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11759 publications

PubMed DOI Crossref
Targeting IMPDH to inhibit SAMHD1 in KMT2A-rearranged leukaemia.
Klootsema Y, Tsesmetzis N, Sharma S, ..., Lilienthal I, Herold N
Cell Cycle 25 (1) 1-19 [2026-12-00; online 2025-12-15]
PubMed DOI Crossref
Grey matter structural asymmetry and premenstrual dysphoric disorder
Bücklein-Ehlers E, Dubol M, Derntl B, ..., Fallgatter A, Comasco E
Neuropsychobiology - (-) 1-22 [2026-08-06; online 2026-08-06]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Biologically informed neural network models are robust to spurious interactions via self-pruning.
Nordenstorm O, Baghdassarian H, Xu X, Lauffenburger DA, Nilsson A
Bioinformatics 42 (8) - [2026-08-03; online 2026-07-26]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Global metabolomics profiling of glucuronides in human plasma, fecal, and cerebrospinal fluid samples.
Tsiara I, Correia MSP, Yang F, ..., Löhr JM, Globisch D
Anal Bioanal Chem 418 (16) 5059-5070 [2026-08-00; online 2025-09-01]
PubMed DOI Crossref
Escitalopram and brain reactivity to aggressive stimuli in premenstrual dysphoric disorder.
Dubol M, Gröndal M, Schmidt F, ..., Sundstrøm I, Comasco E
Br J Psychiatry - (-) 1-9 [2026-07-28; online 2026-07-28]
Erika Comasco SciLifeLab Fellow
DOI Crossref
The business case for investing in biodiversity data
Hasan F, Nyström J, Alström P, ..., Ronquist F, Roslin T
- - (-) - [2026-07-03; online 2026-07-03]
PubMed DOI Crossref
Impairment of Executive Functions in Premenstrual Syndrome: State or Trait?
Gnaiger AM, Werlein P, Gruschwitz P, ..., Hidalgo-Lopez E, Pletzer B
Biol Psychiatry Glob Open Sci 6 (4) 100730 [2026-07-00; online 2026-07-00]
Erika Comasco SciLifeLab Fellow
DOI Crossref
The time dimension matters: Improving mode of action classification with live-cell imaging
Forsgren E, Rietdijk J, Holmberg D, ..., Spjuth O, Jonsson P
Artificial Intelligence in the Life Sciences 9 (-) 100152 [2026-06-00; online 2026-06-00]
DOI Crossref
Seeking knowledge or efficiency: Profiling students’ AI-use through survey-based latent class analysis
Hugerth MW, Hugerth LW
Computers and Education: Artificial Intelligence 10 (-) 100531 [2026-06-00; online 2026-06-00]
PubMed DOI Crossref
Older people's health literacy on COVID-related health behaviours during the pandemic - Results from the SWEOLD 2021 study in Sweden.
Kayser Leeoza N, Wångdahl J, Lennartsson C, Agerholm J
Scand J Public Health 54 (4) 323-330 [2026-06-00; online 2025-07-16]
PubMed DOI Crossref
Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus).
Tørresen OK, Tooming-Klunderud A, Skage M, ..., Mysterud A, Jakobsen KS
J. Hered. 117 (3) 557-565 [2026-05-06; online 2025-11-03]
PubMed DOI Crossref
Mitochondrial ETF insufficiency drives neoplastic growth by selectively optimizing cancer bioenergetics
Papadopoli D, Palia R, Jovanovic P, ..., Pollak M, Topisirovic I
Elife 14 (-) - [2026-05-05; online 2026-05-05]
PubMed DOI Crossref
Timing Matters: Leveraging Positron Emission Tomography Imaging and Hormonal Cycles for Precision Psychiatry in Female Mental Health.
May E, Comasco E, Tiepolt S, ..., Villringer A, Sacher J
Biol. Psychiatry 99 (9) 713-727 [2026-05-01; online 2026-02-23]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Streamlining the Histopathologic Workflow in Diabetic Kidney Disease with Artificial Intelligence.
Matsoukas C, Tomic TT, Tonelius P, ..., Smith K, Söderberg M
J. Am. Soc. Nephrol. 37 (5) 974-983 [2026-05-01; online 2025-11-12]
PubMed DOI Crossref
Women at the heart of mental science: commentary, Pinto da Costa et al.
Pinto da Costa M, de Cates AN, Dhamala E, ..., Upthegrove R, Comasco E
Br J Psychiatry 228 (5) 484-486 [2026-05-00; online 2026-02-11]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Detecting TP53 mutations in paired liquid and tissue biopsies from patients with high-grade serous ovarian carcinoma.
Widjaja AO, Micallef P, Lycke M, ..., Linder A, Sundfeldt K
Int. J. Cancer 158 (8) 2043-2050 [2026-04-15; online 2025-12-09]
PubMed DOI Crossref
Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer
Moreno-Rodriguez T, Zhang M, Lundberg A, ..., Sandhu S, Quigley DA
Genome Biol. 27 (1) - [2026-04-15; online 2026-04-15]
Arian Lundberg DDLS Fellow
PubMed DOI Crossref
Androgen receptor splice variant 7 expression levels distinguish AR-mutated from nonmutated metastatic castration-resistant prostate cancers
Paschalis A, Figueiredo I, Bogdan D, ..., Gaughan L, de Bono J
J. Clin. Invest. 136 (7) - [2026-04-01; online 2026-04-01]
Arian Lundberg DDLS Fellow
PubMed DOI Crossref
Personality and cortical architecture in premenstrual dysphoric disorder
Bücklein-Ehlers E, Dubol M, Derntl B, ..., Sundström-Poromaa I, Comasco E
Arch Womens Ment Health 29 (2) - [2026-04-00; online 2026-03-09]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Engineering biomimetic tissue barrier models on chips: From design and fabrication to applications in disease modeling and drug screening.
Nasiri R, Madadelahi M, Nikmaneshi MR, ..., Khademhosseini A, Herland A
Biomaterials 327 (-) 123739 [2026-04-00; online 2025-09-23]
PubMed DOI Crossref
A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.
Laman Trip DS, van Oostrum M, Memon D, ..., Wollscheid B, Beltrao P
Nat. Biotechnol. 44 (4) 654-667 [2026-04-00; online 2025-05-02]
PubMed DOI Crossref
Autoantibodies neutralizing type I IFNs in patients with fulminant herpes simplex virus hepatitis.
Gervais A, Marchal A, Boucherit S, ..., Casanova JL, Jouanguy E
J. Exp. Med. 223 (3) - [2026-03-02; online 2025-12-05]
PubMed DOI Crossref
Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries.
Antonopoulos K, Nordenstorm O, Nilsson A
PLoS Comput Biol 22 (3) e1014100 [2026-03-00; online 2026-03-18]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Proteome-scale autoantibody profiling in PSC: Associations with clinical phenotypes and evidence for neuroendocrine deregulations.
Cornillet M, Båve AL, Sun D, ..., Halfvarson J, Bergquist A
JHEP Rep 8 (3) 101719 [2026-03-00; online 2025-12-23]
PubMed DOI Crossref
Low-dose testosterone administration and oestrogen synthase availability in the female brain: A pilot study.
Dubol M, Jonasson M, Takahashi K, ..., Sundström-Poromaa I, Comasco E
J Neuroendocrinol 38 (3) e70154 [2026-03-00; online 2026-03-03]
Erika Comasco SciLifeLab Fellow
DOI Crossref
Effects of acute cold and heat shocks on the protein profile of crayfish hemolymph: Implications for crustacean adaptation to thermal stress
Mengal K, Kor G, Siino V, Levander F, Niksirat H
Aquaculture Reports 46 (-) 103265 [2026-03-00; online 2026-03-00]
PubMed DOI Crossref
Early gonadotoxic effects of cyclophosphamide on the prepubertal testis and the feasibility of reducing toxicity through combined antioxidant therapy
Eskafinoghani A, Palomares AR, Hao X, ..., Lundberg A, Rodriguez-Walberg KA
Reprod. Toxicol. 140 (-) 109156 [2026-03-00; online 2026-03-00]
Arian Lundberg DDLS Fellow
PubMed DOI Crossref
Biomarker discovery study design consistent with the receiver-operator characteristic.
Ekström J, Stoimenov I, Åkerrén Ögren J, Sjöblom T
Comput Methods Programs Biomed 276 (-) 109215 [2026-03-00; online 2025-12-20]
PubMed DOI Crossref
Fibrillarin-dependent 2'-O-methylation modulates RPS28 ribosome incorporation and oncogenic translation.
Groza P, Kumari K, Esteva-Socias M, ..., Tuorto F, Aguilo F
Cancer Lett. 639 (-) 218124 [2026-02-28; online 2025-11-17]
PubMed DOI Crossref
Conformational Trajectory of the Molecular Chameleon Grazoprevir From Formulation to Target-Bound.
Wieske LHE, Bu G, Erdélyi M, ..., Gonen T, Danelius ER
Chemistry 32 (8) e02256 [2026-02-23; online 2025-12-18]
PubMed DOI Crossref
The role of gene-environment interactions in endocrine-sensitive life stages for shaping mental health: focus on the RE-MEND project
Abualia K, Cediel-Ulloa A, Allsopp P, ..., Rüegg J, Antczak P
Front Psychiatry 17 (-) 1738584 [2026-02-20; online 2026-02-20]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Understanding excipient interactions unlocks untapped potential of RNA-lipid nanoparticles in dry powder formulations for local pulmonary delivery.
Martini N, Deßloch L, Sych T, ..., Merkel OM, Winkeljann B
J Control Release 390 (-) 114539 [2026-02-10; online 2025-12-12]
PubMed DOI Crossref
High-throughput screening of estrogen receptor activity in personalized mixtures of persistent organic pollutants detected in the blood of Swedish adults.
Reis L, Strand D, Höglund A, ..., Martin JW, Karlsson O
Environ. Res. 290 (-) 123388 [2026-02-01; online 2025-11-20]
PubMed DOI Crossref
Structural and functional modulation of human kynurenine aminotransferase I enhances selenium-driven redox metabolism for cancer therapy.
Selvam AK, Sun R, Sandalova T, ..., Achour A, Björnstedt M
Redox Biol 89 (-) 103967 [2026-02-00; online 2025-12-09]
PubMed DOI Crossref
Spatial architecture of development and disease.
Lázár E, Lundeberg J
Nat. Rev. Genet. 27 (2) 118-136 [2026-02-00; online 2025-09-30]
PubMed DOI Crossref
Single-shot design of a cyclic peptide inhibitor of HIV membrane fusion.
Daumiller D, Giammarino F, Li Q, ..., Ceña Diez R, Bryant P
Antiviral Res. 246 (-) 106336 [2026-02-00; online 2025-12-20]
DOI Crossref
Organocatalytic Michael Addition of β-Ketoesters and Ethenesulfonyl Fluoride: Access to Chiral δ-Sultones via SuFEx Chemistry
Govender KB, Kruger HG, Govender T, ..., Arvidsson PI, Naicker T
Synthesis 58 (03) 303-312 [2026-02-00; online 2025-12-09]
PubMed DOI Crossref
Multiplexed single-molecule characterization at the library scale.
Panfilov M, Mao G, Guo J, ..., Sabantsev A, Deindl S
Nat Protoc 21 (2) 749-774 [2026-02-00; online 2025-06-04]
PubMed DOI Crossref
Loss of Y chromosome in Alzheimer's patients co-occurs with somatic mutations beyond CHIP drivers.
Rychlicka-Buniowska E, Sarkisyan D, Horbacz M, ..., Filipowicz N, Dumanski JP
Life Sci. Alliance 9 (2) - [2026-02-00; online 2025-12-10]
PubMed DOI Crossref
Comorbidities and mutations including single- and multihit TET2 mutations in relation to outcome in chronic myelomonocytic leukaemia-A population-based study.
Kynning MK, Westerberg E, Forsell L, ..., Ejerblad E, Ungerstedt J
Br. J. Haematol. 208 (2) 514-523 [2026-02-00; online 2025-11-25]
PubMed DOI Crossref
Albacarcin V adds EPLIN as a novel and promising target for the treatment of female cancers and pediatric medulloblastoma.
Krahulcová L, Lindell E, Lu X, ..., Sjöblom T, Zhang X
Biochem. Pharmacol. 244 (-) 117625 [2026-02-00; online 2025-12-06]
PubMed DOI Crossref
Ambient temperature exposure on inflammatory blood proteins-A longitudinal self-sampling survey in young Swedish adults.
Yu Z, Björkander S, Bendes A, ..., Schwenk JM, Melén E
iScience 29 (1) 114383 [2026-01-16; online 2025-12-08]
PubMed DOI Crossref
Nonlinear transcriptional responses to gradual modulation of transcription factor dosage
Domingo J, Minaeva M, Morris JA, ..., Sanjana NE, Lappalainen T
Elife 13 (-) - [2026-01-14; online 2026-01-14]
PubMed DOI Crossref
Heterocyclic scaffold-fused dimethoxy-dibenzocyclooctynes for photoactivatable click chemistry.
Larsson NA, Jo T, Bremberg U, ..., Odell LR, Fürth D
Org. Biomol. Chem. 24 (1) 120-126 [2026-01-07; online 2026-01-07]
PubMed DOI Crossref
Dimensionality reduction of genetic data using contrastive learning.
Thor F, Nettelblad C
Genetics 232 (1) - [2026-01-07; online 2025-04-08]
PubMed DOI Crossref
Controlled dynamic remodeling of the spliceosome active site enables the first step of splicing.
Martino G, Manigrasso J, La Sala G, Marcia M, De Vivo M
Proc. Natl. Acad. Sci. U.S.A. 123 (1) e2522293123 [2026-01-06; online 2025-12-31]
PubMed DOI Crossref
Loss of ErbB3 redirects Integrin β1 from early endosomal recycling to secretion in extracellular vesicles.
Rodrigues-Junior DM, Sáez-Ibáñez AR, Terabayashi T, ..., Moustakas A, Ferby I
J. Cell Biol. 225 (1) - [2026-01-05; online 2025-12-05]
PubMed DOI Crossref
Origin and Evolution of Key Enzymes in the Anammox Pathway Revisited.
Hägglund E, Jiménez-González A, Hagström E, ..., Guy L, Andersson SGE
Genome Biol Evol 18 (1) - [2026-01-02; online 2025-12-18]
PubMed DOI Crossref
A High-Resolution Subcellular Map of Proteins in Cells with Motile Cilia.
Bertilsson F, Hikmet F, Hansen JN, ..., Méar L, Lindskog C
J. Proteome Res. 25 (1) 231-243 [2026-01-02; online 2025-12-18]
PubMed DOI Crossref
Ultraprocessed Food Consumption and Risk of Early-Onset Colorectal Cancer Precursors Among Women
Wang C, Du M, Kim H, ..., Cao Y, Chan AT
JAMA Oncol 12 (1) 49 [2026-01-01; online 2026-01-01]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Electrochemical dual-sensing of lactate and glucose using NiO nanoparticles with cross-sensitivity calibration.
Nasiri R, Guagliano G, Van Gastel D, ..., Russom A, Herland A
Talanta 297 (Pt B) 128678 [2026-01-01; online 2025-08-11]
PubMed DOI Crossref
Validation of fibroblast activation protein and α-smooth muscle actin as prognostic biomarkers in prostate cancer through AI-assisted image analysis of dual-marker IHC.
Säilä J, Lehto TP, Rannikko A, ..., Mirtti T, Pellinen T
J Pathol Clin Res 12 (1) e70068 [2026-01-00; online 2025-12-18]
PubMed DOI Crossref
Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells
Schaepe JM, Fries T, Doughty BR, ..., Marklund E, Greenleaf WJ
Cell 189 (1) 307-322.e23 [2026-01-00; online 2026-01-00]
Emil Marklund SciLifeLab Fellow
PubMed DOI Crossref
Putative multiple myeloma susceptibility genes identified by exome sequencing of 347 familial and early-onset cases.
Pertesi M, Demangel D, Niroula A, ..., Intergroupe Francophone du Myélome (IFM) , Nilsson B
Leukemia 40 (1) 235-240 [2026-01-00; online 2025-11-18]
PubMed DOI Crossref
Orthostatic Tremor Is Evoked by Muscle Load Without the Need for Orthostatic Position.
Af Edholm K, Uribarri G, Sundgren M, Svenningsson A, Fransén E
Mov Disord Clin Pract 13 (1) 208-215 [2026-01-00; online 2025-08-01]
PubMed DOI Crossref
Non-coding somatic single-nucleotide variations affecting glioblastoma-specific enhancer elements regulate tumor-promoting gene networks.
Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, ..., Forsberg-Nilsson K, Marzese DM
Genes Dis 13 (1) 101762 [2026-01-00; online 2025-07-05]
PubMed DOI Crossref
Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease.
Jin S, Cenier A, Wetzel D, ..., Patel VC, Schirmer M
Nat. Microbiol 11 (1) 211-227 [2026-01-00; online 2025-12-29]
PubMed DOI Crossref
Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.
Kretsch RC, Albrecht R, Andersen ES, ..., Moult J, Kryshtafovych A
Proteins 94 (1) 51-78 [2026-01-00; online 2025-09-04]
DOI Crossref
Engineering of an Ancestral McbA with Enhanced Domain Mobility Extends Biocatalytic Amide Synthesis Scope
Söderberg E, Molenaar MR, Zaczyk K, ..., Hayes MA, Syrén P
Adv. Synth. Catal. 368 (2) - [2026-01-00; online 2025-11-24]
PubMed DOI Crossref
Engaging the Community: CASP Special Interest Groups.
Elofsson A, Kretsch RC, Magnus M, Montelione GT
Proteins 94 (1) 432-434 [2026-01-00; online 2025-04-30]
PubMed DOI Crossref
Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis.
Vaivade A, Sreenivasan AP, Erngren I, ..., Burman J, Kultima K
Environ Int 207 (-) 109993 [2026-01-00; online 2025-12-11]
PubMed DOI Crossref
Clonal Hematopoiesis and Major Adverse Cardiac Events in People With HIV: Insights From the REPRIEVE Trial
Xue L, Bhattacharya R, Uddin MM, ..., Grinspoon SK, Natarajan P
Arterioscler. Thromb. Vasc. Biol. 46 (1) 168-177 [2026-01-00; online 2026-01-00]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.
Kretsch RC, Posani E, Baulin EF, ..., Case DA, Das R
Proteins 94 (1) 381-402 [2026-01-00; online 2025-11-08]
PubMed DOI Crossref
Author Correction: A roadmap for equitable reuse of public microbiome data.
Hug LA, Hatzenpichler R, Moraru C, ..., Data Reuse Consortium , Probst AJ
Nat. Microbiol 11 (1) 335 [2026-01-00; online 2025-11-06]
PubMed DOI Crossref
AlphaFold3 at CASP16.
Elofsson A
Proteins 94 (1) 154-166 [2026-01-00; online 2025-08-25]
DOI Crossref
A matter of salt: Global assessment of the effect of salt ionic composition as a driver of aquatic bacterial diversity
Szabó A, Székely AJ, Boros E, ..., Bertilsson S, Felföldi T
Limnol Oceanogr Letters 11 (1) - [2026-01-00; online 2025-12-14]
PubMed DOI Crossref
4D Flow MRI Velocity and Turbulence Mapping in Mild Valvular Heart Disease.
Bianchessi T, Trenti C, Carlhäll CJ, ..., Viola F, Dyverfeldt P
J Magn Reson Imaging 63 (1) 222-232 [2026-01-00; online 2025-08-20]
PubMed DOI Crossref
Template-based RNA structure prediction advanced through a blind code competition.
Lee Y, He S, Oda T, ..., Zhang S, Das R
bioRxiv - (-) - [2025-12-30; online 2025-12-30]
DOI Crossref
The collision of two genomes threatens global food security
North HL, Montejo-Kovacevich G, Amado D, ..., Omoto C, Jiggins CD
- - (-) - [2025-12-25; online 2025-12-25]
Gabriela Montejo-Kovacevich SciLifeLab Fellow
PubMed DOI Crossref
Retrospective validation of an artificial intelligence system for diagnostic assessment of prostate biopsies on the ProMort cohort: study protocol.
Ji X, Zelic R, Aspegren O, ..., Akre O, Kartasalo K
BMJ Open 15 (12) e111361 [2025-12-24; online 2025-12-24]
PubMed DOI Crossref
Maturation of human intestinal epithelial cell layers fortifies the apical surface against Salmonella attack.
van Rijn JM, Lopes ACC, Dienhart FSV, ..., Di Martino ML, Sellin ME
Cell Reports 44 (12) 116579 [2025-12-23; online 2025-11-21]
DOI Crossref
Data availability impacts the predictive accuracy of pressure-based biodiversity models
Nyström J, Smith JR, Mandle L, ..., Schön TB, Andermann T
- - (-) - [2025-12-23; online 2025-12-23]
PubMed DOI Crossref
The gut microbiome in early pregnancy is associated with the severity of nausea and vomiting: a nested case‒control study.
González-Valdivia C, Tong B, Hjalmarsson S, ..., Brusselaers N, Hugerth LW
Gut Microbes Rep 3 (1) 2603861 [2025-12-22; online 2025-12-22]
PubMed DOI Crossref
LIPA, a risk locus for coronary artery disease: decoding the variant-to-function relationship.
Li F, Flynn E, Ha P, ..., Lappalainen T, Zhang H
Eur. Heart J. 46 (48) 5273-5288 [2025-12-22; online 2025-08-19]
PubMed DOI Crossref
Protocol for image-based monitoring of de novo RNA synthesis at DNA double-strand breaks in human cell lines.
Pappas G, Gram HH, Bartek J, Galanos P
STAR Protoc 6 (4) 104157 [2025-12-19; online 2025-10-22]
PubMed DOI Crossref
Protocol for generation of endothelial cells from human-derived iPSCs and integration into mouse brain explants.
Erzar I, Noll N, Lugano R, ..., Arce M, Magnusson PU
STAR Protoc 6 (4) 104239 [2025-12-19; online 2025-12-05]
PubMed DOI Crossref
Insight into Malt1 activation mechanism through synergetic approach of AlphaFold, MD Simulation and NMR dynamic analyses.
Lesovoy D, Agback T, Roshchin K, ..., Orekhov V, Agback P
bioRxiv - (-) - [2025-12-19; online 2025-12-19]
PubMed DOI Crossref
Improved Identification of Large-effect Rare Genetic Variants using Haplotype Aggregated Allele-specific Expression Data.
Ganapathy KR, Broly M, Silverstein S, ..., Lappalainen T, Mohammadi P
medRxiv - (-) - [2025-12-18; online 2025-12-18]
PubMed DOI Crossref
Prenatal Exposure to Phthalates, Bisphenols and Their Mixtures and Early Childhood Allergic Conditions and Asthma: Results from the APrON Cohort.
Bartram E, England-Mason G, Martin JW, ..., Soomro MH, APrON Study Team
Int J Environ Res Public Health 22 (12) - [2025-12-17; online 2025-12-17]
DOI Crossref
The vaginal microbiota and gynaecological health study - VaMiGyn - description of a population-based Swedish cohort
Norenhag J, Edfeldt G, Stålberg K, ..., Engstrand L, Olovsson M
npj Womens Health 3 (1) - [2025-12-16; online 2025-12-16]
PubMed DOI Crossref
SARS-CoV-2 Spike Protein Amyloid Fibrils Impair Fibrin Formation and Fibrinolysis.
Westman H, Hammarström P, Nyström S
Biochemistry 64 (24) 4818-4829 [2025-12-16; online 2025-11-26]
PubMed DOI Crossref
Macrophages as central mediators of sympathetic neuro-immune interplay in autoimmunity.
Muntjewerff EM, Josyula VS, Lehmair F, Christoffersson G
Front Immunol 16 (-) 1654382 [2025-12-16; online 2025-12-16]
PubMed DOI Crossref
Minimal structural perturbation of Histatin 5 in crowded environments: Insights from small-angle X-ray scattering, dynamic light scattering, and computer simulations.
Fagerberg E, Holmqvist P, Lenton S, Pernot P, Skepö M
J Colloid Interface Sci 700 (Pt 1) 138310 [2025-12-15; online 2025-07-07]
PubMed DOI Crossref
PDGFRß targeted positron emission tomography as a non-invasive biomarker for activated hepatic stellate cells: lasts steps before clinical translation.
Yashaswini CN, Mitran B, Papadopoulos N, ..., Friedman SL, Eriksson O
EJNMMI Radiopharm Chem 10 (1) 80 [2025-12-13; online 2025-12-13]
PubMed DOI Crossref
Can we infer excitation-inhibition balance from the spectrum of population activity?
Chakravarty K, Roy S, Sinha A, Kumar A
Commun Biol 9 (1) 51 [2025-12-13; online 2025-12-13]
PubMed DOI Crossref
Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.
Hallgren J, Dharamshi JE, Rodríguez-Gijón A, ..., Garcia SL, Jonas K
Nat Commun 16 (1) 11003 [2025-12-12; online 2025-12-12]
PubMed DOI Crossref
The Advanced Therapies model of Lund an integrated approach to accelerate access for many patients.
Helenius G, Jovinge S, Falk A
Mol Ther Methods Clin Dev 33 (4) 101637 [2025-12-11; online 2025-11-25]
PubMed DOI Crossref
Inter- and intra-individual differences in brain sex map to neuroendocrine profiles.
Bon GM, Kimmig AS, Comasco E, Derntl B, Kaufmann T
bioRxiv - (-) - [2025-12-11; online 2025-12-11]
PubMed DOI Crossref
Insulin-regulated aminopeptidase inhibitor C9 restores cellular activity in methadone-damaged primary cell cultures.
Stam F, Bjurling S, Nylander E, ..., Grönbladh A, Hallberg M
Neurosci. Lett. 869 (-) 138415 [2025-12-10; online 2025-10-10]
PubMed DOI Crossref
Integrating extensive functional annotations and multiomics of cattle enhances climate resilience prediction and mapping.
Xiang R, Breen E, Bolormaa S, ..., Chamberlain AJ, Goddard ME
Proc. Natl. Acad. Sci. U.S.A. 122 (49) e2514736122 [2025-12-09; online 2025-11-24]
PubMed DOI Crossref
Hair follicle gene expression profiling in the SubPopulations and InteRmediate Outcome Measures in COPD Study (SPIROMICS).
Buschur KL, Martorella M, Garcia-Flores R, ..., Barr RG, Lappalainen T
BMC Med Genomics 18 (1) 192 [2025-12-09; online 2025-12-09]
PubMed DOI Crossref
Discovery of Previously Unreported Per- and Polyfluoroalkyl Substances (PFAS) in Pooled Australian Human Serum Using Nontarget Analysis.
Dewapriya P, Nilsson S, Ghorbani Gorji S, ..., Kaserzon SL, Thomas KV
Environ. Sci. Technol. 59 (48) 26081-26091 [2025-12-09; online 2025-11-26]
DOI Crossref
A modular lentiviral system for multiplexed gene perturbation and functional analysis suggests interdependence of hormone receptors in breast cancer growth in vivo
Alam S, Matvienko D, Boström J, ..., Brisken C, Altun M
- - (-) - [2025-12-09; online 2025-12-09]
DOI Crossref
A Critical Review and Evaluation of Blood Microsampling Devices for Exposomics
Thiele S, Martin JW
Environ Sci Technol Lett 12 (12) 1595-1610 [2025-12-09; online 2025-11-07]
PubMed DOI Crossref
Evolvability: progress and key questions
Pélabon C, Agudelo-Cantero GA, Araya Ajoy YG, ..., Walling C, Wright J
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Tissue architecture and immune niches govern ctDNA release in colorectal cancer
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Hormonal Contraceptive Formulations and Breast Cancer Risk in Adolescents and Premenopausal Women.
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Selisistat, a SIRT1 inhibitor, enhances paclitaxel activity in luminal and triple-negative breast cancer: in silico, in vitro, and in vivo studies.
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PRIAMOS: A technique for mixing embedding media for freely adjusting pH value and refractive index (RI) for optical clearing (OC) of whole tissue samples.
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Clinical and transcriptomic characterization of patients with chronic lymphocytic leukemia harboring t(14;19): an ERIC study.
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Clinical Validation of Novel Immunoassays for Plasma Phosphorylated Tau 217, 212, 181, 231, and Brain-Derived Tau Across the Biochemical Spectrum of Alzheimer's Disease.
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Calcium stabilizes the flexible N-terminal domain of the bacterial ion channel DeCLIC.
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Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation.
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Autosomal dominant primary hyperparathyroidism in the Keeshond dog breed is strongly associated with a missense variant in sirtuin-6.
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Antigenic peptide delivery to antigen-presenting cells using a CD40-coiled coil affinity-based platform.
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OncoRisk: A state-of-the-art Web Server for bridging the oncogenic databases and pan-cancer cohorts to the translational oncology
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Chromogranin A and catestatin regulate pancreatic islet homeostasis, endocrine function, and neurotransmitter signaling.
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Commun Biol 8 (1) 1684 [2025-11-26; online 2025-11-26]
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The AML cellular state space unveils NPM1 immune evasion subtypes with distinct clinical outcomes.
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The Swedish Reference Genome Portal: A Hub for Non-Human Eukaryotic Genomic Data Visualisation, Discovery, and Reuse
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Proteomics discovery of MTDH and SND1 interaction vulnerabilities in ovarian cancer.
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Depression is an independent risk factor for stroke reccurence and cognitive impairment in stroke patients.
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Genomic and biogeographic patterns of endemic geckos in the Galapagos Islands reveal population structure and species delimitation on inhabited islands.
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Myxococcus xanthus for active matter studies: a tutorial for its growth and potential applications.
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Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem.
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Maternal exposure to trace elements and perfluoroalkyl acids and their associations with alterations of the hypothalamic-pituitary-adrenal axis.
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Progress and future outlook towards a safe and sustainable production and use of chemicals.
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Identification of protein biomarkers to differentiate between gram-negative and gram-positive infections in adults suspected of sepsis
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Giving an Enzyme Scissors: Serotonin Derivatives as Potent Organocatalytic Switches for DNA Repair Enzyme OGG1.
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CD46 is a cellular receptor for species D human adenovirus.
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A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing
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Targeting the parietal memory network with tDCS in MCI: study protocol for a randomized controlled trial.
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Molecular profiling of ex vivo prostate cancer CAF models captures stromal heterogeneity and drug vulnerabilities.
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Does human cytomegalovirus provide a novel therapeutic target for patients with glioblastoma?
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Unraveling the conformational landscape of amyloid precursor protein intracellular domain.
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Keeping Wnt in check for efficient checkpoint blockade in glioblastoma.
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Neuroimmune interactions in the pancreas in health and disease- Identifying the components of nerve-macrophage association 2911
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IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment.
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Clonal Hematopoiesis and Risk of New-Onset Myocarditis and Pericarditis.
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pHyph, a novel antibiotic-free treatment for bacterial vaginosis, promotes Lactobacillus growth and reduces the abundance of pathogens in the vagina.
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The pcnB gene sustains Shigella flexneri virulence.
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Report on the 2nd MObility for Vesicle research in Europe (MOVE) symposium-2024.
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Proximity extension assay inflammatory profiling cannot distinguish the presence of residual C-peptide in patients with long-standing type 1 diabetes.
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Inflammatory Mediators Related to Vascular Dysfunction are Linked to ICP, PRx, and CPP Following Human Severe Traumatic Brain Injury.
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Differences in the Fecal Metabolome of Autoimmune Pancreatitis Patients
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Cardiovascular Morbidity in Patients Undergoing Successful Surgery for Primary Hyperparathyroidism.
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An anti-CEA affibody showing high-definition staining in human pancreatic cancer tissue sections and selective tumor targeting in vivo.
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Spatial transcriptomics reveals an unexpected impact of tau and tau pathology on the expression of transthyretin.
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Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells.
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Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database.
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Comparative analysis of whole genome amplification kits for single cell genome analysis
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Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.
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Benzylhydroxamic Acids as IRAP Inhibitors: Sulfonamide Variations
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Maternal aggression driven by the transient mobilisation of a dormant hormone-sensitive circuit.
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PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules.
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Childhood brain tumours instruct cranial haematopoiesis and immunotolerance
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Retrospective Validation of an Artificial Intelligence System for Diagnostic Assessment of Prostate Biopsies on the ProMort Cohort: Study Protocol
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POMC-specific modulation of metabolic and immune pathways via melanocortin-3 receptor signaling.
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Metagenomic analysis of viral diversity in Portuguese bats.
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LipiGo: A Versatile DNA-Lipid Nanoparticle Hybrid for Precision Drug Delivery
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GRK-biased adrenergic agonists for the treatment of type 2 diabetes and obesity.
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Targeted ferroptosis induction enhances chemotherapy efficacy in chemoresistant neuroblastoma.
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Impact of early-life human microbiota on the murine host metabolome: insights from a two-generation HMA mouse model and implications for allergic disease.
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Gene copy number variation (gCNV) contributes to adaptation along environmental gradient
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Gain-of-function enhancer variant near KCNB1 causes familial ST-depression syndrome.
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Discovery of novel triphenylphosphonium conjugated pleuromutilin with enhanced anti-MRSA effect and broaden antibacterial spectrum.
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4D flow MRI enhances prototype testing of a total artificial heart.
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Genetic background of neurological disorders with basal ganglia calcification.
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Lab-on-PCB with integrated DNA amplification and electroanalytical detection for point-of-care diagnostics.
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Interdisciplinary Study on Drug-Induced-Phospholipidosis of Repurposing Libraries through Machine Learning and Experimental Evaluation in Different Cell Lines
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Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation.
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Investigating recurrence in pilonidal sinus disease: results of a nationwide, multicenter study in Turkey (PISI TURKEY).
Yalcinkaya A, Yalcinkaya A, Sahin C, ..., Leventoglu S, PISI TURKEY Study Collaboration
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Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem
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Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data
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NPJ Precis Oncol 9 (1) 310 [2025-09-09; online 2025-09-09]
Camilla Engblom SciLifeLab Fellow
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Chemoenzymatic cascade depolymerization of plastics.
Sun S, Syrén PO
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Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads
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Virulence factors and outcomes in bacteremia caused by extended-spectrum β-lactamase-producing uropathogenic Escherichia coli ST131-H30Rx in a Swedish county.
Möller V, Welander J, Nilsson M, ..., Östholm Å, Berglund B
BMC Infect Dis 25 (1) 1103 [2025-09-08; online 2025-09-08]
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Rapid label-free identification of seven bacterial species using microfluidics, single-cell time-lapse phase-contrast microscopy, and deep learning-based image and video classification.
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Thiazole-fused thiazoliniums with ketone warheads as covalent inhibitors targeting Cys44 of SARS-CoV-2 3CLpro.
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Chem. Biol. Interact. 418 (-) 111620 [2025-09-05; online 2025-06-24]
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Hemispheric asymmetry of tau pathology is related to asymmetric amyloid deposition in Alzheimer's Disease.
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The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.
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ProbeST: a custom probe design pipeline for Spatial Transcriptomics
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Pre- and Post-synaptic Mechanisms of Neuronal Inhibition Assessed Through Biochemically Detailed Modeling of GABAB Receptor Signaling.
Mäki-Marttunen T, Kismul JF, Pajo K, ..., Andreassen OA, Kotaleski JH
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Unravelling the Complexity of Sarcopenia Through a Systems Biology Approach.
Ceyhan AB, Altay O, Zhang C, ..., Turkez H, Mardinoglu A
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An In Vivo Fluorescence Image Analysis Tool for Esterase Activity Quantification in Daphnia: Using Calcein AM in Ecotoxicological Studies.
Perez-Liñan A, Abele C, Pierozan P, Breitholtz M, Karlsson O
Environ. Sci. Technol. 59 (34) 18023-18032 [2025-09-02; online 2025-08-21]
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U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis.
Xu W, Cai H, Zhang Q, ..., Ouyang W, Cao G
Genome Biol. 26 (1) 261 [2025-09-01; online 2025-09-01]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Subjective cognitive decline in major depressive patients is associated with altered entropy and connectivity changes of temporal and insular region.
Yulug B, Yalcinkaya A, Safa SS, ..., Hanoglu L, Mardinoglu A
Transl Psychiatry 15 (1) 335 [2025-09-01; online 2025-09-01]
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PKP1 promotes lung cancer by modulating energy metabolism through stabilization of PFKP.
Ritoré-Salazar F, Arenas AM, Matia-González AM, ..., Noguera NI, Medina PP
Biomark Res 13 (1) 112 [2025-09-01; online 2025-09-01]
PubMed DOI Crossref
Understanding the transport of drugs across biomimetic barriers of various phospholipid compositions using a combined experimental and computational approach.
Kabedev A, Tønning MH, Teleki A, Bauer-Brandl A, Jacobsen AC
Colloids Surf B Biointerfaces 253 (-) 114706 [2025-09-00; online 2025-04-21]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Tertiary lymphoid structures in Merkel cell carcinoma facilitate naïve and central memory T-cell infiltration linked to immunotherapy response
Srinivas N, Spassova I, Lei KC, ..., Lui WO, Becker JC
J Immunother Cancer 13 (9) e012224 [2025-09-00; online 2025-09-23]
Camilla Engblom SciLifeLab Fellow
DOI Crossref
Synthesis of Two Neutrophil Elastase Inhibitors by Palladium-mediated [11C]cyanations
Wilson V, Zhang H, Estrada S, ..., Eriksson O, Antoni G
Nuclear medicine and biology 148-149 (-) 109076 [2025-09-00; online 2025-09-00]
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Streptomyces uses both polar and dispersed cell wall synthesis during exploratory growth.
Zambri MP, Baglio CR, Irazoki O, ..., Cava F, Elliot MA
Nat. Microbiol 10 (9) 2245-2256 [2025-09-00; online 2025-08-08]
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SKI regulates rRNA transcription and pericentromeric heterochromatin to ensure centromere integrity and genome stability.
Pola-Véliz V, Carrero D, Sagredo EA, ..., Armisén R, Marcelain K
Neoplasia 67 (-) 101204 [2025-09-00; online 2025-07-02]
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Reply to J Drouin-Chartier and J Lessard-Lord.
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Protein-ligand data at scale to support machine learning.
Edwards AM, Owen DR, Structural Genomics Consortium Target 2035 Working Group
Nat Rev Chem 9 (9) 634-645 [2025-09-00; online 2025-07-23]
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POSTER: AML-570 Predictive Value of Microbiome and Metabolomic Biomarkers in Myeloid Neoplasms
Campagna A, Clasen F, Garcia-Guevara F, ..., Porta MGD, Shoaie S
Clinical Lymphoma Myeloma and Leukemia 25 (-) S190 [2025-09-00; online 2025-09-00]
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P32-07 Can we unravel cocktail effects in skin sensitization? A proteomics-centred approach
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Toxicol. Lett. 411 (-) S426 [2025-09-00; online 2025-09-00]
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Mechanical control of breast cancer malignancy by promotion of mevalonate pathway enzyme synthesis.
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Matrix Biol. 140 (-) 1-15 [2025-09-00; online 2025-06-12]
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Longitudinal big biological data in the AI era.
Mardinoglu A, Turkez H, Shong M, ..., Hood L, Uhlen M
Mol Syst Biol 21 (9) 1147-1165 [2025-09-00; online 2025-08-05]
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Interaction between haploinsufficiency of PTPN2 and patient microbiome promotes autoimmune arthritis in mice.
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J. Autoimmun. 156 (-) 103452 [2025-09-00; online 2025-08-01]
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Illuminating druggable dark matter in RNA virus replication using in situ cryo-EM.
Sharma H, Sorin MN, Sharma KB, Carlson LA
Curr Opin Virol 72 (-) 101475 [2025-09-00; online 2025-07-09]
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Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.
Njoroge SM, Kulohoma BW, Falzon LC, ..., von Mentzer A, Fèvre EM
Microb Genom 11 (9) - [2025-09-00; online 2025-09-25]
Astrid von Mentzer DDLS Fellow
PubMed DOI Crossref
Gene and pathway analysis of genome-wide genetic associations of bladder cancer.
Shi M, Meng X, Xu X, Wang Q
Curr Urol 19 (5) 321-330 [2025-09-00; online 2025-06-05]
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PubMed DOI Crossref
Fluctuating DNA methylation tracks cancer evolution at clinical scale.
Gabbutt C, Duran-Ferrer M, Grant HE, ..., Martin-Subero JI, Graham TA
Nature 645 (8081) 764-773 [2025-09-00; online 2025-09-10]
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Distinct Phenotypes of Peripheral Innate Lymphoid Cells and T Cells in Type 2 and Non-Type 2 Asthma.
Kere MM, Björkander S, Merid SK, ..., Tibbitt CA, Melén E
Clin Transl Allergy 15 (9) e70108 [2025-09-00; online 2025-09-18]
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Determination of ADP/ATP translocase isoform ratios in malignancy and cellular senescence.
Liblova Z, Maurencova D, Salovska B, ..., Vajrychova M, Hodny Z
Mol Oncol 19 (9) 2619-2647 [2025-09-00; online 2025-04-27]
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Contextualizing Telomere Biology Through Biopsychological Plasticity: Insights From the Differential Susceptibility Hypothesis.
Comasco E
Biol Psychiatry Glob Open Sci 5 (5) 100548 [2025-09-00; online 2025-06-07]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Competition and cooperation of assembly sequences in recurrent neural networks.
Stöber TM, Lehr AB, Nikzad A, ..., Fyhn M, Kumar A
PLoS Comput Biol 21 (9) e1013403 [2025-09-00; online 2025-09-12]
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Comorbid posttraumatic stress disorder complicates eating disorder treatment: A nationwide study.
Hübel C, Johansson T, Mundy J, ..., Isomaa R, Birgegård A
Psychiatry Res 351 (-) 116563 [2025-09-00; online 2025-05-24]
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Building immunoglobulin and T cell receptor gene databases for the future
Watson CT, Collins AM, Ohlin M, ..., Lees WD, Yaari G
ImmunoInformatics 19 (-) 100059 [2025-09-00; online 2025-09-00]
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Bispecific brain-penetrant antibodies for treatment of Alzheimer's disease.
Sehlin D, Hultqvist G, Michno W, ..., Lopes van den Broek S, Syvänen S
J Prev Alzheimers Dis 12 (8) 100214 [2025-09-00; online 2025-05-26]
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Author Correction: Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.
Sommerauer C, Gallardo-Dodd CJ, Savva C, ..., Williams C, Kutter C
Mol Syst Biol 21 (9) 1282-1283 [2025-09-00; online 2025-06-12]
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Author Correction: A universal language for finding mass spectrometry data patterns.
Damiani T, Jarmusch AK, Aron AT, ..., Dorrestein PC, Wang M
Nat. Methods 22 (9) 1995 [2025-09-00; online 2025-08-09]
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Aurora 2.0: A fluorogenic dye library for expanding the capability of protein-adaptive differential scanning fluorimetry (paDSF).
Charvat AF, Mason-Chalmers K, Grabinska-Rogala A, ..., Vinueza NR, Gestwicki JE
SLAS Discov 35 (-) 100259 [2025-09-00; online 2025-08-08]
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A Diastereoselective Mizoroki–Heck Reaction for Synthesis of Spirooxindole-Based Nonnatural Amino Acids Using a Boc-Protected Amine Chiral Auxiliary
Larhed M, Lindman J, Puthiyaparambath S, Gising J, Odell LR
Synlett 36 (14) 2009-2013 [2025-09-00; online 2025-04-29]
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A Base-Mediated Rearrangement of the Benzylic 1,5-Hexadipyridynyl Moiety.
Remmerswaal WA, Nguyen TT, Han Z, ..., Zhu W, Erdelyi M
Chempluschem 90 (9) e202500252 [2025-09-00; online 2025-08-04]
Ruisheng Xiong SciLifeLab Fellow
DOI Crossref
Interferon-α–Driven Stratification of B Cell Reveals Metabolic Reprogramming of Double Negative, Naive and Transitional cell subsets and Refines Molecular Classification in Sjögren’s Disease
Iperi C, Rekha AA, Arvidsson G, ..., Jamin C, Bordron A
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Hybrid Sequencing Characterization of Complex Chromosomal Rearrangements.
Lindstrand A, Eisfeldt J
Methods in molecular biology (Clifton, N.J.) 2968 (-) 151-159 [2025-08-30; online 2025-08-30]
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Noscapine-bile acid hybrids as novel anticancer agents.
Babanezhad Harikandei K, Salehi P, Hasanpour Z, ..., Asghari SM, Mardinoglu A
RSC Med Chem 16 (11) 5511-5533 [2025-08-29; online 2025-08-29]
PubMed DOI Crossref
Colchicine and Longitudinal Dynamics of Clonal Hematopoiesis: An Exploratory Substudy of the LoDoCo2 Trial.
Mohammadnia N, Xue L, Vestjens LTW, ..., El Messaoudi S, Honigberg MC
J. Am. Coll. Cardiol. - (-) - [2025-08-29; online 2025-08-29]
Abhishek Niroula DDLS Fellow
DOI Crossref
A novel mechanism for bacterial sporulation based on programmed peptidoglycan degradation
Ramírez Carbó CA, Irazoki O, Venkatesan S, ..., Cava F, Nan B
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DOI Crossref
A novel mechanism for bacterial sporulation based on programmed peptidoglycan degradation
Ramírez Carbó CA, Irazoki O, Venkatesan S, ..., Cava F, Nan B
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Multi-omics Profiling of the Lateral Ventricle Choroid Plexus Reveals Developmental Cellular Remodeling, Early Immune Gene Activation, and a Novel Epithelial Subtype
Fernandes M, Andersson-Li L, Correia E, ..., Sousa JC, Falcão AM
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PubMed DOI Crossref
Cotranslational folding and maturation of HIV-1 protease.
Westerfield J, Nicolaus F, Swanstrom R, von Heijne G
bioRxiv - (-) - [2025-08-27; online 2025-08-27]
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NAIP/NLRC4 inflammasome dynamics in murine enteroids are tuned by NAIP ligand concentration and epithelial cell differentiation.
Andreassen PR, Ernst C, Pimentel Mendes M, ..., Hardt WD, Vorholt JA
Cell Reports 44 (8) 116143 [2025-08-26; online 2025-08-20]
Mikael Sellin SciLifeLab Fellow
DOI Crossref
Streptococcus pyogenes nuclease A interferes with host complement functions
A. Bennig I, Ströbaek J, Mamede R, ..., Björck L, Happonen LJ
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PubMed DOI Crossref
Culture-free detection of bacteria from blood for rapid sepsis diagnosis.
Marino Miguélez MH, Osaid M, Hallström E, ..., Elf J, van der Wijngaart W
NPJ Digit Med 8 (1) 544 [2025-08-25; online 2025-08-25]
PubMed DOI Crossref
Winter microbial community structure and methane-cycling potential in constructed agricultural wetlands across regions and microhabitats.
Liu T, Yngve KL, Futter M, ..., Bertilsson S, Geranmayeh P
FEMS Microbiol. Ecol. 101 (9) - [2025-08-23; online 2025-09-03]
PubMed DOI Crossref
Identification of distinct and shared biomarker panels in different manifestations of cerebral small vessel disease through proteomic profiling.
Hristovska I, Binette AP, Kumar A, ..., Vogel JW, Hansson O
medRxiv - (-) - [2025-08-23; online 2025-08-23]
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Lipid-facilitated opening of the ADAM10 sheddase revealed by enhanced sampling simulations
Schahl A, Haloi N, Carroni M, ..., Delemotte L, Howard RJ
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PubMed DOI Crossref
The power of two: Combining imaging and sequencing as readouts for in vivo pooled genetic screens.
Jiménez C, Crosetto N, Bienko M
Mol. Cell 85 (16) 3006-3008 [2025-08-21; online 2025-08-23]
PubMed DOI Crossref
Lactoferricin enables adenovirus infection of human skeletal muscle cells.
Danskog K, Mistry N, Årdahl C, ..., Lenman A, Arnberg N
Npj Viruses 3 (1) 62 [2025-08-19; online 2025-08-19]
PubMed DOI Crossref
Flame-made nanoparticles for magnetic hyperthermia and MRI in colorectal cancer theranostics.
Zhang Y, Paraskeva C, Chen Q, ..., Koliaraki V, Teleki A
Nanoscale Adv 7 (17) 5284-5299 [2025-08-19; online 2025-07-16]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Mutational insights into human kynurenine aminotransferase 1: modulation of transamination and β-elimination activities across diverse substrates.
Selvam AK, Sun R, Razaghi A, ..., Björnstedt M, Achour A
Biochem. J. 482 (16) 1163-1180 [2025-08-18; online 2025-08-18]
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SOX2 and NR2F1 coordinate the gene expression program of the early postnatal visual thalamus.
Serra L, Nordin A, Jonasson M, ..., Nicolis SK, Mercurio S
Biol Open 14 (8) - [2025-08-15; online 2025-08-01]
DOI Crossref
A cytotoxic gene therapy targeting SOX9-positive therapy-resistant medulloblastoma
Lin T, Hutter S, Vikström E, ..., Giraud G, Swartling FJ
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DOI Crossref
Non-equilibrium dynamics of the neocortex in Parkinson’s disease
Helson P, Benyahiya E, Manikandan S, ..., Mitra D, Kumar A
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PubMed DOI Crossref
Navigating the complexities of drug development for metallo-β-lactamase inhibitors.
Reddy N, Balieiro AM, Silva JRA, ..., Govender T, Naicker T
RSC Med Chem 16 (8) 3393-3415 [2025-08-13; online 2025-05-27]
PubMed DOI Crossref
Immune cell activation produces locally scrambled foci of plasma membrane lipids.
Sputay D, Doktorova M, Chan SH, ..., Levental I, Levental KR
Faraday Discuss 259 (0) 45-59 [2025-08-13; online 2025-08-13]
PubMed DOI Crossref
Exploring the sensitivities of experimental techniques to various types of membrane asymmetry using atomistic simulations.
Heberle FA, Doktorova M
Faraday Discuss 259 (0) 300-320 [2025-08-13; online 2025-08-13]
PubMed DOI Crossref
Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms.
Oncins A, Zaurin R, Toukabri H, ..., Oudelaar AM, Beekman R
Nucleic Acids Res. 53 (15) - [2025-08-11; online 2025-08-23]
PubMed DOI Crossref
Deciphering the RNA recognition by Musashi-1 to design protein and RNA variants for in vitro and in vivo applications.
Pérez-Ràfols A, Pérez-Ropero G, Cerofolini L, ..., Buijs J, Fragai M
Nucleic Acids Res. 53 (15) - [2025-08-11; online 2025-08-13]
PubMed DOI Crossref
Screening scaffold proteins for improved functional delivery of luminal proteins using engineered extracellular vesicles.
Niu Z, Zhou H, Zheng W, ..., Liang X, Andaloussi SEL
J Control Release 384 (-) 113882 [2025-08-10; online 2025-05-26]
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Gain of chromosome 17 is an early genetic abnormality in neuroblastoma with PPM1D emerging as a strong candidate oncogene driving tumor progression.
Milosevic J, Fransson S, Svensson J, ..., Kogner P, Johnsen JI
Cancer Lett. 625 (-) 217769 [2025-08-10; online 2025-05-02]
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Isoform-level profiling of m6A epitranscriptomic signatures in human brain.
Gleeson J, Madugalle SU, Wan CY, ..., De Paoli-Iseppi R, Clark MB
Sci Adv 11 (32) eadp0783 [2025-08-08; online 2025-08-08]
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The evolution of health data ecosystems: An international survey.
Lerner-Ellis JP, Price EM, Subhani S, ..., Bernier F, Boycott KM
Am. J. Hum. Genet. 112 (8) 1769-1777 [2025-08-07; online 2025-07-21]
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Nonlinear transcriptional responses to gradual modulation of transcription factor dosage.
Domingo J, Minaeva M, Morris JA, ..., Sanjana NE, Lappalainen T
bioRxiv - (-) - [2025-08-07; online 2025-08-07]
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Nanobody-mediated modulation of long RSH enzymes Rel and RelA catalysis by restriction of their conformational landscape
Van Nerom K, Ainelo A, Coppieters ’t Wallant K, ..., Hauryliuk V, Garcia-Pino A
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A preclinical study on the influence of linkers in [68Ga]Ga-NOTA-X-RM26 radiotracers for PET imaging of GRPR expression.
Olaniran Håkansson E, Zelepukin IV, Obeid K, ..., Odell LR, Kanellopoulos P
EJNMMI Res 15 (1) 104 [2025-08-07; online 2025-08-07]
PubMed DOI Crossref
Hematopoietic loss of Y chromosome activates immune checkpoints and contributes to impaired senescent cell clearance and renal disease.
Arai Y, Chavkin NW, Arai Y, ..., Forsberg LA, Walsh K
Sci Transl Med 17 (810) eadv4071 [2025-08-06; online 2025-08-06]
PubMed DOI Crossref
Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis arenosa.
Vlček J, Hämälä T, Vives Cobo C, ..., Yant L, Kolář F
Proc. Natl. Acad. Sci. U.S.A. 122 (31) e2501739122 [2025-08-05; online 2025-07-30]
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Two-step detection of Lewy body pathology via smell-function testing and CSF α-synuclein seed amplification.
Mastenbroek SE, Collij LE, Vogel JW, ..., Ossenkoppele R, Hansson O
Nat Commun 16 (1) 7182 [2025-08-05; online 2025-08-05]
PubMed DOI Crossref
Matrix-M adjuvant triggers inflammasome activation and enables antigen cross-presentation through induction of lysosomal membrane permeabilization.
Zarnegar B, Carow B, Eriksson J, ..., Stertman L, Lunderius Andersson C
NPJ Vaccines 10 (1) 184 [2025-08-05; online 2025-08-05]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction.
Nazaretyan L, Rentzsch P, Kircher M
Genome Med 17 (1) 84 [2025-08-04; online 2025-08-04]
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Sex unfolded: sex, asex, sexes.
Roze D, Glémin S, Lenormand T, Van Doninck K
J Evol Biol 38 (7) 787-797 [2025-08-02; online 2025-08-03]
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Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes.
Nordin A, Chakraborty C, Jonasson M, ..., Remeseiro S, Cantù C
Genome Res 35 (8) 1701-1716 [2025-08-01; online 2025-08-01]
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Tractable In Vivo Reprogramming of Tumor Cells to Type 1 Conventional Dendritic Cell-like Cells.
Ascic E, Fontanari G, Thrasyvoulou M, ..., Ballocci T, Pereira CF
J Vis Exp - (222) - [2025-08-01; online 2025-08-01]
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TSC2 loss in neural progenitor cells suppresses mRNA translation of neurodevelopmental genes.
Martin P, Szkop KJ, Robert F, ..., Larsson O, Ramesh V
Brain 148 (8) 2935-2950 [2025-08-01; online 2025-03-05]
PubMed DOI Crossref
Risk of atherosclerotic cardiovascular disease after cancer diagnosis: findings from 3 prospective cohort studies.
Liu Q, Wang Q, Wang K, ..., Song M, Giovannucci E
J. Natl. Cancer Inst. 117 (8) 1707-1716 [2025-08-01; online 2025-05-30]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Cryo-EM structures of ρ1 GABAA receptors with antagonist and agonist drugs.
Fan C, Cowgill J, Howard RJ, Lindahl E
Nat Commun 16 (1) 7077 [2025-08-01; online 2025-08-01]
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Considerations and Software for Successful Immune Cell Deconvolution Using Proteomics Data.
Zamore M, Junior SM, Andree SL, ..., Lindstedt M, Levander F
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AEMB: efficient abundance estimation for metagenomic binning
Pan S, Tolstoganov I, Sahlin K, ..., Zhao XM, Coelho LP
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PubMed DOI Crossref
Tumoral pSMAD2 as a prognostic biomarker in early-stage breast cancer: insights from the randomized SweBCG91RT trial.
Stenmark Tullberg A, Thurfjell V, Kovács A, ..., Karlsson P, Strell C
Breast Cancer Res. Treat. 212 (3) 499-509 [2025-08-00; online 2025-06-09]
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The intracellular free concentration of endocrine disrupting chemicals enables translation between cell-free and cell-based estrogenic activity assays.
Munic Kos V, Arvidsson S, Islam B, ..., Cotgreave I, Artursson P
Environ Toxicol Pharmacol 117 (-) 104750 [2025-08-00; online 2025-06-23]
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The influence of metformin treatment on the circulating proteome.
Connolly B, McCreight L, Slieker RC, ..., IMI-DIRECT , IMI-RHAPSODY
EBioMedicine 118 (-) 105859 [2025-08-00; online 2025-07-19]
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The TP53 tumor suppressor gene: From molecular biology to clinical investigations.
Baliakas P, Soussi T
J. Intern. Med. 298 (2) 78-96 [2025-08-00; online 2025-06-16]
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The Global Neurodegeneration Proteomics Consortium: biomarker and drug target discovery for common neurodegenerative diseases and aging.
Imam F, Saloner R, Vogel JW, ..., Lovestone S, Global Neurodegeneration Proteomics Consortium (GNPC)
Nat. Med. 31 (8) 2556-2566 [2025-08-00; online 2025-07-15]
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Sheathless Elasto-Inertial Focusing of Sub-25 Nm Particles in Straight Microchannels.
Tanriverdi S, Cruz J, Habibi S, ..., Sezgin E, Russom A
Small 21 (33) e2503369 [2025-08-00; online 2025-06-25]
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Shared and disease-specific pathways in frontotemporal dementia and Alzheimer's and Parkinson's diseases.
Ali M, Erabadda B, Chen Y, ..., Winchester L, Cruchaga C
Nat. Med. 31 (8) 2567-2577 [2025-08-00; online 2025-07-15]
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Reprogramming Stars #23: Charting Cell Fate Crossroads from the Interplay Between Epigenetics, Transcription, and 3D Chromatin Architecture-An Interview with Dr. Effie Apostolou.
Apostolou E, Lopes M, Pereira CF
Cell Reprogram 27 (4) 135-142 [2025-08-00; online 2025-08-05]
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Platelet characteristics in extremely preterm infants after fatty acid supplementation: a randomized controlled trial.
Lundgren P, Pivodic A, Nilsson AK, ..., Smith LEH, Hellström A
Pediatr. Res. 98 (2) 680-689 [2025-08-00; online 2024-12-19]
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Mechanistic modeling of cell viability assays with in silico lineage tracing.
Mutsuddy A, Huggins JR, Amrit AK, ..., Calhoun JC, Birtwistle MR
PLoS Comput Biol 21 (8) e1013156 [2025-08-00; online 2025-08-29]
Cemal Erdem DDLS Fellow
PubMed DOI Crossref
Mast Cell Phenotypic Heterogeneity Impacts the Interplay with Pathogenic Salmonella Typhimurium Bacteria.
von Beek C, Prensa GI, Andersson JHM, Pejler G, Sellin ME
Eur. J. Immunol. 55 (8) e70040 [2025-08-00; online 2025-08-21]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Longer scans boost prediction and cut costs in brain-wide association studies.
Ooi LQR, Orban C, Zhang S, ..., Yeo BTT, Alzheimer’s Disease Neuroimaging Initiative
Nature 644 (8077) 731-740 [2025-08-00; online 2025-07-16]
PubMed DOI Crossref
Global and tissue-specific transcriptomic dysregulation in human aging: Pathways and predictive biomarkers.
Arif M, Lehoczki A, Haskó G, ..., Ungvari Z, Pacher P
Geroscience 47 (4) 5917-5936 [2025-08-00; online 2025-04-28]
PubMed DOI Crossref
Germline genetic variation impacts clonal hematopoiesis landscape and progression to malignancy.
Liu J, Tran D, Xue L, ..., Natarajan P, Bolton KL
Nat. Genet. 57 (8) 1872-1880 [2025-08-00; online 2025-07-15]
Abhishek Niroula DDLS Fellow
DOI Crossref
Enzymatic depolymerization of polyamides (nylons): current challenges and future directions
Sun S
Polymer Degradation and Stability 238 (-) 111341 [2025-08-00; online 2025-08-00]
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Elofsson A, Kolodny R
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Detection of antibodies against the African parasite Trypanosoma brucei using synthetic glycosylphosphatidylinositol oligosaccharide fragments.
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CLIPPERs - Clip the right protein - a new tool for targeted proteolysis in bacteria.
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An integrated pipeline for identification and prioritisation of smooth muscle cell-related drug targets in atherosclerosis from large scale multi-omics analyses
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A stratified treatment algorithm in psychiatry: a program on stratified pharmacogenomics in severe mental illness (Psych-STRATA): concept, objectives and methodologies of a multidisciplinary project funded by Horizon Europe.
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Low-fibre diet is associated with high-risk coronary plaque features.
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A multiomics approach reveals novel regulators of plasma factor V levels, highlighting CLEC4M as a clearance receptor.
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Host-Specific Adaptation of Legionella pneumophila to Single and Multiple Hosts.
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Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes.
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From Library to Landscape: Integrative Annotation Workflows for Compound Libraries in Drug Repurposing
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Epigenomic diagnosis and prognosis of Acute Myeloid Leukemia.
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Empowering bioinformatics communities with Nextflow and nf-core.
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Conserved architecture of a functional lncRNA-protein interaction in the DNA damage response pathway
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Comparing Xenium 5K and Visium HD data from identical tissue slide at a pathological perspective.
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J. Exp. Clin. Cancer Res. 44 (1) 219 [2025-07-26; online 2025-07-26]
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cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads.
Petri AJ, Thi-Huyen Nguyen M, Rajwar A, Benson E, Sahlin K
PLoS ONE 20 (7) e0321246 [2025-07-24; online 2025-07-24]
Erik Benson Kristoffer Sahlin SciLifeLab Fellow
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Charting structural brain asymmetry across the human lifespan.
Dorfschmidt L, White S, Gardner M, ..., Seidlitz J, Alexander-Bloch A
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Transcription of GABAA receptor subunits in circulating monocytes and association to emotional brain function in premenstrual dysphoric disorder.
Stiernman L, Comasco E, Johansson M, Bixo M
Transl Psychiatry 15 (1) 255 [2025-07-23; online 2025-07-23]
Erika Comasco SciLifeLab Fellow
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Quantitative evaluation of methods to analyze motion changes in single-particle experiments.
Muñoz-Gil G, Bachimanchi H, Pineda J, ..., Volpe G, Manzo C
Nat Commun 16 (1) 6749 [2025-07-22; online 2025-07-22]
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Design of linear and cyclic peptide binders from protein sequence information.
Li Q, Vlachos EN, Bryant P
Commun Chem 8 (1) 211 [2025-07-22; online 2025-07-22]
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Data meets prior knowledge for interpretable mechanistic inference in biology
Gomez-Cabrero D, Tegnér JN
Nat Mach Intell 7 (7) 987-988 [2025-07-22; online 2025-07-22]
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Circular RNA signature of aggressive CLL with t(14;19)(q32;q13). An ERIC study.
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The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts
Guinet B, Sharif BM, van der Valk T
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A U3 snoRNA is required for the regulation of chromatin dynamics and antiviral response in Drosophila melanogaster.
Jain S, Planells J, Regadas I, ..., Mannervik M, Visa N
Nucleic Acids Res. 53 (14) - [2025-07-19; online 2025-07-30]
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Immune development differs between preterm newborns fed mothers' own milk and donor milk.
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iScience 28 (7) 112918 [2025-07-18; online 2025-06-17]
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Establishing a Malonyl-CoA Biosensor for the Two Model Cyanobacteria Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942.
Cengic I, Hudson EP
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Ex Vivo Drug Sensitivity of Pleural Effusion-Derived Cells from Lung Cancer and Pleural Mesothelioma Patients Is Linked to Clinical Response.
Hutyra-Gram Ötvös R, Krynska H, Gudoityte G, ..., Seashore-Ludlow B, Dobra K
Cancers (Basel) 17 (14) - [2025-07-16; online 2025-07-16]
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Validation of Guidelines for Genetic Investigation of Myeloid Neoplasms with Germline Predisposition: Results from a Prospective Cohort Study.
Tesi B, Robelius A, Baskin B, ..., Hellström-Lindberg E, Baliakas P
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The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.
Lyu L, Fan Y, Vogt JK, ..., Pearson E, Pedersen O
Genome Med 17 (1) 78 [2025-07-15; online 2025-07-15]
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Structure-based discovery of positive allosteric modulators of the A1 adenosine receptor.
Nguyen ATN, Panel N, Vo DD, ..., Carlsson J, May LT
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PET imaging of platelet derived growth factor receptor β in lung fibrosis.
Wegrzyniak O, Lechi F, Rokka J, ..., Eriksson J, Eriksson O
EJNMMI Radiopharm Chem 10 (1) 44 [2025-07-15; online 2025-07-15]
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Arylsulfamates inhibit colonic Bacteroidota growth through a sulfatase-independent mechanism.
Crawford CJ, Tomlinson CWE, Gunawan C, ..., Williams SJ, Cartmell A
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The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets.
Knol JC, Lyu M, Böttger F, ..., Guo T, Jimenez CR
Cancer Cell 43 (7) 1328-1346.e8 [2025-07-14; online 2025-05-29]
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Multidimensional Decomposition and Ensemble Modeling of Histatin 1 and Its Siblings: Detailing Structure and Biological Function Using an Integrative Approach.
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Mosaic loss of chromosome Y and coronary atherosclerosis in men: insights into sex differences in cardiovascular risk from the SCAPIS study
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ApoB-containing lipoproteins: count, type, size, and risk of coronary artery disease.
Morze J, Melloni GEM, Wittenbecher C, ..., Sabatine MS, Marston NA
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Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
A genome resource for the marine annelid Platynereis spp.
Mutemi KN, Simakov O, Pan L, ..., Özpolat BD, Arendt D
BMC Genomics 26 (1) 665 [2025-07-14; online 2025-07-14]
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Anticancer effects and mechanisms of Pulsatilla chinensis, Bupleurum chinense and Polyporus umbellatus on human lung carcinoma and hepatoma cells.
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Pre-clinical safety and efficacy evaluation of Helicobacter Pylori neutrophil-activating protein (NAP)-armed CAR-T cells targeting B cell lymphomas.
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Tumor Acidosis Remodels the Glycocalyx to Control Lipid Scavenging and Ferroptosis
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PARP9-PARP13-PARP14 axis tunes colorectal cancer response to radiotherapy.
Prokarenkaite R, Kuodyte K, Gudoityte G, ..., Stankevicius V, Suziedelis K
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Evaluating Deep Learning Based Structure Prediction Methods on Antibody-Antigen Complexes
Fromm S, Ludaic M, Elofsson A
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Interdisciplinary Study on Drug-Induced-Phospholipidosis of Repurposing Libraries through Machine Learning and Experimental Evaluation in Different Cell Lines
Kuzikov M, Kalman A, Reinshagen J, ..., Gribbon P, Zaliani A
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Determinants of divergent Salmonella and Shigella epithelial colonization strategies resolved in human enteroids and colonoids.
Geiser P, Di Martino ML, Lopes ACC, ..., Eriksson J, Sellin ME
MBio 16 (7) e0091125 [2025-07-09; online 2025-05-30]
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Serum Exosomal Multi-Omic Signatures Stratify Glucose Tolerance in Cystic Fibrosis and Reveal Partial Therapeutic Reprogramming by CFTR Modulators
Umashankar B, Capraro A, Vijayan A, ..., Vafaee F, Waters SA
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Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy.
Sweetapple L, Kosek DM, Banijamali E, ..., Andersson ER, Petzold K
Nucleic Acids Res. 53 (13) - [2025-07-08; online 2025-07-17]
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Seeking Knowledge or Efficiency: Profiling students’ AI-use through survey-based Latent Class Analysis
Hugerth MW, Hugerth LW
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Plasma protein biomarkers of Plasmodium falciparum infection in pregnant women: a high-throughput proteomics study.
Kanoi BN, Waweru H, Kobia FM, ..., Gitaka J, Kamali-Moghaddam M
Front. Cell. Infect. Microbiol. 15 (-) 1594088 [2025-07-08; online 2025-07-08]
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Optimized Artificial Colonic Mucus Enabling Physiologically Relevant Diffusion Studies of Drugs, Particles, and Delivery Systems.
Tjakra M, Chakrapeesirisuk N, Jacobson M, ..., Teleki A, Bergström CAS
Mol. Pharm. 22 (7) 4032-4045 [2025-07-07; online 2025-06-10]
Alexandra Teleki Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Factor XII-driven coagulation traps bacterial infections.
Nickel KF, Jämsä A, Konrath S, ..., Herwald H, Renné T
J. Exp. Med. 222 (7) - [2025-07-07; online 2025-04-22]
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Development and retrospective validation of an artificial intelligence system for diagnostic assessment of prostate biopsies: study protocol.
Mulliqi N, Blilie A, Ji X, ..., Kartasalo K, Eklund M
BMJ Open 15 (7) e097591 [2025-07-07; online 2025-07-07]
DDLS Fellow Kimmo Kartasalo
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In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics
Jensen AEV, Crowell H, Pascual Reguant A, ..., Nilsson M, Marco Salas S
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Genetic mapping in the red mason bee implicates ANTSR as an ancient sex-determining locus in bees and ants
Rönneburg T, Taliadoros D, Olsson A, ..., Seidelmann K, Webster MT
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Toll-like receptor 4 (TLR-4) polymorphisms and asthma risk in rural and urban settings: findings from the UK biobank.
Kisiel MA, Rask-Andersen M, Johansson Å, Ek WE, Rask-Andersen A
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Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra.
Lapin J, Nilsson A, Wilhelm M, Käll L
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Development and in vitro evaluation of 1,4,7-triazacyclononane-coupled β-lactams against metallo-β-lactamase producing bacteria.
Shungube M, Reddy N, Ghazi T, ..., Govender T, Naicker T
RSC Adv. 15 (29) 23427-23440 [2025-07-04; online 2025-07-07]
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Highly Multiplexed Immunoassays for the Validation of Anti-GPCR Antibodies.
Bendes A, Dahl L, Sakmar TP, Schwenk JM, Kotliar IB
Methods in molecular biology (Clifton, N.J.) 2937 (-) 189-199 [2025-07-02; online 2025-07-02]
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Survival and Quality of Life After Isolated Hepatic Perfusion With Melphalan as a Treatment for Uveal Melanoma Liver Metastases: Final Results From the Phase III Randomized Controlled Trial SCANDIUM.
Olofsson Bagge R, Nelson A, Shafazand A, ..., Ny L, Lindnér P
Ann Surg 282 (1) 100-107 [2025-07-01; online 2024-02-29]
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Quantification of Endogenous Steroids and Hormonal Contraceptives in Human Plasma via Surrogate Calibration and UHPLC-MS/MS.
Su M, Drotleff B, Janker T, ..., Derntl B, Lämmerhofer M
Anal. Chem. 97 (25) 13496-13503 [2025-07-01; online 2025-06-20]
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Multi-Omics biological embeddings for ML-models
Otte LB, Hogstrand C, Mardinoglu A, Guo M
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Low nanomolar affinity to major grass pollen allergen Phl p 5 as achieved in an unmutated human antibody-lineage ancestor.
Essén M, Franciskovic E, Sele C, Godzwon M, Ohlin M
Front Immunol 16 (-) 1600778 [2025-07-01; online 2025-07-01]
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High-throughput DNA melt measurements enable improved models of DNA folding thermodynamics.
Ke Y, Sharma E, Wayment-Steele HK, ..., Marklund E, Greenleaf WJ
Nat Commun 16 (1) 5572 [2025-07-01; online 2025-07-01]
Emil Marklund SciLifeLab Fellow
PubMed DOI Crossref
Elevated KRAS protein level is associated with better survival in pancreatic cancer.
Stålberg SM, Silwal-Pandit L, Hamfjord J, ..., Skålhegg BS, Kure EH
BMC Cancer 25 (1) 1080 [2025-07-01; online 2025-07-01]
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Divergence of Leptin Receptor and Interleukin-6 Receptor Subunit b in Early Vertebrate Evolution and Physiological Insights from the Sea Lamprey.
Gong N, Barany A, Norstog JL, ..., McCormick SD, Sheridan MA
Mol. Biol. Evol. 42 (7) - [2025-07-01; online 2025-07-01]
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Benchmarking the AI-based diagnostic potential of plasma proteomics for neurodegenerative disease in 17,170 people.
An L, Pichet-Binette A, Hristovska I, ..., Hansson O, Vogel JW
medRxiv - (-) - [2025-07-01; online 2025-07-01]
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Activation of the ChvG-ChvI pathway promotes survival during cell wall stress in Agrobacterium tumefaciens.
Bouchier JM, Knebel E, Amstutz J, ..., Cava F, Brown PJB
Mol. Biol. Cell 36 (7) ar84 [2025-07-01; online 2025-05-15]
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A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins.
Sharapov S, Timoshchuk A, Zaytseva O, ..., Lauc G, Aulchenko YS
Nat Commun 16 (1) 5525 [2025-07-01; online 2025-07-01]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
When numbers matter: Rethinking the role of gene duplication on short evolutionary timescales.
Lindstedt F, Zhou Q, Milesi P
American journal of botany 112 (7) e70072 [2025-07-00; online 2025-07-09]
Pascal Milesi SciLifeLab Fellow
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Tumor hypoxia shapes natural killer cell anticancer activities.
Retamal MA, Salazar-Onfray F, González FE, Tittarelli A
J. Mol. Med. 103 (7) 755-777 [2025-07-00; online 2025-05-30]
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The value of mental science: we publish what matters.
Malhi GS, Adlington K, Al-Diwani A, ..., Zisman-Ilani Y, Fernandez-Egea E
Br J Psychiatry 227 (1) 429-433 [2025-07-00; online 2025-06-09]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Structural and functional insights into extreme thermal stability and activity of two GH12 domains of a multidomain glycosidase from a hyperthermophilic euryarchaeon.
Zayulina KS, Frolov EN, Stracke C, ..., Shugaeva TE, Kublanov IV
FEBS J. 292 (14) 3771-3794 [2025-07-00; online 2025-04-21]
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Sex programs functional protein level dimorphism in the zebrafish gastrointestinal tract
Niksirat H, Siino V, Steinbach C, Levander F
Aquaculture Reports 42 (-) 102775 [2025-07-00; online 2025-07-00]
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Pharmacogenomics in pediatric oncology patients with solid tumors related to chemotherapy-induced toxicity: A systematic review.
Hansson P, Blacker C, Uvdal H, ..., Green H, Ljungman G
Crit Rev Oncol Hematol 211 (-) 104720 [2025-07-00; online 2025-04-11]
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Nucleotide Binding to the ATP-cone in Anaerobic Ribonucleotide Reductases Allosterically Regulates Activity by Modulating Substrate Binding
Bimai O, Banerjee I, Rozman Grinberg I, ..., Sjöberg BM, Logan DT
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IDDF2025-ABS-0272 Distribution and prognostic impacts of enterobacteriaceae-derived virulence factor genes in colorectal cancer
Shi Z, Zhu T, Ren H, ..., Lin C, Zhong H
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Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management
Söderquist L, Joffard N, Scofield DG, ..., Karrenberg S, Sletvold N
Ecography 2025 (7) - [2025-07-00; online 2025-03-19]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Facile Synthesis of Oxazolidinones as Potential Antibacterial Agents.
Els SP, Govender KB, Sokhela MK, ..., Govender T, Naicker T
ChemistryOpen 14 (7) e202400432 [2025-07-00; online 2025-01-07]
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Emerging antibiotic resistance by various novel proteins/enzymes.
Sun S
Eur. J. Clin. Microbiol. Infect. Dis. 44 (7) 1551-1566 [2025-07-00; online 2025-04-15]
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Defining and benchmarking open problems in single-cell analysis.
Luecken MD, Gigante S, Burkhardt DB, ..., Theis FJ, Krishnaswamy S
Nat. Biotechnol. 43 (7) 1035-1040 [2025-07-00; online 2025-07-02]
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Computational exploration of FOXM1 inhibitors for glioblastoma: an integrated virtual screening and molecular dynamics simulation study.
Swati K, Varma SR, Parameswari RP, ..., Kumar D, Agarwal P
J Biomol Struct Dyn 43 (10) 5199-5217 [2025-07-00; online 2024-02-02]
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CombiANT reader: Deep learning-based automatic image processing tool to robustly quantify antibiotic interactions.
Hallström E, Fatsis-Kavalopoulos N, Bimpis M, ..., Hast A, Andersson DI
PLOS Digit Health 4 (7) e0000669 [2025-07-00; online 2025-07-08]
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Collaborative Duality of CircGLIS3(2) RNA and Protein in human Wound Repair.
Niu G, Toma MA, Geara J, ..., Sommar P, Xu Landén N
Adv Sci (Weinh) 12 (25) e2416784 [2025-07-00; online 2025-04-25]
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Bending the Course of Evolution: How Mutualistic Interactions Affect Macroevolutionary Dynamics of Diversification in Mimetic Ithomiini Butterflies.
Chazot N, Braga MP, Aubier TG, ..., Willmott KR, Elias M
Am Nat 206 (1) 1-15 [2025-07-00; online 2025-05-21]
DDLS Fellow Mariana Pires Braga
PubMed DOI Crossref
Bayesian network imputation methods applied to multi-omics data identify putative causal relationships in a type 2 diabetes dataset containing incomplete data: An IMI DIRECT Study.
Howey R, Adam J, Adamski J, ..., Viñuela A, Cordell HJ
PLoS Genet 21 (7) e1011776 [2025-07-00; online 2025-07-15]
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Author Correction: Large-scale network analysis of the cerebrospinal fluid proteome identifies molecular signatures of frontotemporal lobar degeneration.
Saloner R, Staffaroni AM, Dammer EB, ..., Casaletto KB, ALLFTD Consortium
Nat Aging 5 (7) 1372 [2025-07-00; online 2025-07-08]
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A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen.
Di Martino ML, Jenniches L, Bhetwal A, ..., Barquist L, Sellin ME
Nat. Genet. 57 (7) 1730-1741 [2025-07-00; online 2025-06-12]
Mikael Sellin SciLifeLab Fellow
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Accelerating Simulation-Based Inference with Variational Autoencoders
Nautiyal M, Shternshis A, Hellander A, Singh P
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Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
A novel mechanism for bacterial sporulation based on programmed peptidoglycan degradation.
Ramírez Carbó CA, Irazoki O, Venkatesan S, ..., Cava F, Nan B
bioRxiv - (-) - [2025-06-26; online 2025-06-26]
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Mitotic MTH1 inhibitor karonudib kills epithelial ovarian cancer independent of platinum sensitivity.
Hurley RM, Wagner JM, Kanakkanthara A, ..., Kaufmann SH, Hendrickson AEW
Exp Hematol Oncol 14 (1) 88 [2025-06-23; online 2025-06-23]
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Loss of genome maintenance is linked to mTOR complex 1 signaling and accelerates podocyte damage.
Braun F, Mandel AM, Blomberg L, ..., Schumacher B, Kurschat CE
JCI Insight 10 (12) - [2025-06-23; online 2025-05-20]
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Investigating Inflammation and Tissue Remodeling in ILD with [ 11 C]NES and [ 68 Ga]Ga-FAPI-46 PET Imaging
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ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets.
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IEEE Comput Graph Appl 45 (5) 64-77 [2025-06-20; online 2025-06-20]
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Modeling neuroinflammatory interactions between microglia and astrocytes in a human iPSC-based coculture platform.
Tujula I, Hyvärinen T, Lotila J, ..., Narkilahti S, Hagman S
Cell Commun. Signal 23 (1) 298 [2025-06-20; online 2025-06-20]
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Preclinical development and clinical safety assessment of a synthetic peptide conjugate enabling endogenous antibody binding to promote innate receptor engagement.
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Mol Ther Oncol 33 (2) 200954 [2025-06-18; online 2025-02-20]
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Identification of a Lipid-Exposed Extrahelical Binding Site for Positive Allosteric Modulators of the Dopamine D2 Receptor.
Lim HD, Bartuzi D, Keen AC, ..., Carlsson J, Lane JR
ACS Chem Neurosci 16 (12) 2295-2311 [2025-06-18; online 2025-05-15]
PubMed DOI Crossref
Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health.
Wang J, Zenere A, Wang X, ..., Uhlén M, Zhong W
Genome Med 17 (1) 68 [2025-06-17; online 2025-06-17]
DOI Crossref
The pcnB gene sustains Shigella flexneri virulence
Frisch T, Geiser P, Komi M, ..., Sellin ME, Di Martino ML
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PubMed DOI Crossref
In Vitro Evaluation of Flame-Made Calcium Phosphate Nanoparticles for Antigen Delivery and Immunostimulation.
Maheshwari A, Dookie R, Gaytán MO, Henriques-Normark B, Sotiriou GA
ACS Appl Nano Mater 8 (23) 11986-11996 [2025-06-13; online 2025-05-27]
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Exploring impacts of long-COVID-19 on the lungs: A triad of PET scans for perfusion, inflammation and tissue remodeling
Wegrzyniak O, Eriksson O, Ekbom E, ..., Antoni G, Lipcsey M
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PubMed DOI Crossref
Organocatalytic Switches of DNA Glycosylase OGG1 Catalyze a Highly Efficient AP-Lyase Function.
Kehler M, Zhou K, Kemas AM, ..., Lauschke VM, Michel M
Chemistry 31 (33) e202500382 [2025-06-12; online 2025-05-15]
PubMed DOI Crossref
Genomic insights into the genetic basis of the seed size and weight revealed by the Chinese peanut key landraces.
Wang J, Jiao B, Qu C, ..., Li C, Shan S
Theor Appl Genet 138 (7) 144 [2025-06-11; online 2025-06-11]
PubMed DOI Crossref
Correction: Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.
Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM
Sci Rep 15 (1) 20045 [2025-06-11; online 2025-06-11]
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Flame-Made Doped Iron Oxide Nanoparticles as Tracers for Magnetic Particle Imaging.
Ansari SR, Imhoff ED, Suárez-López YDC, ..., Rinaldi-Ramos CM, Teleki A
Chem Mater 37 (11) 4071-4084 [2025-06-10; online 2025-05-20]
Alexandra Teleki SciLifeLab Fellow
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Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system
Boers D, Chapleur O, Andersson AF, Schnürer A
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The burning glass effect of water droplets triggers a high light-induced calcium response in the chloroplast stroma.
Kuang D, Romand S, Zvereva AS, ..., Costa A, Stael S
Curr. Biol. 35 (11) 2642-2658.e7 [2025-06-09; online 2025-05-20]
DOI Crossref
Blind De Novo Design of Dual Cyclic Peptide Agonists Targeting GCGR and GLP1R
Li Q, Wiita E, Helleday T, Bryant P
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PubMed DOI Crossref
Contrasting Becker and Duchenne muscular dystrophy serum biomarker candidates by using data independent acquisition LC-MS/MS.
Johansson C, Schrama EJ, Kotol D, ..., Spitali P, Al-Khalili Szigyarto C
Skelet Muscle 15 (1) 15 [2025-06-07; online 2025-06-07]
DOI Crossref
Loss of Y chromosome in Alzheimer disease patients co-occurs with clonal hematopoiesis defined by post-zygotic point mutations outside canonical CHIP driver genes
Rychlicka-Buniowska E, Sarkisyan D, Horbacz M, ..., Filipowicz N, Dumanski JP
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PubMed DOI Crossref
Emotion generation and regulation in premenstrual dysphoric disorder: dysregulation of large-scale brain networks across the menstrual cycle.
Stiernman L, Dubol M, Comasco E, ..., Stiernman L, Bixo M
Biol. Psychiatry - (-) - [2025-06-06; online 2025-06-06]
Erika Comasco SciLifeLab Fellow
DOI Crossref
Disruption of undecaprenyl phosphate recycling suppresses ampC beta-lactamase induction in Pseudomonas aeruginosa
Klycheva K, Gyger J, Frund M, ..., Cava F, Fumeaux C
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PubMed DOI Crossref
Differentially expressed transcripts associated with depressive symptoms during pregnancy and postpartum.
Björvang RD, Vrettou M, Bujanda Cundin X, ..., Comasco E, Skalkidou A
Mol. Psychiatry - (-) - [2025-06-05; online 2025-06-05]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Supramolecular Nanochannels: Suprasome-Mediated Delivery of Ionophore to Regulate Transmembrane Zn2+ Ion Transport.
Prusty BM, Srimayee S, Karn R, ..., Winterhalter M, Manna D
Chemistry 31 (31) e202501013 [2025-06-03; online 2025-04-27]
PubMed DOI Crossref
Pathway activation model for personalized prediction of drug synergy.
Trac QT, Huang Y, Erkers T, ..., Pawitan Y, Vu TN
Elife 13 (-) - [2025-06-03; online 2025-06-03]
DOI Crossref
Pathway activation model for personalized prediction of drug synergy
Trac QT, Huang Y, Erkers T, ..., Pawitan Y, Vu TN
Elife 13 (-) - [2025-06-03; online 2025-06-03]
PubMed DOI Crossref
Evaluation of automatic cell free DNA extraction metrics using different blood collection tubes.
Andersson D, Kristiansson H, Luna Santamaría M, ..., Torinsson Naluai Å, Ståhlberg A
Sci Rep 15 (1) 19364 [2025-06-03; online 2025-06-03]
PubMed DOI Crossref
Chemical Switching: A Concept Inspired by Strategies from Biocatalysis and Organocatalysis.
Visnes T, Zhou K, Kemas AM, ..., Lauschke VM, Michel M
Chembiochem 26 (11) e202500220 [2025-06-03; online 2025-05-26]
PubMed DOI Crossref
A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics.
Shi M, Méar L, Karlsson M, ..., Uhlén M, Zhang C
Genome Biol. 26 (1) 152 [2025-06-03; online 2025-06-03]
PubMed DOI Crossref
ColBuilder: flexible structure generation of crosslinked collagen fibrils.
Monego D, Brosz M, Buck J, ..., Sugita Y, Gräter F
Bioinformatics 41 (6) - [2025-06-02; online 2025-05-05]
PubMed DOI Crossref
BiGSM: Bayesian inference of gene regulatory network via sparse modelling.
Qin H, Garbulowski M, Sonnhammer ELL, Chatterjee S
Bioinformatics 41 (6) - [2025-06-02; online 2025-06-09]
PubMed DOI Crossref
A Biological-Systems-Based Analyses Using Proteomic and Metabolic Network Inference Reveals Mechanistic Insights into Hepatic Lipid Accumulation: An IMI-DIRECT Study.
Atabaki NN, Coral DE, Pomares-Millan H, ..., Viñuela A, Franks PW
medRxiv - (-) - [2025-06-02; online 2025-06-02]
DOI Crossref
P-499 The Influence of the Rectal, Vaginal, and Seminal Microbiomes on Reproductive Outcome in Assisted Reproduction - A Multicenter Prospective Cohort Study
Behrendt-Møller I, Vomstein TK, Pereira M, ..., Hugerth LW, Nielsen HS
Hum. Reprod. 40 (Supplement_1) - [2025-06-01; online 2025-06-23]
DOI Crossref
P-129 Oxygen levels alter energy metabolism in bovine preimplantation embryos
Boskovic N, Ivask M, Yazgeldi Gunaydin G, ..., Daub CO, Kere J
Hum. Reprod. 40 (Supplement_1) - [2025-06-01; online 2025-06-23]
PubMed DOI Crossref
Effects of the choice of the continuous phase in droplet microfluidics on internal particle manipulation with acoustophoresis.
Shi Q, Baasch T, Liu Z, ..., Barbe L, Tenje M
J Acoust Soc Am 157 (6) 4262-4272 [2025-06-01; online 2025-06-06]
PubMed DOI Crossref
YCharOS protocol for antibody validation.
Monteiro FL, Voskuil JLA, Williams C
Nat Protoc 20 (6) 1389-1390 [2025-06-00; online 2024-12-18]
DOI Crossref
What does oxidative stress look like? Visualizing expression of redox-associated proteins with imaging-based spatial proteomics
Sigaeva A, Gnann C, Lundberg E
Free Radic. Biol. Med. 233 (-) S69 [2025-06-00; online 2025-06-00]
PubMed DOI Crossref
Vestibular modulation by stimulant derivatives in a pentameric ligand-gated ion channel.
Karlsson E, Andén O, Fan C, ..., Delarue M, Lindahl E
Br J Pharmacol 182 (12) 2790-2802 [2025-06-00; online 2025-03-11]
PubMed DOI Crossref
Using TCR-CAR dual signaling for precise cancer targeting.
Shahbazy M, Leo IR, Faridi P, Caron E
Trends Immunol. 46 (6) 435-437 [2025-06-00; online 2025-05-13]
PubMed DOI Crossref
Trajectories and dimensional phenotypes of depressive symptoms throughout pregnancy and postpartum in relation to prior premenstrual symptoms.
Schleimann-Jensen E, Sundström-Poromaa I, Meltzer-Brody S, ..., Skalkidou A, Comasco E
Br J Psychiatry 226 (6) 401-409 [2025-06-00; online 2025-06-20]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Toward clinical long-read genome sequencing for rare diseases.
Eisfeldt J, Ek M, Nordenskjöld M, Lindstrand A
Nat. Genet. 57 (6) 1334-1343 [2025-06-00; online 2025-05-07]
PubMed DOI Crossref
Subjective, behavioural and physiological correlates of stress in women using hormonal contraceptives.
Bürger Z, Kordowich C, Kübbeler J, ..., Derntl B, Kogler L
Br J Psychiatry 226 (6) 392-400 [2025-06-00; online 2025-06-13]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Shaping the future of precision medicine: plasma proteomics to uncover insights in thrombosis.
Johansson E, Iglesias MJ, Odeberg J, Edfors F
Expert Rev Proteomics 22 (6) 237-254 [2025-06-00; online 2025-06-13]
PubMed DOI Crossref
Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold.
Lidbrink SE, Howard RJ, Haloi N, Lindahl E
PLoS Comput Biol 21 (6) e1013187 [2025-06-00; online 2025-06-27]
PubMed DOI Crossref
Reprogramming Stars #22: Cellular Reprogramming as a Route for Decoding Neurodegenerative Disorders-An Interview with Dr. Janelle Drouin-Ouellet.
Drouin-Ouellet J, Lopes M, Pereira CF
Cell Reprogram 27 (3) 95-101 [2025-06-00; online 2025-05-20]
PubMed DOI Crossref
Psychiatric symptoms on the ovarian hormone roller-coaster.
Comasco E, Epperson CN, Kulkarni J
Br J Psychiatry 226 (6) 329-330 [2025-06-00; online 2025-06-18]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Postdiagnosis physical activity and dietary inflammatory and insulinemic potential with overall survival in men with nonmetastatic prostate cancer.
Lee DH, Rezende LFM, Ferrari G, ..., Mucci LA, Giovannucci EL
Eur. J. Epidemiol. 40 (6) 669-679 [2025-06-00; online 2025-05-28]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
NAT2 activity increases cytotoxicity of anthracycline antibiotics and HDAC inhibitors.
Rameika N, Tsiara I, Zhang X, ..., Globisch D, Sjöblom T
Biochim Biophys Acta Mol Basis Dis 1871 (5) 167755 [2025-06-00; online 2025-03-13]
PubMed DOI Crossref
Multimodal cell maps as a foundation for structural and functional genomics.
Schaffer LV, Hu M, Qian G, ..., Lundberg E, Ideker T
Nature 642 (8066) 222-231 [2025-06-00; online 2025-04-09]
PubMed DOI Crossref
Magnetic microfiber hyperthermia for synergistic antimicrobial activity against methicillin-resistant Staphylococcus aureus.
Ansari SR, Grimm D, Ramachandran RV, ..., Sotiriou GA, Teleki A
Mater Today Bio 32 (-) 101862 [2025-06-00; online 2025-05-12]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Large-scale network analysis of the cerebrospinal fluid proteome identifies molecular signatures of frontotemporal lobar degeneration.
Saloner R, Staffaroni AM, Dammer EB, ..., Casaletto KB, ALLFTD Consortium
Nat Aging 5 (6) 1143-1158 [2025-06-00; online 2025-05-16]
PubMed DOI Crossref
Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder.
Strom NI, Gerring ZF, Galimberti M, ..., Derks EM, Mattheisen M
Nat. Genet. 57 (6) 1389-1401 [2025-06-00; online 2025-05-13]
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Fish are poor sentinels for surveillance of riverine antimicrobial resistance.
Tskhay F, Köbsch C, Elena AX, ..., Berendonk TU, Klümper U
One Health 20 (-) 101026 [2025-06-00; online 2025-04-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Emerging multi-drug resistant and extended-spectrum β-lactamase (ESBL)-positive enterotoxigenic E. coli (ETEC) clones circulating in aquatic environments and in patients.
Joffré E, Martín-Rodríguez AJ, Justh de Neczpal A, von Mentzer A, Sjöling Å
One Health 20 (-) 100968 [2025-06-00; online 2025-01-10]
Astrid von Mentzer DDLS Fellow
PubMed DOI Crossref
Bioinspired Nanochitin-Based Porous Constructs for Light-Driven Whole-Cell Biotransformations.
Arumughan V, Medipally H, Torris A, ..., Kourist R, Kontturi E
Adv. Mater. Weinheim 37 (22) e2413058 [2025-06-00; online 2025-02-03]
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AI-first structural identification of pathogenic protein target interfaces.
Saluri M, Landreh M, Bryant P
PLoS Comput Biol 21 (6) e1013168 [2025-06-00; online 2025-06-26]
PubMed DOI Crossref
A universal language for finding mass spectrometry data patterns.
Damiani T, Jarmusch AK, Aron AT, ..., Dorrestein PC, Wang M
Nat. Methods 22 (6) 1247-1254 [2025-06-00; online 2025-05-12]
PubMed DOI Crossref
No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts.
Cerca J, Díaz PJ, Goubert C, ..., Rieseberg LH, Martin MD
Mobile DNA 16 (1) 23 [2025-05-31; online 2025-05-31]
PubMed DOI Crossref
KRIT1 heterozygous mutations are sufficient to induce a pathological phenotype in patient-derived iPSC models of cerebral cavernous malformation.
Arce M, Erzar I, Yang F, ..., Latini R, Magnusson PU
Cell Reports 44 (5) 115576 [2025-05-27; online 2025-04-14]
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Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales
Hallgren J, Dharamshi JE, Rodríguez-Gijón A, ..., Garcia SL, Jonas K
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Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol
Gschwind R, Bonnet M, Abramova A, ..., Bengtsson-Palme J, Ruppe E
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DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
1000 conifer genomes: Genome innovation, organisation and diversity
Nilsson O, Kalman TA, Delhomme N, ..., Nystedt B, Street N
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Age and Alzheimer's disease affect functional connectivity along separate axes of functional brain organization.
Rittmo J, Franzmeier N, Strandberg O, ..., Hansson O, Vogel JW
bioRxiv - (-) - [2025-05-25; online 2025-05-25]
DOI Crossref
From Structure to Immunogenicity: Decoding Correlated Dynamics at the Peptide MHC interface to Understand TCR Recognition
Resink T, Sala BM, Sun R, ..., Ljunggren HG, Achour A
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PubMed DOI Crossref
Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence.
Perez CR, Garmilla A, Nilsson A, ..., Lauffenburger DA, Birnbaum ME
Cell Syst 16 (5) 101260 [2025-05-21; online 2025-04-10]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Association of matrix metalloproteinase 7 and the alpha-chain of fibrinogen at baseline with response to methotrexate at 3 months in patients with early rheumatoid arthritis.
Hambardzumyan K, Hamsten C, Lourido L, ..., Jakobsson PJ, Idborg H
BMC Rheumatol 9 (1) 56 [2025-05-21; online 2025-05-21]
DOI Crossref
Pathway activation model for personalized prediction of drug synergy
Trac QT, Huang Y, Erkers T, ..., Pawitan Y, Vu TN
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PubMed DOI Crossref
Error in Affiliations.
JAMA 333 (19) 1733 [2025-05-20; online 2025-04-23]
PubMed DOI Crossref
Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.
Doktorova M, Daum S, Reagle TR, ..., Kenworthy AK, Levental I
Proc. Natl. Acad. Sci. U.S.A. 122 (20) e2417024122 [2025-05-20; online 2025-05-13]
PubMed DOI Crossref
Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World.
Seal S, Mahale M, García-Ortegón M, ..., Carpenter AE, Bender A
Chem. Res. Toxicol. 38 (5) 759-807 [2025-05-19; online 2025-05-02]
PubMed DOI Crossref
Gender differences in global antimicrobial resistance
Salehi M, Laitinen V, Bhanushali S, ..., Pärnänen K, Lahti L
NPJ Biofilms Microbiomes 11 (1) 79 [2025-05-19; online 2025-05-19]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Genetic Isolation among Four Lineages of Silene nutans.
Postel Z, Martin H, Roux C, ..., Vekemans X, Touzet P
Plant Cell Physiol. 66 (4) 514-528 [2025-05-17; online 2024-09-26]
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Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach.
Menz G, Engblom S
Bull. Math. Biol. 87 (6) 74 [2025-05-16; online 2025-05-16]
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Chromosome-level genome assembly of Norwegian wild alpine reindeer ( Rangifer tarandus tarandus )
Tørresen OK, Tooming-Klunderud A, Skage M, ..., Mysterud A, Jakobsen KS
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Cell shapes decode molecular phenotypes in image-based spatial proteomics.
Le T, Leineweber WD, Viana MP, ..., Rafelski SM, Lundberg E
bioRxiv - (-) - [2025-05-16; online 2025-05-16]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Uracil-induced replication stress drives mutations, genome instability, anti-cancer treatment efficacy, and resistance.
Mortusewicz O, Haslam J, Gad H, Helleday T
Mol. Cell 85 (10) 1897-1906 [2025-05-15; online 2025-05-17]
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Ribosomes modulate transcriptome abundance via generalized frameshift and out-of-frame mRNA decay.
Zhang Y, Nersisyan L, Fürst E, ..., Piazza I, Pelechano V
Mol. Cell 85 (10) 2017-2031.e7 [2025-05-15; online 2025-05-17]
PubMed DOI Crossref
Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes.
Beckwith KS, Brunner A, Morero NR, Jungmann R, Ellenberg J
Cell 188 (10) 2656-2669.e17 [2025-05-15; online 2025-03-24]
PubMed DOI Crossref
Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA.
Bobadilla Ugarte P, Halter S, Mutte SK, ..., Westphal AH, Swarts DC
Mol. Cell 85 (10) 1920-1937.e10 [2025-05-15; online 2025-04-26]
DOI Crossref
Community-promoted antibiotic resistance genes show increased dissemination among pathogens
Lund D, Johnning A, Holmström M, ..., Bengtsson-Palme J, Kristiansson E
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DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A systematic implementation of padlock probing-based rolling circle amplification in an integrated microfluidic device for quantitative biomolecular analyses.
Caneira CRF, Rosa RR, Chu V, ..., Soares RRG, Conde JP
Anal. Chim. Acta 1351 (-) 343834 [2025-05-15; online 2025-02-23]
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Uridine cytidine kinases dictate the therapeutic response of molnupiravir via its bioactivation
Shu H, Sharm S, Alam S, ..., Rudd SG, Zhang SM
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PubMed DOI Crossref
Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.
Baek JW, Lim S, Park N, ..., Koh A, Lee S
NPJ Biofilms Microbiomes 11 (1) 78 [2025-05-14; online 2025-05-14]
DOI Crossref
AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI
Cunha I, Panconi L, Bauer S, ..., Le Marois A, Griffié J
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PubMed DOI Crossref
The developmental factor TBX3 engages with the Wnt/β-catenin transcriptional complex in colorectal cancer to regulate metastasis genes.
Jauregi-Miguel A, Söderholm S, Weiss T, ..., Sheng G, Cantù C
Proc. Natl. Acad. Sci. U.S.A. 122 (19) e2419691122 [2025-05-13; online 2025-05-09]
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Plasma membrane labelling efficiency, internalization and partitioning of functionalized fluorescent lipids as a function of lipid structure
Sezgin E
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PubMed DOI Crossref
Loss of lipid asymmetry facilitates plasma membrane blebbing by decreasing membrane lipid packing.
Wang HY, Rumin A, Doktorova M, ..., Levental KR, Levental I
Proc. Natl. Acad. Sci. U.S.A. 122 (19) e2417145122 [2025-05-13; online 2025-05-05]
DOI Crossref
Elevated KRAS protein level is associated with better survival in pancreatic cancer
Stålberg SM, Silwal-Pandit L, Hamfjord J, ..., Skålhegg BS, Kure EH
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PubMed DOI Crossref
Correction: Senataxin prevents replicative stress induced by the Myc oncogene.
Sberna S, Filipuzzi M, Bianchi N, ..., Curti L, Campaner S
Cell Death Dis 16 (1) 377 [2025-05-12; online 2025-05-12]
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Chemically Recyclable and Enzymatically Degradable Thermostable Polyesters with Inherent Strain from α-Pinene-Derived Chiral Diols
Ranjani G, Subramaniyan S, Lopez-Lorenzo X, Hakkarainen M, Syrén PO
ACS Sustainable Chem. Eng. 13 (18) 6696-6705 [2025-05-12; online 2025-04-25]
PubMed DOI Crossref
The effectiveness of selection in a species affects the direction of amino acid frequency evolution.
McShea H, Wheeler AL, Goodman P, ..., Huttley G, Masel J
bioRxiv - (-) - [2025-05-10; online 2025-05-10]
PubMed DOI Crossref
Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours.
Tran BM, Larsson J, Grip A, Karempudi P, Elf J
Nat Commun 16 (1) 4366 [2025-05-10; online 2025-05-10]
PubMed DOI Crossref
Mechanisms of autoimmune-mediated paraneoplastic syndromes: immune tolerance and disease pathogenesis.
Pérez-Bucio C, Behere A, Landegren N
Front Immunol 16 (-) 1608934 [2025-05-09; online 2025-05-09]
PubMed DOI Crossref
Evaluation of unsupervised learning algorithms for the classification of behavior from pose estimation data.
Mlost J, Dawli R, Liu X, Costa AR, Pollak Dorocic I
Patterns (N Y) 6 (5) 101237 [2025-05-09; online 2025-04-22]
Iskra Pollak Dorocic SciLifeLab Fellow
PubMed DOI Crossref
The Central Role of Ribosomal Proteins in p53 Regulation.
Lindström MS
Cancers (Basel) 17 (10) - [2025-05-08; online 2025-05-08]
PubMed DOI Crossref
INLAomics for Scalable and Interpretable Spatial Multiomic Data Integration.
Arnroth L, Vickovic S
bioRxiv - (-) - [2025-05-08; online 2025-05-08]
PubMed DOI Crossref
Genome-wide association study of myocarditis and pericarditis following COVID-19 vaccination.
Cavalli M, Eriksson N, Baron T, ..., Hallberg P, Wadelius M
NPJ Vaccines 10 (1) 88 [2025-05-08; online 2025-05-08]
PubMed DOI Crossref
Topology-based metrics for finding the optimal sparsity in gene regulatory network inference.
Lundqvist N, Garbulowski M, Hillerton T, Sonnhammer ELL
Bioinformatics 41 (5) - [2025-05-06; online 2025-03-24]
PubMed DOI Crossref
De novo clustering of large long-read transcriptome datasets with isONclust3.
Petri AJ, Sahlin K
Bioinformatics 41 (5) - [2025-05-06; online 2025-04-23]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Single-Shot Design of a Cyclic Peptide Inhibitor of HIV-1 Membrane Fusion with EvoBind
Daumiller D, Giammarino F, Li Q, ..., Ceña Diez R, Bryant P
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Limits of deep-learning-based RNA prediction methods
Ludaic M, Elofsson A
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Gene regulatory networks linked to GABA signalling emerge as relevant for glioblastoma pathogenesis
Nissen I, Dakhel S, Chakraborty C, ..., Erdem C, Remeseiro S
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Cemal Erdem DDLS Fellow
DOI Crossref
Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits
Kvastad L, Kollotzek A, Saghaleyni R, ..., Cao T, Lappalainen T
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PubMed DOI Crossref
Open-Source and FAIR Research Software for Proteomics.
Perez-Riverol Y, Bittremieux W, Noble WS, ..., Käll L, Fondrie WE
J. Proteome Res. 24 (5) 2222-2234 [2025-05-02; online 2025-04-23]
PubMed DOI Crossref
Mosaic loss of Y chromosome and mortality after coronary angiography.
Weyrich M, Zewinger S, Sarakpi T, ..., Speer T, Zeiher AM
Eur. Heart J. 46 (17) 1603-1616 [2025-05-02; online 2025-02-12]
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How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate.
Freestone J, Käll L, Noble WS, Keich U
J. Proteome Res. 24 (5) 2266-2279 [2025-05-02; online 2025-03-31]
PubMed DOI Crossref
Dual-Nuclide Biodistribution and Therapeutic Evaluation of a Novel Antibody-Based Radiopharmaceutical in Anaplastic Thyroid Cancer Xenografts.
Lundgren Mortensen AC, Berglund H, Jha P, ..., Frejd FY, Nestor M
Mol. Cancer Ther. 24 (5) 753-762 [2025-05-02; online 2025-02-20]
PubMed DOI Crossref
Analysis of canine gene constraint identifies new variants for orofacial clefts and stature.
Buckley RM, Bilgen N, Harris AC, ..., Boyko AR, Ostrander EA
Genome Res 35 (5) 1080-1093 [2025-05-02; online 2025-05-02]
PubMed DOI Crossref
Cryo-EM structure of the human monocarboxylate transporter 10.
Bågenholm V, Nordlin KP, Pasquadibisceglie A, ..., Pedersen PA, Gourdon P
Structure 33 (5) 891-902.e4 [2025-05-01; online 2025-03-19]
PubMed DOI Crossref
Using machine learning to investigate the influence of the prenatal chemical exposome on neurodevelopment of young children.
England-Mason G, MacEachern SJ, Amador K, ..., Forkert ND, Dewey D
Neurotoxicology 108 (-) 218-230 [2025-05-00; online 2025-04-11]
PubMed DOI Crossref
Unraveling the influence of astrocytes on endothelial cell transcription: Towards understanding blood-brain barrier in vitro models' dynamics.
Zamproni LN, Gökçe B, Venckute Larsson J, ..., Porcionatto MA, Herland A
Brain Res Bull 224 (-) 111328 [2025-05-00; online 2025-03-31]
PubMed DOI Crossref
The multifaceted role of post-translational modifications of LSD1 in cellular processes and disease pathogenesis.
Li Y, Wang B, Zheng Y, ..., Gao Y, Chen X
Genes Dis 12 (3) 101307 [2025-05-00; online 2024-04-15]
PubMed DOI Crossref
The Role of Artificial Intelligence in the Evaluation of Prostate Pathology.
Egevad L, Camilloni A, Delahunt B, ..., Eklund M, Kartasalo K
Pathol Int 75 (5) 213-220 [2025-05-00; online 2025-04-14]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
The Epstein-Barr virus deubiquitinase BPLF1 regulates stress-induced ribosome UFMylation and reticulophagy.
Liu J, Nagy N, Ayala-Torres C, ..., Larsson O, Masucci MG
Autophagy 21 (5) 996-1018 [2025-05-00; online 2025-01-22]
DOI Crossref
Sustained Release of Proteins Using Region‐Specific Tunable Degradability in Hydrogels through 3D Photopatterning and Complimentary Labile Bond Chemistry
Kivijärvi T, Cerrato CP, Kohlan TB, ..., Arsenian‐Henriksson M, Finne‐Wistrand A
Adv. Funct. Mater. 35 (22) - [2025-05-00; online 2025-01-19]
PubMed DOI Crossref
Structural and antigen-binding surface definition of an anti-CD93 monoclonal antibody for the treatment of degenerative vascular eye diseases.
Raucci L, Perrone CD, Barbera S, ..., Galvagni F, Orlandini M
Int J Biol Macromol 309 (Pt 4) 143118 [2025-05-00; online 2025-04-12]
PubMed DOI Crossref
Spatial miRNomics: towards the integration of microRNAs in spatial biology.
Robles-Remacho A, Nilsson M
Nat. Rev. Genet. 26 (5) 291-292 [2025-05-00; online 2025-02-07]
PubMed DOI Crossref
Reply to the Letter to the Editor regarding "Early detection of pancreatic cancer: Study design and analytical considerations in biomarker discovery and early phase validation studies".
Mahoney DM, Smith LM, Wang QL, ..., Oberg AL, PCDC Biostatistics Subcommittee
Pancreatology 25 (3) 487-488 [2025-05-00; online 2025-05-10]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Rare and low-frequency variants in families with otitis media.
Santos-Cortez RLP, Elling CL, Gomez HZ, ..., Hafrén L, Ryan AF
J. Mol. Med. 103 (5) 559-570 [2025-05-00; online 2025-04-04]
PubMed DOI Crossref
Psychiatric genetics in the diverse landscape of Latin American populations.
Bruxel EM, Rovaris DL, Belangero SI, ..., Giusti-Rodríguez P, Montalvo-Ortiz JL
Nat. Genet. 57 (5) 1074-1088 [2025-05-00; online 2025-04-02]
PubMed DOI Crossref
Precision nutrition for cardiometabolic diseases.
Guasch-Ferré M, Wittenbecher C, Palmnäs M, ..., Sargent JL, Merino J
Nat. Med. 31 (5) 1444-1453 [2025-05-00; online 2025-04-30]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Plasticity of the mammalian integrated stress response.
Chen CW, Papadopoli D, Szkop KJ, ..., Topisirovic I, Hatzoglou M
Nature 641 (8065) 1319-1328 [2025-05-00; online 2025-03-26]
PubMed DOI Crossref
Physical Color Calibration of Digital Pathology Scanners for Robust Artificial Intelligence-Assisted Cancer Diagnosis.
Ji X, Salmon R, Mulliqi N, ..., Eklund M, Kartasalo K
Mod. Pathol. 38 (5) 100715 [2025-05-00; online 2025-01-16]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
MEA-seqX: High-Resolution Profiling of Large-Scale Electrophysiological and Transcriptional Network Dynamics.
Emery BA, Hu X, Klütsch D, ..., Kempermann G, Amin H
Adv Sci (Weinh) 12 (20) e2412373 [2025-05-00; online 2025-04-30]
PubMed DOI Crossref
Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts.
Kimmel M, Tong B, Devall AE, ..., Skalkidou A, Hugerth LW
Biol Psychiatry Glob Open Sci 5 (3) 100453 [2025-05-00; online 2025-01-30]
PubMed DOI Crossref
In Vitro Elimination of Highly Multidrug-Resistant Bacteria by the Lactic Acid Bacterial Drug Candidate ILP100.
Lofton-Tomenius H, Pang Y, Pallin A, ..., Roos S, Phillipson M
Infect Dis Ther 14 (5) 1119-1131 [2025-05-00; online 2025-03-31]
PubMed DOI Crossref
Identification and interpretation of risk factors for Charcot foot. Reply to Milbourn VEL, Bus SA, Game F, van Netten JJ [letter].
Tsatsaris G, Ekberg NR, Fall T, Catrina SB
Diabetologia 68 (5) 1078-1079 [2025-05-00; online 2025-02-20]
PubMed DOI Crossref
Error Reduction in Leukemia Machine Learning Classification With Conformal Prediction.
Lysenkova Wiklander M, Zachariah D, Krali O, Nordlund J
JCO Clin Cancer Inform 9 (-) e2400324 [2025-05-00; online 2025-05-28]
PubMed DOI Crossref
Dairy intake, plasma metabolome, and risk of type 2 diabetes in a population-based cohort.
Zhang S, Janzi S, Du Y, ..., Borné Y, Sonestedt E
Am. J. Clin. Nutr. 121 (5) 1137-1148 [2025-05-00; online 2025-04-03]
PubMed DOI Crossref
Cell-intrinsic metabolic phenotypes identified in patients with glioblastoma, using mass spectrometry imaging of 13C-labelled glucose metabolism.
Tsyben A, Dannhorn A, Hamm G, ..., Mair R, Brindle KM
Nat Metab 7 (5) 928-939 [2025-05-00; online 2025-05-19]
DOI Crossref
Advancing transdisciplinary research on Madagascar's grassy biomes to support resilience in ecosystems and livelihoods
Phelps LN, Razanatsoa E, Davis DS, ..., Vorontsova MS, Lehmann CER
Ecological Monographs 95 (2) - [2025-05-00; online 2025-07-15]
DOI Crossref
Small molecule bioactivity benchmarks are often well-predicted by counting cells
Seal S, Dee W, Shah A, ..., Bender A, Carpenter AE
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PubMed DOI Crossref
Maternal uniparental disomy of chromosome 7: how chromosome 7-encoded imprinted genes contribute to the Silver-Russell phenotype.
Begemann M, Lengyel A, Pinti E, ..., Kraft F, Eggermann T
Clin Epigenetics 17 (1) 70 [2025-04-30; online 2025-04-30]
DOI Crossref
High Content Imaging Applications of Advanced and Translational Disease Models in Drug Discovery and Development
Cui W, Haffa M, Massai F, ..., Axelsson H, Seashore-Ludlow B
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PubMed DOI Crossref
Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization.
Abramsson ML, Corey RA, Skerle JL, ..., Stansfeld PJ, Landreh M
Elife 14 (-) - [2025-04-30; online 2025-04-30]
DOI Crossref
Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Skerle JL, ..., Stansfeld PJ, Landreh M
Elife 14 (-) - [2025-04-30; online 2025-04-30]
DOI Crossref
Author response: Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Skerle JL, ..., Stansfeld PJ, Landreh M
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PubMed DOI Crossref
The overlooked trio: sleep duration, sampling time and physical exercise alter levels of olink-assessed blood biomarkers of cardiovascular risk.
Brandão LEM, Zhang L, Grip A, ..., Benedict C, Cedernaes J
Biomark Res 13 (1) 67 [2025-04-29; online 2025-04-29]
Daniel Espes SciLifeLab Fellow
PubMed DOI Crossref
GenePioneer: a comprehensive Python package for identification of essential genes and modules in cancer.
Haerianardakani A, Taheri G
Bioinform Adv 5 (1) vbaf094 [2025-04-29; online 2025-04-29]
PubMed DOI Crossref
Quantifying Acyl Chain Interdigitation in Simulated Bilayers via Direct Transbilayer Interactions.
Chaisson EH, Heberle FA, Doktorova M
J Chem Inf Model 65 (8) 3879-3885 [2025-04-28; online 2025-04-16]
DOI Crossref
Mitochondrial Dysfunction Induces Hepatic Lipid Accumulation and Inflammatory Responses in mtDNA Mutator Mice
Ross JM, Kim A, Berthod K, ..., Olson L, Coppotelli G
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DOI Crossref
Low anabolic independence emerges when cultivating more than three bacterial species together
Pacheco-Valenciana A, Tausch A, Veseli I, ..., Andersson AF, Garcia SL
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DOI Crossref
Multiplexed Deep Visual Proteomics Unveils Spatial Heterogeneity and Rare Endocrine States in Human Adult Pancreatic Islets
Mardamshina M, Dorka N, Thielert M, ..., Mann M, Lundberg E
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DOI Crossref
The time dimension matters: Improving mode of action classification with live-cell imaging
Forsgren E, Rietdijk J, Holmberg D, ..., Spjuth O, Jonsson P
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Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem
Khodadadi Z, Trpevski D, Lindroos R, Hellgren Kotaleski J
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Author response: Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem
Khodadadi Z, Trpevski D, Lindroos R, Hellgren Kotaleski J
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PubMed DOI Crossref
Astrocytic lipid droplets contain MHCII and may act as cogs in the antigen presentation machinery.
Beretta C, Dakhel A, Eltom K, ..., Michno WP, Erlandsson A
J Neuroinflammation 22 (1) 117 [2025-04-24; online 2025-04-24]
PubMed DOI Crossref
The evaluation of biogenic silica in brackish and freshwater strains reveals links between phylogeny and silica accumulation in picocyanobacteria.
Aguilera A, Lundin D, Charalampous E, ..., Farnelid H, Pinhassi J
Applied and environmental microbiology 91 (4) e0252724 [2025-04-23; online 2025-03-27]
PubMed DOI Crossref
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry.
Schulte D, Šiborová M, Käll L, Snijder J
Elife 14 (-) - [2025-04-23; online 2025-04-23]
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Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry
Schulte D, Šiborová M, Käll L, Snijder J
Elife 14 (-) - [2025-04-23; online 2025-04-23]
PubMed DOI Crossref
Mechanisms of chemotherapy failure in refractory/relapsed acute myeloid leukemia: the role of cytarabine resistance and mitochondrial metabolism.
Yeon Chae S, Jang SY, Kim J, ..., Kim JS, Kim HI
Cell Death Dis 16 (1) 331 [2025-04-23; online 2025-04-23]
PubMed DOI Crossref
A rich conformational palette underlies human CaV2.1-channel availability.
Wang K, Nilsson M, Angelini M, ..., Elinder F, Pantazis A
Nat Commun 16 (1) 3815 [2025-04-23; online 2025-04-23]
PubMed DOI Crossref
Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen.
Stomper J, Niroula A, Belizaire R, ..., Bandaru TS, Ebert BL
Cell Reports 44 (4) 115494 [2025-04-22; online 2025-04-02]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Omics Approach for Personalised Prevention of Type 2 Diabetes Mellitus for African and European Populations (OPTIMA): a protocol paper.
Goedecke JH, Danquah I, Abidha CA, ..., Landberg R, Olsson T
BMJ Open 15 (4) e099108 [2025-04-22; online 2025-04-22]
Clemens Wittenbecher DDLS Fellow
DOI Crossref
Genetics of canine cancer: a guide for the veterinary oncologist
Arendt ML, van der Heiden AD, Pensch R, Lindblad-Toh K
Vet. Oncol. 2 (1) - [2025-04-22; online 2025-04-22]
PubMed DOI Crossref
Discovery of an ene-reductase initiating resveratrol catabolism in gut microbiota and its application in disease treatment.
Dong Z, Yu P, Li J, ..., Gu Y, Yang Y
Cell Reports 44 (4) 115517 [2025-04-22; online 2025-04-04]
DOI Crossref
Abstract 5300: Spatially resolved integrated omics profiling for ADC targets in urothelial carcinoma
Panshikar P, O´Roberts E, Krantz D, ..., Ullén A, Stadler C
Cancer Res. 85 (8_Supplement_1) 5300-5300 [2025-04-21; online 2025-04-21]
DOI Crossref
Abstract 176: Simultaneous spatial characterisation of copy number change and immune cell profiling using DNA FISH and multiplexed immunofluorescence
O'Roberts EM, Panshikar P, Li-Wang X, ..., Bienko M, Stadler C
Cancer Res. 85 (8_Supplement_1) 176-176 [2025-04-21; online 2025-04-21]
DOI Crossref
Nanobinders for Synaptotagmin 1 enable the analysis of synaptic vesicle dynamics in rodent and human models
Goel R, Jevdokimenko K, Rehm R, ..., Rizzoli SO, Fornasiero EF
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DOI Crossref
A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila
Papachristos K, Miller WJ, Klasson L
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PubMed DOI Crossref
Dynamically chiral phosphonic acid-type metallo-β-lactamase inhibitors.
Gulyás KV, Zhou L, Salamonsen D, ..., Zhu W, Erdélyi M
Commun Chem 8 (1) 119 [2025-04-19; online 2025-04-19]
PubMed DOI Crossref
Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.
Kretsch RC, Albrecht R, Andersen ES, ..., Moult J, Kryshtafovych A
bioRxiv - (-) - [2025-04-18; online 2025-04-18]
DOI Crossref
Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution
Zervakis PI, Postel Z, Losvik A, ..., Churcher A, Slotte T
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PubMed DOI Crossref
Functionalized gold nanoflowers on carbon screen-printed electrodes: an electrochemical platform for biosensing hemagglutinin protein of influenza A H1N1 virus.
Torres-Méndez CE, Nandi S, Martinovic K, ..., Mestres G, Kamali-Moghaddam M
Beilstein J Nanotechnol 16 (-) 540-550 [2025-04-16; online 2025-04-16]
DOI Crossref
AlphaFold3 at CASP16
Elofsson A
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PubMed DOI Crossref
Integrated computational and biosensor-based strategies for the discovery of allosteric SMYD3 ligands using diperodon as a starting point.
FitzGerald EA, Rachman MM, Cederfelt D, ..., Koehler K, Danielson UH
Bioorg. Med. Chem. 121 (-) 118134 [2025-04-15; online 2025-02-25]
DOI Crossref
In Vitro Evaluation of Flame-Made Calcium Phosphate Nanoparticles for Antigen Delivery and Immunostimulation
Maheshwari A, Dookie R, Gaytán MO, Henriques-Normark B, Sotiriou GA
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Phenotypic Antibiotic Susceptibility Testing at the limit of one bacterial cell
Johansson L, Ahmad I, Larsson J, ..., Fange D, Elf J
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DOI Crossref
A Systematic Host-Centric Approach to Identifying Repurposed Drugs for Viral Infections
Tampere M, Asp E, Rietdijk J, ..., Seashore-Ludlow B, Östling P
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PubMed DOI Crossref
Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor.
Haloi N, Karlsson E, Delarue M, Howard RJ, Lindahl E
Sci Adv 11 (15) eadr0797 [2025-04-11; online 2025-04-11]
PubMed DOI Crossref
Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder.
Strom NI, Gerring ZF, Galimberti M, ..., Derks EM, Mattheisen M
medRxiv - (-) - [2025-04-08; online 2025-04-08]
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Cotranslational membrane insertion of the voltage-sensitive K+ channel KvAP.
Westerfield JM, Kozojedová P, Juli C, Metola A, von Heijne G
Proc. Natl. Acad. Sci. U.S.A. 122 (14) e2412492122 [2025-04-08; online 2025-03-31]
DOI Crossref
Revisiting the African mtDNA Landscape: A Continental Update from Complete Mitochondrial Genomes
Lankheet I, Chowdhury A, Tellgren-Roth C, ..., Malmström H, Schlebusch CM
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G-quadruplex profiling in complex tissues using single-cell CUT&Tag
Lyu J, Hetey S, Castelo-Branco G, Bartosovic M, Elsässer SJ
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PubMed DOI Crossref
Vaccine-enhanced competition permits rational bacterial strain replacement in the gut.
Lentsch V, Woller A, Rocker A, ..., Diard M, Slack E
Science (New York, N.Y.) 388 (6742) 74-81 [2025-04-04; online 2025-04-03]
PubMed DOI Crossref
Long-term gamma-aminobutyric acid (GABA) treatment fails to regain beta-cell function in longstanding type 1 diabetes in a randomized trial.
Hill H, Lundkvist P, Tsatsaris G, ..., Espes D, Carlsson PO
Sci Rep 15 (1) 11530 [2025-04-04; online 2025-04-04]
Daniel Espes SciLifeLab Fellow
DOI Crossref
Revealing molecular determinants of ligand efficacy and affinity at the D 2 dopamine receptor through molecular dynamics simulations
Chen Y, Kahlous NA, Saarinen M, ..., Delemotte L, Carlsson J
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Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra
Lapin J, Nilsson A, Wilhelm M, Käll L
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PubMed DOI Crossref
Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions.
Shiver AL, Sun J, Culver R, ..., Deutschbauer AM, Huang KC
Cell 188 (7) 2003-2021.e19 [2025-04-03; online 2025-03-10]
DOI Crossref
Computational design of constitutively active mutants of Dopamine D2 receptor inspired by ligand-independent activation mechanisms
Chen Y, Saarinen M, Naraine A, ..., Svenningsson P, Delemotte L
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PubMed DOI Crossref
Affinity maturation and optimization of CD44v6-targeting antibodies for molecular radiotherapy.
Mortensen ACL, Hofström C, Persson H, ..., Frejd FY, Nestor M
Nucl. Med. Biol. 144-145 (-) 109012 [2025-04-03; online 2025-04-03]
PubMed DOI Crossref
Oxygen level alters energy metabolism in bovine preimplantation embryos.
Boskovic N, Ivask M, Yazgeldi Gunaydin G, ..., Daub CO, Kere J
Sci Rep 15 (1) 11327 [2025-04-02; online 2025-04-02]
PubMed DOI Crossref
Mapping Lesions That Cause Psychosis to a Human Brain Circuit and Proposed Stimulation Target.
Pines AR, Frandsen SB, Drew W, ..., Silbersweig D, Siddiqi SH
JAMA Psychiatry 82 (4) 368-378 [2025-04-01; online 2025-02-12]
PubMed DOI Crossref
How sub-optimal are the neural representations: show me your null model.
Lenninger M, Kumar A
J. Neurophysiol. 133 (4) 1083-1085 [2025-04-01; online 2025-02-27]
PubMed DOI Crossref
Exploiting NRF2-ARE pathway activation in papillary renal cell carcinoma.
Angori S, Lakshminarayanan H, Banaei-Esfahani A, ..., Schraml P, Moch H
Int. J. Cancer 156 (7) 1457-1469 [2025-04-01; online 2024-12-20]
PubMed DOI Crossref
Author Correction: Characterization of a second class Ie ribonucleotide reductase.
John J, Lundin D, Branca RM, ..., Lebrette H, Högbom M
Commun Biol 8 (1) 532 [2025-04-01; online 2025-04-01]
PubMed DOI Crossref
Visualization for Diagnostic Review of Copy Number Variants in Complex DNA Sequencing Data.
Stahlbom E, Molin J, Lundstrom C, Ynnerman A
IEEE Trans Vis Comput Graph 31 (4) 2211-2222 [2025-04-00; online 2025-02-27]
PubMed DOI Crossref
The need to implement FAIR principles in biomolecular simulations.
Amaro RE, Åqvist J, Bahar I, ..., Zacharias M, Orozco M
Nat. Methods 22 (4) 641-645 [2025-04-00; online 2025-04-03]
PubMed DOI Crossref
The impact of pharmacotherapy for premenstrual dysphoric disorder on sleep.
Meth EMS, Nôga DA, Dubol M, ..., Sundström-Poromaa I, Benedict C
Sleep Med Rev 80 (-) 102069 [2025-04-00; online 2025-02-07]
DOI Crossref
Synthesis of novel tetrahydrobenzo[b]thiophene-3-carbonitrile (THBTC)-based heterocycles: Structural insights, reactivity profiles, and in-silico bioactivity studies
Sebhaoui J, Ashraf S, Iqbal S, ..., Turkez H, Mardinoglu A
Journal of Molecular Structure 1326 (-) 141110 [2025-04-00; online 2025-04-00]
PubMed DOI Crossref
Reprogramming Stars #21: RNA Regulatory Mechanisms That Instruct Cell Identity-An Interview with Dr. Bruno Di Stefano.
Di Stefano B, Lopes M, Pereira CF
Cell Reprogram 27 (2) 47-52 [2025-04-00; online 2025-03-20]
PubMed DOI Crossref
Putting cancer immunotherapy into spatial context in the clinic.
Engblom C, Lundeberg J
Nat. Biotechnol. 43 (4) 471-476 [2025-04-00; online 2025-04-15]
Camilla Engblom SciLifeLab Fellow
PubMed DOI Crossref
Progress in the Identification and Design of Novel Antimicrobial Peptides Against Pathogenic Microorganisms.
Sun S
Probiotics Antimicrob Proteins 17 (2) 918-936 [2025-04-00; online 2024-11-18]
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Occurrence and spread of carbapenemase‐producing Enterobacterales (CPE) in the food chain in the EU/EFTA. Part 1: 2025 update
Allende A, Álvarez‐Ordóñez A, Bortolaia V, ..., Rabbås H, Peixe L
EFSA J 23 (4) - [2025-04-00; online 2025-04-00]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Formulation and Characterization of Novel Ionizable and Cationic Lipid Nanoparticles for the Delivery of Splice-Switching Oligonucleotides.
Ojansivu M, Barriga HMG, Holme MN, ..., Barauskas J, Stevens MM
Adv. Mater. Weinheim 37 (17) e2419538 [2025-04-00; online 2025-03-16]
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Flow cytometry reveals constant lymphocyte proportions after long-term cryopreservation of whole blood in TransFix® cell stabilization reagent.
Faresjö M, Johansson J, Islander U, Tompa A
J. Immunol. Methods 539 (-) 113853 [2025-04-00; online 2025-03-23]
PubMed DOI Crossref
Enabling global image data sharing in the life sciences.
Bajcsy P, Bhattiprolu S, Börner K, ..., Taylor A, Keppler A
Nat. Methods 22 (4) 672-676 [2025-04-00; online 2025-03-28]
PubMed DOI Crossref
Benchmarking of Quantitative Proteomics Workflows for Limited Proteolysis Mass Spectrometry.
Koudelka T, Bassot C, Piazza I
Mol. Cell Proteomics 24 (4) 100945 [2025-04-00; online 2025-03-13]
PubMed DOI Crossref
A burden of rare copy number variants in obsessive-compulsive disorder.
Halvorsen MW, de Schipper E, Bäckman J, ..., Mataix-Cols D, Crowley JJ
Mol. Psychiatry 30 (4) 1510-1517 [2025-04-00; online 2024-10-27]
PubMed DOI Crossref
Evolutionary rescue of spherical mreB deletion mutants of the rod-shape bacterium Pseudomonas fluorescens SBW25.
Yulo PRJ, Desprat N, Gerth ML, ..., Rainey PB, Hendrickson HL
Elife 13 (-) - [2025-03-31; online 2025-03-31]
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Evolutionary rescue of spherical mreB deletion mutants of the rod-shape bacterium Pseudomonas fluorescens SBW25
Yulo PRJ, Desprat N, Gerth ML, ..., Rainey PB, Hendrickson HL
Elife 13 (-) - [2025-03-31; online 2025-03-31]
DOI Crossref
Genomic Erosion Through the Lens of Comparative Genomics
Wang X, Fontsere C, Caballero XA, ..., Pacheco C, Morales HE
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Solution architecture of G3BP1 reveals pH-dependent conformational switching underlying liquid-liquid phase separation
Han X, Sun R, Graewert MA, ..., Svergun D, Achour A
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Predicting retention on immobilized artificial membrane chromatography: Lipophilicity-based versus lipophilicity-independent models.
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J Chromatogr A 1745 (-) 465752 [2025-03-29; online 2025-02-04]
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Development of DARPin T cell engagers for specific targeting of tumor-associated HLA/peptide complexes
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A Multi-Omic Phenobank Reveals Axes of Glioblastoma Growth, Invasion, and Therapeutic Vulnerability
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Measures of Homozygosity and Relationship to Genetic Diversity in the Bearded Collie Breed.
Belanger JM, Gershony LC, Bell JS, ..., Famula TR, Oberbauer AM
Genes (Basel) 16 (4) - [2025-03-27; online 2025-03-27]
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Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Škerle J, ..., Stansfeld PJ, Landreh M
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Author response: Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
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Ectopic germinal centers in the nasal turbinates contribute to B cell immunity to intranasal viral infection and vaccination.
Gailleton R, Mathew NR, Reusch L, ..., Bemark M, Angeletti D
Proc. Natl. Acad. Sci. U.S.A. 122 (12) e2421724122 [2025-03-25; online 2025-03-20]
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Combination treatment with anti-RANKL and antibiotics for preventing joint destruction in septic arthritis.
Hu Z, Deshmukh M, Jarneborn A, ..., Mohammad M, Jin T
JCI Insight 10 (6) - [2025-03-24; online 2025-03-24]
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Clinical utility of the FilmArray® meningitis/encephalitis panel in children with suspected central nervous system infection in a low-resource setting - a prospective study in Southwestern Uganda.
Rasti R, Kumbakumba E, Nanjebe D, ..., Alfvén T, Gaudenzi G
BMC Infect Dis 25 (1) 396 [2025-03-22; online 2025-03-22]
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Author Correction: Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.
Shafighi S, Geras A, Jurzysta B, ..., Lagergren J, Szczurek E
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Unlocking protein networks with Predictomes: The SPOC advantage.
Elofsson A
Mol. Cell 85 (6) 1050-1051 [2025-03-20; online 2025-03-22]
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Transcriptional architecture and Pol II regulation at promoters, enhancers, and enhancer clusters in Canis lupus familiaris
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Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation
Jin C, Lundstrøm J, Cori CR, ..., Khoo KH, Bojar D
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DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Pathway activation model for personalized prediction of drug synergy
Trac QT, Huang Y, Erkers T, ..., Pawitan Y, Vu TN
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PubMed DOI Crossref
Lab-in-a-Fiber detection and capture of cells.
Varela JC, Harish AV, Maniewski P, ..., Russom A, Laurell F
Sci Rep 15 (1) 9694 [2025-03-20; online 2025-03-20]
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Comparative Analysis of Salivary and Serum Inflammatory Mediator Profiles in Patients With Rheumatoid Arthritis and Periodontitis.
Fei C, Eriksson K, Fei G, ..., Jansson L, Yucel-Lindberg T
Mediators Inflamm. 2025 (-) 7739833 [2025-03-20; online 2025-03-20]
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Author response: Pathway activation model for personalized prediction of drug synergy
Trac QT, Huang Y, Erkers T, ..., Pawitan Y, Vu TN
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PubMed DOI Crossref
Survival and adaptative strategies of Enterotoxigenic E. coli (ETEC) to the freshwater environment.
Sjöling Å, Ashokkumar E, Bjurnemark C, ..., Zhu B, Joffré E
Res Sq - (-) - [2025-03-19; online 2025-03-19]
Astrid von Mentzer DDLS Fellow
PubMed DOI Crossref
Senataxin prevents replicative stress induced by the Myc oncogene.
Sberna S, Filipuzzi M, Bianchi N, ..., Curti L, Campaner S
Cell Death Dis 16 (1) 187 [2025-03-19; online 2025-03-19]
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Early gonadotoxic effects of cyclophosphamide on the prepubertal testis and the feasibility of reducing toxicity through combined antioxidant therapy
Eskafinoghani A, Reyes Palomares A, Hao X, ..., Lundberg A, Rodriguez-Walberg KA
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Arian Lundberg DDLS Fellow
DOI Crossref
Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data
Oskolkov N, Jin C, Clinton SL, ..., Heintzman PD, van der Valk T
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Characterizing the Sulfated and Glucuronidated (Poly)phenol Metabolome for Dietary Biomarker Discovery.
Tsiara I, Hervás Povo B, Alotaibi W, ..., Rodriguez-Mateos A, Globisch D
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Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Schulte D, Šiborová M, Käll L, Snijder J
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Author response: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Schulte D, Šiborová M, Käll L, Snijder J
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Immune-Coagulation Dynamics in Severe COVID-19: Insights from Autoantibody Profiling and Transcriptomics
Ambikan AT, Cederholm A, Rezene S, ..., Landegren N, Gupta S
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Disrupted bone microenvironment and immune recovery following total body irradiation in a murine model
Sághy T, Gupta P, Horkeby K, ..., Chagin AS, Engdahl C
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Targeting TUBG1 in RB1-negative tumors.
Lindström L, Zhou J, Villoutreix BO, ..., Olsson R, Alvarado-Kristensson M
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Markers of inflammation predicts long-term mortality in patients with acute coronary syndrome - a cohort study.
Odeberg J, Halling A, Ringborn M, ..., Odeberg H, Lindblad U
BMC Cardiovasc Disord 25 (1) 190 [2025-03-15; online 2025-03-15]
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Construction of an atlas of transcription factor binding during mouse development identifies popular regulatory regions.
Nordin A, Zambanini G, Enar Jonasson M, ..., Pagella P, Cantù C
Development 152 (6) - [2025-03-15; online 2025-03-24]
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Pharmacological inhibition of MutT homolog 1 (MTH1) in allergic airway inflammation as a novel treatment strategy.
Adler A, Bergwik J, Padra M, ..., Berglund UW, Egesten A
Respir. Res. 26 (1) 101 [2025-03-14; online 2025-03-14]
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LN’s -Test: A Principled Approach to -Testing in Single-Cell RNA Sequencing
Kviman O, Jun SH, Lagergren J
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PubMed DOI Crossref
Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells
Kang W, Yip WH, Li-Wang X, ..., Carninci P, Bienko M
bioRxiv - (-) - [2025-03-14; online 2025-03-14]
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Common connective tissue disorder and anti-cytokine autoantibodies are enriched in idiopathic multicentric castleman disease patients.
Feng A, Gonzalez MV, Kalaycioglu M, ..., Fajgenbaum DC, Utz PJ
Front Immunol 16 (-) 1528465 [2025-03-13; online 2025-03-13]
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Antisecretory factor as add-on treatment for newly diagnosed glioblastoma, IDH wildtype: study protocol for a randomized double-blind placebo-controlled trial.
Ehinger E, Darabi A, Visse E, ..., Bengzon J, Siesjö P
Trials 26 (1) 86 [2025-03-13; online 2025-03-13]
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Visible-Light-Switchable Molecular Glues for Reversible Control of Protein Function.
Zhang J, Herzog LK, Li S, Chen X, Wu YW
Chemistry 31 (15) e202403808 [2025-03-12; online 2025-01-21]
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Cover Feature: Visible‐Light‐Switchable Molecular Glues for Reversible Control of Protein Function (Chem. Eur. J. 15/2025)
Zhang J, Herzog LK, Li S, Chen X, Wu Y
Chemistry 31 (15) - [2025-03-12; online 2025-03-12]
DOI Crossref
An artificial motor protein that walks along a DNA track
Nilsson P, Robertson NO, Gustafsson N, ..., Linke H, Curmi PMG
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DOI Crossref
Abstract A017: Enhanced efficacy of anti-mesothelin CAR T cells in ovarian cancer through drug combinations: Impact of treatment kinetics, co-stimulatory domain, and donor variability
Pizarro LR, Poiret T, Gudoitytė G, ..., Magalhaes I, Erkers T
Cancer Res. 85 (5_Supplement) A017-A017 [2025-03-11; online 2025-03-11]
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Abstract 072: Plasma Metabolome Predicts Long-term Body Weight Gain and Type 2 Diabetes in Non-Obese Individuals
Wu Z, Liu B, Li J, ..., Hu Y, Sun Q
Circulation 151 (Suppl_1) - [2025-03-11; online 2025-03-11]
Clemens Wittenbecher DDLS Fellow
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cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads
Petri AJ, Thi-Huyen Nguyen M, Rajwar A, Benson E, Sahlin K
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Towards high atom economy in whole-cell redox biocatalysis: up-scaling light-driven cyanobacterial ene-reductions in a flat panel photobioreactor.
Grimm HC, Erlsbacher P, Medipally H, ..., Paul CE, Kourist R
Green Chem. 27 (11) 2907-2920 [2025-03-10; online 2025-01-14]
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Droplet microfluidics-based detection of very rare antibiotic-resistant subpopulation in clinical isolates of Escherichia coli from bloodstream infections
Agnihotri SN, Fatsis-Kavalopoulos N, Windhager J, Tenje M, Andersson DI
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Regulatory Effects of RNA-Protein Interactions Revealed by Reporter Assays of Bacteria Grown on Solid Media.
Pérez-Ropero G, Dolcemascolo R, Pérez-Ràfols A, ..., Rodrigo G, Buijs J
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Predicting allergy and postpartum depression from an incomplete compositional microbiome
Shternshis A, Tong B, Skalkidou A, ..., Hugerth LW, Singh P
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Prashant Singh SciLifeLab Fellow
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Organelle-Specific Thiochromenocarbazole Imide Derivative as a Heavy-Atom-Free Type I Photosensitizer for Biomolecule-Triggered Image-Guided Photodynamic Therapy.
Saczuk K, Kassem A, Dudek M, ..., Cabanetos C, Deiana M
J Phys Chem Lett 16 (9) 2273-2282 [2025-03-06; online 2025-02-23]
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Amino Acid Properties, Substitution Rates, and the Nearly Neutral Theory.
James JE, Lascoux M
Genome Biol Evol 17 (3) - [2025-03-06; online 2025-02-20]
PubMed DOI Crossref
Synthesis and biological assessment of BUB1B inhibitors for the treatment of clear cell renal cell carcinoma.
El Hafi M, Bouzian Y, Parvizi N, ..., Turkez H, Mardinoglu A
Eur J Med Chem 285 (-) 117247 [2025-03-05; online 2025-01-09]
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Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities.
Cao L, Garcia SL, Wurzbacher C
J Hazard Mater 485 (-) 136811 [2025-03-05; online 2024-12-06]
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adiposetissue.org: A knowledge portal integrating clinical and experimental data from human adipose tissue.
Zhong J, Zareifi D, Weinbrenner S, ..., Mejhert N, Rydén M
Cell Metab. 37 (3) 566-569 [2025-03-04; online 2025-02-20]
PubMed DOI Crossref
Regulation of gene expression through protein-metabolite interactions.
Hornisch M, Piazza I
NPJ Metab Health Dis 3 (1) 7 [2025-03-04; online 2025-03-04]
PubMed DOI Crossref
Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis.
Brunner A, Morero NR, Zhang W, ..., Beckwith KS, Ellenberg J
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DOI Crossref
Investigating Interaction Dynamics of an Enantioselective Peptide‐Catalyzed Acylation Reaction
Brauser M, Petzold K, Thiele CM
Angewandte Chemie 137 (10) - [2025-03-03; online 2024-12-12]
PubMed DOI Crossref
Investigating Interaction Dynamics of an Enantioselective Peptide-Catalyzed Acylation Reaction.
Brauser M, Petzold K, Thiele CM
Angew. Chem. Int. Ed. Engl. 64 (10) e202421062 [2025-03-03; online 2024-12-12]
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Androgen Receptor Inhibition Increases MHC Class I Expression and Improves Immune Response in Prostate Cancer.
Chesner LN, Polesso F, Graff JN, ..., Feng FY, Moran AE
Cancer Discov 15 (3) 481-494 [2025-03-03; online 2024-12-09]
Arian Lundberg DDLS Fellow
DOI Crossref
Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies
Williams EC, Franzén L, Lindvall MO, ..., Tan J, Mohorianu I
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The non-canonical Smoothened-AMPK axis regulates Smaug1 biomolecular condensates.
Thomas MG, Fernández-Alvarez AJ, Giménez M, ..., Grecco HE, Boccaccio GL
J. Cell. Sci. 138 (5) - [2025-03-01; online 2025-03-14]
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Dynamics of non-Newtonian agarose gel droplet formation in two-phase microfluidic systems
Agnihotri SN, Das PK, Tolboom F, ..., Persson C, Tenje M
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PubMed DOI Crossref
Transcriptional enhancers in human neuronal differentiation provide clues to neuronal disorders.
Yoshihara M, Coschiera A, Bachmann JA, ..., Sahlén P, Kere J
EMBO Rep. 26 (5) 1212-1237 [2025-03-00; online 2025-02-13]
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Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs.
Minaeva M, Domingo J, Rentzsch P, Lappalainen T
NAR Genomics and Bioinformatics 7 (1) lqae178 [2025-03-00; online 2025-01-07]
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Spatial, temporal and numerical regulation of polar flagella assembly in Pseudomonas putida.
Pulido-Sánchez M, Leal-Morales A, López-Sánchez A, Cava F, Govantes F
Microbiol Res 292 (-) 128033 [2025-03-00; online 2024-12-19]
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Recent advances in precision nutrition and cardiometabolic diseases.
Martínez-González MA, Planes FJ, Ruiz-Canela M, ..., Razquin C, Hu FB
Rev Esp Cardiol (Engl Ed) 78 (3) 263-271 [2025-03-00; online 2024-09-30]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Nelarabine in T-cell acute lymphoblastic leukemia: intracellular metabolism and molecular mode-of-action.
Hormann FM, Rudd SG
Leukemia 39 (3) 531-542 [2025-03-00; online 2025-02-17]
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MiR-186-5p inhibition restores synaptic transmission and neuronal network activity in a model of chronic stress.
Rodrigues B, Leitão RA, Santos M, ..., Pinheiro PS, Carvalho AL
Mol. Psychiatry 30 (3) 1034-1046 [2025-03-00; online 2024-09-05]
PubMed DOI Crossref
Machine learning detection of heteroresistance in Escherichia coli.
Guliaev A, Hjort K, Rossi M, ..., Guy L, Andersson DI
EBioMedicine 113 (-) 105618 [2025-03-00; online 2025-02-21]
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Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR).
Loughran G, Andreev DE, Terenin IM, ..., Dmitriev SE, Baranov PV
Nat. Struct. Mol. Biol. 32 (3) 418-430 [2025-03-00; online 2025-03-03]
DOI Crossref
Enzymatic degradation of phthalate esters in the environment: Advances, challenges and opportunities
Sun S, Syrén PO
Chem Eng J 508 (-) 160640 [2025-03-00; online 2025-03-00]
PubMed DOI Crossref
Click Chemistry-Based Bioconjugation of Iron Oxide Nanoparticles.
Asad S, Ahl D, Suárez-López YDC, ..., Phillipson M, Teleki A
Small 21 (11) e2407883 [2025-03-00; online 2025-02-09]
Alexandra Teleki SciLifeLab Fellow
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Baseline characteristics and 1-year outcome by left ventricular function in the CABG PREFERS.
Löfström U, Linde C, Eriksson MJ, ..., Persson H, Hage C
Eur Heart J Open 5 (2) oeaf014 [2025-03-00; online 2025-03-05]
PubMed DOI Crossref
Bacterial peptidoglycan recycling.
Gilmore MC, Cava F
Trends Microbiol. 33 (3) 340-353 [2025-03-00; online 2024-11-29]
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Avances en nutrición de precisión y enfermedades cardiometabólicas
Martínez-González MA, Planes FJ, Ruiz-Canela M, ..., Razquin C, Hu FB
Revista Española de Cardiología 78 (3) 263-271 [2025-03-00; online 2025-03-00]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
An Evaluation Into the Robustness of Grading of Pleural Mesothelioma Outside of Specialist Centres.
Prabhakaran S, Hocking AJ, Irani Y, ..., Moffat D, Klebe S
APMIS 133 (3) e70006 [2025-03-00; online 2025-02-28]
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Adaptive ultrasonic actuation for dynamic formation and characterization of 3D cell cultures
Hammarström B, Olofsson K, Carannante V, ..., Önfelt B, Wiklund M
Sensors and Actuators B: Chemical 427 (-) 137173 [2025-03-00; online 2025-03-00]
PubMed DOI Crossref
The potential radiosensitization target PFKFB3 is related to response to radiotherapy in SweBCG91RT: a randomized clinical trial with long-term follow-up.
Egelberg M, De Marchi T, Schultz N, ..., Killander F, Niméus E
BMC Cancer 25 (1) 374 [2025-02-28; online 2025-02-28]
PubMed DOI Crossref
Sulfilimines: An Underexplored Bioisostere for Drug Design?
Arvidsson PI
J Med Chem 68 (4) 4056-4058 [2025-02-27; online 2025-01-31]
DOI Crossref
Structure and dynamics of a multidomain ligand-gated ion channel revealed under acidic conditions
Andén O, Rovšnik U, Lycksell M, ..., Howard RJ, Lindahl E
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Isolation of individual natural killer cells from deep, high-aspect ratio microwell arrays - an evaluative study
Verron Q, Sandström N, van Ooijen H, ..., Frisk T, Önfelt B
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Geographical variation in mitogenomes of the largetooth sawfish Pristis pristis : challenges and perspectives for conservation efforts
Rodrigues AÉS, Brito RMS, Charvet P, ..., Ready JS, Sales JBL
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CombiCTx: Screening diffusion gradients of anti-cancer drug combinations
Stelzl C, Lerma-Clavero A, Camenisch S, ..., Kreuger J, O’Callaghan P
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DOI Crossref
Calcium stabilization of a flexible N-terminal domain in a pentameric ligand-gated ion channel
Fan C, Lycksell M, Zhuang Y, Howard RJ, Lindahl E
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PubMed DOI Crossref
Editorial: Allergen-specific antibodies: from basic science to clinical application.
Flicker S, Ohlin M, Atanasio A, Pomés A
Front Allergy 6 (-) 1568735 [2025-02-26; online 2025-02-26]
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Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets.
Leo IR, Kunold E, Audrey A, ..., Lehtiö J, Jafari R
Nat Commun 16 (1) 1948 [2025-02-25; online 2025-02-25]
PubMed DOI Crossref
Evaluating feature extraction in ovarian cancer cell line co-cultures using deep neural networks.
Sharma O, Gudoityte G, Minozada R, ..., Paavolainen L, Seashore-Ludlow B
Commun Biol 8 (1) 303 [2025-02-25; online 2025-02-25]
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Genome-wide profiling of tRNA modifications reveal the presence of divergent signatures in Plasmodium falciparum
Li Q, Veith Y, Christ E, ..., Larsson O, Chan SCL
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Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures
Hawgood M, Urién González B, Agostinho A, ..., Blom H, Lemmens B
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Retinal tau phosphorylation in Alzheimer’s disease: a mass spectrometry study
Santiago J, Poceviciute D, Vogel J, Brinkmalm G, Wennström M
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PubMed DOI Crossref
Uncovering pre-cytokinetic block in cancer cells under shear stress using a disturbed flow-generating device.
Beresova L, Vitecek J, Protivánková I, ..., Bartek J, Mistrik M
Sci Rep 15 (1) 6457 [2025-02-22; online 2025-02-22]
PubMed DOI Crossref
Characterization of a second class Ie ribonucleotide reductase.
John J, Lundin D, Branca RM, ..., Lebrette H, Högbom M
Commun Biol 8 (1) 281 [2025-02-22; online 2025-02-22]
PubMed DOI Crossref
WNK1-dependent water influx is required for CD4+ T cell activation and T cell-dependent antibody responses.
Biggs O'May J, Vanes L, de Boer LL, ..., Köchl R, Tybulewicz VLJ
Nat Commun 16 (1) 1857 [2025-02-21; online 2025-02-21]
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Sheathless elasto-inertial focusing of sub-25 nm particles in straight microchannels
Tanriverdi S, Cruz J, Habibi S, ..., Sezgin E, Russom A
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PubMed DOI Crossref
Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes.
Grau B, Kormos R, Bañó-Polo M, ..., DeGrado WF, Mingarro I
Sci Adv 11 (8) eads6804 [2025-02-21; online 2025-02-19]
PubMed DOI Crossref
Functional-proteomics-based investigation of the cellular response to farnesyltransferase inhibition in lung cancer.
Pan Y, Berkovska O, Marathe S, ..., Lehtiö J, Orre LM
iScience 28 (2) 111864 [2025-02-21; online 2025-01-21]
PubMed DOI Crossref
Development of an In Situ G Protein-Coupled Receptor Fragment Molecule Screening Approach with High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance.
Petracco E, Ferré G, Kabelka I, ..., Allais F, Eddy MT
ACS chemical biology 20 (2) 401-411 [2025-02-21; online 2025-01-21]
PubMed DOI Crossref
Biological signatures in the Alzheimer's continuum discriminate between diagnosis-related and -unrelated associations to ATN categories.
Alanko V, Mravinacová S, Hall A, ..., Månberg A, Matton A
Brain Commun 7 (2) fcaf078 [2025-02-21; online 2025-02-21]
PubMed DOI Crossref
First-in-human experience with GRPR antagonist [68Ga]Ga-NOTA-PEG2-RM26 in prostate and breast cancer patients using PET/CT.
Bjäreback A, Jonmarker O, Tzortzakakis A, ..., Axelsson R, Tran TA
EJNMMI Res 15 (1) 12 [2025-02-20; online 2025-02-20]
PubMed DOI Crossref
Data-driven resources and computational tools in non-model plant species.
Street NR
Physiol Plant 177 (1) e70133 [2025-02-20; online 2025-02-20]
PubMed DOI Crossref
Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.
De Martinis ECP, Alves VF, Pereira MG, ..., Dannborg M, Bengtsson-Palme J
Front Immunol 16 (-) 1488699 [2025-02-20; online 2025-02-20]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE.
Teichmann L, Wenne M, Luitwieler S, ..., Bengtsson-Palme J, Ter Kuile B
PLoS ONE 20 (2) e0312223 [2025-02-19; online 2025-02-19]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A new understanding of Acanthamoeba castellanii: dispelling the role of bacterial pore-forming toxins in cyst formation and amoebicidal actions.
Yabrag A, Ullah N, Baryalai P, ..., Wai SN, Nadeem A
Cell death discovery 11 (1) 66 [2025-02-19; online 2025-02-19]
PubMed DOI Crossref
Integrative proteo-transcriptomic characterization of advanced fibrosis in chronic liver disease across etiologies.
Yang H, Atak D, Yuan M, ..., Mardinoglu A, Zeybel M
Cell Rep Med 6 (2) 101935 [2025-02-18; online 2025-01-30]
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Evolutionary rescue of spherical mreB deletion mutants of the rod-shape bacterium Pseudomonas fluorescens SBW25
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The cellular state space of AML unveils novel NPM1 subtypes with distinct clinical outcomes and immune evasion properties
Lilljebjörn H, Peña-Martínez P, Thorsson H, ..., Orsmark-Pietras C, Fioretos T
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Synthesis and Characterization of Memantine-Loaded Niosomes for Enhanced Alzheimer's Disease Targeting.
Turkez H, Oner S, Yıldırım OC, ..., Di Stefano A, Mardinoglu A
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PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity
Larralde M, Zeller G, Carroll LM
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DDLS Fellow Laura Carroll
PubMed DOI Crossref
Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis.
Salgueiro-Toledo VC, Bertol J, Gutierrez C, ..., Sanz J, Prados-Rosales R
Elife 13 (-) - [2025-02-17; online 2025-02-17]
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Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis
Salgueiro-Toledo VC, Bertol J, Gutierrez C, ..., Sanz J, Prados-Rosales R
Elife 13 (-) - [2025-02-17; online 2025-02-17]
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Maternal concentrations of perfluoroalkyl sulfonates and alterations in white matter microstructure in the developing brains of young children.
England-Mason G, Reardon AJF, Reynolds JE, ..., Lebel C, Dewey D
Environ. Res. 267 (-) 120638 [2025-02-15; online 2024-12-15]
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Towards an interpretable deep learning model of cancer.
Nilsson A, Meimetis N, Lauffenburger DA
NPJ Precis Oncol 9 (1) 46 [2025-02-14; online 2025-02-14]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Sub-5 nm Silicon Nanopore Sensors: Scalable Fabrication via Self-Limiting Metal-Assisted Chemical Etching.
De Ferrari F, Raja SN, Herland A, Niklaus F, Stemme G
ACS Appl Mater Interfaces 17 (6) 9047-9058 [2025-02-12; online 2025-01-30]
PubMed DOI Crossref
Secure and federated quantitative trait loci mapping with privateQTL.
Choi YA, Kim Y, Miao P, Lappalainen T, Gürsoy G
Cell Genom 5 (2) 100769 [2025-02-12; online 2025-02-14]
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Imaging Single Particle Profiler to Study Nanoscale Bioparticles Using Conventional Confocal Microscopy.
Sych T, Görgens A, Steiner L, ..., El Andaloussi S, Sezgin E
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Dynamical organization of vimentin intermediate filaments in living cells revealed by MoNaLISA nanoscopy.
Smoler M, Pennacchietti F, De Rossi MC, ..., Testa I, Levi V
Biosci. Rep. 45 (2) - [2025-02-12; online 2025-02-12]
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Cryo-EM ligand building using generative AI and molecular dynamics
Haloi N, Howard RJ, Lindahl E
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PubMed DOI Crossref
NLRP3-mediated glutaminolysis controls microglial phagocytosis to promote Alzheimer's disease progression.
McManus RM, Komes MP, Griep A, ..., Latz E, Heneka MT
Immunity 58 (2) 326-343.e11 [2025-02-11; online 2025-02-03]
PubMed DOI Crossref
Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats.
Yang H, Zhang C, Kim W, ..., Turkez H, Mardinoglu A
Elife 13 (-) - [2025-02-11; online 2025-02-11]
DOI Crossref
Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats
Yang H, Zhang C, Kim W, ..., Turkez H, Mardinoglu A
Elife 13 (-) - [2025-02-11; online 2025-02-11]
PubMed DOI Crossref
In vivo engineering of murine T cells using the evolved adeno-associated virus variant Ark313.
Nyberg WA, Wang CH, Ark J, ..., Asokan A, Eyquem J
Immunity 58 (2) 499-512.e7 [2025-02-11; online 2025-02-04]
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Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies.
Mo S, Zhu Y, Braga MP, ..., Zhang P, Wang H
Syst. Biol. 74 (1) 141-157 [2025-02-10; online 2024-11-01]
DDLS Fellow Mariana Pires Braga
DOI Crossref
Modular Photoswitchable Molecular Glues for Chemo‐Optogenetic Control of Protein Function in Living Cells
Zhang J, Herzog LK, Corkery DP, ..., Li Y, Wu Y
Angewandte Chemie 137 (7) - [2025-02-10; online 2025-01-21]
PubMed DOI Crossref
Modular Photoswitchable Molecular Glues for Chemo-Optogenetic Control of Protein Function in Living Cells.
Zhang J, Herzog LK, Corkery DP, ..., Li Y, Wu YW
Angew. Chem. Int. Ed. Engl. 64 (7) e202416456 [2025-02-10; online 2025-01-21]
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Enhanced Computational and Experimental Approaches for Comparative Analysis of the Human Mycobiome
Begum N, Lee S, Almeida M, ..., Shoiae S, Moyes DL
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DOI Crossref
Spectral STED microscopy improves spectral sensitivity with polarity-sensitive probes and enables correlative measurements of membrane order and anomalous lipid diffusion
Urbančič I, Schneider F, Galiani S, Sezgin E, Eggeling C
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DOI Crossref
Modeling cryo-EM structures in alternative states with generative AI and density-guided simulations
Shugaeva T, Howard RJ, Haloi N, Lindahl E
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PubMed DOI Crossref
Design, Synthesis, and Computational Evaluation of 3,4-Dihydroquinolin-2(1H)-One Analogues as Potential VEGFR2 Inhibitors in Glioblastoma Multiforme.
Buhlak S, Abad N, Akachar J, ..., Türkez H, Mardinoglu A
Pharmaceuticals (Basel, Switzerland) 18 (2) - [2025-02-08; online 2025-02-08]
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Disparate and shared transcriptomic signatures associated with cortical atrophy in genetic behavioral variant frontotemporal degeneration.
Shen T, Vogel JW, Van Deerlin VM, ..., Irwin DJ, McMillan CT
Mol Neurodegener 20 (1) 17 [2025-02-07; online 2025-02-07]
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Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide 15 N( 1 H) NMR Relaxation
Lesovoy D, Roshchin K, Sala BM, ..., Orekhov V, Agback P
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PubMed DOI Crossref
Molecular basis of proton sensing by G protein-coupled receptors.
Howard MK, Hoppe N, Huang XP, ..., Coyote-Maestas W, Manglik A
Cell 188 (3) 671-687.e20 [2025-02-06; online 2025-01-02]
PubMed DOI Crossref
Localized Nanopore Fabrication in Silicon Nitride Membranes by Femtosecond Laser Exposure and Subsequent Controlled Breakdown.
Leva CV, Jain S, Kistermann K, ..., Niklaus F, Raja SN
ACS Appl Mater Interfaces 17 (5) 8737-8748 [2025-02-05; online 2025-01-27]
PubMed DOI Crossref
Interpopulational Variation in Cyclotide Production in Heavy-Metal-Treated Pseudometallophyte (Viola tricolor L.).
Miszczak R, Slazak B, Sychta K, ..., Nilsson A, Słomka A
Plants (Basel) 14 (3) - [2025-02-05; online 2025-02-05]
PubMed DOI Crossref
Identification of bioactive compounds with popular single-atom modifications: Comprehensive analysis and implications for compound design.
Feng B, Yu H, Dong X, Díaz-Holguín A, Hu H
Eur J Med Chem 283 (-) 117051 [2025-02-05; online 2024-11-13]
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Repeated positron emission tomography tracing neutrophil elastase in a porcine intensive-care sepsis model.
Wilske F, Eriksson O, Amini RM, ..., Castegren M, Antoni G
Intensive Care Med Exp 13 (1) 14 [2025-02-04; online 2025-02-04]
PubMed DOI Crossref
Correction: Neuropilin-1 controls vascular permeability through juxtacrine regulation of endothelial adherens junctions.
Pal S, Su Y, Nwadozi E, Claesson-Welsh L, Richards M
Angiogenesis 28 (2) 16 [2025-02-04; online 2025-02-04]
PubMed DOI Crossref
P-type accumulation mode organic electrochemical transistor biosensor for xanthine detection in fish.
Lin Y, Kroon R, Zeglio E, Herland A
Biosens Bioelectron 269 (-) 116928 [2025-02-01; online 2024-11-09]
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Tumor-Associated Macrophages Improve The Efficacy Of SMAC Mimetics Combined With Chemotherapy In Ovarian Cancer
Coelho R, Seashore-Ludlow B, Schütz S, ..., Heinzelmann-Schwarz V, Jacob F
International Journal of Gynecological Cancer 35 (2) 101462 [2025-02-00; online 2025-02-00]
PubMed DOI Crossref
TP53: the unluckiest of genes?
Joerger AC, Stiewe T, Soussi T
Cell Death Differ. 32 (2) 219-224 [2025-02-00; online 2024-10-23]
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Rheumatoid Arthritis Related B-Cell Changes Are Found Already in the Risk-RA Phase.
de Vries C, Huang W, Sharma RK, ..., Lundberg K, Malmström V
Eur. J. Immunol. 55 (2) e202451391 [2025-02-00; online 2025-02-11]
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ProHap enables human proteomic database generation accounting for population diversity.
Vašíček J, Kuznetsova KG, Skiadopoulou D, ..., Käll L, Vaudel M
Nat. Methods 22 (2) 273-277 [2025-02-00; online 2024-12-09]
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Mechanisms of neutralization of toxSAS from toxin-antitoxin modules.
Dominguez-Molina L, Kurata T, Cepauskas A, ..., Hauryliuk V, Garcia-Pino A
Nat. Chem. Biol. 21 (2) 182-192 [2025-02-00; online 2024-06-04]
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Machine learning prediction of tau-PET in Alzheimer's disease using plasma, MRI, and clinical data.
Karlsson L, Vogel J, Arvidsson I, ..., Mattsson-Carlgren N, Hansson O
Alzheimers Dement 21 (2) e14600 [2025-02-00; online 2025-02-22]
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Let it shine: Autofluorescence of Papanicolaou-stain improves AI-based cytological oral cancer detection.
Lian W, Lindblad J, Runow Stark C, Hirsch JM, Sladoje N
Comput Biol Med 185 (-) 109498 [2025-02-00; online 2024-12-10]
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Impact of initial business model on the growth trajectory of new technology-based firms: a path dependency perspective
Löfsten H, Isaksson A, Rannikko H, Tornikoski E, Buffart M
J Technol Transf 50 (1) 29-61 [2025-02-00; online 2024-05-06]
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Genome-scale models in human metabologenomics.
Mardinoglu A, Palsson BØ
Nat. Rev. Genet. 26 (2) 123-140 [2025-02-00; online 2024-09-19]
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Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework.
Saraiva BM, Cunha I, Brito AD, ..., Jacquemet G, Henriques R
Nat. Methods 22 (2) 283-286 [2025-02-00; online 2025-01-02]
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Cerebrospinal fluid levels of NfM in relation to NfL and pNfH as prognostic markers in amyotrophic lateral sclerosis.
Olofsson J, Bergström S, Mravinacová S, ..., Nilsson P, Månberg A
Amyotroph Lateral Scler Frontotemporal Degener 26 (1-2) 113-123 [2025-02-00; online 2024-11-22]
PubMed DOI Crossref
Cell Painting: a decade of discovery and innovation in cellular imaging.
Seal S, Trapotsi MA, Spjuth O, ..., Bender A, Carpenter AE
Nat. Methods 22 (2) 254-268 [2025-02-00; online 2024-12-05]
PubMed DOI Crossref
Ceftazidime-avibactam tolerance and persistence among difficult-to-treat KPC-producing Klebsiella pneumoniae clinical isolates from bloodstream infections.
Abichabki N, Gaspar GG, Bortolato LR, ..., Darini ALC, Andrade LN
Eur. J. Clin. Microbiol. Infect. Dis. 44 (2) 343-353 [2025-02-00; online 2024-11-30]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
BPS2025 - Lipid and voltage regulation of Na+/H+ exchangers
Drew D
Biophysical Journal 124 (3) 352a [2025-02-00; online 2025-02-00]
DOI Crossref
BPS2025 - Cholesterol has a unique binding fingerprint in Kv7.5
Pan R, Kusay AS, Frampton DJA, Delemotte L, Liin SI
Biophysical Journal 124 (3) 123a [2025-02-00; online 2025-02-00]
DOI Crossref
BPS2025 - Cardiotoxic effects of synthetic cannabinoid receptor agonists: Inhibition of hERG and Kv7.1/KCNE1 channels with proposed hERG binding site
Frampton DJA, Pipatpolkai T, Sridhar A, ..., Ottosson NE, Liin SI
Biophysical Journal 124 (3) 277a-278a [2025-02-00; online 2025-02-00]
PubMed DOI Crossref
Author Correction: Cell Painting: a decade of discovery and innovation in cellular imaging.
Seal S, Trapotsi MA, Spjuth O, ..., Bender A, Carpenter AE
Nat. Methods 22 (2) 447 [2025-02-00; online 2024-12-13]
PubMed DOI Crossref
Adaptation of Escherichia coli to ciprofloxacin and enrofloxacin: Differential proteomics of the SOS response and RecA-independent mechanisms.
Teichmann L, Pasman R, Luitwieler S, ..., Bengtsson-Palme J, Ter Kuile B
Int. J. Antimicrob. Agents 65 (2) 107420 [2025-02-00; online 2024-12-30]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Acute Vestibular Syndrome Unmasking an RFC1-Spectrum Disorder.
Verrecchia L, Alm V, Thonberg H, ..., Nilsson D, Paucar M
Neurol Genet 11 (1) e200238 [2025-02-00; online 2025-01-16]
DOI Crossref
A Microfluidic Platform for In Situ Studies of Bacteria Electroporation
Volkov IL, Khaji Z, Johansson M, Tenje M
Adv Materials Technologies 10 (4) - [2025-02-00; online 2024-11-27]
PubMed DOI Crossref
A Heparan Sulfate Mimetic RAFT Copolymer Inhibits SARS-CoV-2 Infection and Ameliorates Viral-Induced Inflammation.
Ling J, Lundkvist Å, Guerrini M, ..., Li JP, Li J
Adv Sci (Weinh) 12 (6) e2411737 [2025-02-00; online 2024-12-16]
PubMed DOI Crossref
Trogocytosis of chimeric antigen receptors between T cells is regulated by their transmembrane domains.
Barbera S, Schuiling MJA, Sanjaya NA, ..., Essand M, Dimberg A
Sci Immunol 10 (103) eado2054 [2025-01-31; online 2025-01-31]
PubMed DOI Crossref
Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells.
Schaepe JM, Fries T, Doughty BR, ..., Marklund E, Greenleaf WJ
bioRxiv - (-) - [2025-01-30; online 2025-01-30]
PubMed DOI Crossref
Photosynthesis in Synechocystis sp. PCC 6803 is not optimally regulated under very high CO2.
Carrasquer-Alvarez E, Hoffmann UA, Geissler AS, ..., Hudson EP, Frigaard NU
Appl. Microbiol. Biotechnol. 109 (1) 33 [2025-01-30; online 2025-01-30]
DOI Crossref
Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats
Yang H, Zhang C, Kim W, ..., Turkez H, Mardinoglu A
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DOI Crossref
Author response: Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats
Yang H, Zhang C, Kim W, ..., Turkez H, Mardinoglu A
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PubMed DOI Crossref
The genetic architecture of resistance to flubendiamide insecticide in Helicoverpa armigera (Hübner).
Amado D, Koch EL, Cordeiro EMG, ..., Jiggins CD, Omoto C
PLoS ONE 20 (1) e0318154 [2025-01-29; online 2025-01-29]
Gabriela Montejo-Kovacevich SciLifeLab Fellow
PubMed DOI Crossref
Cellular and immune landscape of chronic liver diseases: insights from immunophenotyping.
Soleimani S, Albayrak O, Somay K, ..., Dayangac M, Zeybel M
Front Mol Biosci 11 (-) 1521811 [2025-01-29; online 2025-01-29]
PubMed DOI Crossref
Evolution of complexity through regulatory variation at a single gene.
Ferreira MS
Proc. Natl. Acad. Sci. U.S.A. 122 (4) e2424050122 [2025-01-28; online 2025-01-21]
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Probing the Hidden Photoisomerization of a Symmetric Phosphaalkene Switch
Deka R, Steen JD, Hilbers MF, ..., Orthaber A, Crespi S
Angewandte Chemie 137 (5) - [2025-01-27; online 2024-12-13]
Ruisheng Xiong SciLifeLab Fellow
PubMed DOI Crossref
Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains.
Osterholz H, Stevens A, Abramsson ML, ..., Leppert A, Landreh M
JACS Au 5 (1) 281-290 [2025-01-27; online 2025-01-08]
DOI Crossref
Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI
Bjärterot P, Nilsson A, Shariatgorji R, ..., Käll L, Andrén PE
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DOI Crossref
FlashFold: a standalone command-line tool for accelerated protein structure and stoichiometry prediction
Saha CK, Roghanian M, Häussler S, Guy L
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PubMed DOI Crossref
Telomemore enables single-cell analysis of cell cycle and chromatin condensation.
Yakovenko I, Mihai IS, Selinger M, ..., Forsell M, Henriksson J
Nucleic Acids Res. 53 (3) - [2025-01-24; online 2025-01-29]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.
Zgadzay Y, Mirabello C, Wanes G, ..., Gahura O, Amunts A
bioRxiv - (-) - [2025-01-24; online 2025-01-24]
DOI Crossref
Multiomic profiling of metastatic potential in estrogen receptor-positive human epidermal growth factor-negative breast cancer
Mosquim S, Zamore M, Vallon-Christersson J, Rydén L, Levander F
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PubMed DOI Crossref
Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing.
Tetzlaff SK, Reyhan E, Layer N, ..., Heiland DH, Venkataramani V
Cell 188 (2) 390-411.e36 [2025-01-23; online 2024-12-06]
PubMed DOI Crossref
Proper 5'-3' cotranslational mRNA decay in yeast requires import of Xrn1 to the nucleus.
Jordán-Pla A, Zhang Y, García-Martínez J, ..., Pelechano V, Pérez-Ortín JE
PLoS ONE 20 (1) e0308195 [2025-01-22; online 2025-01-22]
PubMed DOI Crossref
First-in-human, multicenter, open-label, phase I study of ATOR-1017 (evunzekibart), a 4-1BB antibody, in patients with advanced solid malignancies.
Carneiro A, Hahn A, Ellmark P, ..., Yachnin J, Ullenhag GJ
J Immunother Cancer 13 (1) - [2025-01-22; online 2025-01-22]
PubMed DOI Crossref
Emotion regulation-based internet-delivered cognitive behavioural therapy for premenstrual dysphoric disorder: study protocol for a randomised controlled trial in Sweden.
Hoppe JM, Weise C, Kleinstaeuber M, ..., Andersson G, Buhrman M
BMJ Open 15 (1) e091649 [2025-01-22; online 2025-01-22]
Erika Comasco SciLifeLab Fellow
DOI Crossref
All-Optical Strategies to Minimize Photo-Bleaching in Reversibly Switchable Fluorescent Proteins
Marín-Aguilera G, Pennacchietti F, Volpato A, ..., Widengren J, Testa I
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PubMed DOI Crossref
Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response.
Teichmann L, Luitwieler S, Bengtsson-Palme J, Ter Kuile B
BMC Microbiol. 25 (1) 37 [2025-01-21; online 2025-01-21]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Oligodendroglia vulnerability in the human dorsal striatum in Parkinson’s disease
Barba-Reyes JM, Harder L, Salas SM, ..., Serrano-Pozo A, Muñoz-Manchado AB
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Single-Cell Morphological Profiling Reveals Insights into Programmed Cell Death
Frey B, Holmberg D, Byström P, ..., Carreras-Puigvert J, Spjuth O
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PubMed DOI Crossref
Syngap1 promotes cognitive function through regulation of cortical sensorimotor dynamics.
Vaissiere T, Michaelson SD, Creson T, ..., Fontolan L, Rumbaugh G
Nat Commun 16 (1) 812 [2025-01-18; online 2025-01-18]
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Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Schulte D, Šiborová M, Käll L, Snijder J
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Protocol to infer off-target effects of drugs on cellular signaling using interactome-based deep learning.
Meimetis N, Lauffenburger DA, Nilsson A
STAR Protoc 6 (1) 103573 [2025-01-16; online 2025-01-16]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Immune dynamics throughout life in relation to sex hormones and perspectives gained from gender-affirming hormone therapy.
Yalcinkaya A, Yalcinkaya R, Sardh F, Landegren N
Front Immunol 15 (-) 1501364 [2025-01-16; online 2025-01-16]
DOI Crossref
Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Škerle J, ..., Stansfeld PJ, Landreh M
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Author response: Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Škerle J, ..., Stansfeld PJ, Landreh M
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Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis
Vlček J, Hämälä T, Cobo CV, ..., Yant L, Kolář F
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PubMed DOI Crossref
Liquid crystal nanoparticles for oral combination antibiotic therapies: A strategy towards protecting commensal gut bacteria during treatment.
He X, Karlsson PA, Xiong R, ..., Bergström CAS, Hubert M
J Colloid Interface Sci 678 (Pt B) 287-300 [2025-01-15; online 2024-08-31]
Ruisheng Xiong SciLifeLab Fellow
PubMed DOI Crossref
Lipoproteins and lipoprotein lipid composition are associated with stages of dysglycemia and subclinical coronary atherosclerosis.
Gigante B, Chen Q, Björkbacka H, ..., Haglöw JT, Östgren CJ
Int. J. Cardiol. 419 (-) 132698 [2025-01-15; online 2024-11-03]
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Front Cover: Conformational Selection in Enzyme‐Catalyzed Depolymerization of Bio‐based Polyesters (ChemBioChem 2/2025)
Lopez‐Lorenzo X, Ranjani G, Syrén P
Chembiochem 26 (2) - [2025-01-14; online 2025-01-29]
PubMed DOI Crossref
Conformational Selection in Enzyme-Catalyzed Depolymerization of Bio-based Polyesters.
Lopez-Lorenzo X, Ranjani G, Syrén PO
Chembiochem 26 (2) e202400456 [2025-01-14; online 2024-09-17]
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Advancing Chronic Liver Disease Diagnoses: Targeted Proteomics for the Non-Invasive Detection of Fibrosis
Villanueva Raisman A, Kotol D, Altay O, ..., Zeybel M, Edfors F
Livers 5 (1) 2 [2025-01-14; online 2025-01-14]
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Functionalized gold nanoflowers on carbon screen-printed electrodes: an electrochemical platform for biosensing hemagglutinin protein of influenza A H1N1 virus
Torres Méndez CE, Nandi S, Martinovic K, ..., Mestres G, Kamali-Moghaddam M
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PubMed DOI Crossref
Characterization of the oxygen-tolerant formate dehydrogenase from Clostridium carboxidivorans.
Brouwer EM, Medipally HKR, Schwab S, ..., Nowaczyk MM, Hagemann M
Front Microbiol 15 (-) 1527626 [2025-01-13; online 2025-01-13]
PubMed DOI Crossref
White matter integrity upon progesterone antagonism in individuals with premenstrual dysphoric disorder: A randomized placebo-controlled diffusion tensor imaging study.
Kaltsouni E, Gu X, Wikström J, ..., Sundström-Poromaa I, Comasco E
Prog Neuropsychopharmacol Biol Psychiatry 136 (-) 111179 [2025-01-10; online 2024-10-23]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface.
Haloi N, Eriksson Lidbrink S, Howard RJ, Lindahl E
Sci Adv 11 (2) eadq3788 [2025-01-10; online 2025-01-08]
PubMed DOI Crossref
Influenza A Virus H7 nanobody recognizes a conserved immunodominant epitope on hemagglutinin head and confers heterosubtypic protection.
Chen ZS, Huang HC, Wang X, ..., Zhu Q, Angeletti D
Nat Commun 16 (1) 432 [2025-01-09; online 2025-01-09]
DOI Crossref
DTPPI: predicting drug interactions using a weighted drug-protein network
Szydlik S, Taheri G
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DDLS Fellow Golnaz Taheri
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Cardiovascular events following coronavirus disease 2019 vaccination in adults: a nationwide Swedish study.
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Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis
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FunCoup 6: advancing functional association networks across species with directed links and improved user experience.
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Author response: Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis
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TCR clonality and TCR clonal expansion in the in situ microenvironment of non-small cell lung cancer
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Human iPSC-based coculture model reveals neuroinflammatory crosstalk between microglia and astrocytes
Tujula I, Hyvärinen T, Lotila J, ..., Narkilahti S, Hagman S
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A propofol binding site in the voltage sensor domain mediates inhibition of HCN1 channel activity.
Burtscher V, Wang L, Cowgill J, ..., Evers AS, Chanda B
Sci Adv 11 (1) eadr7427 [2025-01-03; online 2025-01-03]
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Sci Rep 15 (1) 417 [2025-01-02; online 2025-01-02]
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Schulte T, Magdaong NCM, Di Valentin M, ..., Carbonera D, Hofmann E
Biochim Biophys Acta Bioenerg 1866 (1) 149510 [2025-01-01; online 2024-09-24]
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Hank EC, D'Arcy-Evans N, Scaletti ER, ..., Helleday T, Michel M
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Lin H, Zhong C, Wen R, ..., Alessi DS, He Y
Water Res 268 (Pt B) 122674 [2025-01-01; online 2024-10-21]
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Hasselrot T, Alvendal C, Hunt S, ..., Bohm-Starke N, Broliden K
Am. J. Reprod. Immunol. 93 (1) e70040 [2025-01-00; online 2025-01-08]
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Two decades of bacterial ecology and evolution in a freshwater lake.
Rohwer RR, Kirkpatrick M, Garcia SL, ..., McMahon KD, Baker BJ
Nat. Microbiol 10 (1) 246-257 [2025-01-00; online 2025-01-03]
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The human and non-human primate developmental GTEx projects.
Coorens THH, Guillaumet-Adkins A, Kovner R, ..., Van Hoose PM, dGTEx Consortium
Nature 637 (8046) 557-564 [2025-01-00; online 2025-01-15]
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Yuan M, Zhang C, Von Feilitzen K, ..., Uhlén M, Mardinoglu A
EBioMedicine 111 (-) 105495 [2025-01-00; online 2024-12-10]
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Ten simple rules for good model-sharing practices.
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PLoS Comput Biol 21 (1) e1012702 [2025-01-00; online 2025-01-10]
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Corbella M, Moreira C, Bello-Madruga R, ..., Blair JMA, Sancho-Vaello E
Protein Sci. 34 (1) e5258 [2025-01-00; online 2024-12-11]
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Lu WT, Zalmas LP, Bailey C, ..., Kanu N, Swanton C
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Canal-Garcia A, Branca RM, Francis PT, ..., Pereira JB, Bereczki E
Alzheimers Dement 21 (1) e14375 [2025-01-00; online 2024-12-23]
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Bencker C, Gschwandtner L, Nayman S, ..., Bixo M, Comasco E
Front Neuroendocrinol 76 (-) 101160 [2025-01-00; online 2024-11-06]
Erika Comasco SciLifeLab Fellow
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International multicenter validation of AI-driven ultrasound detection of ovarian cancer.
Christiansen F, Konuk E, Ganeshan AR, ..., Smith K, Epstein E
Nat. Med. 31 (1) 189-196 [2025-01-00; online 2025-01-02]
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Ernst MPT, Versluis J, Valk PJM, ..., Ripperger T, Raaijmakers MHGP
Hemasphere 9 (1) e70057 [2025-01-00; online 2025-01-16]
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Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations.
Funk JS, Klimovich M, Drangenstein D, ..., Joerger AC, Stiewe T
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Capacity and limitations of microfluidic flow to increase solute transport in three-dimensional cell cultures.
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Vaidya S, Saha D, Rode DKH, ..., Cava F, Drescher K
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Aurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context.
Gries A, Santhana Kumar K, Kuttler F, ..., Allalou A, Baumgartner M
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The FunCoup Cytoscape App: multi-species network analysis and visualization.
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Yulo PRJ, Desprat N, Gerth ML, ..., Rainey PB, Hendrickson HL
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Click chemistry-based dual nanosystem for microRNA-122 detection with single-base specificity from tumour cells.
Robles-Remacho A, Martos-Jamai I, Tabraue-Chávez M, ..., Diaz-Mochon JJ, Sanchez-Martin RM
J Nanobiotechnology 22 (1) 791 [2024-12-23; online 2024-12-23]
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HAPP: High-Accuracy Pipeline for Processing deep metabarcoding data
Sundh J, Granqvist E, Iwaszkiewicz-Eggebrecht E, ..., Andersson AF, Ronquist F
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Microbial Dynamics: Assessing Skincare Regimens' Impact on the Facial Skin Microbiome and Skin Health Parameters.
Wagner N, Valeriano VD, Diou-Hirtz S, ..., Schuppe-Koistinen I, Gillbro JM
Microorganisms 12 (12) - [2024-12-21; online 2024-12-21]
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GenePioneer: A Comprehensive Python Package for Identification of Essential Genes and Modules in Cancer
Taheri G, Haerianardakani A
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DDLS Fellow Golnaz Taheri
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Ex Vivo Drug Responses and Molecular Profiles of 597 Pediatric Acute Lymphoblastic Leukemia Patients
Enblad AP, Krali O, Gezelius H, ..., Lönnerholm G, Nordlund J
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Biologically inspired bioactive hydrogels for scarless corneal repair.
Huang J, Jiang T, Qie J, ..., Yao K, Han H
Sci Adv 10 (51) eadt1643 [2024-12-20; online 2024-12-18]
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Molecular and functional profiling of primary normal ovarian cells defines insights into cancer development and drug responses.
Piki E, Dini A, Rantanen F, ..., Murumägi A, Ungureanu D
Mol Ther Oncol 32 (4) 200903 [2024-12-19; online 2024-11-08]
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Crystallographic and NMR Study of Streptococcus pneumonia LCP Protein PsrSp Indicate the Importance of Dynamics in Four Long Loops for Ligand Specificity
Sandalova T, Sala BM, Moche M, ..., Agback P, Achour A
Crystals 14 (12) 1094 [2024-12-19; online 2024-12-19]
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Paracentrotus lividus sea urchin gonadal extract mitigates neurotoxicity and inflammatory signaling in a rat model of Parkinson's disease.
Nagy NS, Helal M, Alsawy ES, ..., Al-Sherif SS, Essawy AE
PLoS ONE 19 (12) e0315858 [2024-12-18; online 2024-12-18]
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Non-linear transcriptional responses to gradual modulation of transcription factor dosage
Domingo J, Minaeva M, Morris JA, ..., Sanjana NE, Lappalainen T
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Flexible and robust cell type annotation for highly multiplexed tissue images.
Sun H, Yu S, Casals AM, ..., Lundberg E, Murphy RF
bioRxiv - (-) - [2024-12-17; online 2024-12-17]
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Gaps between Open Science activities and actual recognition systems: Insights from an international survey.
Grattarola F, Shmagun H, Erdmann C, ..., Kim J, Mabile L
PLoS ONE 19 (12) e0315632 [2024-12-16; online 2024-12-16]
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AI-first structural identification of pathogenic protein targets
Saluri M, Landreh M, Bryant P
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Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning.
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
NPJ Syst Biol Appl 10 (1) 148 [2024-12-13; online 2024-12-13]
Avlant Nilsson DDLS Fellow
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Neuropilin-1 controls vascular permeability through juxtacrine regulation of endothelial adherens junctions.
Pal S, Su Y, Nwadozi E, Claesson-Welsh L, Richards M
Angiogenesis 28 (1) 7 [2024-12-12; online 2024-12-12]
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How to build the virtual cell with artificial intelligence: Priorities and opportunities.
Bunne C, Roohani Y, Rosen Y, ..., Leskovec J, Quake SR
Cell 187 (25) 7045-7063 [2024-12-12; online 2024-12-14]
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CSF levels of brain-derived proteins correlate with brain ventricular volume in cognitively healthy 70-year-olds.
Bergström S, Mravinacová S, Lindberg O, ..., Skoog I, Månberg A
Clin Proteomics 21 (1) 65 [2024-12-12; online 2024-12-12]
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The Role of BAZ2-dependent Chromatin Remodeling in Suppressing G4 DNA Structures and Associated Genomic Instability
Vandeuren AL, O’Dare K, Wilson RHC, ..., Reed SH, Day TA
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EchoTilt: An Acoustofluidic Method for the Capture and Enrichment of Nanoplastics Directed Toward Drinking Water Monitoring.
Costa M, van der Geer L, Joaquim M, ..., Wiklund M, Russom A
Micromachines (Basel) 15 (12) - [2024-12-11; online 2024-12-11]
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Activation of the ChvG-ChvI pathway promotes multiple survival strategies during cell wall stress in Agrobacterium tumefaciens
Bouchier JM, Knebel E, Amstutz J, ..., Cava F, Brown PJB
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The impact of Parkinson's disease on striatal network connectivity and corticostriatal drive: An in silico study.
Carannante I, Scolamiero M, Hjorth JJJ, ..., Chachólski W, Kotaleski JH
Netw Neurosci 8 (4) 1149-1172 [2024-12-10; online 2024-12-10]
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XRN1 supplies free nucleotides to feed alphavirus replication
Ruscica V, Iselin L, Hull R, ..., Davis I, Castello A
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Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response
Lafranchi L, Spinner A, Hornisch M, ..., Piazza I, Elsässer SJ
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From early methods for DNA diagnostics to genomes and epigenomes at high resolution during four decades - a personal perspective.
Syvänen AC
Ups. J. Med. Sci. 129 (-) - [2024-12-09; online 2024-12-09]
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Elucidating acquired PARP inhibitor resistance in advanced prostate cancer.
Seed G, Beije N, Yuan W, ..., Carreira S, de Bono J
Cancer Cell 42 (12) 2113-2123.e4 [2024-12-09; online 2024-11-21]
Arian Lundberg DDLS Fellow
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Plasma proteomics for novel biomarker discovery in childhood tuberculosis
Fossati A, Wambi P, Jaganath D, ..., Zar HJ, Swaney DL
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Andrea Fossati DDLS Fellow
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The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends.
Geyer PE, Hornburg D, Pernemalm M, ..., Deutsch EW, Schwenk JM
J. Proteome Res. 23 (12) 5279-5295 [2024-12-06; online 2024-10-31]
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Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group.
Prediger C, Ferreira EA, Zorzato SV, ..., Yassin A, Madi-Ravazzi L
Mol. Biol. Evol. 41 (12) - [2024-12-06; online 2024-12-11]
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"Head-to-Toe" Lipid Properties Govern the Binding and Cargo Transfer of High-Density Lipoprotein.
Weber F, Axmann M, Sezgin E, ..., Stangl H, Plochberger B
Membranes (Basel) 14 (12) - [2024-12-06; online 2024-12-06]
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SARS-CoV-2 N protein recruits G3BP to double membrane vesicles to promote translation of viral mRNAs.
Long S, Guzyk M, Perez Vidakovics L, ..., Achour A, McInerney GM
Nat Commun 15 (1) 10607 [2024-12-05; online 2024-12-05]
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A landscape of X-inactivation during human T cell development.
Gylemo B, Bensberg M, Hennings V, ..., Ekwall O, Nestor CE
Nat Commun 15 (1) 10527 [2024-12-04; online 2024-12-04]
Antonio Lentini DDLS Fellow
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Improved Localization of Insulinomas Using 68Ga-NODAGA-Exendin-4 PET/CT.
Boss M, Eriksson O, Mikkola K, ..., Hermans J, Gotthardt M
Journal of nuclear medicine : official publication, Society of Nuclear Medicine 65 (12) 1959-1964 [2024-12-03; online 2024-12-03]
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Identification of SPP1 + macrophages as an immune suppressor in hepatocellular carcinoma using single-cell and bulk transcriptomics.
Jin H, Kim W, Yuan M, ..., Zhang C, Mardinoglu A
Front Immunol 15 (-) 1446453 [2024-12-03; online 2024-12-03]
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Correction: Candidate serum protein biomarkers for active pulmonary tuberculosis diagnosis in tuberculosis endemic settings.
Ayalew S, Wegayehu T, Wondale B, ..., Fredolini C, Mihret A
BMC Infect Dis 24 (1) 1380 [2024-12-03; online 2024-12-03]
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The paradox of predictability provides a bridge between micro- and macroevolution.
Tsuboi M, Sztepanacz J, De Lisle S, ..., Love AC, Houle D
J Evol Biol 37 (12) 1413-1432 [2024-12-02; online 2024-08-31]
DDLS Fellow Lisandro Milocco
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Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex.
Chung Y, Yim C, Pereira GP, ..., Souza PCT, Kim H
J. Cell Biol. 223 (12) - [2024-12-02; online 2024-11-20]
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PET imaging of GABAA receptors in pancreatic islets by [11C]flumazenil.
Maloum-Rami F, Cheung P, Antoni G, ..., Eriksson O, Espes D
EJNMMI Res 14 (1) 122 [2024-12-02; online 2024-12-02]
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Notarnicola A, Preger C, Lundström SL, ..., Lundberg IE, Fernandes-Cerqueira C
Arthritis Res Ther 26 (1) 206 [2024-12-02; online 2024-12-02]
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Characterising and preventing the gut microbiota's inactivation of trifluridine, a colorectal cancer drug.
McCoubrey LE, Shen C, Mwasambu S, ..., Globisch D, Basit AW
Eur J Pharm Sci 203 (-) 106922 [2024-12-01; online 2024-10-03]
Daniel Globisch SciLifeLab Fellow
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Visual classification of tau‐PET detects four subtypes with different long‐term outcomes
Boccalini C, Mathoux G, Hristovska I, ..., Vogel JW, Garibotto V
Alzheimers Dement 20 (S2) - [2024-12-00; online 2025-01-09]
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Unlocking Tau PET Accessibility: a Machine Learning‐Based Prediction of Tau Pathology from Plasma, MRI and Clinical Variables
Karlsson L, Vogel JW, Strandberg O, ..., Mattsson‐Carlgren N, Hansson O
Alzheimers Dement 20 (S2) - [2024-12-00; online 2025-01-09]
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Ultra-processed food consumption, plasma metabolite profile, and risk of all-cause and cause-specific mortality in a population-based cohort.
Du Y, Zhang S, Schjølberg JS, ..., Sonestedt E, Borné Y
Clin Nutr 43 (12) 184-193 [2024-12-00; online 2024-10-20]
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Transport mechanism of DgoT, a bacterial homolog of SLC17 organic anion transporters.
Dmitrieva N, Gholami S, Alleva C, ..., Alfonso-Prieto M, Fahlke C
EMBO J. 43 (24) 6740-6765 [2024-12-00; online 2024-10-25]
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The mTOR‐4E‐BP1 axis controls microglia inflammatory and neurodegenerative responses
Bermudez S, Choi J, Kim S, ..., Healy LM, Sonenberg N
Alzheimers Dement 20 (S1) - [2024-12-00; online 2025-01-03]
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The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota?
Hofmann S, Podsiadlowski L, Andermann T, ..., Jablonski D, Schmidt J
Mol. Phylogenet. Evol. 201 (-) 108166 [2024-12-00; online 2024-08-09]
DDLS Fellow Tobias Andermann
DOI Crossref
Targeting Alzheimer's disease with novel dual-function 3,5-diaryl-4,5-dihydro-1H-pyrazole-1-carbothioamide derivatives
Katsogiannou A, Karta D, Di Stefano A, ..., Vassiliou S, Cacciatore I
European Journal of Medicinal Chemistry Reports 12 (-) 100235 [2024-12-00; online 2024-12-00]
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Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome.
Singh V, Moran JC, Itoh Y, ..., Barrientos A, Amunts A
Nat. Struct. Mol. Biol. 31 (12) 1838-1847 [2024-12-00; online 2024-08-12]
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SenNet recommendations for detecting senescent cells in different tissues.
Suryadevara V, Hudgins AD, Rajesh A, ..., Dou Z, Neretti N
Nat. Rev. Mol. Cell Biol. 25 (12) 1001-1023 [2024-12-00; online 2024-06-03]
Sanja Vickovic SciLifeLab Fellow
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Role of human plasma metabolites in prediabetes and type 2 diabetes from the IMI-DIRECT study.
Sharma S, Dong Q, Haid M, ..., Pearson ER, Grallert H
Diabetologia 67 (12) 2804-2818 [2024-12-00; online 2024-09-30]
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Risk factors for Charcot foot development in individuals with diabetes mellitus.
Tsatsaris G, Rajamand Ekberg N, Fall T, Catrina SB
Diabetologia 67 (12) 2702-2710 [2024-12-00; online 2024-09-13]
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Reviewability and supportability: New complementary principles to empower research software practices.
Zhang H, Maillo A, Khan SA, ..., Gomez-Cabrero D, Tegnér J
Comput Struct Biotechnol J 23 (-) 3989-3998 [2024-12-00; online 2024-11-06]
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Regional Amyloid Load Predicts Tau and Atrophy Dynamics
Chaggar P, Vogel JW, Binette AP, ..., Hansson O, Goriely A
Alzheimers Dement 20 (S2) - [2024-12-00; online 2025-01-09]
DOI Crossref
Proteomics analysis characterizing new markers related to Aβ plaques and tau tangles pathologies
Binette AP, Wennström M, Strandberg O, ..., Vogel JW, Hansson O
Alzheimers Dement 20 (S2) - [2024-12-00; online 2025-01-09]
PubMed DOI Crossref
Probe set selection for targeted spatial transcriptomics.
Kuemmerle LB, Luecken MD, Firsova AB, ..., Samakovlis C, Theis FJ
Nat. Methods 21 (12) 2260-2270 [2024-12-00; online 2024-11-18]
PubMed DOI Crossref
Optimising in-cell NMR acquisition for nucleic acids.
Annecke HTP, Eidelpes R, Feyrer H, ..., Dasgupta R, Petzold K
J Biomol NMR 78 (4) 249-264 [2024-12-00; online 2024-08-20]
PubMed DOI Crossref
Novel tetrahydronaphthalen-1-yl-phenethyl ureas: synthesis and dual antibacterial-anticancer activities.
Akbaba Y, Kacı FN, Arslan ME, ..., Mardinoğlu A, Türkez H
J Enzyme Inhib Med Chem 39 (1) 2286925 [2024-12-00; online 2023-12-07]
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New developments for the Quest for Orthologs benchmark service.
Altenhoff A, Nevers Y, Tran V, ..., Ebersberger I, Sonnhammer E
NAR Genomics and Bioinformatics 6 (4) lqae167 [2024-12-00; online 2024-12-11]
DOI Crossref
Multiplex detection of meningitis pathogens by a vertical flow paper microarray and signal enhancement suitable for low-resource settings: Proof of concept
Réu P, Gaudenzi G, Nanjebe D, ..., Boum II Y, Russom A
Talanta Open 10 (-) 100357 [2024-12-00; online 2024-12-00]
DOI Crossref
Individual variation in proteomic cascades along the Alzheimer’s disease spectrum
Vogel JW, Vilkaite G, Binette AP, ..., Mattsson‐Carlgren N, Hansson O
Alzheimers Dement 20 (S2) - [2024-12-00; online 2025-01-09]
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Improved precision of Alzheimer’s disease fluid biomarkers when using Amyloid‐β40 or non‐phosphorylated tau as a reference
Karlsson L, Janelidze S, Horie K, ..., Mattsson‐Carlgren N, Hansson O
Alzheimers Dement 20 (S2) - [2024-12-00; online 2025-01-09]
DOI Crossref
Impact of regional MAPT, APOE, and Aβ on tau propagation in Alzheimer’s disease: Insights from a connectome‐based simulation model
Xiao Y, Strandberg O, Bazinet V, ..., Hansson O, Vogel JW
Alzheimers Dement 20 (S8) - [2024-12-00; online 2025-01-09]
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Exploratory insights from the immuno-oncology hollow fiber assay: A pilot approach bridging In Vitro and In Vivo models.
Selvin T, Berglund M, Åkerström A, ..., Andersson CR, Fryknäs M
SLAS Technol 29 (6) 100232 [2024-12-00; online 2024-12-03]
PubMed DOI Crossref
Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Bilev E, Wild N, Momayyezi P, ..., Achour A, Hammer Q
PLoS Pathog 20 (12) e1012755 [2024-12-00; online 2024-12-09]
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Early detection of pancreatic cancer: Study design and analytical considerations in biomarker discovery and early phase validation studies.
Smith LM, Mahoney DW, Bamlet WR, ..., Koay EJ, Oberg AL
Pancreatology 24 (8) 1265-1279 [2024-12-00; online 2024-10-29]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Diagnosing Monogenic Stroke at Younger Age.
Ilinca A, Kafantari E, Wallenius J, ..., Puschmann A, Lindgren AG
Stroke 55 (12) 2846-2855 [2024-12-00; online 2024-11-05]
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Designing from biobased to closed-loop circularity: Flexible dynamic polyimine-amide networks
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Data‐driven progression patterns of Aβ, tau, α‐synuclein and vascular pathology in a clinical population
Mastenbroek SE, Collij LE, Vogel JW, ..., Ossenkoppele R, Hansson O
Alzheimers Dement 20 (S2) - [2024-12-00; online 2025-01-09]
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Cyclophilin D plays a critical role in the survival of senescent cells.
Protasoni M, López-Polo V, Stephan-Otto Attolini C, ..., Kovatcheva M, Serrano M
EMBO J. 43 (23) 5972-6000 [2024-12-00; online 2024-10-24]
PubMed DOI Crossref
CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference.
Safinianaini N, De Souza CPE, Roth A, ..., Toosi H, Lagergren J
Comput Biol Chem 113 (-) 108257 [2024-12-00; online 2024-10-23]
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Benzylhydroxamic acids as inhibitors of insulin regulated aminopeptidase (IRAP)
Beveridge J, Söderström M, Prieto-Díaz R, ..., Larhed M, Gising J
European Journal of Medicinal Chemistry Reports 12 (-) 100215 [2024-12-00; online 2024-12-00]
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Author Correction: A virally encoded tRNA neutralizes the PARIS antiviral defence system.
Burman N, Belukhina S, Depardieu F, ..., Wiedenheft B, Isaev A
Nature 636 (8043) E8 [2024-12-00; online 2024-12-05]
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A framework for sharing of clinical and genetic data for precision medicine applications.
Elhussein A, Baymuradov U, NYGC ALS Consortium , ..., Natarajan K, Gürsoy G
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Deteriorated mechanics of left ventricular diastolic filling one year after coronary artery bypass grafting
Norderfeldt J, Sundqvist MG, Maret E, ..., Eriksson MJ, Ugander M
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Aquaporin-4 as a cerebrospinal fluid biomarker of Alzheimer's disease.
Gómez de San José N, Halbgebauer S, Steinacker P, ..., Parnetti L, Otto M
Transl Neurodegener 13 (1) 57 [2024-11-29; online 2024-11-29]
PubMed DOI Crossref
The ROCK-1/2 inhibitor RKI-1447 blocks N-MYC, promotes cell death, and emerges as a synergistic partner for BET inhibitors in neuroblastoma.
Pepich A, Tümmler C, Abu Ajamieh S, ..., Johnsen JI, Wickström M
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Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix.
Kurt S, Bouchard-Côté A, Lagergren J
Bioinformatics 40 (12) - [2024-11-28; online 2024-11-21]
PubMed DOI Crossref
Author Correction: Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes.
Diamanti K, Visvanathar R, Pereira MJ, ..., Wadelius C, Ahlström H
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A Swedish dietary guideline index, gut microbial α-diversity and prevalence of metabolic syndrome - observations in the Swedish CArdioPulmonary bioImage Study (SCAPIS).
Ericson U, Hellstrand S, Larsson A, ..., Fall T, Orho-Melander M
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Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis.
Salgueiro V, Bertol J, Gutierrez C, ..., Sanz J, Prados-Rosales R
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Cryo-EM structure of single-layered nucleoprotein-RNA complex from Marburg virus.
Zinzula L, Beck F, Camasta M, ..., Plitzko JM, Baumeister W
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Contemporary menopausal hormone therapy and risk of cardiovascular disease: Swedish nationwide register based emulated target trial.
Johansson T, Karlsson T, Bliuc D, ..., Center JR, Johansson Å
BMJ 387 (-) e078784 [2024-11-27; online 2024-11-27]
PubMed DOI Crossref
The association between novel urinary kidney damage biomarkers and coronary atherosclerosis in an apparently healthy population.
Lin YT, Wuopio J, Larsson A, ..., Fall T, Ärnlöv J
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Microneedles loaded with lipid nanocarriers for local treatment of vulvovaginal candidiasis
Udayakumar P, Škalko-Basnet N, Salas Cotaquispe CF, ..., Du J, Teleki A
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Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Co-occurring mutations identify prognostic subgroups of microsatellite stable colorectal cancer.
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Mol Cancer 23 (1) 264 [2024-11-25; online 2024-11-25]
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Naltrexone blocks alcohol-induced effects on kappa-opioid receptors in the plasma membrane.
Oasa S, Sezgin E, Ma Y, ..., Vukojević V, Terenius L
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The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans.
Stevens I, Silao FG, Huch S, ..., Ljungdahl PO, Pelechano V
Sci Rep 14 (1) 29012 [2024-11-22; online 2024-11-22]
SciLifeLab Fellow Vicente Pelechano
PubMed DOI Crossref
Response to Letter to Editor by A. Derbalah et al.: the role of automation in enhancing reproducibility and interoperability of PBPK models.
Domínguez-Romero E, Mazurenko S, Scheringer M, ..., Županič A, Suarez-Diez M
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PubMed DOI Crossref
Bridging the gap: Integrating cutting-edge techniques into biological imaging with deepImageJ.
Fuster-Barceló C, García-López-de-Haro C, Gómez-de-Mariscal E, ..., Sage D, Muñoz-Barrutia A
Biol Imaging 4 (-) e14 [2024-11-22; online 2024-11-22]
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Flipping a switch on BRD4: How to control the do-it-all.
van Hout FAH, Vihervaara A
Mol. Cell 84 (22) 4257-4259 [2024-11-21; online 2024-11-23]
Anniina Vihervaara SciLifeLab Fellow
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Single-molecule states link transcription factor binding to gene expression.
Doughty BR, Hinks MM, Schaepe JM, ..., Bintu L, Greenleaf WJ
Nature - (-) - [2024-11-20; online 2024-11-20]
Emil Marklund SciLifeLab Fellow
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SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF Resulting in Drastic Soluble Protein Depletion.
Christ W, Kapell S, Sobkowiak MJ, ..., El Andaloussi S, Ezzat K
ACS Chem Neurosci 15 (22) 4095-4104 [2024-11-20; online 2024-11-07]
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Complete genome sequences of the prosthecate dimorphic bacteria Brevundimonas intermedia CB63T and Brevundimonas staleyi FWC43T.
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Microbiol Resour Announc - (-) e0105024 [2024-11-20; online 2024-11-20]
Kristina Jonas SciLifeLab Fellow
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A Phylogenomic Analysis of Genipa (Rubiaceae) Using Target Sequence Capture Data
Ridley R, Persson C, Oxelman B, Andermann T, Bacon CD
Systematic Botany 49 (3) 617-625 [2024-11-19; online 2024-11-19]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
The Role of Water Networks in Phosphodiesterase Inhibitor Dissociation and Kinetic Selectivity.
Blaazer AR, Singh AK, Zara L, ..., Brown DG, de Esch IJP
ChemMedChem 19 (22) e202400417 [2024-11-18; online 2024-09-12]
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Host-specific adaptation of Legionella pneumophila to single and multiple hosts
Moreno AB, Paranjape K, Cederblom M, ..., Andersson DI, Guy L
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Enterotoxigenic Escherichia coli in Blantyre, Malawi.
Ashton PM, Katuah ZJ, Botomani A, ..., Msefula C, Jere KC
Access Microbiol 6 (11) - [2024-11-18; online 2024-11-18]
Astrid von Mentzer DDLS Fellow
PubMed DOI Crossref
Cooperative role of LSD1 and CHD7 in regulating differentiation of mouse embryonic stem cells.
Malla S, Martinez-Gamero C, Kumari K, ..., Roman AC, Aguilo F
Sci Rep 14 (1) 28495 [2024-11-18; online 2024-11-18]
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A dispensable SepIVA orthologue in Streptomyces venezuelae is associated with polar growth and not cell division.
Sen BC, Mavi PS, Irazoki O, ..., Cava F, Flärdh K
BMC Microbiol. 24 (1) 481 [2024-11-18; online 2024-11-18]
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tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation in Plasmodium falciparum.
Li Q, Vetter L, Veith Y, ..., Larsson O, Chun-Leung Chan S
iScience 27 (11) 111167 [2024-11-15; online 2024-10-12]
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A comparative analysis of blastoid models through single-cell transcriptomics.
Balubaid A, Alsolami S, Kiani NA, ..., Li M, Tegner J
iScience 27 (11) 111122 [2024-11-15; online 2024-10-11]
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JAK2-mutant clonal hematopoiesis is associated with venous thromboembolism.
Zon RL, Sekar A, Clapham K, ..., Natarajan P, Ebert BL
Blood 144 (20) 2149-2154 [2024-11-14; online 2024-08-05]
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From Virtual Screens to Cellular Target Engagement: New Small Molecule Ligands for the Immune Checkpoint LAG-3.
Fuchs N, Calvo-Barreiro L, Talagayev V, ..., Wolber G, Gabr MT
ACS Med. Chem. Lett. 15 (11) 1884-1890 [2024-11-14; online 2024-10-15]
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Colchicine prevents accelerated atherosclerosis in TET2-mutant clonal haematopoiesis.
Zuriaga MA, Yu Z, Matesanz N, ..., Natarajan P, Fuster JJ
Eur. Heart J. 45 (43) 4601-4615 [2024-11-14; online 2024-09-01]
Abhishek Niroula DDLS Fellow
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Abstract PR002: Hypoxia-induced epigenetic changes coordinate transcription start site selection and translational control through remodeling of 5’UTRs
Watt K, Dauber B, Szkop KJ, ..., Larsson O, Postovit LM
Mol. Cancer Ther. 23 (11_Supplement) PR002-PR002 [2024-11-14; online 2024-11-14]
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Tertiary Lymphoid Structures in Central Nervous System Disorders.
Vaccaro A, de Alves Pereira B, van de Walle T, Dimberg A
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Annotated genome sequences of Salmonella Haifa, Salmonella Bangkok, and Salmonella Reading, isolated from chicken meat in South Africa.
Mathole M, Carroll L, Khabo-Mmekoa C, Mabogoane N, Matle I
Microbiol Resour Announc 13 (11) e0028424 [2024-11-12; online 2024-10-09]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Single cell long read whole genome sequencing reveals somatic transposon activity in human brain.
Izydorczyk MB, Kalef-Ezra E, Horner DW, ..., Sedlazeck FJ, Proukakis C
medRxiv - (-) - [2024-11-11; online 2024-11-11]
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CNSC-11. INVESTIGATION OF GLIOBLASTOMA NEURON-TUMOR NETWORKS WITH RABIES-BASED RETROGRADE TRACING
Tetzlaff SK, Reyhan E, Bengtson CP, ..., Saez-Rodriguez J, Venkataramani V
Neuro-oncology 26 (Supplement_8) viii42-viii42 [2024-11-11; online 2024-11-11]
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Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules.
de Weerd HA, Guala D, Gustafsson M, ..., Lubovac-Pilav Z, Magnusson R
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Inhibition of IRAP Enhances the Expression of Pro-Cognitive Markers Drebrin and MAP2 in Rat Primary Neuronal Cells.
Stam F, Bjurling S, Nylander E, ..., Grönbladh A, Hallberg M
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AlphaFold with conformational sampling reveals the structural landscape of homorepeats.
Bonet DF, Ranyai S, Aswad L, ..., Landreh M, Lama D
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Unraveling the Bivalent and Rapid Interactions Between a Multivalent RNA Recognition Motif and RNA: A Kinetic Approach.
Pérez-Ropero G, Pérez-Ràfols A, Martelli T, Danielson UH, Buijs J
Biochemistry 63 (21) 2816-2829 [2024-11-05; online 2024-10-14]
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Targeting the SWI/SNF Chromatin Remodeling Complex Subunit SMARCA4 in ALL
Ayyadevara VSSA, Paik A, Perencsik R, ..., Geng H, Hurtz C
Blood 144 (Supplement 1) 4216-4216 [2024-11-05; online 2024-11-05]
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Standalone single- and bi-layered human skin 3D models supported by recombinant silk feature native spatial organization.
Gkouma S, Bhalla N, Frapard S, ..., Widhe M, Hedhammar M
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Resistance to FLT3 Inhibitors in FLT3-Mutated AML Is Associated with CD45RA+CD200- leukemic Cells and Can be Overcome By Combination with SMAC Mimetics
Struyf N, Gezelius H, Lundmark A, ..., Kallioniemi O, Erkers T
Blood 144 (Supplement 1) 1565-1565 [2024-11-05; online 2024-11-05]
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Plasma Proteomics Differentiates between Patients with B-Cell Lymphomas
Babačić H, Chowdhury NM, Berglund M, ..., Pernemalm M, Hellström M
Blood 144 (Supplement 1) 4370-4370 [2024-11-05; online 2024-11-05]
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Mutations in BCORCCND2NRAS and XPO1 Predict Clinical Outcomes upon MRD-Guided Venetoclax Plus Ibrutinib in Relapsed and Refractory Chronic Lymphocytic Leukemia
Brieghel C, Dubois J, Buhl IK, ..., Kater AP, Niemann CU
Blood 144 (Supplement 1) 586-586 [2024-11-05; online 2024-11-05]
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Mutation-Specific Differences in the Relationship between Obesity and Clonal Hematopoiesis, with a Focus on JAK2V617F and MPN Prevention
Rolles B, Sekar A, Serrano-Ron L, ..., Hormoz S, Mullally A
Blood 144 (Supplement 1) 872-872 [2024-11-05; online 2024-11-05]
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Mapping the Spatial Proteome of Individual Leukemia Cells Undergoing Fludarabine Treatment
Nordlund J, Globisch M, Gezelius H, ..., Raine A, Andersson C
Blood 144 (Supplement 1) 2212-2212 [2024-11-05; online 2024-11-05]
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Differential Response to ATR/Chk1 Inhibition in Preleukemia and Transformed Leukemia in an MLL-ENL Model of Leukemogenesis Reflects Enrichment for Myc-Transcriptional Program
Chaloupkova P, Janotka L, Gursky J, ..., Bartek J, Divoky V
Blood 144 (Supplement 1) 5725-5725 [2024-11-05; online 2024-11-05]
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Deciphering the Heterogeneity of Acute Myeloid Leukemia through Chromatin Accessibility Profiling
Ochi Y, Liew-Littorin M, Nannya Y, ..., Lehmann S, Ogawa S
Blood 144 (Supplement 1) 639-639 [2024-11-05; online 2024-11-05]
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Clinical Relevance of the Integrative Analysis of Gut Microbiome and Metabolomics in Myeloid Neoplasms: Correlations with Genomic Profiles, Treatment Response/Complications and Clinical Outcome
Campagna A, Clasen F, Portlock T, ..., Della Porta MG, Shoaie S
Blood 144 (Supplement 1) 104-104 [2024-11-05; online 2024-11-05]
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CCDC28A deficiency causes head-tail coupling defects and immotility in murine spermatozoa.
Stojanovic N, Hernández RO, Ramírez NT, ..., Hernández AH, Shibuya H
Sci Rep 14 (1) 26808 [2024-11-05; online 2024-11-05]
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BMI trajectories from birth to young adulthood associate with distinct cardiometabolic profiles.
Wang G, Wei D, Kebede Merid S, ..., Bergström A, Melén E
BMC Med 22 (1) 510 [2024-11-05; online 2024-11-05]
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A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS.
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Prelude to malignancy: A gene expression signature in normal mammary gland from breast cancer patients suggests pre-tumorous alterations and is associated with adverse outcomes.
Andreou M, Jąkalski M, Duzowska K, ..., Mieczkowski J, Piotrowski A
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EMhub: a web platform for data management and on-the-fly processing in scientific facilities.
de la Rosa-Trevin JM, Sharov G, Fleischmann S, ..., Fernandez IS, Carroni M
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The genetic landscape of neuro-related proteins in human plasma.
Repetto L, Chen J, Yang Z, ..., Navarro P, Shen X
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Sustained immune activation and impaired epithelial barrier integrity in the ectocervix of women with chronic HIV infection.
Franzén Boger M, Hasselrot T, Kaldhusdal V, ..., Broliden K, Tjernlund A
PLoS Pathog 20 (11) e1012709 [2024-11-00; online 2024-11-19]
Gisele Miranda SciLifeLab Fellow
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J Allergy Clin Immunol Glob 3 (4) 100332 [2024-11-00; online 2024-08-30]
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Photothermal induction of pyroptosis in malignant glioma spheroids using (16-mercaptohexadecyl)trimethylammonium bromide-modified cationic gold nanorods.
Zarska M, Novak O, Jakubcova T, ..., Proska J, Hodny Z
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Massive parallel sequencing-based non-invasive prenatal test (NIPT) identifies aberrations on chromosome 13.
Sobol M, Aravidis C, Hessel H, Lindqvist A, Baranowska Körberg I
Eur J Obstet Gynecol Reprod Biol 302 (-) 370-374 [2024-11-00; online 2024-10-06]
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Loss of heterozygosity of CYP2D6 enhances the sensitivity of hepatocellular carcinomas to talazoparib.
Zhang X, Rameika N, Zhong L, ..., Globisch D, Sjöblom T
EBioMedicine 109 (-) 105368 [2024-11-00; online 2024-10-04]
Daniel Globisch SciLifeLab Fellow
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Integration across biophysical scales identifies molecular and cellular correlates of person-to-person variability in human brain connectivity.
Ng B, Tasaki S, Greathouse KM, ..., Gaiteri C, Herskowitz JH
Nat. Neurosci. 27 (11) 2240-2252 [2024-11-00; online 2024-10-31]
DDLS Fellow Jacob W Vogel
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Epigenetic regulation by polycomb repressive complex 1 promotes cerebral cavernous malformations.
Pham VC, Rödel CJ, Valentino M, ..., Pagani M, Abdelilah-Seyfried S
EMBO Mol Med 16 (11) 2827-2855 [2024-11-00; online 2024-10-14]
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Early-life chemical exposome: Comprehensive strategies for wide-scope screening of organic compounds
Guerrini C, Sunyer-Caldú A, Gil-Solsona R, ..., Gago-Ferrero P, Ramírez N
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Biosens Bioelectron 261 (-) 116518 [2024-10-01; online 2024-06-22]
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Eichelmann F, Prada M, Sellem L, ..., Schulze MB, Wittenbecher C
Nat. Med. 30 (10) 2867-2877 [2024-10-00; online 2024-07-11]
Clemens Wittenbecher DDLS Fellow
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Mi J, Ren L, Andersson O
Trends in molecular medicine 30 (10) 932-949 [2024-10-00; online 2024-06-01]
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Emerging methods and applications in 3D genomics.
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Design and evaluation of novel inhibitors for the treatment of clear cell renal cell carcinoma.
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Blood lipid profiling indicates that dietary fat quality is associated with cardiometabolic risk.
Nat. Med. 30 (10) 2735-2736 [2024-10-00; online 2024-08-31]
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Bayesian polynomial neural networks and polynomial neural ordinary differential equations.
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PLoS Comput Biol 20 (10) e1012414 [2024-10-00; online 2024-10-10]
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Author Correction: Immune system adaptation during gender-affirming testosterone treatment.
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A virally encoded tRNA neutralizes the PARIS antiviral defence system.
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A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract.
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A cocktail of histidine, carnosine, cysteine and serine reduces adiposity and improves metabolic health and adipose tissue immunometabolic function in ovariectomized rats.
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MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families, and updated covariance models
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The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer.
Gallardo-Dodd CJ, Kutter C
Hum Genomics 18 (1) 109 [2024-09-27; online 2024-09-27]
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Syngap1 Promotes Cognitive Function through Regulation of Cortical Sensorimotor Dynamics.
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SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.
Tolstoganov I, Chen Z, Pevzner P, Korobeynikov A
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Introducing synthetic thermostable RNase inhibitors to single-cell RNA-seq.
Noble JC, Lentini A, Hagemann-Jensen M, Sandberg R, Reinius B
Nat Commun 15 (1) 8373 [2024-09-27; online 2024-09-27]
Antonio Lentini DDLS Fellow
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Antimicrobial Dihydroflavonols and Isoflavans Isolated from the Root Bark of Dalbergia gloveri.
Kiganda I, Wieske LHE, Nchiozem-Ngnitedem VA, ..., Yenesew A, Erdelyi M
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Targeting mutant p53: Evaluation of novel anti-p53 R175H monoclonal antibodies as diagnostic tools
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Discovery of 2-Aryl-4-aminoquinazolin-Based LSD1 Inhibitors to Activate Immune Response in Gastric Cancer.
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Single-cell dissection of the human blood-brain barrier and glioma blood-tumor barrier.
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Gastrin-releasing peptide receptor as theranostic target in estrogen-receptor positive breast cancer: A preclinical study of the theranostic pair [55Co]Co- and [177Lu]Lu-DOTA-RM26.
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The Organelle in the Ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses
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Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health
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Making PBPK models more reproducible in practice.
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Improved sub-genomic RNA prediction with the ARTIC protocol.
Baudeau T, Sahlin K
Nucleic Acids Res. 52 (17) e82 [2024-09-23; online 2024-08-16]
Kristoffer Sahlin SciLifeLab Fellow
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A machine learning-based prediction of tau load and distribution in Alzheimer's disease using plasma, MRI and clinical variables.
Karlsson L, Vogel J, Arvidsson I, ..., Mattsson-Carlgren N, Hansson O
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Microgravity Effect on Pancreatic Islets.
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FunCoup 6: advancing functional association networks across species with directed links and improved user experience
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Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.
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Integrating amyloid and tau imaging with proteomics and genomics in Alzheimer's disease.
Vilkaite G, Vogel J, Mattsson-Carlgren N
Cell Rep Med 5 (9) 101735 [2024-09-17; online 2024-09-19]
DDLS Fellow Jacob W Vogel
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Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection.
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Conserved Evolutionary Response to Whole Genome Duplication in Angiosperms Revealed Using High Resolution Gene Expression Profiling
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BCL2 expression is enriched in advanced prostate cancer with features of lineage plasticity.
Westaby D, Jiménez-Vacas JM, Figueiredo I, ..., de Bono J, Sharp A
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Arian Lundberg DDLS Fellow
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Aurora B and Aurora C pools at two chromosomal regions collaboratively maintain chromosome alignment and prevent aneuploidy at the second meiotic division in mammalian oocytes.
Kouznetsova A, Valentiniene S, Liu JG, ..., Brismar H, Höög C
Front Cell Dev Biol 12 (-) 1470981 [2024-09-17; online 2024-09-17]
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An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.
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Cancer Res. 84 (18) 3086-3100 [2024-09-16; online 2024-07-11]
Arian Lundberg DDLS Fellow
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Maternal pre-pregnancy BMI influences the associations between bisphenol and phthalate exposures and maternal weight changes and fat accumulation.
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The CHCHD2-CHCHD10 protein complex is modulated by mitochondrial dysfunction and alters lipid homeostasis in the mouse brain
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Sequence variants influencing the regulation of serum IgG subclass levels.
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Abhishek Niroula DDLS Fellow
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Nasal transcriptomic profiling reveals distinct patterns in Type 2 Asthma
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Cigarette smoking, but not snuff usage, is associated with a systemic inflammatory profile in young adults
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Biomarkers in ICU-treated Covid-19 patients 4 and 10 months after discharge: evidence for persistent inflammation and remodeling
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Microbial dietary preference and interactions affect the export of lipids to the deep ocean.
Behrendt L, Alcolombri U, Hunter JE, ..., Stocker R, Van Mooy BAS
Science (New York, N.Y.) 385 (6714) eaab2661 [2024-09-13; online 2024-09-13]
Lars Behrendt SciLifeLab Fellow
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Discovery of a 6-Aminobenzo[b]thiophene 1,1-Dioxide Derivative (K2071) with a Signal Transducer and Activator of Transcription 3 Inhibitory, Antimitotic, and Senotherapeutic Activities.
Oleksak P, Rysanek D, Vancurova M, ..., Musilek K, Hodny Z
ACS pharmacology & translational science 7 (9) 2755-2783 [2024-09-13; online 2024-08-12]
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Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats
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Degradation of PET microplastic particles to monomers in human serum by PETase.
Lopez-Lorenzo X, Hueting D, Bosshard E, Syrén PO
Faraday Discuss 252 (0) 387-402 [2024-09-11; online 2024-09-11]
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Control of bacterial cell wall autolysins by peptidoglycan crosslinking mode.
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Nat Commun 15 (1) 7937 [2024-09-11; online 2024-09-11]
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Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma.
Nagarajan D, Parracho RT, Corujo D, ..., Buschbeck M, Mao Y
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Automated Image-Based Fluorescence Screening of Mitochondrial Membrane Potential in Daphnia magna: An Advanced Ecotoxicological Testing Tool.
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Environ. Sci. Technol. 58 (36) 15926-15937 [2024-09-10; online 2024-08-27]
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Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT.
Takada H, Fujiwara K, Atkinson GC, Chiba S, Hauryliuk V
Nucleic Acids Res. 52 (16) 9854-9866 [2024-09-09; online 2024-06-29]
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Long-term longitudinal analysis of 4,187 participants reveals insights into determinants of clonal hematopoiesis.
Uddin MM, Saadatagah S, Niroula A, ..., Ballantyne CM, Natarajan P
Nat Commun 15 (1) 7858 [2024-09-09; online 2024-09-09]
Abhishek Niroula DDLS Fellow
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Bacterial transcriptional repressor NrdR – a flexible multifactorial nucleotide sensor
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Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold
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The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder
Weibel CA, Wheeler AL, James JE, ..., McShea H, Masel J
Elife 12 (-) - [2024-09-06; online 2024-09-06]
DDLS Fellow Jennifer James
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Hyper-recombination in ribosomal DNA is driven by long-range resection-independent RAD51 accumulation.
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Nat Commun 15 (1) 7797 [2024-09-06; online 2024-09-06]
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Divergent mechanisms of steroid inhibition in the human ρ1 GABAA receptor.
Fan C, Cowgill J, Howard RJ, Lindahl E
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Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer
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Claudia Kutter SciLifeLab Fellow
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Genetic ablation of adhesion ligands mitigates rejection of allogeneic cellular immunotherapies.
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Cell Stem Cell 31 (9) 1376-1386.e8 [2024-09-05; online 2024-07-08]
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Exploring the structural landscape of DNA maintenance proteins.
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Development of a three-dimensional scoring model for the assessment of continuous glucose monitoring data in type 1 diabetes.
Dawnbringer J, Hill H, Lundgren M, ..., Carlsson PO, Espes D
BMJ Open Diabetes Res Care 12 (4) - [2024-09-05; online 2024-09-05]
Daniel Espes SciLifeLab Fellow
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Deep learning segmentation model produces accurate biodiversity predictions at 10 m spatial resolution
Andermann T, Häggmark J, Olsson P, Högström A
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DDLS Fellow Tobias Andermann
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Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes.
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Mol. Biol. Evol. 41 (9) - [2024-09-04; online 2024-09-20]
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Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.
Doktorova M, Daum S, Ebenhan J, ..., Kenworthy AK, Levental I
bioRxiv - (-) - [2024-09-04; online 2024-09-04]
DDLS Fellow Milka Doktorova
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The Oxidation of Electron-Rich Arenes Using a H2O2-Proline System.
Chetty LC, Kruger HG, Arvidsson PI, ..., Govender T, Naicker T
ACS Omega 9 (35) 37155-37162 [2024-09-03; online 2024-08-22]
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Regional distribution of mechanical strain and macrophage-associated lung inflammation after ventilator-induced lung injury: an experimental study.
Liggieri F, Chiodaroli E, Pellegrini M, ..., Eriksson O, Perchiazzi G
Intensive Care Med Exp 12 (1) 77 [2024-09-03; online 2024-09-03]
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Nationwide prospective audit for the evaluation of appendicitis risk prediction models in adults: right iliac fossa treatment (RIFT)-Turkey.
Yalcinkaya A, Yalcinkaya A, Balci B, ..., Leventoglu S, RIFT TURKEY Study Collaboration
BJS Open 8 (5) - [2024-09-03; online 2024-10-09]
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Multi-ancestry polygenic risk scores for venous thromboembolism.
Jee YH, Thibord F, Dominguez A, ..., Kraft P, INVENT Consortium
Hum. Mol. Genet. 33 (18) 1584-1591 [2024-09-03; online 2024-06-16]
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Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach.
Sharma KD, Doktorova M, Waxham MN, Heberle FA
Biophys. J. 123 (17) 2877-2891 [2024-09-03; online 2024-04-30]
DDLS Fellow Milka Doktorova
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Novel Calcium Phosphate Promotes Interbody Bony Fusion in a Porcine Anterior Cervical Discectomy and Fusion Model.
Östman M, Försth P, Hedenqvist P, ..., Höglund O, Forterre F
Spine (Phila Pa 1976) 49 (17) 1179-1186 [2024-09-01; online 2024-01-12]
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ECCB2024: The 23rd European Conference on Computational Biology.
Kukkonen-Macchi A, Hautaniemi S, Heil KF, ..., Nyrönen TH, Elo LL
Bioinformatics 40 (Suppl 2) ii1-ii3 [2024-09-01; online 2024-09-04]
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quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data.
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Nat. Methods 21 (9) 1603-1607 [2024-09-00; online 2024-07-04]
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Unveiling structural features, chemical reactivity, and bioactivity of a newly synthesized purine derivative through crystallography and computational approaches
Abad N, Buhlak S, Hajji M, ..., Turkez H, Mardinoglu A
Journal of Molecular Structure 1311 (-) 138400 [2024-09-00; online 2024-09-00]
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The one-carbon metabolic enzyme MTHFD2 promotes resection and homologous recombination after ionizing radiation.
Marttila P, Bonagas N, Chalkiadaki C, ..., Mortusewicz O, Helleday T
Mol Oncol 18 (9) 2179-2195 [2024-09-00; online 2024-03-27]
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Synthesis, spectroscopic characterization, DFT and molecular docking of N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl) naphthalene-1-sulfonamide derivatives
Ashraf S, Iqbal S, Sebhaoui J, ..., Turkez H, Mardinoglu A
Journal of Molecular Structure 1312 (-) 138470 [2024-09-00; online 2024-09-00]
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Spatial metatranscriptomics resolves host-bacteria-fungi interactomes.
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Spatial landscapes of cancers: insights and opportunities.
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Nat Rev Clin Oncol 21 (9) 660-674 [2024-09-00; online 2024-07-23]
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Serial Lift-Out: sampling the molecular anatomy of whole organisms.
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Nat. Methods 21 (9) 1684-1692 [2024-09-00; online 2023-12-18]
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Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles
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Mol. Ecol. 33 (17) - [2024-09-00; online 2024-08-15]
Pascal Milesi SciLifeLab Fellow
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Prognostic genome and transcriptome signatures in colorectal cancers.
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Plasma levels of complement components C5 and C9 are associated with thrombin generation.
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P25-13 Effects of personalized mixtures of POPs on steroidogenesis and viability in H295R cells
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P25-12 Effects of personalized chemical mixture on endocrine disruption based on estrogen nuclear receptors
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P12-14 Male exposure to di-n-butyl phthalate induces persistent and transgenerational adverse effects on mouse liver transcriptome
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P06-14 Single-nucleus RNA-sequencing of the testis in dibutyl phthalate-exposed mice
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OC01.04: *AI‐driven ultrasound detection of ovarian cancer that generalises: an international multicentre validation study
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Ultrasound in Obstet & Gyne 64 (S1) 2-2 [2024-09-00; online 2024-09-09]
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Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs.
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Major cardiovascular events and death in parents of children with type 1 diabetes: a register-based matched cohort study in Sweden.
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Diabetologia 67 (9) 1828-1837 [2024-09-00; online 2024-06-26]
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Ironing out protein synthesis: METTL17 is an Fe-S cluster checkpoint for mitochondrial translation
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Biochim Biophys Acta Bioenerg 1865 (-) 149421 [2024-09-00; online 2024-09-00]
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Increased levels of thymidine kinase 1 in malignant cell-derived extracellular vesicles.
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Cancer Med 13 (18) e70255 [2024-09-00; online 2024-09-24]
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Tiemann JK, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
Elife 12 (-) - [2024-08-30; online 2024-08-30]
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Mutsuddy A, Huggins JR, Amrit A, ..., Calhoun JC, Birtwistle MR
bioRxiv - (-) - [2024-08-26; online 2024-08-26]
Cemal Erdem DDLS Fellow
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Comparing Lipinskis Rule of 5 and Machine Learning Based Prediction of Fraction Absorbed for Assessing Oral Absorption in Humans
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Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
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Size-related variability of oxygen consumption rates in individual human hepatic cells.
Botte E, Cui Y, Magliaro C, ..., Behrendt L, Ahluwalia A
Lab Chip 24 (17) 4128-4137 [2024-08-20; online 2024-08-20]
Lars Behrendt SciLifeLab Fellow
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Quantification of membrane fluidity in bacteria using TIR-FCS.
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Multi-layered dosage compensation of the avian Z chromosome
Papanicolaou N, Lentini A, Wettersten S, ..., Wright D, Reinius B
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Antonio Lentini DDLS Fellow
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Detection of protein-protein interactions by bio-orthogonal fluorogenic proximity probes
Torell A, Larsson NA, Phillipson S, Odell LR, Fürth D
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DNA methylation patterns contribute to changes of cellular differentiation pathways in leukocytes with LOY from patients with Alzheimer’s disease
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Therapeutic application of extracellular vesicular EGFR isoform D as a co-drug to target squamous cell cancers with tyrosine kinase inhibitors.
Toh SY, Leong HS, Chong FT, ..., Tan DSW, Iyer NG
Dev. Cell 59 (16) 2189-2202.e8 [2024-08-19; online 2024-07-31]
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Sleep maintains excitatory synapse diversity in the cortex and hippocampus.
Koukaroudi D, Qiu Z, Fransén E, ..., Seibt J, Grant SGN
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Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data.
Seal S, Williams D, Hosseini-Gerami L, ..., Spjuth O, Bender A
Chem. Res. Toxicol. 37 (8) 1290-1305 [2024-08-19; online 2024-07-09]
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Hugerth LW, Krog MC, Vomstein K, ..., Nielsen HS, Schuppe-Koistinen I
Microbiome 12 (1) 153 [2024-08-19; online 2024-08-19]
DDLS Fellow Luisa Hugerth
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Halama A, Zaghlool S, Thareja G, ..., Schmidt F, Suhre K
Nat Commun 15 (1) 7111 [2024-08-19; online 2024-08-19]
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Curti L, Rohban S, Bianchi N, ..., Parazzoli D, Campaner S
Nat Commun 15 (1) 7100 [2024-08-18; online 2024-08-18]
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Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.
Lee H, Langseth CM, Salas SM, ..., Grillo M, Nilsson M
Development 151 (16) - [2024-08-15; online 2024-08-29]
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In sickness and health - a questionnaire based study regarding immune mediated diseases and neoplasia in Swedish Nova Scotia Duck Tolling Retrievers.
Nilsson M, Kozyrev SV, Lindblad-Toh K, Rönnberg H, Hansson-Hamlin H
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Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.
Erb IK, Suarez C, Frank EM, ..., Lindberg E, Paul CJ
FEMS Microbes 5 (-) xtae024 [2024-08-14; online 2024-08-14]
DDLS Fellow Johan Bengtsson-Palme
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Distinct bacterial and protist plankton diversity dynamics uncovered through DNA-based monitoring in the Baltic Sea area
Jurdzinski KT, Latz MA, Torstensson A, ..., Karlson B, Andersson AF
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Sun W-S, Torrens G, Ter Beek J, Cava F, Berntsson RP-A
MBio 15 (8) e0048824 [2024-08-14; online 2024-06-28]
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Eriksen R, White MC, Dawed AY, ..., Frost G, Pearson ER
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Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer.
Zhu X, Farsh T, Vis D, ..., van der Heijden MS, Feng FY
J. Clin. Invest. 134 (19) - [2024-08-13; online 2024-08-13]
Arian Lundberg DDLS Fellow
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Four decades of research on Viktor Mutt’s neuropeptides with focus on galanin
Hökfelt T, Barde S, Zhong W, Xu ZQD, Alberts P
PEAS 73 (3) 170-192 [2024-08-12; online 2024-08-12]
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A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.
Takada H, Paternoga H, Fujiwara K, ..., Wilson DN, Hauryliuk V
Nucleic Acids Res. 52 (14) 8483-8499 [2024-08-12; online 2024-05-30]
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Sex-Specific Associations between Prenatal Exposure to Bisphenols and Phthalates and Infant Epigenetic Age Acceleration.
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Epigenomes 8 (3) - [2024-08-10; online 2024-08-10]
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Duplexed CeTEAM drug biosensors reveal determinants of PARP inhibitor selectivity
Pires MJ, Lovric A, Alam S, ..., Altun M, Valerie NCK
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Pathway activation model for personalized prediction of drug synergy
Trac QT, Huang Y, Erkers T, ..., Pawitan Y, Vu TN
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Stimulated emission depletion microscopy
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Nat Rev Methods Primers 4 (1) - [2024-08-08; online 2024-08-08]
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Insights into the mechanisms driven by H3K4 KMTs in pancreatic cancer.
LaRue-Nolan KC, Raja Arul GL, Sigafoos AN, Shi J, Fernandez-Zapico ME
Biochem. J. 481 (15) 983-997 [2024-08-07; online 2024-07-30]
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Hypoxic-Ischemic Insult Alters Polyamine and Neurotransmitter Abundance in the Specific Neonatal Rat Brain Subregions.
Mácha H, Luptáková D, Juránek I, Andrén PE, Havlíček V
ACS Chem Neurosci 15 (15) 2811-2821 [2024-08-07; online 2024-07-26]
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Extensively acquired antimicrobial resistant bacteria restructure the individual microbial community in post-antibiotic conditions
Baek JW, Lim S, Park N, ..., Koh A, Lee S
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Association of polygenic scores for autism with volumetric MRI phenotypes in cerebellum and brainstem in adults.
Mohammad S, Gentreau M, Dubol M, ..., Mwinyi J, Schiöth HB
Mol Autism 15 (1) 34 [2024-08-07; online 2024-08-07]
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Applying Spatial Metabolomics To Investigate Age- and Drug-Induced Neurochemical Changes.
Vallianatou T, Angerer TB, Kaya I, ..., Svenningsson P, Andrén PE
ACS Chem Neurosci 15 (15) 2822-2829 [2024-08-07; online 2024-07-29]
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β-Carboline-based light and pH dual stimuli-responsive ion transporters induce cancer cell death.
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Chem. Commun. (Camb.) 60 (64) 8419-8422 [2024-08-06; online 2024-08-06]
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Hydrogen production by a fully de novo enzyme.
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Allosteric inhibition of CFTR gating by CFTRinh-172 binding in the pore.
Gao X, Yeh HI, Yang Z, ..., Kappes JC, Hwang TC
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Integrating Natural and Engineered Genetic Variation to Decode Regulatory Influence on Blood Traits
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Deciphering the genetics and mechanisms of predisposition to multiple myeloma.
Went M, Duran-Lozano L, Halldorsson GH, ..., Houlston R, Nilsson B
Nat Commun 15 (1) 6644 [2024-08-05; online 2024-08-05]
Abhishek Niroula DDLS Fellow
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Multiplexed mapping of the interactome of GPCRs with receptor activity-modifying proteins.
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Sci Adv 10 (31) eado9959 [2024-08-02; online 2024-07-31]
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Understanding the interplay between dNTP metabolism and genome stability in cancer.
Yagüe-Capilla M, Rudd SG
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Oral administration of CXCL12-expressing Limosilactobacillus reuteri improves colitis by local immunomodulatory actions in preclinical models.
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GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention.
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Effects of oral contraceptives and menopausal hormone therapy on the risk of rheumatoid arthritis: a prospective cohort study.
Hadizadeh F, Johansson T, Johansson Å, Karlsson T, Ek WE
Rheumatology (Oxford) 63 (8) 2101-2108 [2024-08-01; online 2023-09-29]
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The brittle star genome illuminates the genetic basis of animal appendage regeneration.
Parey E, Ortega-Martinez O, Delroisse J, ..., Oliveri P, Marlétaz F
Nat Ecol Evol 8 (8) 1505-1521 [2024-08-00; online 2024-07-19]
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Structure-based virtual screening of vast chemical space as a starting point for drug discovery.
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SMYD5 methylation of rpL40 links ribosomal output to gastric cancer.
Park J, Wu J, Szkop KJ, ..., Gozani O, Mazur PK
Nature 632 (8025) 656-663 [2024-08-00; online 2024-07-24]
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Role of estrogen signaling in fibroblastic reticular cells for innate and adaptive immune responses in antigen-induced arthritis.
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Immunol. Cell Biol. 102 (7) 578-592 [2024-08-00; online 2024-05-10]
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Mechanistic screening of reproductive toxicity in a novel 3D testicular co-culture model shows significant impairments following exposure to low-dibutyl phthalate concentrations.
Almamoun R, Pierozan P, Karlsson O
Arch. Toxicol. 98 (8) 2695-2709 [2024-08-00; online 2024-05-20]
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Maternal exposure to bisphenols, phthalates, perfluoroalkyl acids, and trace elements and their associations with gestational diabetes mellitus in the APrON cohort.
Soomro MH, England-Mason G, Reardon AJF, ..., Dewey D, APrON Study Team
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Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes.
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Annu Rev Biomed Data Sci 7 (1) 369-389 [2024-08-00; online 2024-07-24]
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Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis.
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Nat. Genet. 56 (8) 1725-1736 [2024-08-00; online 2024-07-01]
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Maculopathy and adult-onset ataxia in patients with biallelic MFSD8 variants.
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Mol Genet Genomic Med 12 (8) e2505 [2024-08-00; online 2024-08-07]
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Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer.
Zhao SG, Bootsma M, Zhou S, ..., Lupien M, Feng FY
Nat. Genet. 56 (8) 1689-1700 [2024-08-00; online 2024-07-17]
Arian Lundberg DDLS Fellow
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Genotyping oral contraceptive users for venous thromboembolism risk.
Lo Faro V, Johansson Å
Am J Obstet Gynecol 231 (2) e80 [2024-08-00; online 2024-05-01]
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Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae).
Hofmann S, Rödder D, Andermann T, ..., Schmidt J, Podsiadlowski L
Mol. Ecol. 33 (15) e17446 [2024-08-00; online 2024-07-01]
DDLS Fellow Tobias Andermann
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Epidemiological and environmental investigation of the 'big four' Vibrio species, 1994 to 2021: a Baltic Sea retrospective study.
Gyraitė G, Kataržytė M, Bučas M, ..., Lastauskienė E, Labrenz M
Euro Surveill 29 (32) - [2024-08-00; online 2024-08-09]
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Direct presentation of inflammation-associated self-antigens by thymic innate-like T cells induces elimination of autoreactive CD8+ thymocytes.
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Nat. Immunol. 25 (8) 1367-1382 [2024-08-00; online 2024-07-11]
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Development and implementation of assays to monitor human adenovirus F40/41 in wastewater: Trends preceding, during, and following the non-A-to-E hepatitis outbreak in Stockholm.
Perez-Zabaleta M, Williams C, Cetecioglu Z
Environ Int 190 (-) 108937 [2024-08-00; online 2024-08-05]
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Combining VPS34 inhibitors with STING agonists enhances type I interferon signaling and anti-tumor efficacy.
Yu Y, Bogdan M, Noman MZ, ..., De Milito A, Janji B
Mol Oncol 18 (8) 1904-1922 [2024-08-00; online 2024-03-20]
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BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging.
Lei W, Fuster-Barceló C, Reder G, Muñoz-Barrutia A, Ouyang W
Nat. Methods 21 (8) 1368-1370 [2024-08-00; online 2024-08-10]
DDLS Fellow Wei Ouyang
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Artificial intelligence for high content imaging in drug discovery.
Carreras-Puigvert J, Spjuth O
Curr. Opin. Struct. Biol. 87 (-) 102842 [2024-08-00; online 2024-05-25]
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A suicidal and extensively disordered luciferase with a bright luminescence.
Dijkema FM, Escarpizo-Lorenzana MI, Nordentoft MK, ..., Teilum K, Winther JR
Protein Sci. 33 (8) e5115 [2024-08-00; online 2024-07-18]
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A second space age spanning omics, platforms and medicine across orbits.
Mason CE, Green J, Adamopoulos KI, ..., Mateus J, Beheshti A
Nature 632 (8027) 995-1008 [2024-08-00; online 2024-06-11]
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A Visual Environment for Data Driven Protein Modeling and Validation.
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IEEE Trans Vis Comput Graph 30 (8) 5063-5073 [2024-08-00; online 2024-07-01]
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Inhibition of IRAP Enhance the Expression of Pro-cognitive Markers Drebrin and MAP2 in Rat Primary Neuronal Cells
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Bacteria combine polar- and dispersed-growth to power cell elongation and wall width dynamics
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Genome-wide expression analysis in a Fabry disease human podocyte cell line.
Snanoudj S, Derambure C, Zhang C, ..., Bekri S, Tebani A
Heliyon 10 (14) e34357 [2024-07-30; online 2024-07-09]
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Cryo-EM structures of ρ1 GABA A receptors with antagonist and agonist drugs
Fan C, Cowgill J, Howard RJ, Lindahl E
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Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis.
Schulte T, Chaves-Sanjuan A, Speranzini V, ..., Palladini G, Ricagno S
Nat Commun 15 (1) 6359 [2024-07-28; online 2024-07-28]
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Selective lysis of acute myeloid leukemia cells by CD34/CD3 bispecific antibody through the activation of γδ T-cells.
Al Agrafi F, Gaballa A, Hahn P, ..., Uhlin M, Stikvoort A
Oncoimmunology 13 (1) 2379063 [2024-07-27; online 2024-07-27]
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OCT1 (SLC22A1) transporter kinetics and regulation in primary human hepatocyte 3D spheroids.
Mickols E, Meyer A, Handin N, ..., Karlgren M, Artursson P
Sci Rep 14 (1) 17334 [2024-07-27; online 2024-07-27]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Large-scale proteomics reveals precise biomarkers for detection of ovarian cancer in symptomatic women.
Ivansson E, Hedlund Lindberg J, Stålberg K, ..., Gyllensten U, Enroth S
Sci Rep 14 (1) 17288 [2024-07-27; online 2024-07-27]
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Disparate and shared transcriptomic signatures associated with cortical atrophy in genetic bvFTD.
Shen T, Vogel JW, Van Deerlin VM, ..., Irwin DJ, McMillan CT
medRxiv - (-) - [2024-07-27; online 2024-07-27]
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Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.
Leal JL, Milesi P, Hodková E, ..., Salojärvi J, Lascoux M
Syst. Biol. 73 (2) 392-418 [2024-07-27; online 2024-04-13]
DDLS Fellow Jennifer James Pascal Milesi SciLifeLab Fellow
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Autoantibodies towards HFE and SYT5 in anti-neutrophil cytoplasm antibody-associated vasculitis relapse
Bayati S, Nazeer J, Ng J, ..., Nilsson P, Pin E
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Adaptive Robust Learning using Latent Bernoulli Variables
Karakulev A, Zachariah D, Singh P
Proceedings of the 41st International Conference on Machine Learning, PMLR 235 (-) 23105-23122 [2024-07-27; online 2023-12-04]
Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
Loss of the tumour suppressor LKB1/STK11 uncovers a leptin-mediated sensitivity mechanism to mitochondrial uncouplers for targeted cancer therapy.
Angelopoulou A, Theocharous G, Valakos D, ..., Papaspyropoulos A, Gorgoulis VG
Mol Cancer 23 (1) 147 [2024-07-25; online 2024-07-25]
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Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
Bryant P, Noé F
PLoS Comput Biol 20 (7) e1012253 [2024-07-25; online 2024-07-25]
DDLS Fellow Patrick Bryant
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Distinct Plasma Protein Profiles Distinguish Faster from Slower Disease Progression in HIV-1 and HIV-2 infections
Johansson E, Nazziwa J, Freyhult E, ..., Jansson M, Esbjörnsson J
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MpANT regulates meristem development in Marchantia polymorpha.
Liu W, Yang Z, Cai G, ..., Willemsen V, Xu L
Cell Reports 43 (7) 114466 [2024-07-23; online 2024-07-09]
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High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage.
Lai Y, Koelmel JP, Walker DI, ..., Jones DP, Miller GW
Environ. Sci. Technol. 58 (29) 12784-12822 [2024-07-23; online 2024-07-10]
PubMed DOI Crossref
Protective alleles and precision healthcare in crewed spaceflight.
Rutter LA, MacKay MJ, Cope H, ..., Giacomello S, Mason CE
Nat Commun 15 (1) 6158 [2024-07-22; online 2024-07-22]
DOI Crossref
Glutamine-addiction in cisplatin resistant cancer cells is mediated by SLC7A11 and can be targeted with asparaginase therapy
Wang J, Strauss R, Bartek J, Rudd SG
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PubMed DOI Crossref
Discovery of Cell-Permeable Allosteric Inhibitors of Liver Pyruvate Kinase: Design and Synthesis of Sulfone-Based Urolithins.
Iqbal S, Islam MZ, Ashraf S, ..., Turkez H, Mardinoglu A
Int J Mol Sci 25 (14) - [2024-07-22; online 2024-07-22]
PubMed DOI Crossref
Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.
Lin Z, Schaefer K, Lui I, ..., Sali A, Wells JA
Science (New York, N.Y.) 385 (6706) eadl5763 [2024-07-19; online 2024-07-19]
Andrea Fossati DDLS Fellow
PubMed DOI Crossref
Discovery of a Therapeutic Agent for Glioblastoma Using a Systems Biology-Based Drug Repositioning Approach.
Kaynar A, Ozcan M, Li X, ..., Shoaie S, Mardinoglu A
Int J Mol Sci 25 (14) - [2024-07-18; online 2024-07-18]
PubMed DOI Crossref
Electromigrated Gold Nanogap Tunnel Junction Arrays: Fabrication and Electrical Behavior in Liquid and Gaseous Media.
Raja SN, Jain S, Kipen J, ..., Herland A, Niklaus F
ACS Appl Mater Interfaces 16 (28) 37131-37146 [2024-07-17; online 2024-07-02]
PubMed DOI Crossref
A potential space-making role in cell wall biogenesis for SltB1and DacB revealed by a beta-lactamase induction phenotype in Pseudomonas aeruginosa.
Gyger J, Torrens G, Cava F, Bernhardt TG, Fumeaux C
MBio 15 (7) e0141924 [2024-07-17; online 2024-06-26]
DOI Crossref
Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program
Karppi I, Pessa JC, Rabenius A, ..., Sistonen L, Vihervaara A
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PubMed DOI Crossref
Mapping the contribution of the C-linker domain to gating polarity in CNBD channels.
Lin JL, Chang Y, Tewari D, Cowgill J, Chanda B
Biophys. J. 123 (14) 2176-2184 [2024-07-16; online 2024-04-27]
PubMed DOI Crossref
Divergent evolution of male-determining loci on proto-Y chromosomes of the housefly.
Li X, Visser S, Son JH, ..., Bopp D, Beukeboom LW
Nat Commun 15 (1) 5984 [2024-07-16; online 2024-07-16]
DOI Crossref
Ancient tree-topologies and gene-flow processes among human lineages in Africa
Breton G, Sjödin P, Zervakis PI, ..., Jakobsson M, Verdu P
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PubMed DOI Crossref
An intracellular hydrophobic nexus critical for hERG1 channel slow deactivation.
Stevens-Sostre WA, Flores-Aldama L, Bustos D, ..., Delemotte L, Robertson GA
Biophys. J. 123 (14) 2024-2037 [2024-07-16; online 2024-01-12]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
TMEM16F scramblase regulates angiogenesis via endothelial intracellular signaling.
Shan KZ, Le T, Liang P, ..., Claesson-Welsh L, Yang H
J. Cell. Sci. 137 (14) - [2024-07-15; online 2024-07-18]
PubMed DOI Crossref
Retraction notice to "Combined metabolic activators improve metabolic functions in the animal models of neurodegenerative diseases" [Life Sci. 314 (2023) 121325].
Turkez H, Altay O, Yildirim S, ..., Uhlén M, Mardinoglu A
Life Sci 349 (-) 122712 [2024-07-15; online 2024-05-18]
PubMed DOI Crossref
Discovery and in vitro Evaluation of Novel Serotonin 5-HT2A Receptor Ligands Identified Through Virtual Screening.
Zięba A, Bartuzi D, Stępnicki P, ..., Castro M, Kaczor AA
ChemMedChem 19 (14) e202400080 [2024-07-15; online 2024-05-29]
PubMed DOI Crossref
Advances in development of biomarkers for brain damage and ischemia.
Karimova D, Rostami E, Chubarev VN, ..., Schiöth HB, Rask-Andersen M
Mol. Biol. Rep. 51 (1) 803 [2024-07-13; online 2024-07-13]
PubMed DOI Crossref
SignalP: The Evolution of a Web Server.
Nielsen H, Teufel F, Brunak S, von Heijne G
Methods in molecular biology (Clifton, N.J.) 2836 (-) 331-367 [2024-07-12; online 2024-07-12]
PubMed DOI Crossref
How sex and gender shape functional brain networks.
Matte Bon G, Kraft D, Kaufmann T
Sci Adv 10 (28) eadq3079 [2024-07-12; online 2024-07-12]
DOI Crossref
Cardiomyocyte antisense transcription regulates exon usage in the elastic spring region of Titin to modulate sarcomere function
Celik S, Hyrefelt L, Czuba T, ..., Smith JG, Gidlöf O
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DOI Crossref
Nasal tissue-resident memory CD4 + T cells persist after influenza A virus infection and provide heterosubtypic protection
Mathew NR, Gailleton R, Scharf L, ..., Tang KW, Angeletti D
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PubMed DOI Crossref
Mechanism of phage sensing and restriction by toxin-antitoxin-chaperone systems.
Mets T, Kurata T, Ernits K, ..., Atkinson GC, Hauryliuk V
Cell Host Microbe 32 (7) 1059-1073.e8 [2024-07-10; online 2024-05-30]
DOI Crossref
Evolutionary rescue of spherical mreB deletion mutants of the rod-shape bacterium Pseudomonas fluorescens SBW25
Yulo PRJ, Desprat N, Gerth ML, ..., Rainey PB, Hendrickson HL
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PubMed DOI Crossref
Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.
Mozumdar D, Fossati A, Stevenson E, ..., Swaney DL, Bondy-Denomy J
Cell Host Microbe 32 (7) 1050-1058.e7 [2024-07-10; online 2024-06-12]
Andrea Fossati DDLS Fellow
DOI Crossref
Cerebrospinal fluid levels of NfM in relation to NfL and pNfH as prognostic markers in amyotrophic lateral sclerosis
Olofsson J, Bergström S, Mravinacová S, ..., Nilsson P, Månberg A
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PubMed DOI Crossref
Associations between Microglia and Astrocytic Proteins and Tau Biomarkers across the Continuum of Alzheimer's Disease.
Doroszkiewicz J, Kulczyńska-Przybik A, Dulewicz M, ..., Blennow K, Mroczko B
Int J Mol Sci 25 (14) - [2024-07-09; online 2024-07-09]
PubMed DOI Crossref
Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily.
Digles D, Ingles-Prieto A, Dvorak V, ..., Wiedmer T, Superti-Furga G
Front. Pharmacol. 15 (-) 1401599 [2024-07-09; online 2024-07-09]
PubMed DOI Crossref
Simulating the Skin Permeation Process of Ionizable Molecules.
Lundborg M, Wennberg C, Lindahl E, Norlén L
J Chem Inf Model 64 (13) 5295-5302 [2024-07-08; online 2024-06-25]
PubMed DOI Crossref
Genome-scale metabolic network of human carotid plaque reveals the pivotal role of glutamine/glutamate metabolism in macrophage modulating plaque inflammation and vulnerability.
Jin H, Zhang C, Nagenborg J, ..., Mardinoglu A, Biessen EAL
Cardiovasc Diabetol 23 (1) 240 [2024-07-08; online 2024-07-08]
PubMed DOI Crossref
Broadcasters, receivers, functional groups of metabolites, and the link to heart failure by revealing metabolomic network connectivity.
Yazdani A, Mendez-Giraldez R, Yazdani A, ..., Larson MG, Elsea SH
Metabolomics 20 (4) 71 [2024-07-07; online 2024-07-07]
Clemens Wittenbecher DDLS Fellow
DOI Crossref
Cellular and molecular events organizing the assembly of tertiary lymphoid structures in glioblastoma
Vaccaro A, Yang F, van de Walle T, ..., Ramachandran M, Dimberg A
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PubMed DOI Crossref
ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer.
Bernal YA, Durán E, Solar I, Sagredo EA, Armisén R
Int J Mol Sci 25 (13) - [2024-07-06; online 2024-07-06]
PubMed DOI Crossref
Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding.
Bimai O, Banerjee I, Rozman Grinberg I, ..., Sjöberg BM, Logan DT
Elife 12 (-) - [2024-07-05; online 2024-07-05]
PubMed DOI Crossref
A generalizable data-driven model of atrophy heterogeneity and progression in memory clinic settings.
Baumeister H, Vogel JW, Insel PS, ..., Hansson O, Berron D
Brain 147 (7) 2400-2413 [2024-07-05; online 2024-04-24]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Rapid genome sequencing for critically ill infants: an inaugural pilot study from Turkey.
Guner Yilmaz B, Akgun-Dogan O, Ozdemir O, ..., Ozbek U, Alanay Y
Front Pediatr 12 (-) 1412880 [2024-07-04; online 2024-07-04]
PubMed DOI Crossref
A single-cell transcriptomic study of heterogeneity in human embryonic tanycytes.
Bai Y, Chen Q, Li Y
Sci Rep 14 (1) 15384 [2024-07-04; online 2024-07-04]
PubMed DOI Crossref
Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds.
Wang SZ, Yan Y, Widlund M, ..., Savolainen P, Wang GD
Mol. Biol. Evol. 41 (7) - [2024-07-03; online 2024-06-06]
PubMed DOI Crossref
High Caveolin-1 mRNA expression in triple-negative breast cancer is associated with an aggressive tumor microenvironment, chemoresistance, and poor clinical outcome.
Godina C, Khazaei S, Belting M, ..., Bosch A, Jernström H
PLoS ONE 19 (7) e0305222 [2024-07-03; online 2024-07-03]
PubMed DOI Crossref
Flotillin-mediated stabilization of unfolded proteins in bacterial membrane microdomains.
Ukleja M, Kricks L, Torrens G, ..., Cava F, Lopez D
Nat Commun 15 (1) 5583 [2024-07-03; online 2024-07-03]
PubMed DOI Crossref
Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women.
Bashir Z, Hugerth LW, Krog MC, ..., Fransson E, Nielsen HS
Front. Cell. Infect. Microbiol. 14 (-) 1324794 [2024-07-02; online 2024-07-02]
DDLS Fellow Luisa Hugerth
DOI Crossref
Vaginal Microbiota Transplantation (VMT) for treatment of vaginal dysbiosis without the use of antibiotics – A Double-Blinded Randomized Controlled Trial in healthy women with vaginal dysbiosis
Wrønding T, Vomstein K, DeLong K, ..., Ensign LM, Nielsen HS
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DOI Crossref
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
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PubMed DOI Crossref
High-bandwidth low-current measurement system for automated and scalable probing of tunnel junctions in liquids.
Raja SN, Jain S, Kipen J, ..., Herland A, Niklaus F
Rev Sci Instrum 95 (7) - [2024-07-01; online 2024-07-22]
PubMed DOI Crossref
Deletion of CD44 promotes adipogenesis by regulating PPARγ and cell cycle-related pathways.
Weng X, Jiang H, Walker DJ, ..., Wang J, Kang L
J Endocrinol 262 (1) - [2024-07-01; online 2024-05-20]
PubMed DOI Crossref
Cancer Core Europe: Leveraging Institutional Synergies to Advance Oncology Research and Care Globally.
Carmona J, Chavarria E, Donoghue K, ..., Zwart W, Tabernero J
Cancer Discov 14 (7) 1147-1153 [2024-07-01; online 2024-06-13]
PubMed DOI Crossref
CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses.
Prajapati B, Sokolova M, Sidorenko E, ..., Vihervaara A, Vartiainen MK
J. Cell. Sci. 137 (13) - [2024-07-01; online 2024-07-15]
Anniina Vihervaara SciLifeLab Fellow
DOI Crossref
Author response: MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
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PubMed DOI Crossref
Special issue: TGF-β and epithelial-mesenchymal transition in cancer.
Ten Dijke P, Miyazono K, Heldin CH, Moustakas A
Semin. Cancer Biol. 102-103 (-) 1-3 [2024-07-00; online 2024-06-27]
PubMed DOI Crossref
Smad7 palmitoylation by the S-acyltransferase zDHHC17 enhances its inhibitory effect on TGF-β/Smad signaling.
Voytyuk O, Ohata Y, Moustakas A, Ten Dijke P, Heldin CH
J Biol Chem 300 (7) 107462 [2024-07-00; online 2024-06-12]
PubMed DOI Crossref
On-Chip Neural Induction Boosts Neural Stem Cell Commitment: Toward a Pipeline for iPSC-Based Therapies.
Jain S, Voulgaris D, Thongkorn S, ..., Falk A, Herland A
Adv Sci (Weinh) 11 (25) e2401859 [2024-07-00; online 2024-04-24]
PubMed DOI Crossref
Novel drug targets and molecular mechanisms for sarcopenia based on systems biology.
Ceyhan AB, Ozcan M, Kim W, ..., Zhang C, Mardinoglu A
Biomed. Pharmacother. 176 (-) 116920 [2024-07-00; online 2024-06-13]
PubMed DOI Crossref
Lipid imaging of Alzheimer's disease pathology.
Hanrieder J
J. Neurochem. 168 (7) 1175-1178 [2024-07-00; online 2024-02-19]
PubMed DOI Crossref
Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression.
Zhang M, Sjöström M, Cui X, ..., Feng FY, Quigley DA
Nat. Cell Biol. 26 (7) 1176-1186 [2024-07-00; online 2024-06-13]
Arian Lundberg DDLS Fellow
DOI Crossref
Identification of Gene‐Therapy Responsive Blood Biomarkers in mdx Mouse Model
Johansson C, Boehler JF, Brown KJ, ..., Spitali P, Al‐Khalili Szigyarto C
JCSM Communications 7 (2) 187-198 [2024-07-00; online 2024-12-17]
PubMed DOI Crossref
Exploring BPA alternatives - Environmental levels and toxicity review.
Adamovsky O, Groh KJ, Białk-Bielińska A, ..., Blaha L, Kyriakopoulou K
Environ Int 189 (-) 108728 [2024-07-00; online 2024-05-23]
Lars Behrendt SciLifeLab Fellow
DOI Crossref
Evaluation of activated sludge settling characteristics from microscopy images with deep convolutional neural networks and transfer learning
Borzooei S, Scabini L, Miranda G, ..., Nopens I, Torfs E
Journal of Water Process Engineering 64 (-) 105692 [2024-07-00; online 2024-07-00]
Gisele Miranda SciLifeLab Fellow
PubMed DOI Crossref
Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures.
Martins ASG, Reis SD, Benson E, ..., Pêgo AP, Moreno PMD
Small 20 (29) e2309140 [2024-07-00; online 2024-02-11]
Erik Benson SciLifeLab Fellow
DOI Crossref
Enhanced Cellular Uptake through Nanotopography‐Induced Macropinocytosis
Aramesh M, Yu D, Essand M, Persson C
Adv. Funct. Mater. 34 (28) - [2024-07-00; online 2024-03-13]
PubMed DOI Crossref
Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass.
Choi B, Tafur Rangel A, Kerkhoven EJ, Nygård Y
Metab. Eng. 84 (-) 23-33 [2024-07-00; online 2024-05-23]
PubMed DOI Crossref
Effects and avoidance of photoconversion-induced artifacts in confocal and STED microscopy.
Dasgupta A, Koerfer A, Kokot B, ..., Eggeling C, Carravilla P
Nat. Methods 21 (7) 1171-1174 [2024-07-00; online 2024-06-04]
PubMed DOI Crossref
Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS.
Nordahl L, Akkuratov EE, Heimgärtner J, ..., Wennmalm S, Brismar H
Biochim Biophys Acta Gen Subj 1868 (7) 130619 [2024-07-00; online 2024-04-20]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Corrigendum to "Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning" [eBioMedicine, 2022;83:104214].
Zhang C, Shi M, Kim W, ..., Boren J, Mardinoglu A
EBioMedicine 105 (-) 105224 [2024-07-00; online 2024-06-28]
PubMed DOI Crossref
Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay.
Pérez-Ortín JE, Jordán-Pla A, Zhang Y, ..., Pelechano V, García-Martínez J
Yeast 41 (7) 458-472 [2024-07-00; online 2024-06-14]
SciLifeLab Fellow Vicente Pelechano
PubMed DOI Crossref
Cleanroom-Free Direct Laser Micropatterning of Polymers for Organic Electrochemical Transistors in Logic Circuits and Glucose Biosensors.
Enrico A, Buchmann S, De Ferrari F, ..., Herland A, Zeglio E
Adv Sci (Weinh) 11 (27) e2307042 [2024-07-00; online 2024-01-15]
PubMed DOI Crossref
Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis.
Salignon J, Millan-Ariño L, Garcia MU, Riedel CG
Genomics 116 (4) 110858 [2024-07-00; online 2024-05-11]
PubMed DOI Crossref
Being Breastfed in Infancy and Risk of Colorectal Cancer and Precursor Lesions.
Yuan C, Wang QL, Kim H, ..., Giovannucci EL, Ng K
Clin Gastroenterol Hepatol 22 (7) 1508-1517.e11 [2024-07-00; online 2023-09-06]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
The quantification of zebrafish ocular-associated proteins provides hints for sex-biased visual impairments and perception.
Niksirat H, Siino V, Steinbach C, Levander F
Heliyon 10 (12) e33057 [2024-06-30; online 2024-06-13]
DOI Crossref
Population History and Admixture of the Fulani People from the Sahel
Fortes-Lima CA, Diallo MY, Janoušek V, Černý V, Schlebusch CM
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PubMed DOI Crossref
CPSign: conformal prediction for cheminformatics modeling.
Arvidsson McShane S, Norinder U, Alvarsson J, ..., Carlsson L, Spjuth O
J Cheminform 16 (1) 75 [2024-06-28; online 2024-06-28]
DOI Crossref
Implementing AI in Advanced Recycling of Perovskite Solar Cells
Sprague CI, de la Asunción-Nadal V, García-Fernández A
- - (-) 1-4 [2024-06-25; online 2024-06-25]
PubMed DOI Crossref
Elasto-inertial focusing and particle migration in high aspect ratio microchannels for high-throughput separation.
Tanriverdi S, Cruz J, Habibi S, ..., Tammisola O, Russom A
Microsyst. Nanoeng. 10 (-) 87 [2024-06-25; online 2024-06-25]
PubMed DOI Crossref
Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics.
Chang YC, Gnann C, Steimbach RR, ..., Miller AK, Kuster B
Cell Reports 43 (6) 114272 [2024-06-25; online 2024-05-24]
DOI Crossref
Design of linear and cyclic peptide binders of different lengths from protein sequence information
Li Q, Vlachos EN, Bryant P
- - (-) - [2024-06-22; online 2024-06-22]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
Mass Spectrometry Proteomics Characterization of Plasma Biomarkers for Colorectal Cancer Associated With Inflammation.
Urbiola-Salvador V, Jabłońska A, Miroszewska D, ..., Dumanski JP, Chen Z
Biomark Insights 19 (-) 11772719241257739 [2024-06-20; online 2024-06-20]
PubMed DOI Crossref
Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts.
Bontemps Z, Paranjape K, Guy L
FEMS Microbiol Rev 48 (4) - [2024-06-20; online 2024-07-31]
PubMed DOI Crossref
Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements.
Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, ..., DiNome ML, Marzese DM
Cell. Mol. Life Sci. 81 (1) 274 [2024-06-20; online 2024-06-20]
PubMed DOI Crossref
Identification of fragments targeting SMYD3 using highly sensitive kinetic and multiplexed biosensor-based screening.
FitzGerald EA, Cederfelt D, Lund BA, ..., Dobritzsch D, Danielson UH
RSC Med Chem 15 (6) 1982-1990 [2024-06-19; online 2024-03-20]
DOI Crossref
Discovery of tumour indicating morphological changes in benign prostate biopsies through AI
Chelebian E, Avenel C, Järemo H, ..., Bergh A, Wählby C
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DOI Crossref
SURG-02. INTRAOPERATIVE APPLICATION OF A POLYMER-BASED HYDROGEL AGAINST MEDULLOBLASTOMA GROUP 3 AND ATYPICAL TERATOID/RHABDOID TUMOURS
Moloney C, ElSherbeny A, McCrorie P, ..., Smith SJ, Rahman R
Neuro-oncology 26 (Supplement_4) 0-0 [2024-06-18; online 2024-06-18]
PubMed DOI Crossref
Deciphering the functional specialization of whole-brain spatiomolecular gradients in the adult brain.
Vogel JW, Alexander-Bloch AF, Wagstyl K, ..., Satterthwaite TD, Seidlitz J
Proc. Natl. Acad. Sci. U.S.A. 121 (25) e2219137121 [2024-06-18; online 2024-06-11]
DDLS Fellow Jacob W Vogel
DOI Crossref
DIPG-27. MATCHED PRIMARY-RELAPSE PEDHGG PATIENT-DERIVED XENOGRAFT MODELS TO IDENTIFY THERAPY RESISTANCE PROFILES
Barnerjee S, Zhao M, Rosen G, ..., Holmberg KO, Giraud G
Neuro-oncology 26 (Supplement_4) 0-0 [2024-06-18; online 2024-06-18]
PubMed DOI Crossref
Disease progression modelling reveals heterogeneity in trajectories of Lewy-type α-synuclein pathology.
Mastenbroek SE, Vogel JW, Collij LE, ..., Beach TG, Hansson O
Nat Commun 15 (1) 5133 [2024-06-15; online 2024-06-15]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Cortical morphology variations during the menstrual cycle in individuals with and without premenstrual dysphoric disorder.
Dubol M, Stiernman L, Sundström-Poromaa I, Bixo M, Comasco E
J Affect Disord 355 (-) 470-477 [2024-06-15; online 2024-03-27]
Erika Comasco SciLifeLab Fellow
DOI Crossref
Wide-scale Geographical Analysis of Genetic Ancestry in the South African Coloured Population
Lankheet I, Hammarén R, Caballero LXA, ..., de Jongh M, Schlebusch C
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PubMed DOI Crossref
Human In Vitro Models of Neuroenergetics and Neurometabolic Disturbances: Current Advances and Clinical Perspectives.
Rogal J, Zamproni LN, Nikolakopoulou P, ..., Wredenberg A, Herland A
Stem Cells Transl Med 13 (6) 505-514 [2024-06-14; online 2024-04-08]
DOI Crossref
Author response: Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone allosterically mediates substrate binding to the active site
Bimaï O, Banerjee I, Grinberg IR, ..., Sjöberg BM, Logan DT
- - (-) - [2024-06-14; online 2024-06-14]
DOI Crossref
Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone allosterically mediates substrate binding to the active site
Bimaï O, Banerjee I, Grinberg IR, ..., Sjöberg BM, Logan DT
- - (-) - [2024-06-14; online 2024-06-14]
PubMed DOI Crossref
Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.
de Souza Gama FH, Dutra LA, Hawgood M, ..., Azevedo H, Couñago RM
J Med Chem 67 (11) 8609-8629 [2024-06-13; online 2024-05-23]
PubMed DOI Crossref
Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database.
Gudmundsson S, Singer-Berk M, Stenton SL, ..., MacArthur DG, O'Donnell-Luria A
bioRxiv - (-) - [2024-06-13; online 2024-06-13]
DOI Crossref
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis
Murga M, Lopez-Pernas G, Soliva R, ..., Orozco M, Fernández-Capetillo O
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PubMed DOI Crossref
Construction of the ETECFinder database for the characterization of enterotoxigenic Escherichia coli (ETEC) and revision of the VirulenceFinder web tool at the CGE website.
Scheutz F, Nielsen CH, von Mentzer A
J. Clin. Microbiol. 62 (6) e0057023 [2024-06-12; online 2024-04-24]
Astrid von Mentzer DDLS Fellow
PubMed DOI Crossref
Pharmaceutical Quality by Design Approach to Develop High-Performance Nanoparticles for Magnetic Hyperthermia.
Ansari SR, Suárez-López YDC, Thersleff T, ..., Rinaldi-Ramos CM, Teleki A
ACS Nano 18 (23) 15284-15302 [2024-06-11; online 2024-05-30]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Hemangiosarcoma Cells Promote Conserved Host-derived Hematopoietic Expansion.
Kim JH, Schulte AJ, Sarver AL, ..., Kaufman DS, Modiano JF
Cancer Res Commun 4 (6) 1467-1480 [2024-06-11; online 2024-05-17]
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EchoGrid: High-Throughput Acoustic Trapping for Enrichment of Environmental Microplastics.
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ACS Chem Neurosci 15 (11) 2296-2307 [2024-06-05; online 2024-05-24]
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Chim HY, Elofsson A
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Koutarapu S, Ge J, Dulewicz M, ..., Schöll M, Hanrieder J
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JAMA Cardiol 9 (6) 497-506 [2024-06-01; online 2024-04-10]
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Temperature and water availability drive insect seasonality across a temperate and a tropical region.
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Kiasat A, Prast-Nielsen S, Rautiainen S, ..., Löf Granström A, Gustafsson UO
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Peripheral Blood Mononuclear Cell Gene Expression Associated with Pulmonary Microvascular Perfusion: The Multi-Ethnic Study of Atherosclerosis Chronic Obstructive Pulmonary Disease.
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Mixing Insulating Commodity Polymers with Semiconducting n-type Polymers Enables High-Performance Electrochemical Transistors.
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Mid-pregnancy allopregnanolone levels and trajectories of perinatal depressive symptoms.
Björväng RD, Walldén Y, Fransson E, ..., Sundström-Poromaa I, Skalkidou A
Psychoneuroendocrinology 164 (-) 107009 [2024-06-00; online 2024-02-28]
Erika Comasco SciLifeLab Fellow
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Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells.
Aslanzadeh M, Stanicek L, Tarbier M, ..., Biryukova I, Friedländer MR
NAR Genomics and Bioinformatics 6 (2) lqae045 [2024-06-00; online 2024-05-06]
DDLS Fellow Marcel Tarbier
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Design and synthesis of novel JNK inhibitors targeting liver pyruvate kinase for the treatment of non-alcoholic fatty liver disease and hepatocellular carcinoma
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Bioorganic Chemistry 147 (-) 107425 [2024-06-00; online 2024-06-00]
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DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible.
Hidalgo-Cenalmor I, Pylvänäinen JW, G Ferreira M, ..., Henriques R, Gómez-de-Mariscal E
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Kermpatsou D, Olsson F, Wåhlén E, ..., Lennartsson J, Norlin M
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Turnbull K, Paternoga H, von der Weth E, ..., Wilson DN, Hauryliuk V
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Bryant P, Kelkar A, Guljas A, Clementi C, Noé F
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Hohmann M, Brunner V, Johannes W, ..., Janßen KP, Gulder TAM
Commun Biol 7 (1) 655 [2024-05-28; online 2024-05-28]
DDLS Fellow Laura Carroll
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An Automated Versatile Diagnostic Workflow for Infectious Disease Detection in Low-Resource Settings.
Urrutia Iturritza M, Mlotshwa P, Gantelius J, ..., Jönsson HN, Gaudenzi G
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2-Aryladenine Derivatives as a Potent Scaffold for Adenosine Receptor Antagonists: The 6-Morpholino Derivatives.
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Cheng L, Correia MSP, Higdon SM, ..., Globisch D, Du J
Gut Microbes 16 (1) 2356275 [2024-05-26; online 2024-05-26]
Daniel Globisch SciLifeLab Fellow
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Mitotic MTH1 inhibitor TH1579 induces PD-L1 expression and inflammatory response through the cGAS-STING pathway.
Shen J, Guillén Mancina E, Chen S, ..., Sanjiv K, Helleday T
Oncogenesis 13 (1) 17 [2024-05-25; online 2024-05-25]
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Deep Texture Feature Aggregation on Leaf Microscopy Images for Brazilian Plant Species Recognition
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Nat Commun 15 (1) 4380 [2024-05-23; online 2024-05-23]
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FLT3L governs the development of partially overlapping hematopoietic lineages in humans and mice.
Momenilandi M, Lévy R, Sobrino S, ..., Casanova JL, Béziat V
Cell 187 (11) 2817-2837.e31 [2024-05-23; online 2024-05-03]
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Effectiveness and Cost-effectiveness of Artificial Intelligence-assisted Pathology for Prostate Cancer Diagnosis in Sweden: A Microsimulation Study.
Du X, Hao S, Olsson H, ..., Eklund M, Clements M
Eur Urol Oncol - (-) - [2024-05-23; online 2024-05-23]
DDLS Fellow Kimmo Kartasalo
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Allosteric Cholesterol Site in Glycine Receptors Characterized through Molecular Simulations.
Jalalypour F, Howard RJ, Lindahl E
J Phys Chem B 128 (20) 4996-5007 [2024-05-23; online 2024-05-15]
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Elevated levels of IL-12/IL-23p40 in Nova Scotia Duck Tolling Retrievers with autoimmune disease and lymphoma.
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Diagnosis of Cancer After Recent Weight Loss-Reply.
Wang QL, Yuan C, Wolpin BM
JAMA 331 (19) 1678-1679 [2024-05-21; online 2024-04-24]
DDLS Fellow Qiaoli Wang
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Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Singh V, Itoh Y, Del'Olio S, ..., Taoka M, Amunts A
Nat Commun 15 (1) 4272 [2024-05-20; online 2024-05-20]
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Non-invasive PET imaging of liver fibrogenesis using a RESCA-conjugated Affibody molecule.
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An atlas of protein-protein associations of human tissues prioritizes candidate disease genes
Laman Trip DS, van Oostrum M, Memon D, ..., Wollscheid B, Beltrao P
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Andrea Fossati DDLS Fellow
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The full spectrum of SLC22 OCT1 mutations illuminates the bridge between drug transporter biophysics and pharmacogenomics.
Yee SW, Macdonald CB, Mitrovic D, ..., Giacomini KM, Coyote-Maestas W
Mol. Cell 84 (10) 1932-1947.e10 [2024-05-16; online 2024-05-03]
Lucie Delemotte SciLifeLab Fellow
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Streptolysin O Accelerates the Conversion of Plasminogen to Plasmin
Tang D, Khakzad H, Hjortswang E, ..., Happonen L, Malmström J
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Microfluidic Cartridge for Bead-Based Affinity Assays.
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Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia.
Norenhag J, Edfeldt G, Stålberg K, ..., Schuppe-Koistinen I, Olovsson M
Sci Rep 14 (1) 11183 [2024-05-16; online 2024-05-16]
DDLS Fellow Luisa Hugerth
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Matte Bon G, Kraft D, Comasco E, Derntl B, Kaufmann T
Biol Sex Differ 15 (1) 42 [2024-05-15; online 2024-05-15]
Erika Comasco SciLifeLab Fellow
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Cope JE, Berckx F, Lundmark J, ..., Karlsson I, Weih M
Sci Rep 14 (1) 11099 [2024-05-15; online 2024-05-15]
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Spatial Coherence in DNA Barcode Networks
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Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1
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Iron oxide nanoparticles for treatment and diagnosis of chronic inflammatory diseases: A systematic review.
Ansari SR, Mahajan J, Teleki A
Wiley Interdiscip Rev Nanomed Nanobiotechnol 16 (3) e1963 [2024-05-10; online 2024-05-10]
Alexandra Teleki SciLifeLab Fellow
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TPP1 is associated with risk of advanced precursors and cervical cancer survival.
Wang QL, Gong C, Meng XY, ..., Wu Q, Zhou Y
PLoS ONE 19 (5) e0298118 [2024-05-09; online 2024-05-09]
DDLS Fellow Qiaoli Wang
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Chromatin damage generated by DNA intercalators leads to degradation of RNA Polymerase II.
Espinoza JA, Kanellis DC, Saproo S, ..., Bartek J, Lindström MS
Nucleic Acids Res. 52 (8) 4151-4166 [2024-05-08; online 2024-02-10]
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A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.
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High Resolution Crystal Structure of the Pyruvate Kinase Tetramer in Complex with the Allosteric Activator Mitapivat/AG-348
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GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability
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Adaptive sampling-based structural prediction reveals opening of a GABA receptor through the αβ interface
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MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations.
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Differential expression of plasma proteins in pregnant women exposed to Plasmodium falciparum malaria
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Determinants of the Divergent Salmonella and Shigella Epithelial Colonization Strategies Resolved in Human Enteroids and Colonoids
Geiser P, Martino MLD, Lopes ACC, ..., Eriksson J, Sellin ME
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Ancestral terpene cyclases: From fundamental science to applications in biosynthesis.
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Spatial transcriptomics Visium data for mouse bleomycin model of lung fibrosis
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Evolutionary convergence of sensory circuits in the pallium of amniotes
Rueda-Alaña E, Senovilla-Ganzo R, Grillo M, ..., De Pitta M, García-Moreno F
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CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.
Kurt S, Chen M, Toosi H, ..., Hartman J, Lagergren J
Bioinformatics 40 (5) - [2024-05-02; online 2024-04-28]
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Abstract PO3-25-07: Characterization of tertiary lymphoid structures and its association with response to immune checkpoint inhibitors in triple negative breast cancer using spatial transcriptomics
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Cancer Res. 84 (9_Supplement) PO3-25-07-PO3-25-07 [2024-05-02; online 2024-05-02]
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Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases.
Karlsson L, Vogel J, Arvidsson I, ..., Mattsson-Carlgren N, Hansson O
Nat Commun 15 (1) 3676 [2024-05-01; online 2024-05-01]
DDLS Fellow Jacob W Vogel
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Acquired Multidrug Resistance in AML Is Caused by Low Apoptotic Priming in Relapsed Myeloblasts.
Olesinski EA, Bhatia KS, Wang C, ..., Letai A, Bhatt S
Blood Cancer Discov 5 (3) 180-201 [2024-05-01; online 2024-03-05]
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White matter volume and treatment with selective progesterone receptor modulator in patients with premenstrual dysphoric disorder.
Kaltsouni E, Wikström J, Lanzenberger R, Sundström-Poromaa I, Comasco E
Psychoneuroendocrinology 163 (-) 106977 [2024-05-00; online 2024-01-22]
Erika Comasco SciLifeLab Fellow
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The decanoate esters of nandrolone, testosterone, and trenbolone induce steroid specific memory impairment and somatic effects in the male rat.
Zelleroth S, Stam F, Nylander E, ..., Grönbladh A, Hallberg M
Horm Behav 161 (-) 105501 [2024-05-00; online 2024-02-17]
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Super-sectioning with multi-sheet reversible saturable optical fluorescence transitions (RESOLFT) microscopy.
Bodén A, Ollech D, York AG, Millett-Sikking A, Testa I
Nat. Methods 21 (5) 882-888 [2024-05-00; online 2024-02-23]
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Scuphr: A probabilistic framework for cell lineage tree reconstruction.
Koptagel H, Jun SH, Hård J, Lagergren J
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Ouabain modulates collective cell migration via a Na,K-ATPase activated Ca2+ signal pathway
Brismar H, Senftleben M, Latron E, ..., Edwards S, Ogazon A
Physiology 39 (S1) - [2024-05-00; online 2024-05-00]
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Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting.
Sandell FL, Holzweber T, Street NR, Dohm JC, Himmelbauer H
Plant Biotechnol J 22 (5) 1312-1324 [2024-05-00; online 2024-01-11]
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Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.
Keaton JM, Kamali Z, Xie T, ..., Snieder H, Warren HR
Nat. Genet. 56 (5) 778-791 [2024-05-00; online 2024-04-30]
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Generation of Anterior Segment of the Eye Cells from hiPSCs in Microfluidic Platforms.
Koçak G, Uyulgan S, Polatlı E, ..., Utine CA, Güven S
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Gastrointestinal cancer precursor risk and mortality in pancreatic intraductal papillary mucinous neoplasms: a nationwide cohort study.
Vujasinovic M, Elbe P, Ekheden I, ..., Löhr JM, Ludvigsson JF
Scand. J. Gastroenterol. 59 (5) 600-607 [2024-05-00; online 2024-02-13]
DDLS Fellow Qiaoli Wang
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Disease staging of Alzheimer's disease using a CSF-based biomarker model.
Salvadó G, Horie K, Barthélemy NR, ..., Bateman RJ, Hansson O
Nat Aging 4 (5) 694-708 [2024-05-00; online 2024-03-21]
DDLS Fellow Jacob W Vogel
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von Mentzer A, Svennerholm AM
Trends Microbiol. 32 (5) 448-464 [2024-05-00; online 2023-12-04]
Astrid von Mentzer DDLS Fellow
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Cellular energy regulates mRNA degradation in a codon-specific manner.
Tomaz da Silva P, Zhang Y, Theodorakis E, ..., Pelechano V, Gagneur J
Mol Syst Biol 20 (5) 506-520 [2024-05-00; online 2024-03-15]
SciLifeLab Fellow Vicente Pelechano
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COVID-19 vaccine uptake among young adults: Influence of asthma and sociodemographic factors.
Ödling M, Andersson N, Ekström S, ..., Melén E, Kull I
J Allergy Clin Immunol Glob 3 (2) 100231 [2024-05-00; online 2024-02-20]
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Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.
Shrine N, Guyatt AL, Erzurumluoglu AM, ..., Tobin MD, Wain LV
Nat. Genet. 56 (5) 1032-1033 [2024-05-00; online 2024-04-20]
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Arachidonic acid and docosahexaenoic acid levels correlate with the inflammation proteome in extremely preterm infants.
Klevebro S, Kebede Merid S, Sjöbom U, ..., Hellström A, Nilsson AK
Clin Nutr 43 (5) 1162-1170 [2024-05-00; online 2024-04-03]
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MassiveFold: unveiling AlphaFold’s hidden potential with optimized and parallelized massive sampling
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Drivers Underlying Metastasis and Relapse in Medulloblastoma and Targeting Strategies.
Holmberg KO, Borgenvik A, Zhao M, Giraud G, Swartling FJ
Cancers (Basel) 16 (9) - [2024-04-30; online 2024-04-30]
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Clonal Hematopoiesis of Indeterminate Potential With Loss of Tet2 Enhances Risk for Atrial Fibrillation Through Nlrp3 Inflammasome Activation.
Lin AE, Bapat AC, Xiao L, ..., Ellinor PT, Ebert BL
Circulation 149 (18) 1419-1434 [2024-04-30; online 2024-02-15]
Abhishek Niroula DDLS Fellow
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Mapping Lesions that Cause Psychosis to a Human Brain Circuit and Proposed Stimulation Target
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Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer.
Papakyriacou I, Kutkaite G, Rúbies Bedós M, ..., Menden MP, Mao Y
Nat Commun 15 (1) 3581 [2024-04-27; online 2024-04-27]
SciLifeLab Fellow Yumeng Mao
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Tissue and cellular spatiotemporal dynamics in colon aging.
Daly AC, Cambuli F, Äijö T, ..., Regev A, Vickovic S
bioRxiv - (-) - [2024-04-26; online 2024-04-26]
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New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project.
Tal T, Myhre O, Fritsche E, ..., Torres-Ruiz M, Bartmann K
Front Toxicol 6 (-) 1359507 [2024-04-26; online 2024-04-26]
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Interpreting mammalian evolutionary constraint at synonymous sites in light of the unwanted transcript hypothesis
Christmas MJ, Dong M, Meadows JRS, Kozyrev SV, Lindblad-Toh K
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Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse.
Elofsson A, Han L, Bianchi E, Wright GJ, Jovine L
Elife 13 (-) - [2024-04-26; online 2024-04-26]
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Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse
Elofsson A, Han L, Bianchi E, Wright GJ, Jovine L
Elife 13 (-) - [2024-04-26; online 2024-04-26]
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Loss of Y in regulatory T lymphocytes in the tumor micro-environment of primary colorectal cancers and liver metastases.
Wójcik M, Juhas U, Mohammadi E, ..., Filipowicz N, Dumanski JP
Sci Rep 14 (1) 9458 [2024-04-24; online 2024-04-24]
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Inhibitors of dermatan sulfate epimerase 1 decreased accumulation of glycosaminoglycans in mucopolysaccharidosis type I fibroblasts.
Maccarana M, Li B, Li H, ..., Yu M, Li JP
Glycobiology 34 (6) - [2024-04-24; online 2024-05-18]
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Cell Painting-based bioactivity prediction boosts high-throughput screening hit-rates and compound diversity.
Fredin Haslum J, Lardeau CH, Karlsson J, ..., Smith K, Müllers E
Nat Commun 15 (1) 3470 [2024-04-24; online 2024-04-24]
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Two Novel [68Ga]Ga-Labeled Radiotracers Based on Metabolically Stable [Sar11]RM26 Antagonistic Peptide for Diagnostic Positron Emission Tomography Imaging of GRPR-Positive Prostate Cancer.
Kanellopoulos P, Bezverkhniaia E, Abouzayed A, ..., Tolmachev V, Orlova A
ACS Omega 9 (16) 18608-18616 [2024-04-23; online 2024-04-10]
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Author Correction: scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.
Chen JP, Diekmann C, Wu H, ..., Bienko M, Crosetto N
Nat Commun 15 (1) 3390 [2024-04-22; online 2024-04-22]
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Patient-Specific Measurable Residual Disease Markers Predict Outcome in Patients With Myelodysplastic Syndrome and Related Diseases After Hematopoietic Stem-Cell Transplantation.
Tobiasson M, Pandzic T, Illman J, ..., Dybedal I, Hellström-Lindberg E
J Clin Oncol 42 (12) 1378-1390 [2024-04-20; online 2024-01-17]
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Inference of drug off-target effects on cellular signaling using interactome-based deep learning.
Meimetis N, Lauffenburger DA, Nilsson A
iScience 27 (4) 109509 [2024-04-19; online 2024-03-14]
Avlant Nilsson DDLS Fellow
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Divergent mechanisms of steroid inhibition in the human ρ1 GABAA receptor
Lindahl E, Fan C, Cowgill J, Howard R
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Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates aging in mice.
Sirozh O, Saez-Mas A, Jung B, ..., Lafarga V, Fernandez-Capetillo O
Mol. Cell 84 (8) 1527-1540.e7 [2024-04-18; online 2024-03-22]
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Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood
Sdougkou K, Papazian S, Bonnefille B, ..., Martin LJ, Martin JW
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Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis.
Chung T, Salazar A, Harm G, ..., Carroll LM, Kovac J
Applied and environmental microbiology 90 (4) e0177823 [2024-04-17; online 2024-03-12]
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Microenvironmental reorganization in brain tumors following radiotherapy and recurrence revealed by hyperplexed immunofluorescence imaging.
Watson SS, Duc B, Kang Z, ..., Hausser J, Joyce JA
Nat Commun 15 (1) 3226 [2024-04-15; online 2024-04-15]
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Efficient calculation of orientation-dependent lipid dynamics from membrane simulations.
Doktorova M, Khelashvili G, Brown MF
bioRxiv - (-) - [2024-04-15; online 2024-04-15]
DDLS Fellow Milka Doktorova
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Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient.
King MR, Ruff KM, Lin AZ, ..., Vahey MD, Pappu RV
Cell 187 (8) 1889-1906.e24 [2024-04-11; online 2024-03-18]
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Postel Z, Van Rossum F, Godé C, Schmitt E, Touzet P
Ann. Bot. 133 (3) 427-434 [2024-04-10; online 2023-12-23]
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Multiple pro-viral effects of the host protein G3BP in SARS-CoV-2 Infection
McInerney G, Long S, Vidakovics LP, ..., Guzyk M, Coquet J
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GRPR-Antagonists Carrying DOTAGA-Chelator via Positively Charged Linkers: Perspectives for Prostate Cancer Theranostics.
Obeid K, Kanellopoulos P, Abouzayed A, ..., Maina T, Orlova A
Pharmaceutics 16 (4) - [2024-04-08; online 2024-04-08]
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Drug repositioning for immunotherapy in breast cancer using single-cell analysis.
Mohammadi E, Dashti S, Shafizade N, ..., Mardinoglu A, Sekhavati MH
NPJ Syst Biol Appl 10 (1) 37 [2024-04-08; online 2024-04-08]
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The Discovery of New Inhibitors of Insulin-Regulated Aminopeptidase by a High-Throughput Screening of 400,000 Drug-like Compounds.
Gising J, Honarnejad S, Bras M, ..., Hallberg M, Larhed M
Int J Mol Sci 25 (7) - [2024-04-06; online 2024-04-06]
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Sulfone-based human liver pyruvate kinase inhibitors - Design, synthesis and in vitro bioactivity.
Matić J, Akladios F, Battisti UM, ..., Uhlen M, Grøtli M
Eur J Med Chem 269 (-) 116306 [2024-04-05; online 2024-03-05]
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Pérez-Valero Á, Serna-Diestro J, Tafur Rangel A, ..., Villar CJ, Lombó F
Int J Mol Sci 25 (7) - [2024-04-05; online 2024-04-05]
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Bimaï O, Banerjee I, Grinberg IR, ..., Sjöberg BM, Logan DT
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Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone allosterically mediates substrate binding to the active site
Bimaï O, Banerjee I, Grinberg IR, ..., Sjöberg BM, Logan DT
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Identification of New Ketamine Metabolites and Their Detailed Distribution in the Mammalian Brain.
Vallianatou T, de Souza Anselmo C, Tsiara I, ..., Lundgaard I, Globisch D
ACS Chem Neurosci 15 (7) 1335-1341 [2024-04-03; online 2024-03-20]
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White horses - non-coding sequences drive premature hair greying and predisposition to melanoma.
Andersson L
Ups. J. Med. Sci. 129 (-) - [2024-04-02; online 2024-04-02]
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Utilizing developmental dynamics for evolutionary prediction and control.
Milocco L, Uller T
Proc. Natl. Acad. Sci. U.S.A. 121 (14) e2320413121 [2024-04-02; online 2024-03-26]
DDLS Fellow Lisandro Milocco
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Lin W, Gerullat L, Braadland PR, ..., Hov JR, Globisch D
Angewandte Chemie 136 (14) - [2024-04-02; online 2024-02-29]
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Rapid and Bifunctional Chemoselective Metabolome Analysis of Liver Disease Plasma Using the Reagent 4‐Nitrophenyl‐2‐azirine
Lin W, Gerullat L, Braadland PR, ..., Hov JR, Globisch D
Angewandte Chemie 136 (14) - [2024-04-02; online 2024-01-31]
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Rapid and Bifunctional Chemoselective Metabolome Analysis of Liver Disease Plasma Using the Reagent 4-Nitrophenyl-2H-azirine.
Lin W, Gerullat L, Braadland PR, ..., Hov JR, Globisch D
Angew. Chem. Int. Ed. Engl. 63 (14) e202318579 [2024-04-02; online 2024-01-31]
Daniel Globisch
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Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota.
Odelgard A, Hägglund E, Guy L, Andersson SGE
Genome Biol Evol 16 (4) - [2024-04-02; online 2024-03-28]
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Lin W, Gerullat L, Braadland PR, ..., Hov JR, Globisch D
Angewandte Chemie International Edition 63 (14) - [2024-04-02; online 2024-02-29]
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Synthesis and kinetic evaluation of phosphomimetic inhibitors targeting type B ribose-5-phosphate isomerase from Mycobacterium tuberculosis.
Courtiol-Legourd S, Mariano S, Foret J, ..., Mowbray SL, Salmon L
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Lifetime Duration of Breastfeeding and Cardiovascular Risk in Women With Type 2 Diabetes or a History of Gestational Diabetes: Findings From Two Large Prospective Cohorts.
Birukov A, Guasch-Ferré M, Ley SH, ..., Hu FB, Zhang C
Diabetes Care 47 (4) 720-728 [2024-04-01; online 2024-02-20]
Clemens Wittenbecher DDLS Fellow
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Fast volumetric multifocus structured illumination microscopy of subcellular dynamics in living cells.
Senftleben ML, Bajor A, Hirata E, Abrahamsson S, Brismar H
Biomed Opt Express 15 (4) 2281-2292 [2024-04-01; online 2024-03-11]
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Developmental dyslexia susceptibility genes DNAAF4, DCDC2, and NRSN1 are associated with brain function in fluently reading adolescents and young adults.
Rinne N, Wikman P, Sahari E, ..., Kere J, Alho K
Cereb. Cortex 34 (4) - [2024-04-01; online 2024-04-13]
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Crosstalk between TGF-β and EGF receptors via direct phosphorylation.
Moustakas A
J. Cell Biol. 223 (4) - [2024-04-01; online 2024-03-20]
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A comparison between different human hepatocyte models reveals profound differences in net glucose production, lipid composition and metabolism in vitro.
Bonanini F, Singh M, Yang H, ..., Mardinoglu A, Hankemeier T
Exp. Cell Res. 437 (1) 114008 [2024-04-01; online 2024-03-16]
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Use of an AI Score Combining Cancer Signs, Masking, and Risk to Select Patients for Supplemental Breast Cancer Screening.
Liu Y, Sorkhei M, Dembrower K, ..., Strand F, Smith K
Radiology 311 (1) e232535 [2024-04-00; online 2024-04-09]
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Unexpected effect of halogenation on the water solubility of small organic compounds.
Zhang J, Gulyás KV, Li J, ..., Zhu W, Xu Z
Comput Biol Med 172 (-) 108209 [2024-04-00; online 2024-02-28]
Ruisheng Xiong SciLifeLab Fellow
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Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.
Mücke MM, Hernández-Tejero M, Gu W, ..., Trebicka J, MICROB-PREDICT and PREDICT Study Group of the EASL-CLIF Consortium
Aliment. Pharmacol. Ther. 59 (7) 877-888 [2024-04-00; online 2024-02-27]
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Spatial landmark detection and tissue registration with deep learning.
Ekvall M, Bergenstråhle L, Andersson A, ..., Käll L, Lundeberg J
Nat. Methods 21 (4) 673-679 [2024-04-00; online 2024-03-04]
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Single-cell omics analysis with genome-scale metabolic modeling.
Chen Y, Gustafsson J, Yang J, Nielsen J, Kerkhoven EJ
Curr. Opin. Biotechnol. 86 (-) 103078 [2024-04-00; online 2024-02-15]
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Research Note: Phenotypic trends for the multigenerational advanced intercross of the Virginia body weight lines of chickens.
Siegel PB, Honaker CF, Andersson L
Poult Sci 103 (4) 103480 [2024-04-00; online 2024-01-30]
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Quantitative imaging of doxorubicin diffusion and cellular uptake in biomimetic gels with human liver tumor cells.
Degerstedt O, O'Callaghan P, Clavero AL, ..., Kreuger J, Lennernäs H
Drug Deliv Transl Res 14 (4) 970-983 [2024-04-00; online 2023-10-12]
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Phylogeography, origin and population structure of the self-fertile emerging plant pathogen Phytophthora pseudosyringae.
Mullett MS, Harris AR, Scanu B, ..., Heungens K, Jung T
Mol Plant Pathol 25 (4) e13450 [2024-04-00; online 2024-04-09]
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Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats.
Vass M, Ramasamy KP, Andersson A
Environ. Microbiol. 26 (4) e16618 [2024-04-00; online 2024-04-02]
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In Vitro Cytotoxic, Genotoxic, Embryotoxic and Oxidative Damage Potentials by Empagliflozin
Kenan Cadirci , Turkez H, Tozlu OO, ..., Emsen B, Mardinoglu A
Biol Bull Russ Acad Sci 51 (2) 243-250 [2024-04-00; online 2024-02-09]
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Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests.
Karunarathne P, Zhou Q, Lascoux M, Milesi P
Glob Chang Biol 30 (4) e17262 [2024-04-00; online 2024-03-28]
Pascal Milesi SciLifeLab Fellow
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Genotype-environment associations reveal genes potentially linked to avian malaria infection in populations of an endemic island bird.
Sheppard EC, Martin CA, Armstrong C, ..., Spurgin LG, Richardson DS
Mol. Ecol. 33 (8) e17329 [2024-04-00; online 2024-03-27]
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Genetic interaction mapping reveals functional relationships between peptidoglycan endopeptidases and carboxypeptidases.
Alvarado Obando M, Rey-Varela D, Cava F, Dörr T
PLoS Genet 20 (4) e1011234 [2024-04-00; online 2024-04-10]
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Exploring Biginelli-based scaffolds as A2B adenosine receptor antagonists: Unveiling novel structure-activity relationship trends, lead compounds, and potent colorectal anticancer agents.
Prieto-Díaz R, Fojo-Carballo H, Majellaro M, ..., Gutiérrez-de-Terán H, Sotelo E
Biomed. Pharmacother. 173 (-) 116345 [2024-04-00; online 2024-03-05]
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Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.
Sommerauer C, Gallardo-Dodd CJ, Savva C, ..., Williams C, Kutter C
Mol Syst Biol 20 (4) 374-402 [2024-04-00; online 2024-03-08]
Claudia Kutter SciLifeLab Fellow
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Diverse mechanisms control amino acid-dependent environmental alkalization by Candida albicans.
Silao FGS, Valeriano VD, Uddström E, Falconer E, Ljungdahl PO
Mol. Microbiol. 121 (4) 696-716 [2024-04-00; online 2024-01-04]
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Direct Salmonella injection into enteroid cells allows the study of host-pathogen interactions in the cytosol with high spatiotemporal resolution.
Ernst C, Andreassen PR, Giger GH, ..., Hardt WD, Vorholt JA
PLoS Biol. 22 (4) e3002597 [2024-04-00; online 2024-04-29]
Mikael Sellin SciLifeLab Fellow
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Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes.
Claret JL, Di-Liegro M, Namias A, ..., Milesi P, Labbé P
Heredity (Edinb) 132 (4) 179-191 [2024-04-00; online 2024-01-27]
Pascal Milesi SciLifeLab Fellow
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DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.
Frommelt F, Fossati A, Uliana F, ..., Ciuffa R, Gstaiger M
Nat. Methods 21 (4) 635-647 [2024-04-00; online 2024-03-26]
Andrea Fossati DDLS Fellow
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Compound Absorption in Polymer Devices Impairs the Translatability of Preclinical Safety Assessments.
Kemas AM, Zandi Shafagh R, Taebnia N, ..., Hofmann U, Lauschke VM
Adv Healthc Mater 13 (11) e2303561 [2024-04-00; online 2023-12-10]
PubMed DOI Crossref
CD40 stimulation via CD40 ligand enhances adenovirus-mediated tumour immunogenicity including 'find-me', 'eat-me', and 'kill-me' signalling.
Naseri S, Cordova MM, Wenthe J, ..., Loskog A, Ullenhag GJ
J. Cell. Mol. Med. 28 (7) e18162 [2024-04-00; online 2024-03-18]
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Biomarker-based staging of Alzheimer disease: rationale and clinical applications.
Therriault J, Schindler SE, Salvadó G, ..., Jack CR, Rosa-Neto P
Nat Rev Neurol 20 (4) 232-244 [2024-04-00; online 2024-03-01]
DDLS Fellow Jacob W Vogel
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Automated model building and protein identification in cryo-EM maps.
Jamali K, Käll L, Zhang R, ..., Kimanius D, Scheres SHW
Nature 628 (8007) 450-457 [2024-04-00; online 2024-02-26]
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Modulator of TMB-associated immune infiltration (MOTIF) predicts immunotherapy response and guides combination therapy.
Qian ZY, Pan YQ, Li XX, ..., Wang ZX, Xu RH
Sci Bull (Beijing) 69 (6) 803-822 [2024-03-30; online 2024-01-19]
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Two Different Strategies for Stabilization of Brain Tissue and Extraction of Neuropeptides.
Fridjonsdottir E, Nilsson A, Fricker LD, Andrén PE
Methods in molecular biology (Clifton, N.J.) 2758 (-) 49-60 [2024-03-29; online 2024-03-29]
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Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.
Eisele AS, Tarbier M, Dormann AA, Pelechano V, Suter DM
Nat Commun 15 (1) 2744 [2024-03-29; online 2024-03-29]
DDLS Fellow Marcel Tarbier
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Designing efficient randstrobes for sequence similarity analyses.
Karami M, Soltani Mohammadi A, Martin M, ..., Patro R, Sahlin K
Bioinformatics 40 (4) - [2024-03-29; online 2024-04-05]
Kristoffer Sahlin SciLifeLab Fellow
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Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.
Grones C, Eekhout T, Shi D, ..., Libault M, De Rybel B
Plant Cell 36 (4) 812-828 [2024-03-29; online 2024-01-17]
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Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.
Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM
Sci Rep 14 (1) 7432 [2024-03-28; online 2024-03-28]
DDLS Fellow Johan Bengtsson-Palme
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Long-Term Survival and Immune Response Dynamics in Melanoma Patients Undergoing TAPCells-Based Vaccination Therapy.
Tittarelli A, Pereda C, Gleisner MA, ..., Larrondo M, Salazar-Onfray F
Vaccines (Basel) 12 (4) - [2024-03-27; online 2024-03-27]
DOI Crossref
Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
Tarbier M, Mackowiak SD, Sekar V, ..., Biryukova I, Friedländer MR
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Unboxing the network among long non-coding RNAs and TGF-β signaling in cancer.
Rodrigues-Junior DM, Moustakas A
Ups. J. Med. Sci. 129 (-) - [2024-03-26; online 2024-03-26]
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Salmonella T3SS-2 virulence enhances gut-luminal colonization by enabling chemotaxis-dependent exploitation of intestinal inflammation.
Gül E, Huuskonen J, Abi Younes A, ..., Bakkeren E, Hardt WD
Cell Reports 43 (3) 113925 [2024-03-26; online 2024-03-07]
Mikael Sellin SciLifeLab Fellow
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ProQ-dependent activation of Salmonella virulence genes mediated by post-transcriptional control of PhoP synthesis.
Bergman S, Andresen L, Kjellin J, ..., Sellin ME, Holmqvist E
mSphere 9 (3) e0001824 [2024-03-26; online 2024-02-27]
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Assessing the Fate of Benzophenone-Type UV Filters and Transformation Products during Soil Aquifer Treatment: The Biofilm Compartment as Bioaccumulator and Biodegrader in Porous Media.
Jou-Claus S, Rodríguez-Escales P, Martínez-Landa L, ..., Quintana G, Valhondo C
Environ. Sci. Technol. 58 (12) 5472-5482 [2024-03-26; online 2024-03-11]
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NEDD8 loss causes cancer vulnerability to immune checkpoint blockade in triple-negative breast cancer
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An efficient protocol for extracting thylakoid membranes and total leaf proteins from Posidonia oceanica and other polyphenol-rich plants.
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Twenty years on from Developmental Plasticity and Evolution: middle-range theories and how to test them.
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Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer.
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Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis
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The Calvin Benson cycle in bacteria: New insights from systems biology.
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Asymmetric T-cell division: insights from cutting-edge experimental techniques and implications for immunotherapy.
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Uncovering driver genes in breast cancer through an innovative machine learning mutational analysis method.
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Comput Biol Med 171 (-) 108234 [2024-03-00; online 2024-02-29]
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The risk of venous thromboembolism in oral contraceptive users: the role of genetic factors-a prospective cohort study of 240,000 women in the UK Biobank.
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The immunopathological landscape of human pre-TCRα deficiency: From rare to common variants.
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The exon-junction complex helicase eIF4A3 holds therapeutic potential in acute myeloid leukemia.
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The association of the RSC remodeler complex with chromatin is influenced by the prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae.
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The airway microbiota in siblings with primary ciliary dyskinesia: Related factors and correlation with clinical characteristics.
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Ten simple rules for pushing boundaries of inclusion at academic events.
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Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0.
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Predicting the future of our oceans-Evaluating genomic forecasting approaches in marine species.
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Population genetics for insect conservation and control
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PACMan: A software package for automated single-cell chlorophyll fluorometry.
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Cytometry A 105 (3) 203-213 [2024-03-00; online 2023-10-20]
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P13 Acquired ficolin-3 deficiency in patients with systemic lupus erythematosus
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O16 pQTL analysis of ficolin-3 activity reveals a link between the lectin pathway of complement and hematological disease manifestations in systemic lupus erythematosus
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Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.
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Effect of Aerobic Exercise and Time-Restricted Feeding on Metabolic Markers and Circadian Rhythm in Mice Fed with the High-Fat Diet.
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Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome.
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DEPICTER: Deep representation clustering for histology annotation.
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Association of Somatic TET2 Mutations With Giant Cell Arteritis.
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Arthritis & rheumatology (Hoboken, N.J.) 76 (3) 438-443 [2024-03-00; online 2024-02-02]
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Amyloid-β deposits in human astrocytes contain truncated and highly resistant proteoforms.
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Mol Cell Neurosci 128 (-) 103916 [2024-03-00; online 2024-01-19]
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A D-Y Shaped Neuropeptide Y Mimetic Peptide-Dye Self-Assembly with Maximal Emission Beyond 1300 nm and Glioma Mitochondrial Activity Modulation.
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The clinical spectrum of ataxia telangiectasia in a cohort in Sweden.
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Genetic and molecular architecture of complex traits.
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Risk factors for clonal hematopoiesis of indeterminate potential in people with HIV: a report from the REPRIEVE trial.
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Predictive biomarkers of rapidly developing insulin deficiency in children with type 1 diabetes.
Lundkvist P, Grönberg A, Carlsson PO, Ludvigsson J, Espes D
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Equine enteroid-derived monolayers recapitulate key features of parasitic intestinal nematode infection.
Hellman S, Martin F, Tydén E, ..., Svedberg P, Fossum C
Vet Res 55 (1) 25 [2024-02-27; online 2024-02-27]
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Decoding of the surfaceome and endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche.
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The energy metabolism of Cupriavidus necator in different trophic conditions
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Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank.
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Computational analysis of human medium-chain dehydrogenases/reductases revealing substrate- and coenzyme-binding characteristics.
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Mechanism of phage sensing and abortion by toxin-antitoxin-chaperone systems
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MALT1 inhibition suppresses antigen-specific T cell responses.
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CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.
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Spatial Neurolipidomics at the Single Amyloid-β Plaque Level in Postmortem Human Alzheimer's Disease Brain.
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Applying a modified systematic review and integrated assessment framework (SYRINA) - a case study on triphenyl phosphate.
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Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave.
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Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation.
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Exposure assessment suggests some cytotoxic Bacillus cereus group genotypes can grow over 3 logs in HTST milk throughout the shelf life at temperature abuse conditions
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Delineating functional and molecular impact of ex vivo sample handling in precision medicine.
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Targeting autophagy as a therapeutic strategy in pediatric acute lymphoblastic leukemia.
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Limited parallelism in genetic adaptation to brackish water bodies in European sprat and Atlantic herring
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Targeting OGG1 and PARG radiosensitises head and neck cancer cells to high-LET protons through complex DNA damage persistence.
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Toward ovarian cancer screening with protein biomarkers using dried, self-sampled cervico-vaginal fluid.
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Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.
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Community stability increases the predictability of microeukaryote community coalescence outcomes
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A regulatory element associated to NAFLD in the promoter of DIO1 controls LDL-C, HDL-C and triglycerides in hepatic cells.
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RhoB expression associated with chemotherapy response and prognosis in colorectal cancer.
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Prevalent and persistent new-onset autoantibodies in mild to severe COVID-19
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Chp1 is a dedicated chaperone at the ribosome that safeguards eEF1A biogenesis.
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Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids.
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Continental scientific drilling and microbiology: (extremely) low biomass in bedrock of central Sweden
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Cancer Diagnoses After Recent Weight Loss.
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A New Synthesized Dicarboxylated Oxy-Heparin Efficiently Attenuates Tumor Growth and Metastasis.
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Soluble and multivalent Jag1 DNA origami nanopatterns activate Notch without pulling force.
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Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids.
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Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
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Observation of a single protein by ultrafast X-ray diffraction.
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Universal Biomaterial-on-Chip: a versatile platform for evaluating cellular responses on diverse biomaterial substrates.
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Sensitive and Specific Analyses of Colorectal Cancer Recurrence through Multiplex superRCA Mutation Detection in Blood Plasma
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Precision microbial intervention improves social behavior but not autism severity: A pilot double-blind randomized placebo-controlled trial.
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Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection.
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High-Throughput DNA melt measurements enable improved models of DNA folding thermodynamics
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All SNAP25 molecules in the vesicle-plasma membrane contact zone change conformation during vesicle priming.
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Investigating chromosomal instability in long-term survivors with glioblastoma and grade 4 astrocytoma.
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GDF15 Protects Insulin-Producing Beta Cells against Pro-Inflammatory Cytokines and Metabolic Stress via Increased Deamination of Intracellular Adenosine.
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Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM
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Author Response: Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM
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A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors.
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Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans.
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Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.
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Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse
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Bridging Generalization Gaps in High Content Imaging Through Online Self-Supervised Domain Adaptation
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The role of the 5' sensing function of ribonuclease E in cyanobacteria.
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One Year Weekly Size‐Resolved Air Sampling of SARS‐CoV‐2 in Hospital Corridors and Relations to the Indoor Environment
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Non-invasive imaging of sympathetic innervation of the pancreas in individuals with type 2 diabetes.
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JDLL: a library to run deep learning models on Java bioimage informatics platforms.
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Calcium-gated potassium channel blockade via membrane-facing fenestrations.
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Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice.
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Transfer Learning-Assisted Inverse Modeling in Nanophotonics Based on Mixture Density Networks
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Toward safer and more sustainable by design biocatalytic amide-bond coupling
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Spatial Transcriptomics Reveals an Unexpected Impact of Tau and Tau Pathology on the Expression of Transthyretin
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Multi-Tissue Network Analysis Reveals the Effect of JNK Inhibition on Dietary Sucrose-Induced Metabolic Dysfunction in Rats
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Integrative Proteo-Transcriptomic Characterization of Advanced Fibrosis in Chronic Liver Disease Across Etiologies
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Small vessel disease in primary familial brain calcification with novel truncating PDGFB variants.
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Mitotic MTH1 inhibitor TH1579 induces PD-L1 expression and inflammatory response through the cGAS-STING pathway
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The MHC-E peptide ligands for checkpoint CD94/NKG2A are governed by inflammatory signals, whereas LILRB1/2 receptors are peptide indifferent.
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Mapping of the gene network that regulates glycan clock of ageing.
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ProHap enables proteomic database generation accounting for population diversity
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Rat liver extracellular matrix and perfusion bioreactor culture promote human amnion epithelial cell differentiation towards hepatocyte-like cells.
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Host-Pathogen Interactions in the Plasmodium -Infected Mouse Liver at Spatial and Single-Cell Resolution
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Translational mapping of spatially resolved transcriptomes in human and mouse pulmonary fibrosis
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Humoral immune responses to the monovalent XBB.1.5-adapted BNT162b2 mRNA booster
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A machine learning and live-cell imaging tool kit uncovers small molecules induced phospholipidosis.
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A community-curated, global atlas ofBacillus cereus sensu latogenomes for epidemiological surveillance
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DDLS Fellow Laura Carroll
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Nanotopography boosts cellular uptake by inducing macropinocytosis
Aramesh M, Yu D, Essand M, Persson C
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Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves.
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Nat Commun 14 (1) 8116 [2023-12-19; online 2023-12-19]
DDLS Fellow Tobias Andermann
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Regulation of lactose and galactose growth: Insights from a unique metabolic gene cluster in Candida intermedia
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MacP bypass variants of Streptococcus pneumoniae PBP2a suggest a conserved mechanism for the activation of bifunctional cell wall synthases.
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MBio 14 (6) e0239023 [2023-12-19; online 2023-10-17]
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Evaluation of noninvasive biospecimens for transcriptome studies.
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Protein-Decorated Microbubbles for Ultrasound-Mediated Cell Surface Manipulation.
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Spatial, temporal and numerical regulation of polar flagella assembly in Pseudomonas putida
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Recurring EPHB1 mutations in human cancers alter receptor signalling and compartmentalisation of colorectal cancer cells.
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Preclinical evaluation of Affibody molecule for PET imaging of human pancreatic islets derived from stem cells.
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Metagenomic assemblies tend to break around antibiotic resistance genes
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Modelling Pathogen Response of the Human Immune System in a Reduced State Space
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Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost
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Preclinical Evaluation of a Novel High-Affinity Radioligand [99mTc]Tc-BQ0413 Targeting Prostate-Specific Membrane Antigen (PSMA).
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Postnatal FGFR-signaling establishes gradients of secretory cell identities along the proximal-distal axis of the lung airways
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Variability in single-cell oxygen consumption kinetics
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The complex nature of lncRNA-mediated chromatin dynamics in multiple myeloma.
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Microbial metabolic specificity controls pelagic lipid export efficiency
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The association between the gut microbiome and 24-hour blood pressure measurements in the SCAPIS study
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snPATHO-seq: unlocking the pathology archives
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Novel data-driven subtypes and stages of brain atrophy in the ALS-FTD spectrum.
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Increasing diversity of functional genetics studies to advance biological discovery and human health.
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Experimental design of blending samples to increase precision of 1H NMR urine metabolomics
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T cell migration requires ion and water influx to regulate actin polymerization.
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Nat Commun 14 (1) 7844 [2023-12-06; online 2023-12-06]
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Influences of community engagement and health system strengthening for cholera control in cholera reporting countries.
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Experimental design of blending samples to increase precision of 1H NMR urine metabolomics
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Experimental design of blending samples to increase precision of 1H NMR urine metabolomics
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Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data
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Symmetry-adapted Markov state models of closing, opening, and desensitizing in α7 nicotinic acetylcholine receptors
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Lysicamine Reduces Protein Kinase B (AKT) Activation and Promotes Necrosis in Anaplastic Thyroid Cancer.
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A surfactant lipid layer of endosomal membranes facilitates airway gas filling in Drosophila.
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Multi-Modal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O
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Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research.
Cao L, Garcia SL, Wurzbacher C
Microb Cell Fact 22 (1) 245 [2023-12-02; online 2023-12-02]
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TADA: taxonomy-aware dataset aggregator.
Hägglund E, Andersson SGE, Guy L
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Seeing the Membrane from Both Sides Now: Lipid Asymmetry and Its Strange Consequences.
Doktorova M, Levental I, Heberle FA
Cold Spring Harbor Perspectives in Biology 15 (12) - [2023-12-01; online 2023-12-01]
DDLS Fellow Milka Doktorova
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RNA Pol II Assembly Affects ncRNA Expression
Garrido-Godino AI, Gupta I, Pelechano V, Navarro F
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Prevalence of Charcot Foot in Subjects With Diabetes: A Nationwide Cohort Study.
Tsatsaris G, Rajamand Ekberg N, Fall T, Catrina SB
Diabetes Care 46 (12) e217-e218 [2023-12-01; online 2023-10-24]
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Inputs, amplification and sinks of perfluoroalkyl substances at coastal Antarctica.
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Environ Pollut 338 (-) 122608 [2023-12-01; online 2023-09-22]
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Infectivity of exhaled SARS-CoV-2 aerosols is sufficient to transmit covid-19 within minutes.
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Constant-pH Molecular Dynamics Simulations of Closed and Open States of a Proton-gated Ion Channel
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Utilizing CD44v6 and V600EBRAF-mutation for in vitro targeted combination therapy of thyroid carcinomas.
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Uncovering distinct spatial‐temporal trajectories of Lewy‐type α‐synuclein pathology: a Subtype and Stage Inference model analysis
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Alzheimers Dement 19 (S14) - [2023-12-00; online 2023-12-25]
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The evolving landscape of COVID-19 and post-COVID condition in patients with chronic lymphocytic leukemia: A study by ERIC, the European research initiative on CLL.
Visentin A, Chatzikonstantinou T, Scarfò L, ..., Stamatopoulos K, Ghia P
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Subtype-specific modulation of human KV 7 channels by the anticonvulsant cannabidiol through a lipid-exposed pore-domain site.
Pökl M, Sridhar A, Frampton DJA, ..., Delemotte L, Liin SI
Br J Pharmacol 180 (23) 2956-2972 [2023-12-00; online 2023-07-27]
Lucie Delemotte SciLifeLab Fellow
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Songbird germline-restricted chromosome as a potential arena of genetic conflicts.
Vontzou N, Pei Y, Mueller JC, ..., Schlebusch SA, Suh A
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Shared and disparate transcriptomic signatures associated with cortical atrophy change in genetic behavioral variant frontotemporal degeneration
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Alzheimers Dement 19 (S12) - [2023-12-00; online 2023-12-25]
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Sequential sequencing by synthesis and the next-generation sequencing revolution.
Uhlen M, Quake SR
Trends Biotechnol 41 (12) 1565-1572 [2023-12-00; online 2023-07-21]
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Proteomics Analysis Identifying New Markers Related to Alzheimer’s Disease Pathology In Vivo
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Alzheimers Dement 19 (S14) - [2023-12-00; online 2023-12-25]
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Novel CSF tau biomarkers can be used for disease staging of sporadic Alzheimer’s
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Alzheimers Dement 19 (S14) - [2023-12-00; online 2023-12-25]
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NAD+ regulates nucleotide metabolism and genomic DNA replication.
Munk SHN, Merchut-Maya JM, Adelantado Rubio A, ..., Bartek J, Maya-Mendoza A
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Microbiomes respond predictably to built habitats on the seafloor.
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Mol. Ecol. 32 (23) 6686-6695 [2023-12-00; online 2022-05-26]
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Metabolic exchanges are ubiquitous in natural microbial communities.
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Improved multimer prediction using massive sampling with AlphaFold in CASP15
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Proteins 91 (12) 1734-1746 [2023-12-00; online 2023-08-07]
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Identification of Distinct and Shared Biomarkers in Cerebral Small Vessel Disease (SVD) through Proteomic Profiling of Cerebrospinal Fluid
Hristovska I, Kumar A, Binette AP, ..., Vogel JW, Hansson O
Alzheimers Dement 19 (S24) - [2023-12-00; online 2023-12-25]
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Identification and Characterization of CD8+ CD27+ CXCR3- T Cell Dysregulation and Progression-Associated Biomarkers in Systemic Lupus Erythematosus.
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Adv Sci (Weinh) 10 (35) e2300123 [2023-12-00; online 2023-10-24]
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High-throughput cell spheroid production and assembly analysis by microfluidics and deep learning.
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Assessing the Layer-by-Layer Assembly of Cellulose Nanofibrils and Polyelectrolytes in Pancreatic Tumor Spheroid Formation.
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Worse long term prognosis in new onset HFpEF treated in HF clinics compared to HFrEF and HFmrEF patients; reflecting need for effective treatment in HFpEF. Results from the Stockholm PREFERS Study
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An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond.
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The roles of surround inhibition for the intrinsic function of the striatum, analyzed in silico.
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NIPMAP: niche-phenotype mapping of multiplex histology data by community ecology.
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coRIC map: a framework for the exploration of multifaceted subcellular RNA-binding proteins
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Multi-omics characterization of lymphedema-induced adipose tissue from breast cancer patients
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Enhancers dysfunction in the 3D genome of cancer cells.
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An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses
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PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.
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Genome-wide nascent transcription profiling uncovers gene regulatory elements and dynamic immune responses in the major arbovirus vector Aedes aegypti
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Between but Not Within-Species Variation in the Distribution of Fitness Effects.
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The Role of Small Nucleolar RNAs As Putative Biomarkers of Chemoresistance in Pediatric Acute Lymphoblastic Leukemia
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SRCAP mutations drive clonal hematopoiesis through epigenetic and DNA repair dysregulation.
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Abhishek Niroula DDLS Fellow
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Patients with Chronic Lymphocytic Leukemia Carrying t(14;19) Display a Distinctive Transcriptomic Profile and Adverse Outcome, Which Might be Overcome Continuous Therapy with BTK Inhibitors. an Italian Campus CLL and Eric Study
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Mapping Chemo-Resistance Profiles of Pediatric Acute Leukemia through Integration of Ex-Vivo Drug Screens with Molecular Data
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Laboratories Can Reliably Detect Clinically Relevant Variants in the TP53 Gene below 10 % Allelic Frequency: A Multicenter Study of ERIC, the European Research Initiative on CLL
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Gut Microbial Dysbiosis in Myeloid Neoplasms: Correlations with Clinical and Genomic Features
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Genomic Determinants of Therapy Response in ETV6::RUNX1 Leukemia
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Epigenetic Profiling and Machine Learning for Enhanced Risk Stratification in Pediatric Acute Lymphoblastic Leukemia
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3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer.
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Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.
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Kristoffer Sahlin SciLifeLab Fellow
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Radiotracers for Imaging of Fibrosis: Advances during the Last Two Decades and Future Directions.
Eriksson O, Velikyan I
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Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy.
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Adil Mardinoglu SciLifeLab Fellow
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Identification of nutritional biomarkers through highly sensitive and chemoselective metabolomics.
Lin W, Mellinghaus K, Rodriguez-Mateos A, Globisch D
Food Chem 425 (-) 136481 [2023-11-01; online 2023-06-01]
Daniel Globisch SciLifeLab Fellow
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A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha and Betaproteobacteria
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3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers.
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IUCrJ 10 (Pt 6) 662-670 [2023-11-01; online 2023-11-01]
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The evolution of intramitochondriality in Midichloria bacteria.
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The clinical phenotype of germline RUNX1 mutations in relation to the accompanying somatic variants and RUNX1 isoform expression.
Cabrerizo Granados D, Barbosa I, Baliakas P, Hellström-Lindberg E, Lundin V
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Synthesis, Anti-inflammatory, and Neuroprotective Activity of N-Substituted Phthalimide Derivatives
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Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells.
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Proline catabolism is a key factor facilitating Candida albicans pathogenicity.
Silao FGS, Jiang T, Bereczky-Veress B, ..., Peuckert C, Ljungdahl PO
PLoS Pathog 19 (11) e1011677 [2023-11-00; online 2023-11-02]
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Neutrophil extracellular trap formation is an independent risk factor for occult cancer in patients presenting with venous thromboembolism.
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Neurofilament light chain in plasma as a sensitive diagnostic biomarker of peripheral neurotoxicity: In Vivo mouse studies with oxaliplatin and paclitaxel - NeuroDeRisk project.
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Monoclonal antibodies lock down SARS-CoV-2 spike.
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Leveraging circulating microbial DNA for early cancer detection.
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Trends Cancer 9 (11) 879-882 [2023-11-00; online 2023-09-01]
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Genome and proteomic analysis of risk factors for fatal outcome in children with severe community-acquired pneumonia caused by human adenovirus 7.
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Functional and molecular profiling of hematopoietic stem cells during regeneration.
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Exp. Hematol. 127 (-) 40-51 [2023-11-00; online 2023-09-04]
Abhishek Niroula DDLS Fellow
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Differences and similarities in false interpretations by AI CAD and radiologists in screening mammography.
Salim M, Dembrower K, Eklund M, Smith K, Strand F
Br J Radiol 96 (1151) 20230210 [2023-11-00; online 2023-09-03]
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Author Correction: Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.
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Artificial intelligence for natural product drug discovery.
Mullowney MW, Duncan KR, Elsayed SS, ..., Robinson SL, Medema MH
Nat Rev Drug Discov 22 (11) 895-916 [2023-11-00; online 2023-09-11]
DDLS Fellow Laura Carroll
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A data-driven framework to model the organism-environment system.
Milocco L, Uller T
Evol Dev 25 (6) 439-450 [2023-11-00; online 2023-06-05]
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A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: 'rCNV', a versatile r package for paralogue and CNV detection.
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Mol Ecol Resour 23 (8) 1772-1789 [2023-11-00; online 2023-07-29]
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CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions.
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The α-synuclein PET tracer [18F] ACI-12589 distinguishes multiple system atrophy from other neurodegenerative diseases.
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Of mice and lymphoid aggregates: modeling tertiary lymphoid structures in cancer.
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Multi-omics Quality Assessment in Personalized Medicine through EATRIS
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Two-Photon Polymerization Printing with High Metal Nanoparticle Loading.
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aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow
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Genome Biol. 24 (1) 242 [2023-10-23; online 2023-10-23]
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RNA Polymerase II-mediated transcription is required for repair of ribosomal DNA breaks in nucleolar caps, guarding against genomic instability
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Three-dimensional Co-culture Model for Live Imaging of Pancreatic Islets, Immune Cells, and Neurons in Agarose Gel.
Muntjewerff EM, Josyula VS, Christoffersson G
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Characterization of an in vitro steatosis model simulating activated de novo lipogenesis in MAFLD patients.
Kim W, Li M, Jin H, ..., Zhang C, Mardinoglu A
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Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity
Edelbroek B, Kjellin J, Biryukova I, ..., Friedländer MR, Söderbom F
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Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.
Sounart H, Lázár E, Masarapu Y, ..., Bergmann O, Giacomello S
Genome Biol. 24 (1) 237 [2023-10-19; online 2023-10-19]
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Organic matter lability modifies the vertical structure of methane-related microbial communities in lake sediments.
Rissanen AJ, Jilbert T, Simojoki A, ..., Peura S, Jäntti H
Microbiol Spectr 11 (5) e0195523 [2023-10-17; online 2023-09-12]
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Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment.
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Large-scale causal discovery using interventional data sheds light on the regulatory network architecture of blood traits.
Brown BC, Morris JA, Lappalainen T, Knowles DA
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Automated model building and protein identification in cryo-EM maps.
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Endothelial VEGFR2-PLCγ signaling regulates vascular permeability and antitumor immunity through eNOS/Src.
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Designing efficient randstrobes for sequence similarity analyses
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Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.
Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M
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Comprehensive cell atlas of the first-trimester developing human brain.
Braun E, Danan-Gotthold M, Borm LE, ..., Sundström E, Linnarsson S
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Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription.
Cameron DP, Grosser J, Ladigan S, ..., Hahn SA, Baranello L
Sci Adv 9 (41) eadg5109 [2023-10-13; online 2023-10-13]
Claudia Kutter SciLifeLab Fellow
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Discovery and characterisation of quinazolines and 8-Azaquinazolines as NLRP3 agonists with oral bioavailability in mice.
O' Donovan DH, Baker D, Ciotta G, ..., Tang H, Valge-Archer V
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SciLifeLab Fellow Yumeng Mao
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Saltational episodes of reticulate evolution in the Drosophila saltans species group
Prediger C, Ferreira EA, Zorzato SV, ..., Yassin A, Madi-Ravazzi L
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Inference of drug off-target effects on cellular signaling using Interactome-Based Deep Learning
Meimetis N, Lauffenburger DA, Nilsson A
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Genetic ablation of adhesion ligands averts rejection of allogeneic immune cells.
Hammer Q, Perica K, van Ooijen H, ..., Sadelain M, Malmberg KJ
bioRxiv - (-) - [2023-10-09; online 2023-10-09]
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Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides.
Skiadopoulou D, Vašíček J, Kuznetsova K, ..., Käll L, Vaudel M
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Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles
Zhou Q, Karunarathne P, Andersson-Li L, ..., Lascoux M, Milesi P
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Going local with ancient DNA: A review of human histories from regional perspectives.
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Science (New York, N.Y.) 382 (6666) 53-58 [2023-10-06; online 2023-10-05]
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Bacterial cell surface nanoenvironment requires a specialized chaperone to activate a peptidoglycan biosynthetic enzyme.
Delerue T, Chareyre S, Anantharaman V, ..., Aravind L, Ramamurthi KS
bioRxiv - (-) - [2023-10-06; online 2023-10-06]
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Functional imaging studies of acute administration of classic psychedelics, ketamine, and MDMA: Methodological limitations and convergent results.
Linguiti S, Vogel JW, Sydnor VJ, ..., Dworkin RH, Satterthwaite TD
Neurosci Biobehav Rev 154 (-) 105421 [2023-10-05; online 2023-10-05]
DDLS Fellow Jacob W Vogel
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A fluorophore-conjugated reagent enabling rapid detection, isolation and live tracking of senescent cells.
Magkouta S, Veroutis D, Pousias A, ..., Evangelou K, Gorgoulis VG
Mol. Cell 83 (19) 3558-3573.e7 [2023-10-05; online 2023-10-07]
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Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.
Larsson L, Franzén L, Ståhl PL, Lundeberg J
Bioinformatics 39 (10) - [2023-10-03; online 2023-10-17]
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Long-Term Effects of Perinatal Exposure to a Glyphosate-Based Herbicide on Melatonin Levels and Oxidative Brain Damage in Adult Male Rats.
Cattani D, Pierozan P, Zamoner A, Brittebo E, Karlsson O
Antioxidants (Basel) 12 (10) - [2023-10-03; online 2023-10-03]
Oskar Karlsson SciLifeLab Fellow
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ELIXIR and Toxicology: a community in development.
Martens M, Stierum R, Schymanski EL, ..., Županič A, Willighagen EL
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Sex-Specific Associations between Adiponectin and Leptin Signaling and Pancreatic Cancer Survival.
Babic A, Wang QL, Lee AA, ..., Fuchs CS, Wolpin BM
Cancer Epidemiol Biomarkers Prev 32 (10) 1458-1469 [2023-10-02; online 2023-08-09]
DDLS Fellow Qiaoli Wang
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COMPARISON OF HIGH-THROUGHPUT SINGLE-CELL RNA-SEQ METHODS FOR EX VIVO DRUG SCREENING
Gezelius H, Enblad AP, Lundmark A, ..., Andersson C, Nordlund J
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Biochemical and X-ray analyses of the players involved in the faRel2/aTfaRel2 toxin-antitoxin operon.
Dominguez-Molina L, Talavera A, Cepauskas A, ..., Hauryliuk V, Garcia-Pino A
Acta Crystallogr F Struct Biol Commun 79 (Pt 10) 247-256 [2023-10-01; online 2023-09-20]
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Well-being spectrum traits are associated with polygenic scores for autism.
Mohammad S, de Ruijter MJT, Rukh G, ..., Mwinyi J, Schiöth HB
Autism Res 16 (10) 1891-1902 [2023-10-00; online 2023-08-21]
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Uncovering new families and folds in the natural protein universe.
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Nature 622 (7983) 646-653 [2023-10-00; online 2023-09-13]
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The alpha2 nicotinic acetylcholine receptor, a subunit with unique and selective expression in inhibitory interneurons associated with principal cells.
Hilscher MM, Mikulovic S, Perry S, Lundberg S, Kullander K
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Targeting pan-essential pathways in cancer with cytotoxic chemotherapy: challenges and opportunities.
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SPP1/osteopontin: a driver of fibrosis and inflammation in degenerative ascending aortic aneurysm?
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J. Mol. Med. 101 (10) 1323-1333 [2023-10-00; online 2023-09-12]
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SARS-CoV-2-related mortality decrease in nursing home residents given multiple COVID-19 boosters.
Blom K, Fjällström P, Molnár C, ..., Forsell MNE, Johansson AF
Lancet Infect Dis 23 (10) e393-e394 [2023-10-00; online 2023-09-13]
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Precision medicine in complex diseases-Molecular subgrouping for improved prediction and treatment stratification.
Johansson Å, Andreassen OA, Brunak S, ..., Wheelock CE, Jacobsson B
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On the Path to Optimal Alchemistry.
Lundborg M, Lidmar J, Hess B
Protein J 42 (5) 477-489 [2023-10-00; online 2023-08-31]
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Novel precision medicine approaches and treatment strategies in hematological malignancies.
Rosenquist R, Bernard E, Erkers T, ..., Fioretos T, Smedby KE
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Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias.
Teunissen CE, Kimble L, Bayoumy S, ..., Zetterberg H, MIRIADE consortium
Mol. Cell Proteomics 22 (10) 100629 [2023-10-00; online 2023-08-07]
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Distinct HLA associations with autoantibody-defined subgroups in idiopathic inflammatory myopathies.
Leclair V, Galindo-Feria AS, Rothwell S, ..., Lundberg IE, Diaz-Gallo LM
EBioMedicine 96 (-) 104804 [2023-10-00; online 2023-09-26]
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Crosstalk between small-cell lung cancer cells and astrocytes mimics brain development to promote brain metastasis.
Qu F, Brough SC, Michno W, ..., Pasca AM, Sage J
Nat. Cell Biol. 25 (10) 1506-1519 [2023-10-00; online 2023-10-02]
SciLifeLab Fellow Wojciech Michno
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Connectome-based modelling of neurodegenerative diseases: towards precision medicine and mechanistic insight.
Vogel JW, Corriveau-Lecavalier N, Franzmeier N, ..., Jones DT, Ewers M
Nat Rev Neurosci 24 (10) 620-639 [2023-10-00; online 2023-08-24]
DDLS Fellow Jacob W Vogel
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Blood Proteins are Associated with Aneurysm Growth in Men with Screening Detected Abdominal Aortic Aneurysm
Siika A, Edfors F, Obeberg J, ..., Hultgren R, Roy J
Aorta (Stamford) 11 (05) 1-18 [2023-10-00; online 2024-06-11]
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Antibiotic use and development of nonalcoholic fatty liver disease: A population-based case-control study.
Ebrahimi F, Simon TG, Hagström H, ..., Engstrand L, Ludvigsson JF
Liver Int. 43 (10) 2186-2197 [2023-10-00; online 2023-06-30]
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Benchmarking enrichment analysis methods with the disease pathway network
Buzzao D, Castresana-Aguirre M, Guala D, Sonnhammer ELL
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Protective non-neutralizing mAbs Ab94 and Ab81 retain high-affinity and potent Fc-mediated function against SARS-CoV-2 variants from Omicron to XBB1.5
Izadi A, Godzwon M, Ohlin M, Nordenfelt P
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Genetic differences between primary and metastatic cancer: a pan-cancer whole-genome comparison study.
Zhong L, Zhao Z, Zhang X
Signal Transduct Target Ther 8 (1) 363 [2023-09-29; online 2023-09-29]
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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics
Mc Cartney AM, Formenti G, Mouton A, ..., Waterhouse RM, Mazzoni CJ
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Exploring the morphology of the host cell to open new possibilities for drug repurposing in viral infections
Tampere M, Kalman A, Rietdijk J, ..., Stadler C, Östling P
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Challenges in Permeability Assessment for Oral Drug Product Development.
Koziolek M, Augustijns P, Berger C, ..., Weitschies W, Dressman J
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Absolute Quantification of Pan-Cancer Plasma Proteomes Reveals Unique Signature in Multiple Myeloma.
Kotol D, Woessmann J, Hober A, ..., Uhlén M, Edfors F
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Modulation of lytic molecules restrain serial killing in γδ T lymphocytes.
Sandoz PA, Kuhnigk K, Szabo EK, ..., Uhlin M, Önfelt B
Nat Commun 14 (1) 6035 [2023-09-27; online 2023-09-27]
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177Lu-labeled PSMA targeting therapeutic with optimized linker for treatment of disseminated prostate cancer; evaluation of biodistribution and dosimetry.
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Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility.
Meng XY, Wang QL, Shi MJ, Zhang HY
Bladder Cancer 9 (3) 211-216 [2023-09-25; online 2023-09-25]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Editorial: Endocrine organoids for modeling, drug development, and treatment of cancer and other diseases.
Pidugu VK, Tharappel AM, Kumari S, Sanjiv K
Front Endocrinol (Lausanne) 14 (-) 1292619 [2023-09-25; online 2023-09-25]
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Unmasking AlphaFold: integration of experiments and predictions in multimeric complexes
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Rapid integration of screen-printed electrodes into thermoplastic organ-on-a-chip devices for real-time monitoring of trans-endothelial electrical resistance.
Kawakita S, Li S, Nguyen HT, ..., Dokmeci MR, Khademhosseini A
Biomed Microdevices 25 (4) 37 [2023-09-23; online 2023-09-23]
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Short tandem repeats bind transcription factors to tune eukaryotic gene expression.
Horton CA, Alexandari AM, Hayes MGB, ..., Kundaje A, Fordyce PM
Science (New York, N.Y.) 381 (6664) eadd1250 [2023-09-22; online 2023-09-22]
Emil Marklund SciLifeLab Fellow
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Front Cover: Fast Depolymerization of PET Bottle Mediated by Microwave Pre‐Treatment and An Engineered PETase (ChemSusChem 18/2023)
Guo B, Lopez‐Lorenzo X, Fang Y, ..., Hakkarainen M, Syrén P
ChemSusChem 16 (18) - [2023-09-22; online 2023-09-04]
PubMed DOI Crossref
Fast Depolymerization of PET Bottle Mediated by Microwave Pre-Treatment and An Engineered PETase.
Guo B, Lopez-Lorenzo X, Fang Y, ..., Hakkarainen M, Syrén PO
ChemSusChem 16 (18) e202300742 [2023-09-22; online 2023-08-09]
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Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.
Sekar V, Mármol-Sánchez E, Kalogeropoulos P, ..., Biryukova I, Friedländer MR
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Marc Friedländer SciLifeLab Fellow
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MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
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Building the next generation of virtual cells to understand cellular biology.
Johnson GT, Agmon E, Akamatsu M, ..., Rafelski S, Horwitz R
Biophys. J. 122 (18) 3560-3569 [2023-09-19; online 2023-04-11]
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Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation.
Sporre E, Karlsen J, Schriever K, ..., Edfors F, Hudson EP
Commun Biol 6 (1) 947 [2023-09-18; online 2023-09-18]
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Live Detection of Neural Progenitors and Glioblastoma Cells by an Oligothiophene Derivative.
Ilkhanizadeh S, Gracias A, Åslund AKO, ..., Hermanson O, Nilsson KPR
ACS Appl Bio Mater 6 (9) 3790-3797 [2023-09-18; online 2023-08-30]
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A GPU-based computational framework that bridges neuron simulation and artificial intelligence.
Zhang Y, He G, Ma L, ..., Du K, Huang T
Nat Commun 14 (1) 5798 [2023-09-18; online 2023-09-18]
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Epigenetic coordination of transcriptional and translational programs in hypoxia
Watt K, Dauber B, Szkop KJ, ..., Larsson O, Postovit LM
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Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals.
Wang F, Tessier AJ, Liang L, ..., Hu FB, Guasch-Ferré M
Nat Commun 14 (1) 5744 [2023-09-16; online 2023-09-16]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Mobile phase and column chemistry selection for high sensitivity non-targeted LC/ESI/HRMS screening of water.
Souihi A, Mohai MP, Martin JW, Kruve A
Anal. Chim. Acta 1274 (-) 341573 [2023-09-15; online 2023-06-28]
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Genetic modification of inflammation- and clonal hematopoiesis-associated cardiovascular risk.
Yu Z, Fidler TP, Ruan Y, ..., Tall AR, Natarajan P
J. Clin. Invest. 133 (18) - [2023-09-15; online 2023-09-15]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Enhancing European capabilities for application of multi-omics studies in biology and biomedicine space research.
Manzano A, Weging S, Bezdan D, ..., da Silveira WA, Herranz R
iScience 26 (9) 107289 [2023-09-15; online 2023-07-12]
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Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways.
Pinheiro AS, Tsarouhas V, Senti KA, Arefin B, Samakovlis C
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Identifying genetic regulatory variants that affect transcription factor activity.
Li X, Lappalainen T, Bussemaker HJ
Cell Genom 3 (9) 100382 [2023-09-13; online 2023-08-18]
PubMed DOI Crossref
Identification of essential genes associated with SARS-CoV-2 infection as potential drug target candidates with machine learning algorithms.
Taheri G, Habibi M
Sci Rep 13 (1) 15141 [2023-09-13; online 2023-09-13]
DDLS Fellow Golnaz Taheri
PubMed DOI Crossref
Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection.
Ambikan AT, Elaldi N, Svensson-Akusjärvi S, ..., Mirazimi A, Neogi U
Proc. Natl. Acad. Sci. U.S.A. 120 (37) e2304722120 [2023-09-12; online 2023-09-05]
Adil Mardinoglu SciLifeLab Fellow
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SARS-CoV-2 Omicron Variants and Their Susceptibility Towards Monoclonal Antibodies in a Swedish Cohort During 2022-23, Studied by Next-Generation Sequencing
Haars J, Palanisamy N, Wallin F, ..., Kaden R, Lennerstrand J
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Photoinduced Ring-Opening and Phototoxicity of an Indolin-3-one Derivative.
Doloczki S, Kern C, Holmberg KO, ..., Streuff J, Dyrager C
Chemistry 29 (51) e202300864 [2023-09-12; online 2023-08-09]
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Novel Per- and Polyfluoroalkyl Substances Discovered in Cattle Exposed to AFFF-Impacted Groundwater.
Dewapriya P, Nilsson S, Ghorbani Gorji S, ..., Kaserzon SL, Thomas KV
Environ. Sci. Technol. 57 (36) 13635-13645 [2023-09-12; online 2023-08-30]
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Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application.
Woessmann J, Petrosius V, Üresin N, ..., Edfors F, Schoof EM
Anal. Chem. 95 (36) 13649-13658 [2023-09-12; online 2023-08-28]
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A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration.
Sørensen MES, Zlatogursky VV, Onuţ-Brännström I, ..., Foster RA, Burki F
Curr. Biol. 33 (17) 3571-3584.e6 [2023-09-11; online 2023-08-02]
Fabien Burki SciLifeLab Fellow
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PI-(3,5)P2-mediated oligomerization of the endosomal sodium/proton exchanger NHE9
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Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs.
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CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses
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Application of clinical and molecular profiling data to improve patient outcomes in psoriatic arthritis.
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The Crystal Structure of Tyrosinase from Verrucomicrobium spinosum Reveals It to Be an Atypical Bacterial Tyrosinase.
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Biomolecules 13 (9) - [2023-09-07; online 2023-09-07]
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Risk of estrogen receptor-specific breast cancer by family history of estrogen receptor subtypes and other cancers.
Wang QL, Zhang Y, Zeng E, ..., He W, Czene K
J. Natl. Cancer Inst. 115 (9) 1020-1028 [2023-09-07; online 2023-05-27]
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PubMed DOI Crossref
Long-term longitudinal analysis of 4,187 participants reveals new insights into determinants of incident clonal hematopoiesis.
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EGb 761 reduces Ca2+ influx and apoptosis after pentylenetetrazole treatment in a neuroblastoma cell line.
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Continental scientific drilling and microbiology: (extremely) low biomass in crystalline bedrock of central Sweden
Westmeijer G, Escudero C, Bergin C, ..., Bertilsson S, Dopson M
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Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data.
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Author Correction: A method for Boolean analysis of protein interactions at a molecular level.
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A test of memory for stimulus sequences in great apes.
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PLoS ONE 18 (9) e0290546 [2023-09-06; online 2023-09-06]
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Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation.
Jin H, Zhang C, Zwahlen M, ..., Uhlén M, Mardinoglu A
Nat Commun 14 (1) 5417 [2023-09-05; online 2023-09-05]
Adil Mardinoglu SciLifeLab Fellow
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Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists.
Matricon P, Nguyen AT, Vo DD, ..., May LT, Carlsson J
Eur J Med Chem 257 (-) 115419 [2023-09-05; online 2023-05-01]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
ER-localized Shr3 is a selective co-translational folding chaperone necessary for amino acid permease biogenesis.
Myronidi I, Ring A, Wu F, Ljungdahl PO
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Deciphering early human pancreas development at the single-cell level.
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AFsample: improving multimer prediction with AlphaFold using massive sampling.
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PubMed DOI Crossref
Sex differences in distribution and identity of aromatase gene expressing cells in the young adult rat brain.
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Biol Sex Differ 14 (1) 54 [2023-09-01; online 2023-09-01]
Erika Comasco SciLifeLab Fellow
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Long-chain polyphosphates inhibit type I interferon signaling and augment LPS-induced cytokine secretion in human leukocytes.
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J Leukoc Biol 114 (3) 250-265 [2023-09-01; online 2023-05-24]
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Influenza virus decreases albumin uptake and megalin expression in alveolar epithelial cells.
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Front Immunol 14 (-) 1260973 [2023-09-01; online 2023-09-01]
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Guidelines for microbiome studies in renal physiology.
Muralitharan RR, Snelson M, Meric G, Coughlan MT, Marques FZ
Am. J. Physiol. Renal Physiol. 325 (3) F345-F362 [2023-09-01; online 2023-07-13]
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AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes
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A Two-Step Activation Mechanism Enables Mast Cells to Differentiate their Response between Extracellular and Invasive Enterobacterial Infection
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Whole tumour cell-based vaccines: tuning the instruments to orchestrate an optimal antitumour immune response.
Pérez-Baños A, Gleisner MA, Flores I, ..., Tittarelli A, Salazar-Onfray F
Br. J. Cancer 129 (4) 572-585 [2023-09-00; online 2023-06-24]
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Vesicular glutamate transporter 2 expression in the ventral tegmental area of outbred male rats following exposure to nicotine and alcohol.
Vrettou M, Thalhammer SB, Svensson AL, ..., Nylander I, Comasco E
Drug Alcohol Depend Rep 8 (-) 100180 [2023-09-00; online 2023-07-13]
Erika Comasco SciLifeLab Fellow
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The understory microclimate in agroforestry now and in the future – a case study of Arabica coffee in its native range
Zignol F, Kjellström E, Hylander K, ..., Rodríguez-Gijón A, Tack AJM
Agricultural and Forest Meteorology 340 (-) 109586 [2023-09-00; online 2023-09-00]
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Sex-specific associations between maternal phthalate exposure and neurodevelopmental outcomes in children at 2 years of age in the APrON cohort.
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Neurotoxicology 98 (-) 48-60 [2023-09-00; online 2023-07-29]
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Real-life data of hypoglycemic events in children and adolescents with type 1 diabetes.
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BMJ Open Diabetes Res Care 11 (5) - [2023-09-00; online 2023-09-23]
Daniel Espes SciLifeLab Fellow
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Pubertal sexual development and endpoints for disrupted spermatogenesis in the model Xenopus tropicalis.
Svanholm S, Roza M, Marini D, ..., Karlsson O, Berg C
Reprod. Toxicol. 120 (-) 108435 [2023-09-00; online 2023-07-01]
Oskar Karlsson SciLifeLab Fellow
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OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Moore J, Basurto-Lozada D, Besson S, ..., Theis FJ, Swedlow JR
Histochem Cell Biol 160 (3) 223-251 [2023-09-00; online 2023-07-10]
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Mosaic Loss of Chromosome Y Is Associated With Functional Outcome After Ischemic Stroke.
Dorvall M, Pedersen A, Dumanski JP, ..., Stanne TM, Jern C
Stroke 54 (9) 2434-2437 [2023-09-00; online 2023-07-19]
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Latent anxiety and depression dimensions differ amongst patients with eating disorders: A Swedish nationwide investigation.
Hübel C, Birgegård A, Johansson T, ..., Isomaa R, Herle M
Int J Methods Psychiatr Res 32 (3) e1961 [2023-09-00; online 2023-02-12]
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Laboratory evolution of Synechocystis sp. PCC 6803 for phenylpropanoid production.
Kukil K, Englund E, Crang N, Hudson EP, Lindberg P
Metab. Eng. 79 (-) 27-37 [2023-09-00; online 2023-06-29]
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KRAS G12C Mutant Non-Small Cell Lung Cancer Linked to Female Sex and High Risk of CNS Metastasis: Population-based Demographics and Survival Data From the National Swedish Lung Cancer Registry.
Isaksson J, Berglund A, Louie K, ..., Wagenius G, Botling J
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Inhibition of cystathionine-gamma lyase dampens vasoconstriction in mouse and human intracerebral arterioles.
Peleli M, Lyngso KS, Poulsen FR, ..., Papapetropoulos A, Stubbe J
Acta Physiol 239 (1) e14021 [2023-09-00; online 2023-08-09]
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Infection with COVID-19 is no longer a public emergency: But what about degenerative dementia?
Yulug B, Ayyıldız B, Ayyıldız S, ..., Velioglu HA, Mardinoglu A
J Med Virol 95 (9) e29072 [2023-09-00; online 2023-09-19]
Adil Mardinoglu SciLifeLab Fellow
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Immune system adaptation during gender-affirming testosterone treatment
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Journal of Reproductive Immunology 159 (-) 104065 [2023-09-00; online 2023-09-00]
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High-resolution bioenergetics correlates the length of continuous protonatable diaminoethane motif of four-armed oligo(ethanamino)amide transfectants to cytotoxicity.
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Ghost admixture in eastern gorillas.
Pawar H, Rymbekova A, Cuadros-Espinoza S, ..., Marques-Bonet T, Kuhlwilm M
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Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.
Zhao JH, Stacey D, Eriksson N, ..., Butterworth AS, Peters JE
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GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification.
Lagou V, Jiang L, Ulrich A, ..., Prokopenko I, Meta-Analysis of Glucose and Insulin-Related Traits Consortium (MAGIC)
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Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets.
Angori S, Banaei-Esfahani A, Mühlbauer K, ..., Schraml P, Moch H
Eur Urol Focus 9 (5) 751-759 [2023-09-00; online 2023-03-16]
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Development of microsatellite markers for sister species Linum suffruticosum and Linum tenuifolium in their overlapping ranges.
Olmedo-Vicente E, Désamoré A, Simón-Porcar VI, Slotte T, Arroyo J
Mol. Biol. Rep. 50 (9) 7927-7933 [2023-09-00; online 2023-07-17]
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Single-cell transcriptomics reveals functional insights into a non-model aquatic phytoflagellate and its metabolically linked bacterial community
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Tissue pleiotropic effect of biotin and prebiotic supplementation in established obesity.
Voland L, Yuan M, Lecoutre S, ..., Soula H, Clément K
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Adil Mardinoglu SciLifeLab Fellow
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Pre-existing CD4 T cell help boosts antibody responses but has limited impact on germinal center, antigen-specific B cell frequencies after influenza infection.
Besavilla DF, Reusch L, Enriquez J, Schön K, Angeletti D
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Identification of a new Kir6 potassium channel and comparison of properties of Kir6 subtypes by structural modelling and molecular dynamics.
Criveanu D, Bergqvist CA, Larhammar D, Walczewska-Szewc K
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Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2.
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Role of interneuron subtypes in controlling trial-by-trial output variability in the neocortex.
Guo L, Kumar A
Commun Biol 6 (1) 874 [2023-08-25; online 2023-08-25]
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Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells.
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Sci Adv 9 (34) eadg1610 [2023-08-25; online 2023-08-25]
Claudia Kutter SciLifeLab Fellow
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The Relationships between Cerebrospinal Fluid Glial (CXCL12, CX3CL, YKL-40) and Synaptic Biomarkers (Ng, NPTXR) in Early Alzheimer's Disease.
Kulczyńska-Przybik A, Dulewicz M, Doroszkiewicz J, ..., Blennow K, Mroczko B
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Association of mitochondrial DNA copy number with chronic kidney disease in older adults.
Liu Y, Pan Y, Tian Z, ..., Zhou X, Zhou K
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A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics.
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Sci Data 10 (1) 562 [2023-08-24; online 2023-08-24]
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Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles
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Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis
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Structural insights into opposing actions of neurosteroids on GABAA receptors.
Legesse DH, Fan C, Teng J, ..., Lindahl E, Hibbs RE
Nat Commun 14 (1) 5091 [2023-08-22; online 2023-08-22]
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Prevalence of the human papillomavirus (HPV) types among cervical dysplasia women attending a gynaecological clinic in Sweden.
García FR, Norenhag J, Edfeldt G, ..., Olovsson M, Du J
BJC Rep 1 (1) 11 [2023-08-22; online 2023-08-22]
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Immobilized Enzymes on Magnetic Beads for Separate Mass Spectrometric Investigation of Human Phase II Metabolite Classes.
Tsiara I, Riemer A, Correia MSP, Rodriguez-Mateos A, Globisch D
Anal. Chem. 95 (33) 12565-12571 [2023-08-22; online 2023-08-08]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Bypassing the Identification: MS2Quant for Concentration Estimations of Chemicals Detected with Nontarget LC-HRMS from MS2 Data.
Sepman H, Malm L, Peets P, ..., Breitholtz M, Kruve A
Anal. Chem. 95 (33) 12329-12338 [2023-08-22; online 2023-08-07]
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Allelic variation of KIR and HLA tunes the cytolytic payload and determines functional hierarchy of NK cell repertoires.
Philippon C, Tao S, Clement D, ..., Norman PJ, Malmberg KJ
Blood Adv 7 (16) 4492-4504 [2023-08-22; online 2023-06-16]
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Modeling brain sex in the limbic system as phenotype for female-prevalent mental disorders
Bon GM, Kraft D, Comasco E, Derntl B, Kaufmann T
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Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits.
Brown AA, Fernandez-Tajes JJ, Hong MG, ..., Dermitzakis ET, Viñuela A
Nat Commun 14 (1) 5062 [2023-08-21; online 2023-08-21]
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The acute effect of different NAD+ precursors included in the combined metabolic activators.
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Free Radic. Biol. Med. 205 (-) 77-89 [2023-08-20; online 2023-06-02]
Adil Mardinoglu SciLifeLab Fellow
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Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.
Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S
Nat Commun 14 (1) 5019 [2023-08-18; online 2023-08-18]
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Broadcasters, receivers, functional groups of metabolites and the link to heart failure progression using polygenic factors.
Yazdani A, Mendez-Giraldez R, Yazdani A, ..., Larson M, Elsea S
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Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex.
Chen A, Sun Y, Lei Y, ..., Xu X, Li C
Cell 186 (17) 3726-3743.e24 [2023-08-17; online 2023-07-12]
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A Comparison of Host Responses to Infection with Wild-Type Avian Influenza Viruses in Chickens and Tufted Ducks.
Naguib MM, Eriksson P, Jax E, ..., Järhult JD, Ellström P
Microbiol Spectr 11 (4) e0258622 [2023-08-17; online 2023-06-26]
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Association of the human gut microbiota with vascular stiffness.
Cuadrat RRC, Goris T, Birukov A, ..., Wittenbecher C, Schulze MB
Sci Rep 13 (1) 13348 [2023-08-16; online 2023-08-16]
Clemens Wittenbecher DDLS Fellow
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Using evolutionary constraint to define novel candidate driver genes in medulloblastoma.
Roy A, Sakthikumar S, Kozyrev SV, ..., Lindblad-Toh K, Forsberg-Nilsson K
Proc. Natl. Acad. Sci. U.S.A. 120 (33) e2300984120 [2023-08-15; online 2023-08-07]
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The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems.
Ernits K, Saha CK, Brodiazhenko T, ..., Hauryliuk V, Atkinson GC
Proc. Natl. Acad. Sci. U.S.A. 120 (33) e2305393120 [2023-08-15; online 2023-08-09]
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The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer.
Lundberg A, Zhang M, Aggarwal R, ..., Small EJ, Quigley DA
Cancer Res. 83 (16) 2763-2774 [2023-08-15; online 2023-06-08]
Arian Lundberg DDLS Fellow
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Proinflammatory allogeneic dendritic cells enhance the therapeutic efficacy of systemic anti-4-1BB treatment.
Ali A, Gao M, Iskantar A, ..., Yu D, Jin C
Front Immunol 14 (-) 1146413 [2023-08-15; online 2023-08-15]
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Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations.
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Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries.
Englund E, Schmidt M, Nava AA, ..., Yuzawa S, Keasling JD
Nat Commun 14 (1) 4871 [2023-08-12; online 2023-08-12]
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Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates ageing in mice
Sirozh O, Jung B, Sanchez-Burgos L, ..., Lafarga V, Fernández-Capetillo O
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Local excision versus thrombectomy in thrombosed external hemorrhoids: a multicenter, prospective, observational study.
Yalcinkaya A, Yalcinkaya A, Atici SD, ..., Leventoglu S, T E H Study Collaboration
BMC Surg 23 (1) 228 [2023-08-10; online 2023-08-10]
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Multiset correlation and factor analysis enables exploration of multi-omics data.
Brown BC, Wang C, Kasela S, ..., Knowles DA, Lappalainen T
Cell Genom 3 (8) 100359 [2023-08-09; online 2023-07-10]
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Folded alpha helical putative new proteins from Apilactobacillus kunkeei
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Streptococcus Species Abundance in the Gut Is Linked to Subclinical Coronary Atherosclerosis in 8973 Participants From the SCAPIS Cohort.
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Circulation 148 (6) 459-472 [2023-08-08; online 2023-07-12]
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Feasibility of dopamine as a vector-valued feedback signal in the basal ganglia.
Wärnberg E, Kumar A
Proc. Natl. Acad. Sci. U.S.A. 120 (32) e2221994120 [2023-08-08; online 2023-08-01]
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Epithelial inflammasomes, gasdermins, and mucosal inflammation - Lessons from Salmonella and Shigella infected mice.
Gül E, Fattinger SA, Sellin ME, Hardt WD
Semin Immunol 70 (-) 101812 [2023-08-08; online 2023-08-08]
Mikael Sellin SciLifeLab Fellow
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The ASV Portal Allows for Efficient Handling of DNA Derived Data in the Living Atlas
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Technology platform for facile handling of 3D hydrogel cell culture scaffolds.
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Pathogenic entero- and salivatypes harbour changes in microbiome virulence and antimicrobial resistance genes with increasing chronic liver disease severity
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Spatial tumour gene signature discriminates neoplastic from non-neoplastic compartments in colon cancer: unravelling predictive biomarkers for relapse.
Sallinger K, Gruber M, Müller CT, ..., Kroneis T, El-Heliebi A
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Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.
Almamoun R, Pierozan P, Manoharan L, Karlsson O
Ecotoxicology and Environmental Safety 262 (-) 115321 [2023-08-05; online 2023-08-05]
Oskar Karlsson SciLifeLab Fellow
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Diverse mechanisms control amino acid-dependent environmental alkalization by Candida albicans
Silao FGS, Valeriano VD, Uddström E, Falconer E, Ljungdahl PO
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Chylomicrons Regulate Lacteal Permeability and Intestinal Lipid Absorption.
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Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms.
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Multiple Origins and Genomic Basis of Complex Traits in Sighthounds.
Li WL, Liu YH, Li JX, ..., Wang GD, Zhang YP
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Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia.
Eriksson A, Engvall M, Mathot L, ..., Ladenvall C, Baliakas P
Clin. Cancer Res. 29 (15) 2826-2834 [2023-08-01; online 2023-04-07]
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Separation of transcriptional repressor and activator functions in Drosophila HDAC3.
Tang M, Regadas I, Belikov S, ..., Bienko M, Mannervik M
Development 150 (15) - [2023-08-01; online 2023-08-02]
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Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators.
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Free Radic. Biol. Med. 204 (-) 347-358 [2023-08-01; online 2023-05-26]
Adil Mardinoglu SciLifeLab Fellow
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Umbilical cord-derived mesenchymal stromal cells preserve endogenous insulin production in type 1 diabetes: a Phase I/II randomised double-blind placebo-controlled trial.
Carlsson PO, Espes D, Sisay S, ..., Smith CIE, Svahn MG
Diabetologia 66 (8) 1431-1441 [2023-08-00; online 2023-05-24]
Daniel Espes SciLifeLab Fellow
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Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?
Bengtsson-Palme J, Abramova A, Berendonk TU, ..., Wester AL, Zahra R
Environ Int 178 (-) 108089 [2023-08-00; online 2023-07-05]
DDLS Fellow Johan Bengtsson-Palme
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The salivary microbiota is altered in cervical dysplasia patients and influenced by conization.
Wu S, Cheng L, Pennhag AAL, ..., Andersson S, Du J
Imeta 2 (3) e108 [2023-08-00; online 2023-05-12]
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The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence.
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PLoS Biol. 21 (8) e3002253 [2023-08-00; online 2023-08-31]
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Synthesis of Substituted Indazole Acetic Acids by N−N Bond Forming Reactions
Odell LR, Skillinghaug B, Matt C, ..., Helleday T, Scobie M
Eur. J. Org. Chem. 26 (29) - [2023-08-00; online 2023-05-24]
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Spatial transcriptomics of human placentas reveal distinct RNA patterns associated with morphology and preeclampsia.
Bhalla N, Franzén L, Scheynius A, ..., Lager S, Ståhl PL
Placenta 139 (-) 213-216 [2023-08-00; online 2023-07-05]
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S154: IDENTIFICATION OF NOVEL FACTORS CONTROLLING NON GENETIC CELL PLASTICITY IN CHRONIC MYELOID LEUKEMIA
Baselli G, Alekseenko A, Brinkman E, ..., Sinanis L, Pelechano V
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Round-robin testing of commercial two-photon polymerization 3D printers
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Polygenic risk scores and risk stratification in deep vein thrombosis.
Lo Faro V, Johansson T, Höglund J, Hadizadeh F, Johansson Å
Thromb. Res. 228 (-) 151-162 [2023-08-00; online 2023-06-10]
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PB1709: A COMPLETE DIGITAL KARYOTYPE OF THE B-CELL LEUKEMIA REH CELL LINE RESOLVED BY LONG-READ SEQUENCING
Wiklander ML, Arvidsson G, Bunikis I, ..., Ameur A, Nordlund J
Hemasphere 7 (S3) e656876f [2023-08-00; online 2023-08-08]
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Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.
Quardokus EM, Saunders DC, McDonough E, ..., Börner K, Radtke AJ
Nat. Methods 20 (8) 1174-1178 [2023-08-00; online 2023-07-19]
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OSA Is Associated With the Human Gut Microbiota Composition and Functional Potential in the Population-Based Swedish CardioPulmonary bioImage Study.
Baldanzi G, Sayols-Baixeras S, Theorell-Haglöw J, ..., Lindberg E, Fall T
Chest 164 (2) 503-516 [2023-08-00; online 2023-03-15]
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Mucosal IgA protects against BQ.1 and BQ.1.1 infection.
Marking U, Bladh O, Havervall S, ..., Klingström J, Thålin C
Lancet Infect Dis 23 (8) e272-e273 [2023-08-00; online 2023-07-12]
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Maternal co-exposure to mercury and perfluoroalkyl acid isomers and their associations with child neurodevelopment in a Canadian birth cohort.
Reardon AJF, Hajihosseini M, Dinu I, ..., Martin JW, APrON Study
Environ Int 178 (-) 108087 [2023-08-00; online 2023-07-05]
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Managing leukemia patients via liquid biopsy and super rolling circle amplification (superRCA).
Eriksson A, Chen L, Amini RM, Cavelier L, Landegren U
J. Intern. Med. 294 (2) 228-237 [2023-08-00; online 2023-06-18]
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Historical RNA expression profiles from the extinct Tasmanian tiger.
Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR
Genome Res 33 (8) 1299-1316 [2023-08-00; online 2023-07-18]
Marc Friedländer SciLifeLab Fellow
DOI Crossref
Front Cover: Synthesis of Substituted Indazole Acetic Acids by N−N Bond Forming Reactions (Eur. J. Org. Chem. 29/2023)
Odell LR, Skillinghaug B, Matt C, ..., Helleday T, Scobie M
Eur. J. Org. Chem. 26 (29) - [2023-08-00; online 2023-07-27]
PubMed DOI Crossref
Expansion spatial transcriptomics.
Fan Y, Andrusivová Ž, Wu Y, ..., Lundeberg J, Wang B
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Early-Life and Family Risk Factors for Tic Disorder Persistence into Adulthood.
Mataix-Cols D, Isomura K, Brander G, ..., Sidorchuk A, Fernández de la Cruz L
Mov Disord 38 (8) 1419-1427 [2023-08-00; online 2023-05-29]
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Deep thermal profiling for detection of functional proteoform groups.
Kurzawa N, Leo IR, Stahl M, ..., Savitski MM, Jafari R
Nat. Chem. Biol. 19 (8) 962-971 [2023-08-00; online 2023-03-20]
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D-amino acids signal a stress-dependent run-away response in Vibrio cholerae.
Irazoki O, Ter Beek J, Alvarez L, ..., Berntsson RP, Cava F
Nat. Microbiol 8 (8) 1549-1560 [2023-08-00; online 2023-06-26]
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Cystathionine gamma-lyase (CTH) inhibition attenuates glioblastoma formation.
Peleli M, Antoniadou I, Rodrigues-Junior DM, ..., Moustakas A, Papapetropoulos A
Redox Biol 64 (-) 102773 [2023-08-00; online 2023-06-05]
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Cryo-EM uniqueness in structure determination of macromolecular complexes: A selected structural anthology.
Azinas S, Carroni M
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Biliverdin reductase B is a plasma biomarker for intraplaque hemorrhage and a predictor of ischemic stroke in symptomatic carotid stenosis
Chemaly M, Marlevi D, Iglesias MJ, ..., Kooi ME, Hedin U
Atherosclerosis 379 (-) S180 [2023-08-00; online 2023-08-00]
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A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments.
Abramova A, Berendonk TU, Bengtsson-Palme J
Environ Int 178 (-) 108084 [2023-08-00; online 2023-07-03]
DDLS Fellow Johan Bengtsson-Palme
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Oxidative, Genotoxic and Cytotoxic Damage Potential of Novel Borenium and Borinium Compounds
Oguzkan SB, Turkez H, Ugras HI, Tatar A, Mardinoglu A
Inorganics 11 (8) 324 [2023-07-31; online 2023-07-31]
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Cell Membranes Sustain Phospholipid Imbalance Via Cholesterol Asymmetry
Doktorova M, Symons JL, Zhang X, ..., Levental KR, Levental I
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DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Rapid gene content turnover on the germline-restricted chromosome in songbirds.
Schlebusch SA, Rídl J, Poignet M, ..., Suh A, Reifová R
Nat Commun 14 (1) 4579 [2023-07-29; online 2023-07-29]
PubMed DOI Crossref
Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations.
Grätz L, Kowalski-Jahn M, Scharf MM, ..., Gloriam DE, Schulte G
Nat Commun 14 (1) 4573 [2023-07-29; online 2023-07-29]
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Microaerobic degradation of crude oil and long chain alkanes by a new Rhodococcus strain from Gulf of Mexico.
Juárez K, Reza L, Bretón-Deval L, ..., García-Guevara F, Lara P
World J Microbiol Biotechnol 39 (10) 264 [2023-07-29; online 2023-07-29]
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Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse
Elofsson A, Han L, Bianchi E, Wright GJ, Jovine L
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Control of protein synthesis through mRNA pseudouridylation by dyskerin.
Pederiva C, Trevisan DM, Peirasmaki D, ..., Agostini F, Farnebo M
Sci Adv 9 (30) eadg1805 [2023-07-28; online 2023-07-28]
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Phosphate starvation decouples cell differentiation from DNA replication control in the dimorphic bacterium Caulobacter crescentus
Hallgren J, Koonce K, Felletti M, ..., Turco E, Jonas K
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Immunostimulatory gene therapy targeting CD40, 4-1BB and IL-2R activates DCs and stimulates antigen-specific T-cell and NK-cell responses in melanoma models.
Wenthe J, Eriksson E, Hellström AC, ..., Lövgren T, Loskog A
J Transl Med 21 (1) 506 [2023-07-27; online 2023-07-27]
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Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1
Hank EC, D'Arcy-Evans N, Wallner O, ..., de Vega M, Michel M
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Delineating functional and molecular impact of ex vivo sample handling in precision medicine
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A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder
Weibel CA, Wheeler AL, James JE, Willis SM, Masel J
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DDLS Fellow Jennifer James
PubMed DOI Crossref
Moving beyond the desktop: prospects for practical bioimage analysis via the web.
Ouyang W, Eliceiri KW, Cimini BA
Front Bioinform 3 (-) 1233748 [2023-07-25; online 2023-07-25]
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Kita crispants for systematic image-based genetic screens of complex traits in zebrafish larvae
Mazzaferro E, Metzendorf C, Zhang H, ..., Allalou A, den Hoed M
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Identification of ATF3 as a novel protective signature of quiescent colorectal tumor cells
Zhang X, Lu X, Zhong L, ..., Chen X, Sjoblom T
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A Molecular Basis of Human Brain Connectivity.
Ng B, Tasaki S, Greathouse KM, ..., Gaiteri C, Herskowitz JH
bioRxiv - (-) - [2023-07-24; online 2023-07-24]
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Naltrexone blocks alcohol-induced effects on kappa-opioid receptors in the plasma membrane.
Terenius L, Oasa S, Sezgin E, ..., Martin-Fardon R, Vukojevic V
Res Sq - (-) - [2023-07-21; online 2023-07-21]
Erdinc Sezgin SciLifeLab Fellow
DOI Crossref
Coevolution-driven method for efficiently simulating conformational changes in proteins reveals molecular details of ligand effects in the β2AR receptor
Mitrovic D, Chen Y, Marciniak A, Delemotte L
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PubMed DOI Crossref
Genus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential.
Carroll LM, Pierneef R, Mafuna T, Magwedere K, Matle I
Front Microbiol 14 (-) 1181376 [2023-07-20; online 2023-07-20]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Development of an Effective Functional Lipid Anchor for Membranes (FLAME) for the Bioorthogonal Modification of the Lipid Bilayer of Mesenchymal Stromal Cells.
Sternstein C, Böhm TM, Fink J, ..., Ebert R, Seibel J
Bioconjug. Chem. 34 (7) 1221-1233 [2023-07-19; online 2023-06-16]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Next generation pan-cancer blood proteome profiling using proximity extension assay.
Álvez MB, Edfors F, von Feilitzen K, ..., Fagerberg L, Uhlén M
Nat Commun 14 (1) 4308 [2023-07-18; online 2023-07-18]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Answer to the Hamlet-like dilemma of lipid metabolites causing senile macular degeneration.
Lo Faro V
Cell Rep Med 4 (7) 101077 [2023-07-18; online 2023-07-20]
PubMed DOI Crossref
Adipose tissue and skeletal muscle wasting precede clinical diagnosis of pancreatic cancer.
Babic A, Rosenthal MH, Sundaresan TK, ..., Caan BJ, Wolpin BM
Nat Commun 14 (1) 4317 [2023-07-18; online 2023-07-18]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Novel CSF tau biomarkers can be used for disease staging of sporadic Alzheimer's disease.
Salvadó G, Horie K, Barthélemy NR, ..., Bateman RJ, Hansson O
medRxiv - (-) - [2023-07-16; online 2023-07-16]
PubMed DOI Crossref
Nanopore sequencing of PCR products enables multicopy gene family reconstruction.
Namias A, Sahlin K, Makoundou P, ..., Belkhir K, Weill M
Comput Struct Biotechnol J 21 (-) 3656-3664 [2023-07-16; online 2023-07-16]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability
Seal S, Carreras-Puigvert J, Carpenter AE, Spjuth O, Bender A
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InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins.
Persson E, Sonnhammer ELL
J. Mol. Biol. 435 (14) 168001 [2023-07-15; online 2023-02-09]
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Preclinical Characterization of a Stabilized Gastrin-Releasing Peptide Receptor Antagonist for Targeted Cancer Theranostics.
Abouzayed A, Kanellopoulos P, Gorislav A, ..., Nock BA, Orlova A
Biomolecules 13 (7) - [2023-07-14; online 2023-07-14]
PubMed DOI Crossref
Plasma 25-Hydroxyvitamin D Levels and Survival in Stage III Colon Cancer: Findings from CALGB/SWOG 80702 (Alliance).
Wang QL, Ma C, Yuan C, ..., Meyerhardt JA, Ng K
Clin. Cancer Res. 29 (14) 2621-2630 [2023-07-14; online 2023-06-08]
DDLS Fellow Qiaoli Wang
DOI Crossref
Geographic population structure and distinct population dynamics of globally abundant freshwater bacteria
Hoetzinger M, Hahn MW, Andersson LY, ..., Puente-Sánchez F, Bertilsson S
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The Escherichia coli chromosome moves to the replisome
Gras K, Fange D, Elf J
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PubMed DOI Crossref
Editorial: The blood-brain barrier in brain tumors: molecular mechanisms and therapeutic strategies.
Zhang L, Dimberg A, Rasouli J
Front Neurol 14 (-) 1225594 [2023-07-13; online 2023-07-13]
PubMed DOI Crossref
Cortex-wide topography of 1/f-exponent in Parkinson's disease.
Helson P, Lundqvist D, Svenningsson P, Vinding MC, Kumar A
NPJ Parkinsons Dis 9 (1) 109 [2023-07-13; online 2023-07-13]
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N-Glycomic Profiling of Microsatellite Unstable Colorectal Cancer.
Ukkola I, Nummela P, Heiskanen A, ..., Kytölä S, Ristimäki A
Cancers (Basel) 15 (14) - [2023-07-11; online 2023-07-11]
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Limited diversity of epibiont bdelloid rotifers and no pattern of codiversification with the highly diverse endemic amphipods of a coastal zone of Lake Baikal
Fontaneto D, Sottoriva E, Rodríguez-Gijón A, ..., Timoshkin OA, Ivanenko VN
The European Zoological Journal 90 (1) 354-365 [2023-07-11; online 2023-05-23]
PubMed DOI Crossref
Automated simulation-based membrane protein refinement into cryo-EM data.
Yvonnesdotter L, Rovšnik U, Blau C, ..., Howard RJ, Lindahl E
Biophys. J. 122 (13) 2773-2781 [2023-07-11; online 2023-06-05]
DOI Crossref
Author response: Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways
Pinheiro AS, Tsarouhas V, Senti KA, Arefin B, Samakovlis C
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PubMed DOI Crossref
A data-driven study of Alzheimer's disease related amyloid and tau pathology progression.
Aksman LM, Oxtoby NP, Scelsi MA, ..., Altmann A, ADNI
Brain - (-) - [2023-07-11; online 2023-07-11]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Establishing mammalian GLUT kinetics and lipid composition influences in a reconstituted-liposome system.
Suades A, Qureshi A, McComas SE, ..., Carlsson J, Drew D
Nat Commun 14 (1) 4070 [2023-07-10; online 2023-07-10]
Jens Carlsson SciLifeLab Fellow
DOI Crossref
A Career in Catalysis: Bernhard Hauer
Nebel BA, Breuer M, Schneider A, ..., Weissenborn MJ, Nestl BM
ACS Catal 13 (13) 8861-8889 [2023-07-07; online 2023-06-20]
PubMed DOI Crossref
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.
Erdem C, Gross SM, Heiser LM, Birtwistle MR
Nat Commun 14 (1) 3991 [2023-07-06; online 2023-07-06]
Cemal Erdem DDLS Fellow
PubMed DOI Crossref
Genetic Investigation of Consanguineous Pakistani Families Segregating Rare Spinocerebellar Disorders.
Saadi SM, Cali E, Khalid LB, ..., Fatima A, Iqbal Z
Genes (Basel) 14 (7) - [2023-07-06; online 2023-07-06]
PubMed DOI Crossref
Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning.
Mitrovic D, McComas SE, Alleva C, ..., Drew D, Delemotte L
Elife 12 (-) - [2023-07-05; online 2023-07-05]
PubMed DOI Crossref
Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5.
McComas SE, Reichenbach T, Mitrovic D, ..., Delemotte L, Drew D
Elife 12 (-) - [2023-07-05; online 2023-07-05]
DOI Crossref
Free energy landscapes of KcsA inactivation
Pérez-Conesa S, Delemotte L
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DOI Crossref
Free energy landscapes of KcsA inactivation
Pérez-Conesa S, Delemotte L
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PubMed DOI Crossref
Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function.
Laudette M, Lindbom M, Arif M, ..., Levin MC, Borén J
Cardiovasc Res 119 (7) 1537-1552 [2023-07-04; online 2023-03-08]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Birth Weight Is Associated With Clonal Hematopoiesis of Indeterminate Potential and Cardiovascular Outcomes in Adulthood.
Schuermans A, Nakao T, Ruan Y, ..., Natarajan P, Honigberg MC
J Am Heart Assoc 12 (13) e030220 [2023-07-04; online 2023-06-22]
Abhishek Niroula DDLS Fellow
DOI Crossref
Author Response: Free energy landscapes of KcsA inactivation
Pérez-Conesa S, Delemotte L
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PubMed DOI Crossref
Diabetes, metformin use, and survival in esophageal cancer: a population-based cohort study.
Wang QL, Santoni G, Lagergren J
JNCI Cancer Spectr 7 (4) - [2023-07-03; online 2023-06-14]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes.
Zhu W, Shenoy A, Kundrotas P, Elofsson A
Bioinformatics 39 (7) - [2023-07-01; online 2023-07-05]
PubMed DOI Crossref
Weak antagonistic fitness effects can maintain an inversion polymorphism.
Pei Y, Forstmeier W, Knief U, Kempenaers B
Mol. Ecol. 32 (13) 3575-3585 [2023-07-00; online 2023-04-28]
PubMed DOI Crossref
Sex-specific microglia state in the Neuroligin-4 knock-out mouse model of autism spectrum disorder.
Guneykaya D, Ugursu B, Logiacco F, ..., Kettenmann H, Wolf SA
Brain Behav. Immun. 111 (-) 61-75 [2023-07-00; online 2023-03-29]
PubMed DOI Crossref
Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications.
Pasin C, Consiglio CR, Huisman JS, ..., Kouyos RD, Bonhoeffer S
R Soc Open Sci 10 (7) 221628 [2023-07-00; online 2023-07-05]
Camila Consiglio DDLS Fellow
PubMed DOI Crossref
Mucosal immune responses following a fourth SARS-CoV-2 vaccine dose.
Bladh O, Marking U, Havervall S, ..., Klingström J, Thålin C
Lancet Microbe 4 (7) e488 [2023-07-00; online 2023-04-20]
PubMed DOI Crossref
How Hi-C ignited the era of 3D genome biology.
Bienko M
Nat. Rev. Genet. 24 (7) 418 [2023-07-00; online 2023-02-03]
Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
HLA Class I Genotype Is Associated with Relapse Risk after Allogeneic Stem Cell Transplantation for NPM1-Mutated Acute Myeloid Leukemia.
Narayan R, Niroula A, Wang T, ..., Spellman S, Lee SJ
Transplant Cell Ther 29 (7) 452.e1-452.e11 [2023-07-00; online 2023-03-29]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.
Blau C, Yvonnesdotter L, Lindahl E
PLoS Comput Biol 19 (7) e1011255 [2023-07-00; online 2023-07-31]
PubMed DOI Crossref
Evaluating the utility of brightfield image data for mechanism of action prediction.
Harrison PJ, Gupta A, Rietdijk J, ..., Spjuth O, Sintorn IM
PLoS Comput Biol 19 (7) e1011323 [2023-07-00; online 2023-07-25]
PubMed DOI Crossref
Esr1+ hypothalamic-habenula neurons shape aversive states.
Calvigioni D, Fuzik J, Le Merre P, ..., Carlén M, Meletis K
Nat. Neurosci. 26 (7) 1245-1255 [2023-07-00; online 2023-06-22]
Antonio Lentini DDLS Fellow
PubMed DOI Crossref
Entropy predicts sensitivity of pseudorandom seeds.
Maier BD, Sahlin K
Genome Res 33 (7) 1162-1174 [2023-07-00; online 2023-05-22]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Efficient mapping of accurate long reads in minimizer space with mapquik.
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R
Genome Res 33 (7) 1188-1197 [2023-07-00; online 2023-06-30]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Efficient Resource Scheduling for Distributed Infrastructures Using Negotiation Capabilities
Chu J, Singh P, Toor S
IEEE CLOUD 2023 - (-) 486-492 [2023-07-00; online 2023-07-00]
Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
Cannabis-derived products antagonize platinum drugs by altered cellular transport.
Buchtova T, Beresova L, Chroma K, ..., Bartek J, Mistrik M
Biomed. Pharmacother. 163 (-) 114801 [2023-07-00; online 2023-05-01]
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Author Correction: Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
Allesøe RL, Lundgaard AT, Hernández Medina R, ..., Brunak S, IMI DIRECT Consortium
Nat. Biotechnol. 41 (7) 1026 [2023-07-00; online 2023-05-03]
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A structural and resting-state functional connectivity investigation of the pulvinar in elderly individuals and Alzheimer's disease patients.
Velioglu HA, Ayyildiz B, Ayyildiz S, ..., Bayraktaroglu Z, Yulug B
Alzheimers Dement 19 (7) 2774-2789 [2023-07-00; online 2022-12-28]
PubMed DOI Crossref
A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the USA lost the ability to produce pertussis-like toxin ArtAB.
Carroll LM, Piacenza N, Cheng RA, Wiedmann M, Guldimann C
Microb Genom 9 (7) - [2023-07-00; online 2023-07-04]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.
Petri AJ, Sahlin K
Bioinformatics 39 (39 Suppl 1) i222-i231 [2023-06-30; online 2023-06-30]
Kristoffer Sahlin SciLifeLab Fellow
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The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes
Abalde S, Tellgren-Roth C, Heintz J, Pettersson OV, Jondelius U
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Novel conformational filter allows unambiguous identification of specific conformational ensembles for the large NS3pro/NS2B Dengue-associated protease; Implications for the appropriate choice of protein conformations in drug discovery
Agback T, Lesovoy D, Han X, ..., Achour A, Agback P
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Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection
Böhne A, Fernández R, Leonard JA, ..., Vinnere Pettersson O, Struck TH
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The bacterial lectin LecA from P. aeruginosa alters membrane organization by dispersing ordered domains
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Commun Phys 6 (1) - [2023-06-29; online 2023-06-29]
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The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct.
Getz EW, Lanclos VC, Kojima CY, ..., Faircloth BC, Thrash JC
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Modulation of Pore Opening of Eukaryotic Sodium Channels by π-Helices in S6.
Choudhury K, Delemotte L
J Phys Chem Lett 14 (25) 5876-5881 [2023-06-29; online 2023-06-21]
Lucie Delemotte SciLifeLab Fellow
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Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.
Kasela S, Aguet F, Kim-Hellmuth S, ..., Graham Barr R, Lappalainen T
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Inhibition of MYC translation through targeting of the newly identified PHB-eIF4F complex as a therapeutic strategy in CLL.
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Blood 141 (26) 3166-3183 [2023-06-29; online 2023-04-21]
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Glutamate spillover drives robust all-or-none dendritic plateau potentials-an in silico investigation using models of striatal projection neurons.
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Development of new approach methods for the identification and characterization of endocrine metabolic disruptors-a PARC project.
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Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?
Chaisson EH, Heberle FA, Doktorova M
Membranes (Basel) 13 (7) - [2023-06-29; online 2023-06-29]
DDLS Fellow Milka Doktorova
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The ACE2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion.
Cervantes M, Hess T, Morbioli GG, Sengar A, Kasson PM
Chem Sci 14 (25) 6997-7004 [2023-06-28; online 2023-06-05]
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In vitro models to study natural killer cell dynamics in the tumor microenvironment.
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Front Immunol 14 (-) 1135148 [2023-06-28; online 2023-06-28]
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Synthesis and biological evaluation of novel β-lactam-metallo β-lactamase inhibitors.
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Loss of Y in regulatory T lymphocytes in the tumor micro-environment of primary colorectal cancers and liver metastases
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Interplay between VSD, pore, and membrane lipids in electromechanical coupling in HCN channels.
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Elife 12 (-) - [2023-06-21; online 2023-06-21]
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Persistent immunosuppressive effects of dibutyl phthalate exposure in adult male mice.
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Sci. Total Environ. 878 (-) 162741 [2023-06-20; online 2023-03-11]
Oskar Karlsson SciLifeLab Fellow
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Loss of chromosome Y in regulatory T cells
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Demographic Reconstruction of the Western Sheep Expansion from Whole-Genome sequences
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Structure and dynamics of differential ligand binding in the human ρ-type GABA A receptor
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Rigorous software pipeline for clinical somatic mutation analyses of solid tumors
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Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.
An Y, Braga MP, Garcia SL, Grudzinska-Sterno M, Hambäck PA
Microb. Ecol. - (-) - [2023-06-14; online 2023-06-14]
Sarahi Garcia SciLifeLab Fellow
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Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration.
Correia JC, Jannig PR, Gosztyla ML, ..., Yeo GW, Ruas JL
bioRxiv - (-) - [2023-06-13; online 2023-06-13]
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Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain.
Zhang Y, Miller JA, Park J, ..., Lein ES, Scheuermann RH
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A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function
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Population-based cohort study of oral contraceptive use and risk of depression.
Johansson T, Vinther Larsen S, Bui M, ..., Karlsson T, Johansson Å
Epidemiol Psychiatr Sci 32 (-) e39 [2023-06-12; online 2023-06-12]
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Orthogonal proteomics methods warrant the development of Duchenne muscular dystrophy biomarkers.
Johansson C, Hunt H, Signorelli M, ..., Uhlén M, Szigyarto CA
Clin Proteomics 20 (1) 23 [2023-06-12; online 2023-06-12]
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High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler.
Sych T, Schlegel J, Barriga HMG, ..., Stevens MM, Sezgin E
Nat. Biotechnol. - (-) - [2023-06-12; online 2023-06-12]
Erdinc Sezgin SciLifeLab Fellow
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Adiposity and sex-specific cancer risk.
Rask-Andersen M, Ivansson E, Höglund J, ..., Karlsson T, Johansson Å
Cancer Cell 41 (6) 1186-1197.e4 [2023-06-12; online 2023-06-14]
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Autoencoder Model for Translating Omics Signatures
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
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Avlant Nilsson DDLS Fellow
DOI Crossref
Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases
Karlsson L, Vogel J, Arvidsson I, ..., Mattsson-Carlgren N, Hansson O
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More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases.
Gaballa A, Wiedmann M, Carroll LM
Front. Cell. Infect. Microbiol. 13 (-) 1060519 [2023-06-08; online 2023-06-08]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Deconvolution of spatial sequencing provides accurate characterization of hESC-derived DA transplants in vivo.
Rájová J, Davidsson M, Avallone M, ..., Parmar M, Björklund T
Mol Ther Methods Clin Dev 29 (-) 381-394 [2023-06-08; online 2023-05-04]
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The full spectrum of OCT1 (SLC22A1) mutations bridges transporter biophysics to drug pharmacogenomics.
Yee SW, Macdonald C, Mitrovic D, ..., Giacomini KM, Coyote-Maestas W
bioRxiv - (-) - [2023-06-07; online 2023-06-07]
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Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism.
Iglesias MJ, Sanchez-Rivera L, Ibrahim-Kosta M, ..., Trégouët DA, Odeberg J
Nat Commun 14 (1) 3280 [2023-06-07; online 2023-06-07]
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Generation of Amber Suppression Cell Lines Using CRISPR-Cas9.
Meineke B, Elsässer SJ
Methods in molecular biology (Clifton, N.J.) 2676 (-) 169-180 [2023-06-06; online 2023-06-06]
SciLifeLab Fellow Simon Elsässer
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Engineered display of ganglioside-sugars on protein elicits a clonally and structurally constrained B cell response
Deimel LP, Xue X, Khan A, ..., Davis BG, Sattentau QJ
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Contrasting outcomes of genome reduction in mikrocytids and microsporidians.
Žárský V, Karnkowska A, Boscaro V, ..., Burki F, Keeling PJ
BMC Biol. 21 (1) 137 [2023-06-06; online 2023-06-06]
Fabien Burki SciLifeLab Fellow
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Temporal transcriptome analysis of the endothelial response to tumour necrosis factor
Struck E, Belova T, Hsieh P, ..., Dusart P, Butler L
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RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.
Øvrebø Ø, Ojansivu M, Kartasalo K, ..., Holme MN, Stevens MM
BMC Bioinformatics 24 (1) 237 [2023-06-05; online 2023-06-05]
DDLS Fellow Kimmo Kartasalo
DOI Crossref
Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference
Lobo V, Nowak I, Fernandez C, ..., Angeletti D, Sarshad AA
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Evaluation of plasma Short chain fatty acid levels as markers for Inflammatory bowel disease.
Kiasat A, Rautiainen S, Prast-Nielsen S, ..., Gustafsson UO, Löf Granström A
Scand. J. Gastroenterol. 58 (11) 1246-1252 [2023-06-05; online 2023-06-05]
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Ribosome clustering and surface layer reorganization in the microsporidian host-invasion apparatus
Sharma H, Jespersen N, Ehrenbolger K, Carlson LA, Barandun J
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Jonas Barandun SciLifeLab Fellow
DOI Crossref
ACCELEROMETER-BASED SEDENTARY BEHAVIOUR AND PHYSICAL ACTIVITY ARE ASSOCIATED WITH THE GUT MICROBIOTA IN 8507 INDIVIDUALS FROM THE POPULATION-BASED SCAPIS
Baldanzi G, Sayols-Baixeras S, Ekblom-Bak E, ..., Orho-Melander M, Fall T
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Wnt signaling regulates MFSD2A-dependent drug delivery through endothelial transcytosis in glioma.
Xie Y, He L, Zhang Y, ..., Wang L, Zhang L
Neuro-oncology 25 (6) 1073-1084 [2023-06-02; online 2023-01-03]
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Whole-genome informed circulating tumor DNA analysis by multiplex digital PCR for disease monitoring in B-cell lymphomas: a proof-of-concept study.
Haider Z, Wästerlid T, Spångberg LD, ..., Tham E, Smedby KE
Front Oncol 13 (-) 1176698 [2023-06-02; online 2023-06-02]
PubMed DOI Crossref
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data.
Seal S, Yang H, Trapotsi MA, ..., Spjuth O, Bender A
J Cheminform 15 (1) 56 [2023-06-02; online 2023-06-02]
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Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages and bacterial genes
Hugerth LW, Krog MC, Vomstein K, ..., Nielsen HS, Schuppe-Koistinen I
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Abstract A051: The spatial landscape of clonal somatic copy number alterations in benign and malignant prostate epithelia
Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J
Cancer Res. 83 (11_Supplement) A051-A051 [2023-06-02; online 2023-06-02]
PubMed DOI Crossref
Reply to: Obsessive-Compulsive Disorder, Tic Disorders, and Early-Life Infections.
Zhang T, Brander G, Isung J, ..., Mataix-Cols D, Fernández de la Cruz L
Biol. Psychiatry 93 (11) e37-e38 [2023-06-01; online 2022-12-09]
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Prenatal and Early Childhood Infections and Subsequent Risk of Obsessive-Compulsive Disorder and Tic Disorders: A Nationwide, Sibling-Controlled Study.
Zhang T, Brander G, Isung J, ..., Mataix-Cols D, Fernández de la Cruz L
Biol. Psychiatry 93 (11) 1023-1030 [2023-06-01; online 2022-07-18]
PubMed DOI Crossref
Obesity-induced inflammation exacerbates clonal hematopoiesis.
Pasupuleti SK, Ramdas B, Burns SS, ..., Natarajan P, Kapur R
J. Clin. Invest. 133 (11) - [2023-06-01; online 2023-06-01]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Isolated Hepatic Perfusion With Melphalan for Patients With Isolated Uveal Melanoma Liver Metastases: A Multicenter, Randomized, Open-Label, Phase III Trial (the SCANDIUM Trial).
Olofsson Bagge R, Nelson A, Shafazand A, ..., Ny L, Lindnér P
J Clin Oncol 41 (16) 3042-3050 [2023-06-01; online 2023-03-20]
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First-in-human (FIH) phase I dose escalation study (part A) of the first oral allosteric modulator of phosphoinositide 3-kinase inhibitor delta (PI3Kδ) roginolisib in patients with advanced cancer and dose confirmation in uveal melanoma (part B).
Di Giacomo AM, Santangelo F, Amato G, ..., Evans TRJ, Maio M
J Clin Oncol 41 (16_suppl) 3110-3110 [2023-06-01; online 2023-06-01]
PubMed DOI Crossref
Barcoded Consortium Infections: A Scalable, Internally Controlled Method to Study Host Cell Binding and Invasion by Pathogenic Bacteria.
Di Martino ML, Sellin ME
Methods in molecular biology (Clifton, N.J.) 2674 (-) 295-311 [2023-06-01; online 2023-06-01]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Analysis of Breast Cancer Family History, Estrogen Receptor Status, and Breast Cancer Outcomes in Sweden.
Zhang Y, Wang QL, Zeng E, He W, Czene K
JAMA Netw Open 6 (6) e2318053 [2023-06-01; online 2023-06-01]
DDLS Fellow Qiaoli Wang
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A survey of mapping algorithms in the long-reads era.
Sahlin K, Baudeau T, Cazaux B, Marchet C
Genome Biol. 24 (1) 133 [2023-06-01; online 2023-06-01]
Kristoffer Sahlin SciLifeLab Fellow
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Two‐view attention‐guided convolutional neural network for mammographic image classification
Sun L, Wen J, Wang J, ..., Wu J, Xu Y
CAAI Trans on Intel Tech 8 (2) 453-467 [2023-06-00; online 2022-04-22]
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The role of eIF4F-driven mRNA translation in regulating the tumour microenvironment.
Bartish M, Abraham MJ, Gonçalves C, ..., Rolny C, Del Rincón SV
Nat. Rev. Cancer 23 (6) 408-425 [2023-06-00; online 2023-05-04]
PubMed DOI Crossref
The Long Noncoding RNA LINC00958 Is Induced in Psoriasis Epidermis and Modulates Epidermal Proliferation.
Luo L, Pasquali L, Srivastava A, ..., Pivarcsi A, Sonkoly E
J. Invest. Dermatol. 143 (6) 999-1010 [2023-06-00; online 2023-01-12]
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Tailoring 3' UTRs alters metastatic potential.
Watt K, Postovit LM
Nat. Cell Biol. 25 (6) 805-807 [2023-06-00; online 2023-05-09]
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Replacement of dietary saturated with unsaturated fatty acids is associated with beneficial effects on lipidome metabolites: a secondary analysis of a randomized trial.
Sellem L, Eichelmann F, Jackson KG, ..., Schulze MB, Lovegrove JA
Am. J. Clin. Nutr. 117 (6) 1248-1261 [2023-06-00; online 2023-04-11]
Clemens Wittenbecher DDLS Fellow
DOI Crossref
Relation of different CSF biosignatures to clinical phenotypes in a memory clinic cohort
Alanko V, Mravinacová S, Kivipelto M, ..., Nilsson P, Sandebring‐Matton A
Alzheimers Dement 19 (S2) - [2023-06-00; online 2023-06-16]
PubMed DOI Crossref
Protein Profiling in Presymptomatic Individuals Separates Myeloperoxidase-Antineutrophil Cytoplasmic Antibody and Proteinase 3-Antineutrophil Cytoplasmic Antibody Vasculitides.
Brink M, Berglin E, Mohammad AJ, ..., Lejon K, Rantapää-Dahlqvist S
Arthritis & rheumatology (Hoboken, N.J.) 75 (6) 996-1006 [2023-06-00; online 2023-04-09]
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Progress at protein structure prediction, as seen in CASP15.
Elofsson A
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POS1468 A HIGH GENETIC RISK OF SLE IS ASSOCIATED WITH AN INCREASED RISK OF MYOCARDIAL INFARCTION AND IMPAIRED KIDNEY FUNCTION; A COMBINED OBSERVATIONAL AND MENDELIAN RANDOMIZATION STUDY
Reid S, Sandling J, Pucholt P, ..., Ronnblom L, Leonard D
Ann Rheum Dis 82 (-) 1088-1089 [2023-06-00; online 2023-06-00]
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POS1438 ANALYSIS OF THE PLASMA PROTEOME PROVIDES MECHANISTIC INSIGHTS INTO THE PATHOPHYSIOLOGY OF ANCA-ASSOCIATED VASCULITIS
Hellbacher E, Van Hoef V, Johansson A, ..., Rantapää Dahlqvist S, Dahlqvist J
Ann Rheum Dis 82 (-) 1073 [2023-06-00; online 2023-06-00]
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POS0603 AUTOANTIBODIES AGAINST A SUBUNIT OF MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX I IN INCLUSION BODY MYOSITIS
Notarnicola A, Hellstrom C, Horuluoglu B, ..., Nilsson P, Lundberg IE
Ann Rheum Dis 82 (-) 574 [2023-06-00; online 2023-06-00]
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POS0538 THE IMPACT OF IMMUNOMODULATING TREATMENT ON THE SEROLOGICAL IMMUNOGENICITY FOLLOWING THREE DOSES OF COVID-19 VACCINE AND PERSISTENCE OF IMMUNOGENICITY OF TWO VACCINE DOSES IN PATIENTS WITH INFLAMMATORY RHEUMATIC DISEASES - A SWEDISH STUDY (COVID19-REUMA)
Frodlund M, Nived P, Chatzidionysiou K, ..., Klareskog L, Kapetanovic MC
Ann Rheum Dis 82 (-) 533 [2023-06-00; online 2023-06-00]
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POS0214 IN-DEPTH ANALYSIS OF DISEASE MANIFESTATIONS IN ANCA-ASSOCIATED VASCULITIDES IDENTIFIES DISTINCT CLINICAL PHENOTYPES, EMPHASIZING THE IMPACT OF SEX AND AGE AT DIAGNOSIS
Lindberg H, Rantapää Dahlqvist S, Norling O, ..., Knight A, Dahlqvist J
Ann Rheum Dis 82 (-) 334 [2023-06-00; online 2023-06-00]
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PLASMA PROTEIN PROFILING USING MULTIPLEX EXTENSION ASSAY IN DLBCL. A DESCRIPTIVE STUDY EXPLORING PLASMA PROTEIN PATTERN EVOLUTION IN DLBCL TREATED WITH R‐CHOP
Sabaa AHA, Mörth C, Molin D, ..., Eriksson A, Enblad G
Hematological Oncology 41 (S2) 631-633 [2023-06-00; online 2023-06-09]
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OxLDL sensitizes platelets for increased formation of extracellular vesicles capable of finetuning macrophage gene expression.
Maaninka K, Neuvonen M, Kerkelä E, ..., Öörni K, Siljander PR
Eur J Cell Biol 102 (2) 151311 [2023-06-00; online 2023-03-15]
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OTX2 duplications: a recurrent cause of oculo-auriculo-vertebral spectrum.
Celse T, Tingaud-Sequeira A, Dieterich K, ..., Rooryck C, Coutton C
J. Med. Genet. 60 (6) 620-626 [2023-06-00; online 2022-11-11]
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OP0021 STRATIFICATION OF PATIENTS WITH SJÖGREN'S SYNDROME BY JOINT MULTI-MODAL ANALYSIS OF CIRCULATING B CELLS
Arvidsson G, Czarnewski P, Johansson A, ..., Nordmark G, Syvänen AC
Ann Rheum Dis 82 (-) 13-14 [2023-06-00; online 2023-06-00]
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Mobility and the spatial spread of sars-cov-2 in Belgium.
Rollier M, Miranda GHB, Vergeynst J, ..., Belgian Collaborative Group on covid-19 Hospital Surveillance , Baetens JM
Math Biosci 360 (-) 108957 [2023-06-00; online 2023-02-17]
Gisele Miranda SciLifeLab Fellow
PubMed DOI Crossref
Intraluminal neutrophils limit epithelium damage by reducing pathogen assault on intestinal epithelial cells during Salmonella gut infection.
Gül E, Enz U, Maurer L, ..., Sellin ME, Hardt WD
PLoS Pathog 19 (6) e1011235 [2023-06-00; online 2023-06-29]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.
Eme L, Tamarit D, Caceres EF, ..., Baker BJ, Ettema TJG
Nature 618 (7967) 992-999 [2023-06-00; online 2023-06-14]
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In situ architecture of the ER-mitochondria encounter structure.
Wozny MR, Di Luca A, Morado DR, ..., Vanni S, Kukulski W
Nature 618 (7963) 188-192 [2023-06-00; online 2023-05-10]
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High-throughput biochemistry in RNA sequence space: predicting structure and function.
Marklund E, Ke Y, Greenleaf WJ
Nat. Rev. Genet. 24 (6) 401-414 [2023-06-00; online 2023-01-12]
Emil Marklund SciLifeLab Fellow
PubMed DOI Crossref
Engineered bacteria to accelerate wound healing: an adaptive, randomised, double-blind, placebo-controlled, first-in-human phase 1 trial.
Öhnstedt E, Vågesjö E, Fasth A, ..., Roos S, Phillipson M
EClinicalMedicine 60 (-) 102014 [2023-06-00; online 2023-05-25]
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Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer.
Wadensten E, Wessman S, Abel F, ..., Gisselsson D, Genomic Medicine Sweden Childhood Cancer Working Group
JCO Precis Oncol 7 (-) e2300039 [2023-06-00; online 2023-06-29]
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Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.
Bargheet A, Klingenberg C, Esaiassen E, ..., Bengtsson-Palme J, Pettersen VK
EBioMedicine 92 (-) 104613 [2023-06-00; online 2023-05-13]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Deterministic evolution and stringent selection during preneoplasia.
Karlsson K, Przybilla MJ, Kotler E, ..., Kuo CJ, Curtis C
Nature 618 (7964) 383-393 [2023-06-00; online 2023-05-31]
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Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT).
Feodoroff M, Mikkonen P, Turunen L, ..., Kallioniemi O, Pietiäinen V
SLAS Discov 28 (4) 138-148 [2023-06-00; online 2023-03-20]
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Classification of Hypoglycemic Events in Type 1 Diabetes Using Machine Learning Algorithms.
Cederblad L, Eklund G, Vedal A, ..., Carlsson PO, Espes D
Diabetes Ther 14 (6) 953-965 [2023-06-00; online 2023-04-13]
Daniel Espes SciLifeLab Fellow
PubMed DOI Crossref
Chemical safety and the exposome
Karlsson O
Emerging Contaminants 9 (2) 100225 [2023-06-00; online 2023-06-00]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Caveolin-1 genotypes as predictor for locoregional recurrence and contralateral disease in breast cancer.
Godina C, Tryggvadottir H, Bosch A, ..., Isaksson K, Jernström H
Breast Cancer Res. Treat. 199 (2) 335-347 [2023-06-00; online 2023-04-05]
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Author Correction: The power of genetic diversity in genome-wide association studies of lipids.
Graham SE, Clarke SL, Wu KH, ..., Sun YV, Willer CJ
Nature 618 (7965) E19-E20 [2023-06-00; online 2023-05-27]
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Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers.
Yuan Y, Ju YS, Kim Y, ..., Liang H, PCAWG Consortium
Nat. Genet. 55 (6) 1078 [2023-06-00; online 2023-03-23]
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Associations between maternal folate status and choline intake during pregnancy and neurodevelopment at 3-4 years of age in the Alberta Pregnancy Outcomes and Nutrition (APrON) study.
Irvine N, England-Mason G, Field CJ, ..., Dewey D, APrON Study Team
J Dev Orig Health Dis 14 (3) 402-414 [2023-06-00; online 2023-03-20]
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The impact of TLR2 and aging on the humoral immune response to Staphylococcus aureus bacteremia in mice.
Gupta P, Hu Z, Kopparapu PK, ..., Jin T, Engdahl C
Sci Rep 13 (1) 8850 [2023-05-31; online 2023-05-31]
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Spatially resolved multiomics on the neuronal effects induced by spaceflight
Masarapu Y, Cekanaviciute E, Andrusivova Z, ..., Costes S, Giacomello S
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A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology.
Petersen J, Englmaier L, Artemov AV, ..., Gusev O, Adameyko I
Nat Commun 14 (1) 3092 [2023-05-29; online 2023-05-29]
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Assessing the role of trypsin in quantitative plasma- and single-cell proteomics towards clinical application
Woessmann J, Petrosius V, Üresin N, ..., Edfors F, Schoof EM
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Chemoselective bicyclobutane-based mass spectrometric detection of biological thiols uncovers human and bacterial metabolites.
Kaur A, Lin W, Dovhalyuk V, ..., Sellin ME, Globisch D
Chem Sci 14 (20) 5291-5301 [2023-05-24; online 2023-04-06]
Daniel Globisch Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Biliverdin Reductase B Is a Plasma Biomarker for Intraplaque Hemorrhage and a Predictor of Ischemic Stroke in Patients with Symptomatic Carotid Atherosclerosis.
Chemaly M, Marlevi D, Iglesias MJ, ..., Kooi ME, Hedin U
Biomolecules 13 (6) - [2023-05-24; online 2023-05-24]
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Targeting NETs using dual-active DNase1 variants.
Englert H, Göbel J, Khong D, ..., Fuchs TA, Renné T
Front Immunol 14 (-) 1181761 [2023-05-23; online 2023-05-23]
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Clonal Hematopoiesis of Indeterminate Potential Predicts Adverse Outcomes in Patients With Atherosclerotic Cardiovascular Disease.
Gumuser ED, Schuermans A, Cho SMJ, ..., Natarajan P, Honigberg MC
J. Am. Coll. Cardiol. 81 (20) 1996-2009 [2023-05-23; online 2023-05-18]
Abhishek Niroula DDLS Fellow
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Author Correction: An online atlas of human plasma metabolite signatures of gut microbiome composition.
Dekkers KF, Sayols-Baixeras S, Baldanzi G, ..., Orho-Melander M, Fall T
Nat Commun 14 (1) 2971 [2023-05-23; online 2023-05-23]
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Antibodies from serum and CSF of multiple sclerosis patients bind to oligodendroglial and neuronal cell-lines.
Nazir FH, Wiberg A, Müller M, Mangsbo S, Burman J
Brain Commun 5 (3) fcad164 [2023-05-23; online 2023-05-23]
DOI Crossref
Half-cost array-based genotyping of SNPs in bread wheat from pooled experiments and imputation
Clouard C, Nettelblad C
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Design of Drug Efficacy Guided by Free Energy Simulations of the β2 -Adrenoceptor.
Panel N, Vo DD, Kahlous NA, ..., Gmeiner P, Carlsson J
Angew. Chem. Int. Ed. Engl. 62 (22) e202218959 [2023-05-22; online 2023-04-20]
Jens Carlsson Lucie Delemotte SciLifeLab Fellow
DOI Crossref
Design of Drug Efficacy Guided by Free Energy Simulations of the β 2 ‐Adrenoceptor
Panel N, Vo DD, Kahlous NA, ..., Gmeiner P, Carlsson J
Angewandte Chemie 135 (22) - [2023-05-22; online 2023-04-20]
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Atlas of mRNA translation and decay for bacteria.
Huch S, Nersisyan L, Ropat M, ..., Engstrand L, Pelechano V
Nat. Microbiol - (-) - [2023-05-22; online 2023-05-22]
SciLifeLab Fellow Vicente Pelechano
PubMed DOI Crossref
Drug repositioning targeting glutaminase reveals drug candidates for the treatment of Alzheimer's disease patients.
Bayraktar A, Li X, Kim W, ..., Shoaie S, Mardinoglu A
J Transl Med 21 (1) 332 [2023-05-20; online 2023-05-20]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Development and Characterization of Novel Selective, Non-Basic Dopamine D2 Receptor Antagonists for the Treatment of Schizophrenia.
Stępnicki P, Wośko S, Bartyzel A, ..., Castro M, Kaczor AA
Molecules 28 (10) - [2023-05-20; online 2023-05-20]
Jens Carlsson SciLifeLab Fellow
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Membranes in focus.
Sezgin E, Levental I
Biophys. J. - (-) - [2023-05-19; online 2023-05-19]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Genome sequencing with comprehensive variant calling identifies structural variants and repeat expansions in a large fraction of individuals with ataxia and/or neuromuscular disorders.
Ek M, Nilsson D, Engvall M, ..., Lindstrand A, Kvarnung M
Front Neurol 14 (-) 1170005 [2023-05-18; online 2023-05-18]
DOI Crossref
Author response: Interplay between VSD, pore, and membrane lipids in electromechanical coupling in HCN channels
Elbahnsi A, Cowgill J, Burtscher V, ..., Chanda B, Delemotte L
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Syndecan-4 is a maestro of gastric cancer cell invasion and communication that underscores poor survival.
Poças J, Marques C, Gomes C, ..., Costa-Silva B, Magalhães A
Proc. Natl. Acad. Sci. U.S.A. 120 (20) e2214853120 [2023-05-16; online 2023-05-08]
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Author response: Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5
McComas SE, Reichenbach T, Mitrovic D, ..., Delemotte L, Drew D
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Are single-peaked tuning curves tuned for speed rather than accuracy?
Lenninger M, Skoglund M, Herman PA, Kumar A
Elife 12 (-) - [2023-05-16; online 2023-05-16]
PubMed DOI Crossref
Relationship between iron deficiency and expression of genes involved in iron metabolism in human myocardium and skeletal muscle.
Cabrera C, Frisk C, Löfström U, ..., Persson B, Ekström M
Int. J. Cardiol. 379 (-) 82-88 [2023-05-15; online 2023-03-15]
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Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy.
Ollila HM, Sharon E, Lin L, ..., Ye CJ, Mignot EJ
Nat Commun 14 (1) 2709 [2023-05-15; online 2023-05-15]
DOI Crossref
Striking allelic diversity despite structural homogeneity of ace-1 duplications in Anopheles mosquitoes
Claret JL, Di-Liegro M, Namias A, ..., Milesi P, Labbé P
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Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.
Doye JPK, Fowler H, Prešern D, ..., Poppleton E, Snodin BEK
Methods in molecular biology (Clifton, N.J.) 2639 (-) 93-112 [2023-05-11; online 2023-05-11]
Erik Benson SciLifeLab Fellow
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Sensitive quantification of short-chain fatty acids combined with global metabolomics in microbiome cultures.
Lin W, García FR, Norin EL, ..., Du J, Globisch D
Chem. Commun. (Camb.) 59 (39) 5843-5846 [2023-05-11; online 2023-05-11]
Daniel Globisch SciLifeLab Fellow
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Image recovery from unknown network mechanisms for DNA sequencing-based microscopy.
Fernandez Bonet D, Hoffecker IT
Nanoscale 15 (18) 8153-8157 [2023-05-11; online 2023-05-11]
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Rapid Traversal of Ultralarge Chemical Space using Machine Learning Guided Docking Screens
Luttens A, Cabeza de Vaca I, Sparring L, Norinder U, Carlsson J
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Author response: Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning
Mitrovic D, McComas SE, Alleva C, ..., Drew D, Delemotte L
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A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens.
Schlegel J, Porebski B, Andronico L, ..., Fernandez-Capetillo O, Sezgin E
Nano Lett. 23 (9) 3701-3707 [2023-05-10; online 2023-03-09]
PubMed DOI Crossref
Plasma protein changes reflect colorectal cancer development and associated inflammation.
Urbiola-Salvador V, Jabłońska A, Miroszewska D, ..., Li B, Chen Z
Front Oncol 13 (-) 1158261 [2023-05-09; online 2023-05-09]
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Ball-and-Chain Inactivation in Potassium Channels.
Sukomon N, Fan C, Nimigean CM
Annu Rev Biophys 52 (-) 91-111 [2023-05-09; online 2023-01-10]
PubMed DOI Crossref
Data-driven neuropathological staging and subtyping of TDP-43 proteinopathies.
Young AL, Vogel JW, Robinson JL, ..., Lee EB, Hansson O
Brain - (-) - [2023-05-08; online 2023-05-08]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Comparison of Group-Level and Individualized Brain Regions for Measuring Change in Longitudinal Tau Positron Emission Tomography in Alzheimer Disease.
Leuzy A, Binette AP, Vogel JW, ..., Hansson O, Alzheimer’s Disease Neuroimaging Initiative
JAMA Neurol - (-) - [2023-05-08; online 2023-05-08]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Moore J, Basurto-Lozada D, Besson S, ..., Theis FJ, Swedlow JR
bioRxiv - (-) - [2023-05-07; online 2023-05-07]
PubMed DOI Crossref
Identifying miRNA-mRNA regulatory networks on extreme n-6/n-3 polyunsaturated fatty acid ratio expression profiles in porcine skeletal muscle.
Manaig YJY, Criado-Mesas L, Esteve-Codina A, ..., Sánchez A, Folch JM
PLoS ONE 18 (5) e0283231 [2023-05-04; online 2023-05-04]
PubMed DOI Crossref
A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic data sets.
Vlasschaert C, Mack T, Heimlich JB, ..., Jaiswal S, Bick AG
Blood 141 (18) 2214-2223 [2023-05-04; online 2023-01-19]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Multiplexed selectivity screening of anti-GPCR antibodies.
Dahl L, Kotliar IB, Bendes A, ..., Sakmar TP, Schwenk JM
Sci Adv 9 (18) eadf9297 [2023-05-03; online 2023-05-03]
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The GRPR Antagonist [99mTc]Tc-maSSS-PEG2-RM26 towards Phase I Clinical Trial: Kit Preparation, Characterization and Toxicity.
Abouzayed A, Borin J, Lundmark F, ..., Chernov V, Orlova A
Diagnostics (Basel) 13 (9) - [2023-05-02; online 2023-05-02]
PubMed DOI Crossref
Nontarget Analysis of Polluted Surface Waters in Bangladesh Using Open Science Workflows.
Bonnefille B, Karlsson O, Rian MB, ..., Islam MS, Martin JW
Environ. Sci. Technol. 57 (17) 6808-6824 [2023-05-02; online 2023-04-21]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
MYCN Amplification Is Associated with Reduced Expression of Genes Encoding γ-Secretase Complex and NOTCH Signaling Components in Neuroblastoma.
Agarwal P, Glowacka A, Mahmoud L, ..., Larsson LG, Alzrigat M
Int J Mol Sci 24 (9) - [2023-05-02; online 2023-05-02]
PubMed DOI Crossref
Lab-in-a-fiber-based integrated particle separation and counting.
Kumar T, Harish AV, Etcheverry S, ..., Laurell F, Russom A
Lab Chip 23 (9) 2286-2293 [2023-05-02; online 2023-05-02]
PubMed DOI Crossref
Fe and C additions decrease the dissolution rate of silicon nitride coatings and are compatible with microglial viability in 3D collagen hydrogels.
Echeverri E, Skjöldebrand C, O'Callaghan P, ..., Hulsart-Billström G, Persson C
Biomater Sci 11 (9) 3144-3158 [2023-05-02; online 2023-05-02]
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Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.
Paulat NS, Storer JM, Moreno-Santillán DD, ..., Karlsson EK, Ray DA
Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-18]
PubMed DOI Crossref
Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians.
Ovchinnikov V, Uliano-Silva M, Wilkinson M, ..., Durbin R, O'Connell MJ
Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-05-17]
PubMed DOI Crossref
Modelling Brain in a Chip.
Ashammakhi N, Nasiri R, Contag CH, Herland A
J Craniofac Surg 34 (3) 845-847 [2023-05-01; online 2023-03-24]
PubMed DOI Crossref
Helicobacter pylori Seropositivity, ABO Blood Type, and Pancreatic Cancer Risk From 5 Prospective Cohorts.
Lee AA, Wang QL, Kim J, ..., Yuan C, Wolpin BM
Clin Transl Gastroenterol 14 (5) e00573 [2023-05-01; online 2023-05-01]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Comparison of CX-4945 and SGC-CK2-1 as inhibitors of CSNK2 using quantitative phosphoproteomics: Triple SILAC in combination with inhibitor-resistant CSNK2.
Menyhart D, Gyenis L, Jurcic K, ..., Topisirovic I, Litchfield DW
Curr Res Chem Biol 3 (-) - [2023-05-01; online 2023-05-01]
DOI Crossref
Anti-IL-6R prevents experimental type 1 diabetes
Luo Z, Hamze N, Berggren E, ..., Sandler S, Singh K
J. Immunol. 210 (Supplement_1) 165.20-165.20 [2023-05-01; online 2023-05-01]
DOI Crossref
Adrenomedullin promotes interneuron migration in a dual human model for hypoxic interneuronopathy of prematurity
Michno WP, Puno A, Li L, ..., Willsey AJ, Pasca AM
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SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.
Grüttner J, van Rijn JM, Geiser P, ..., Sellin ME, Svärd SG
PLoS Pathog 19 (5) e1011372 [2023-05-00; online 2023-05-04]
Mikael Sellin SciLifeLab Fellow
DOI Crossref
Topic: AS06-Prognosis/AS06a-Prognostic factors of outcome and risk assessment: COMPARISON OF MRD-MARKERS USING MUTATION-SPECIFIC DDPCR IN BONE MARROW AND PERIPHERAL BLOOD AFTER ALLOGENEIC STEM CELL TRANSPLANTATION IN PATIENTS WITH MDS
Lindholm C, Tobiasson M, Pandzic T, ..., Dybedal I, Hellstrom-Lindberg E
Leuk. Res. 128 (-) 107227 [2023-05-00; online 2023-05-00]
PubMed DOI Crossref
The association between genetically elevated polyunsaturated fatty acids and risk of cancer.
Haycock PC, Borges MC, Burrows K, ..., Martin RM, Fatty Acids in Cancer Mendelian Randomization Collaboration
EBioMedicine 91 (-) 104510 [2023-05-00; online 2023-04-20]
PubMed DOI Crossref
Revisiting the role of serine metabolism in hepatic lipogenesis.
Yang H, Zhang C, Turkez H, ..., Boren J, Mardinoglu A
Nat Metab 5 (5) 760-761 [2023-05-00; online 2023-05-11]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Prediction of risk for myeloid malignancy in clonal hematopoiesis.
Weeks LD, Niroula A, Neuberg D, ..., Natarajan P, Ebert BL
NEJM Evid 2 (5) - [2023-05-00; online 2023-04-25]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Plasma lipidome and risk of atrial fibrillation: results from the PREDIMED trial.
Toledo E, Wittenbecher C, Razquin C, ..., Hu FB, Martínez-González MA
J Physiol Biochem 79 (2) 355-364 [2023-05-00; online 2023-04-01]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
New Pharmacological Approaches to the Management of Premenstrual Dysphoric Disorder.
Sundström-Poromaa I, Comasco E
CNS Drugs 37 (5) 371-379 [2023-05-00; online 2023-05-12]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Neither Gastric Bypass Surgery Nor Diet-Induced Weight-Loss Affect OATP1B1 Activity as Measured by Rosuvastatin Oral Clearance.
Hovd M, Robertsen I, Johnson LK, ..., Jansson-Löfmark R, Christensen H
Clin Pharmacokinet 62 (5) 725-735 [2023-05-00; online 2023-03-29]
PubMed DOI Crossref
Naturally occurring dipeptide from elite controllers with dual anti-HIV-1 mechanism.
Ceña-Diez R, Narayanan A, Ray S, ..., van Domselaar R, Sönnerborg A
Int. J. Antimicrob. Agents 61 (5) 106792 [2023-05-00; online 2023-03-15]
PubMed DOI Crossref
Migraine, inflammatory bowel disease and celiac disease: A Mendelian randomization study.
Welander NZ, Rukh G, Rask-Andersen M, ..., Schiöth HB, Mwinyi J
Headache 63 (5) 642-651 [2023-05-00; online 2023-01-27]
PubMed DOI Crossref
Itch receptor MRGPRX4 interacts with the receptor activity-modifying proteins.
Kotliar IB, Ceraudo E, Kemelmakher-Liben K, ..., Schwenk JM, Sakmar TP
J Biol Chem 299 (5) 104664 [2023-05-00; online 2023-03-30]
PubMed DOI Crossref
Intrinsic lipolysis rate for systematic design of lipid-based formulations
Jacobsen AC, Kabedev A, Sinko PD, ..., Bergström CAS, Teleki A
Drug Deliv. and Transl. Res. 13 (5) 1288-1304 [2023-05-00; online 2022-10-08]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Interobserver reproducibility of cribriform cancer in prostate needle biopsies and validation of International Society of Urological Pathology criteria.
Egevad L, Delahunt B, Iczkowski KA, ..., Eklund M, Kartasalo K
Histopathology 82 (6) 837-845 [2023-05-00; online 2023-01-25]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Insulin thermostability in a real-world setting.
Pendsey S, James S, Garrett TJ, ..., Forsander G, Ogle GD
The Lancet Diabetes & Endocrinology 11 (5) 310-312 [2023-05-00; online 2023-03-29]
DOI Crossref
Impaired thymic AIRE expression underlies autoantibodies against type I IFNs in humans with inborn errors of the alternative NF-κB pathway
Voyer TL, Gervais A, Rosain J, ..., Casanova JL, Puel A
Clin. Immunol. 250 (-) 109369 [2023-05-00; online 2023-05-00]
PubMed DOI Crossref
Hepatic Innervations and Nonalcoholic Fatty Liver Disease.
Adori M, Bhat S, Gramignoli R, ..., Uhlèn M, Adori C
Semin Liver Dis 43 (2) 149-162 [2023-05-00; online 2023-05-08]
DOI Crossref
Expansion microscopy and biorthogonal labeling with non-canonical amino acids enables cluster analysis of Na, K-ATPase in the plasma membrane
Edwards S, Bauer S, Graef P, ..., Elsässer S, Brismar H
Physiology 38 (S1) - [2023-05-00; online 2023-05-00]
PubMed DOI Crossref
Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma.
Graves OK, Kim W, Özcan M, ..., Mardinoglu A, Li X
Biomed. Pharmacother. 161 (-) 114486 [2023-05-00; online 2023-03-10]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Discovering CRISPR-Cas off-target breaks.
Jiménez C, Crosetto N
Nat. Methods 20 (5) 641-642 [2023-05-00; online 2023-04-07]
PubMed DOI Crossref
Cotranslational folding of human growth hormone in vitro and in Escherichia coli.
Mermans D, Nicolaus F, Baygin A, von Heijne G
FEBS Lett. 597 (10) 1355-1362 [2023-05-00; online 2022-12-22]
PubMed DOI Crossref
Conditionally activated affibody-based prodrug targeting EGFR demonstrates improved tumour selectivity.
Dahlsson Leitao C, Mestre Borras A, Xu T, ..., Vorobyeva A, Löfblom J
J Control Release 357 (-) 185-195 [2023-05-00; online 2023-03-31]
DOI Crossref
Click chemistry, FRET-FCS, and expansion microscopy reveal that Na, K-ATPase forms complexes in the plasma membrane
Brismar H, Edwards S, Bauer S, ..., Elsässer S, Wennmalm S
Physiology 38 (S1) - [2023-05-00; online 2023-05-00]
PubMed DOI Crossref
Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH.
Schulte T, Panas MD, Han X, ..., Achour A, McInerney GM
Open Biol 13 (5) 220369 [2023-05-00; online 2023-05-10]
DOI Crossref
Biomarker screening in children and adolescents reveals that CUB domain-containing protein 1 is associated with obesity and that hepatocyte growth factor is associated with weight gain
Manell H, Shen Q, Chowdhury A, ..., Bergsten P, Forslund A
Obesity Medicine 39 (-) 100481 [2023-05-00; online 2023-05-00]
PubMed DOI Crossref
Apoptotic cell death in disease-Current understanding of the NCCD 2023.
Vitale I, Pietrocola F, Guilbaud E, ..., Kroemer G, Galluzzi L
Cell Death Differ. 30 (5) 1097-1154 [2023-05-00; online 2023-04-26]
PubMed DOI Crossref
Acute nicotine exposure blocks aromatase in the limbic brain of healthy women: A [11C]cetrozole PET study.
Dubol M, Immenschuh J, Jonasson M, ..., Sundström-Poromaa I, Comasco E
Compr Psychiatry 123 (-) 152381 [2023-05-00; online 2023-03-05]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Pancreatic cancer is associated with medication changes prior to clinical diagnosis.
Zhang Y, Wang QL, Yuan C, ..., Kraft P, Wolpin BM
Nat Commun 14 (1) 2437 [2023-04-28; online 2023-04-28]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Lipoprotein Particles as Shuttles for Hydrophilic Cargo.
Weber F, Axmann M, Horner A, ..., Weghuber J, Plochberger B
Membranes (Basel) 13 (5) - [2023-04-28; online 2023-04-28]
PubMed DOI Crossref
Exploration of Novel Urolithin C Derivatives as Non-Competitive Inhibitors of Liver Pyruvate Kinase.
Battisti UM, Monjas L, Akladios F, ..., Mardinoğlu A, Grøtli M
Pharmaceuticals (Basel, Switzerland) 16 (5) - [2023-04-28; online 2023-04-28]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Mapping of the gene network that regulates glycan clock of ageing
Frkatović-Hodžić A, Miškec K, Mijakovac A, ..., Zoldoš V, Lauc G
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PubMed DOI Crossref
Reconfigurable self-assembled DNA devices.
Benson E, Bath J
Sci Robot 8 (77) eadh8148 [2023-04-26; online 2023-04-26]
Erik Benson SciLifeLab Fellow
PubMed DOI Crossref
Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase.
Englund E, Schmidt M, Nava AA, ..., Yuzawa S, Keasling JD
Journal of the American Chemical Society 145 (16) 8822-8832 [2023-04-26; online 2023-04-14]
DOI Crossref
Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM
Bergh C, Rovšnik U, Howard RJ, Lindahl E
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PubMed DOI Crossref
Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates.
Gunn BM, McNamara RP, Wood L, ..., Simon JK, Alter G
Cell Reports 42 (4) 112402 [2023-04-25; online 2023-04-15]
Avlant Nilsson DDLS Fellow
DOI Crossref
Genomic, transcriptomic and epigenomic sequencing data of the B- cell leukemia cell line REH
Wiklander ML, Övernäs E, Lagensjö J, ..., Liljedahl U, Nordlund J
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PubMed DOI Crossref
Size matters: the impact of nucleus size on results from spatial transcriptomics.
Mohammadi E, Chojnowska K, Bieńkowski M, ..., Piotrowski A, Mieczkowski J
J Transl Med 21 (1) 270 [2023-04-21; online 2023-04-21]
PubMed DOI Crossref
Normalization of hepatic ChREBP activity does not protect against liver disease progression in a mouse model for Glycogen Storage Disease type Ia.
Rutten MGS, Lei Y, Hoogerland JH, ..., van de Sluis B, Oosterveer MH
Cancer Metab 11 (1) 5 [2023-04-21; online 2023-04-21]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
GABA, glucose and insulin orchestrate CD4 + T cells effector functions
Jin Z, Hammoud H, Bhandage A, ..., Kamali-Moghaddam M, Birnir B
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PubMed DOI Crossref
Time-Lapse Imaging of Inflammasome-Dependent Cell Death and Extrusion in Enteroid-Derived Intestinal Epithelial Monolayers.
Geiser P, van Rijn JM, Sellin ME
Methods in molecular biology (Clifton, N.J.) 2641 (-) 203-221 [2023-04-19; online 2023-04-19]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Development of top-down cortical propagations in youth.
Pines A, Keller AS, Larsen B, ..., Fair DA, Satterthwaite TD
Neuron 111 (8) 1316-1330.e5 [2023-04-19; online 2023-02-17]
DDLS Fellow Jacob W Vogel
DOI Crossref
Comparing the Performance of SYCL Runtimes for Molecular Dynamics Applications
Alekseenko A, Páll S
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PubMed DOI Crossref
Monitoring beta cell survival after intrahepatic islet transplantation using dynamic exendin PET imaging: a proof-of-concept study in individuals with type 1 diabetes.
Jansen TJP, Buitinga M, Boss M, ..., de Koning EJP, Gotthardt M
Diabetes - (-) - [2023-04-17; online 2023-04-17]
Olof Eriksson SciLifeLab Fellow
DOI Crossref
Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins
Unneberg P, Larsson M, Olsson A, ..., Meyer B, Wallberg A
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PubMed DOI Crossref
ERβ in Granulosa Cell Tumors and Its Clinical Potential.
Birgersson M, Indukuri R, Antonson P, ..., Archer A, Williams C
Endocrinology 164 (6) - [2023-04-17; online 2023-04-19]
PubMed DOI Crossref
Microscopy-based phenotypic monitoring of MDA-MB-231 spheroids allows the evaluation of phenotype-directed therapy.
Mahmoud L, Cougnoux A, Bekiari C, ..., Gsell L, Hausser J
Exp. Cell Res. 425 (2) 113527 [2023-04-15; online 2023-03-06]
Jean Hausser SciLifeLab Fellow
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Emotion-induced brain activation across the menstrual cycle in individuals with premenstrual dysphoric disorder and associations to serum levels of progesterone-derived neurosteroids.
Stiernman L, Dubol M, Comasco E, ..., Johansson M, Bixo M
Transl Psychiatry 13 (1) 124 [2023-04-14; online 2023-04-14]
Erika Comasco SciLifeLab Fellow
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Azido-Ceramides, a Tool to Analyse SARS-CoV-2 Replication and Inhibition-SARS-CoV-2 Is Inhibited by Ceramides.
Brenner D, Geiger N, Schlegel J, ..., Bodem J, Seibel J
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Abstract LB362: Epigenome-wide DNA methylation alterations precede diagnosis since birth and affect prognosis of pediatric B-cell acute lymphoblastic leukemia
Ghantous A, Nusslé SG, Nassar F, ..., Munthe-Kaas MC, Herceg Z
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The Drug Efficacy Testing in Ex Vivo 3D Cultures (DETECt) platform enables rapid identification of effective drugs and drug combinations for ovarian cancer patients
Seashore-Ludlow B, Åkerlund E, Gudoityte G, ..., Kallioniemi O, Joneborg U
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Molecular profiling of high-level athlete skeletal muscle after acute exercise – a systems biology approach
Reitzner SM, Emanuelsson EB, Arif M, ..., Chapman MA, Sundberg CJ
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Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry.
Truong P, The M, Käll L
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Exploring High-Throughput Immunoassays for Biomarker Validation in Rheumatic Diseases in the Context of the Human Proteome Project.
Fuentes M, Ruiz-Romero C, Misiego S, ..., Nilsson P, Blanco FJ
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Electrochemically Etched Tapered-Tip Stainless-Steel Electrospray-Ionization Emitters for Capillary Electrophoresis-Mass Spectrometry.
Aerts JT, Andrén PE, Jansson ET
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M-Ionic: Prediction of metal ion binding sites from sequence using residue embeddings
Shenoy A, Kalakoti Y, Sundar D, Elofsson A
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Free energy landscapes of KcsA inactivation
Pérez-Conesa S, Delemotte L
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CRISPR-Cas9-mediated genome engineering exaggerates genomic deletion at 10q23.31 including the<i>PTEN</i>gene locus mimicking cancer profiles
Geng K, Merino LG, Veiga RG, ..., Brinkman EK, Kutter C
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Claudia Kutter SciLifeLab Fellow
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The genetic legacy of the expansion of Bantu-speaking peoples in Africa
Fortes-Lima CA, Burgarella C, Hammarén R, ..., Bostoen K, Schlebusch CM
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Investigation of 2-Hydroxypropyl-β-Cyclodextrin Treatment in a Neuronal-Like Cell Model of Niemann-Pick Type C Using Quantitative Proteomics.
Cougnoux A, Pergande MR, Serna-Perez F, Cologna SM
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Evaluation of Circulating Plasma Proteins in Breast Cancer: A Mendelian Randomization Analysis
Malarstig A, Grassman F, Dahl L, ..., Czene K, Hedman A
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Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.
James JE, Nelson PG, Masel J
Mol. Biol. Evol. 40 (4) - [2023-04-04; online 2023-03-23]
DDLS Fellow Jennifer James
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Abstract 705: Potentiation of immunotherapy by LSD1 modulation
Emond WB, Sawant R, Geitmann M, ..., Hellström M, Koehler KF
Cancer Res. 83 (7_Supplement) 705-705 [2023-04-04; online 2023-04-04]
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Abstract 2929: Modular peptide cargo delivery by targeting CD40 enables ligandome driven, precision immunotherapy via the Adaptable Drug Affinity Conjugate (ADAC™) technology
Mebrahtu A, Lauren I, Veerman R, ..., Rockberg J, Mangsbo S
Cancer Res. 83 (7_Supplement) 2929-2929 [2023-04-04; online 2023-04-04]
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Abstract 1793: Single-cell RNA analysis reveal effector-like CD8+ CAR-T cell subpopulations associated with response in lymphoma patients
Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M
Cancer Res. 83 (7_Supplement) 1793-1793 [2023-04-04; online 2023-04-04]
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Supplementary file from Leukocyte Differentiation by Histidine-Rich Glycoprotein/Stanniocalcin-2 Complex Regulates Murine Glioma Growth through Modulation of Antitumor Immunity
Roche FP, Pietilä I, Kaito H, ..., Welsh M, Claesson-Welsh L
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Supplementary file from Leukocyte Differentiation by Histidine-Rich Glycoprotein/Stanniocalcin-2 Complex Regulates Murine Glioma Growth through Modulation of Antitumor Immunity
Roche FP, Pietilä I, Kaito H, ..., Welsh M, Claesson-Welsh L
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Supplementary Materials from A Pragmatic Definition of Therapeutic Synergy Suitable for Clinically Relevant &lt;i&gt;In Vitro&lt;/i&gt; Multicompound Analyses
Kashif M, Andersson C, Åberg M, ..., Larsson R, Gustafsson MG
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Supplementary Materials from A Pragmatic Definition of Therapeutic Synergy Suitable for Clinically Relevant &lt;i&gt;In Vitro&lt;/i&gt; Multicompound Analyses
Kashif M, Andersson C, Åberg M, ..., Larsson R, Gustafsson MG
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Mucosal and Plasma Metabolomes in New-onset Paediatric Inflammatory Bowel Disease: Correlations with Disease Characteristics and Plasma Inflammation Protein Markers.
Nyström N, Prast-Nielsen S, Correia M, ..., Schuppe-Koistinen I, Halfvarson J
J Crohns Colitis 17 (3) 418-432 [2023-04-03; online 2022-10-12]
Daniel Globisch SciLifeLab Fellow
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IL-1 receptor-associated kinase-3 acts as an immune checkpoint in myeloid cells to limit cancer immunotherapy.
Tunalı G, Rúbies Bedós M, Nagarajan D, ..., Papakyriacou I, Mao Y
J. Clin. Invest. 133 (7) - [2023-04-03; online 2023-04-03]
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Data from SOX9 Defines Distinct Populations of Cells in SHH Medulloblastoma but Is Not Required for Math1-Driven Tumor Formation
Adolphe C, Millar A, Kojic M, ..., Genovesi LA, Wainwright BJ
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Data from Inhibition of Oxidized Nucleotide Sanitation By TH1579 and Conventional Chemotherapy Cooperatively Enhance Oxidative DNA Damage and Survival in AML
Centio A, Estruch M, Reckzeh K, ..., Helleday T, Theilgaard-Mönch K
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Data from Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions
Kim JH, Megquier K, Thomas R, ..., Lindblad-Toh K, Modiano JF
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Retention time and fragmentation predictors increase confidence in variant peptide identification
Skiadopoulou D, Vašíček J, Kuznetsova K, Käll L, Vaudel M
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Plasma Lipidomic n-6 Polyunsaturated Fatty Acids and Type 2 Diabetes Risk in the EPIC-Potsdam Prospective Cohort Study.
Prada M, Eichelmann F, Wittenbecher C, Kuxhaus O, Schulze MB
Diabetes Care 46 (4) 836-844 [2023-04-01; online 2023-02-15]
Clemens Wittenbecher DDLS Fellow
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Low-Carbohydrate Diet Scores and Mortality Among Adults With Incident Type 2 Diabetes.
Hu Y, Liu G, Yu E, ..., Hu FB, Sun Q
Diabetes Care 46 (4) 874-884 [2023-04-01; online 2023-02-15]
Clemens Wittenbecher DDLS Fellow
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Heparan sulfate proteoglycan in Alzheimer's disease: aberrant expression and functions in molecular pathways related to amyloid-β metabolism.
Ozsan McMillan I, Li JP, Wang L
Am. J. Physiol., Cell Physiol. 324 (4) C893-C909 [2023-04-01; online 2023-03-06]
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Epithelial and microbial determinants of colonic drug distribution.
Hammar R, Sellin ME, Artursson P
Eur J Pharm Sci 183 (-) 106389 [2023-04-01; online 2023-01-20]
Mikael Sellin SciLifeLab Fellow
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Voices of the new generation: normalizing career choices outside academia.
Sezgin E
Nat. Rev. Mol. Cell Biol. 24 (4) 237 [2023-04-00; online 2023-01-20]
Erdinc Sezgin SciLifeLab Fellow
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The liver kinase B1 supports mammary epithelial morphogenesis by inhibiting critical factors that mediate epithelial-mesenchymal transition.
Tzavlaki K, Ohata Y, Morén A, ..., Heldin CH, Moustakas A
J. Cell. Physiol. 238 (4) 790-812 [2023-04-00; online 2023-02-15]
Mikael Sellin SciLifeLab Fellow
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Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird.
Martin CA, Sheppard EC, Illera JC, ..., Spurgin LG, Richardson DS
Mol. Ecol. 32 (8) 1972-1989 [2023-04-00; online 2023-02-10]
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Optimizing insect metabarcoding using replicated mock communities.
Iwaszkiewicz-Eggebrecht E, Granqvist E, Buczek M, ..., Ronquist F, Łukasik P
Methods Ecol Evol 14 (4) 1130-1146 [2023-04-00; online 2023-02-13]
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Novel therapeutic approaches for pleural mesothelioma identified by functional ex vivo drug sensitivity testing.
Ollila-Raj H, Murumägi A, Pellinen T, ..., Mäyränpää MI, Ilonen I
Lung Cancer 178 (-) 213-219 [2023-04-00; online 2023-03-01]
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NUDT22 promotes cancer growth through pyrimidine salvage.
Walter M, Mayr F, Hanna BMF, ..., Helleday T, Herr P
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Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression.
Mattis KK, Krentz NAJ, Metzendorf C, ..., den Hoed M, Gloyn AL
Diabetologia 66 (4) 674-694 [2023-04-00; online 2023-01-12]
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Heterologous inactivated virus/mRNA vaccination response to BF.7, BQ.1.1, and XBB.1.
Zuo F, Sun R, Abolhassani H, ..., Marcotte H, Pan-Hammarström Q
Lancet Reg Health West Pac 33 (-) 100762 [2023-04-00; online 2023-04-12]
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Gray matter hypoperfusion is a late pathological event in the course of Alzheimer's disease.
Ahmadi K, Pereira JB, Berron D, ..., Mutsaerts HJ, Hansson O
J. Cereb. Blood Flow Metab. 43 (4) 565-580 [2023-04-00; online 2022-11-22]
DDLS Fellow Jacob W Vogel
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Dynamic antagonism between key repressive pathways maintains the placental epigenome.
Weigert R, Hetzel S, Bailly N, ..., Smith ZD, Meissner A
Nat. Cell Biol. 25 (4) 579-591 [2023-04-00; online 2023-04-06]
SciLifeLab Fellow Simon Elsässer
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Dietary intake of total, heme and non-heme iron and the risk of colorectal cancer in a European prospective cohort study.
Aglago EK, Cross AJ, Riboli E, ..., Tsilidis KK, Jenab M
Br. J. Cancer 128 (8) 1529-1540 [2023-04-00; online 2023-02-09]
Clemens Wittenbecher DDLS Fellow
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Deep mutational scan of a drug efflux pump reveals its structure-function landscape.
Meier G, Thavarasah S, Ehrenbolger K, ..., Barandun J, Seeger MA
Nat. Chem. Biol. 19 (4) 440-450 [2023-04-00; online 2022-11-28]
Jonas Barandun SciLifeLab Fellow
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Deep learning for protein complex structure prediction.
Bryant P
Curr. Opin. Struct. Biol. 79 (-) 102529 [2023-04-00; online 2023-01-31]
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Decreased frontal and orbital volumes and increased cerebellar volumes in patients with anosmia Of Unknown origin: A subtle connection?
Avnioglu S, Sahin C, Cankaya S, ..., Velioglu HA, Yulug B
J Psychiatr Res 160 (-) 86-92 [2023-04-00; online 2023-01-11]
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Clonal haematopoiesis and risk of chronic liver disease.
Wong WJ, Emdin C, Bick AG, ..., Ebert BL, Natarajan P
Nature 616 (7958) 747-754 [2023-04-00; online 2023-04-12]
Abhishek Niroula DDLS Fellow
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CD93 maintains endothelial barrier function by limiting the phosphorylation and turnover of VE-cadherin.
Lugano R, Vemuri K, Barbera S, ..., Claesson-Welsh L, Dimberg A
FASEB J. 37 (4) e22894 [2023-04-00; online 2023-03-25]
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Brain temperature in healthy and diseased conditions: A review on the special implications of MRS for monitoring brain temperature.
Yulug B, Velioglu HA, Sayman D, Cankaya S, Hanoglu L
Biomed. Pharmacother. 160 (-) 114287 [2023-04-00; online 2023-01-27]
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Author Correction: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing.
Cikes D, Elsayad K, Sezgin E, ..., Banka S, Penninger JM
Nat Metab 5 (4) 711 [2023-04-00; online 2023-04-07]
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An atlas of genetic scores to predict multi-omic traits.
Xu Y, Ritchie SC, Liang Y, ..., Butterworth AS, Inouye M
Nature 616 (7955) 123-131 [2023-04-00; online 2023-03-29]
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A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken.
Bi H, Tranell J, Harper DC, ..., Globisch D, Andersson L
PLoS Genet 19 (4) e1010724 [2023-04-00; online 2023-04-17]
Daniel Globisch SciLifeLab Fellow
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Unraveling Neuro-Proteogenomic Landscape and Therapeutic Implications for Human Behaviors and Psychiatric Disorders.
Repetto L, Chen J, Yang Z, ..., Navarro P, Shen X
Res Sq - (-) - [2023-03-31; online 2023-03-31]
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Supplementary Figure 1 from Downregulation of SMG-1 in HPV-Positive Head and Neck Squamous Cell Carcinoma Due to Promoter Hypermethylation Correlates with Improved Survival
Gubanova E, Brown B, Ivanov SV, ..., Yarbrough WG, Issaeva N
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Data from Downregulation of SMG-1 in HPV-Positive Head and Neck Squamous Cell Carcinoma Due to Promoter Hypermethylation Correlates with Improved Survival
Gubanova E, Brown B, Ivanov SV, ..., Yarbrough WG, Issaeva N
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Data from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Borgenvik A, Holmberg KO, Bolin S, ..., Weishaupt H, Swartling FJ
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Data from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Borgenvik A, Holmberg KO, Bolin S, ..., Weishaupt H, Swartling FJ
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Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer
Sjöberg E, Meyrath M, Milde L, ..., Augsten M, Östman A
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Data from &lt;i&gt;SETD2&lt;/i&gt; Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma
Sakthikumar S, Elvers I, Kim J, ..., Marinescu VD, Lindblad-Toh K
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Data from &lt;i&gt;SETD2&lt;/i&gt; Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma
Sakthikumar S, Elvers I, Kim J, ..., Marinescu VD, Lindblad-Toh K
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Prognostic whole-genome and transcriptome signatures in colorectal cancers
Nunes L, Li F, Wu M, ..., Lin C, Sjöblom T
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Do lipids tune B cell signaling?
Urbančič I, Eggeling C, Sezgin E
Nat. Chem. Biol. - (-) - [2023-03-30; online 2023-03-30]
Erdinc Sezgin SciLifeLab Fellow
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Data from 6-Thioguanine Selectively Kills BRCA2-Defective Tumors and Overcomes PARP Inhibitor Resistance
Issaeva N, Thomas HD, Djurenovic T, ..., Curtin NJ, Helleday T
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Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton
Grujcic V, Saarenpää S, Sundh J, ..., Foster RA, Andersson AF
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Selective Serotonin Reuptake Inhibitors within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane.
Nichols AL, Blumenfeld Z, Luebbert L, ..., Dougherty DA, Lester HA
J. Neurosci. 43 (13) 2222-2241 [2023-03-29; online 2023-03-03]
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Prediction of the Human Pharmacokinetics of 30 Modern Antibiotics Using the ANDROMEDA Software
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
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Diverticulosis is not associated with altered gut microbiota nor is it predictive of future diverticulitis: a population-based colonoscopy study.
Alexandersson BT, Hugerth LW, Hedin C, ..., Andreasson A, Schmidt PT
Scand. J. Gastroenterol. 58 (10) 1131-1138 [2023-03-29; online 2023-03-29]
DDLS Fellow Luisa Hugerth
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The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken
Höglund A, Henriksen R, Churcher AM, ..., Jensen P, Wright D
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Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia
Krali O, Marincevic-Zuniga Y, Arvidsson G, ..., Syvänen AC, Nordlund J
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Mapping pQTLs of circulating inflammatory proteins identifies drivers of immune-related disease risk and novel therapeutic targets
Zhao JH, Stacey D, Eriksson N, ..., Butterworth AS, Peters JE
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Linking prokaryotic genome size variation to metabolic potential and environment.
Rodríguez-Gijón A, Buck M, Andersson AF, ..., Nascimento FJA, Garcia SL
ISME Commun 3 (1) 25 [2023-03-27; online 2023-03-27]
Sarahi Garcia SciLifeLab Fellow
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Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery
Meineke B, Heimgärtner J, Caridha R, ..., Landreh M, Elsässer SJ
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Correlative Chemical Imaging and Spatial Chemometrics Delineate Alzheimer Plaque Heterogeneity at High Spatial Resolution.
Wehrli PM, Ge J, Michno W, ..., Blennow K, Hanrieder J
JACS Au 3 (3) 762-774 [2023-03-27; online 2023-03-07]
SciLifeLab Fellow Wojciech Michno
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Modulation of Pore Opening of Eukaryotic Sodium Channels by π-helices in S6
Choudhury K, Delemotte L
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Costunolide and Parthenolide Ameliorate MPP+ Induced Apoptosis in the Cellular Parkinson's Disease Model.
Arslan ME, Türkez H, Sevim Y, ..., Öner S, Mardinoğlu A
Cells 12 (7) - [2023-03-24; online 2023-03-24]
Adil Mardinoglu SciLifeLab Fellow
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standard-GEM: standardization of open-source genome-scale metabolic models
Anton M, Almaas E, Benfeitas R, ..., Zeidan AA, Kerkhoven EJ
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Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release
Wang Z, Himanen SV, Haikala HM, ..., Vihervaara A, Barborič M
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Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.
Mutsuddy A, Erdem C, Huggins JR, ..., Feltus FA, Birtwistle MR
Bioinform Adv 3 (1) vbad039 [2023-03-23; online 2023-03-23]
Cemal Erdem DDLS Fellow
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Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia
Paulat NS, Storer JM, Moreno-Santillán DD, ..., Karlsson EK, Ray DA
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Whole‐cell Mediated Carboxylation of 2‐Furoic Acid Towards the Production of Renewable Platform Chemicals and Biomaterials
Lopez‐Lorenzo X, Asem H, Stamm A, ..., Hakkarainen M, Syrén P
ChemCatChem 15 (6) - [2023-03-22; online 2023-02-21]
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The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems
Ernits K, Saha CK, Brodiazhenko T, ..., Hauryliuk V, Atkinson GC
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Recurring EPHB1 mutations in human cancers alter receptor signalling and compartmentalisation of colorectal cancer cells
Kundu S, Nunes L, Adler J, ..., Stoimenov I, Sjöblom T
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PD-L1ATTAC mice reveal the potential of depleting PD-L1 expressing cells in cancer therapy.
Fueyo-Marcos E, Lopez-Pernas G, Fustero-Torre C, ..., Fernández-Capetillo O, Murga M
Aging (Albany NY) 15 (6) 1791-1807 [2023-03-22; online 2023-03-22]
DOI Crossref
The association of the RSC remodeler complex with chromatin depends on prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae
Cuevas-Bermúdez A, Martínez-Fernández V, Garrido-Godino AI, ..., Pelechano V, Navarro F
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Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics.
Doktorova M, Khelashvili G, Ashkar R, Brown MF
Biophys. J. 122 (6) 984-1002 [2023-03-21; online 2022-12-05]
DDLS Fellow Milka Doktorova
DOI Crossref
Application of the ANDROMEDA Software for Prediction of the Human Pharmacokinetics of Modern Anticancer Drugs
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
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PubMed DOI Crossref
Targeting Glioblastoma-Associated Macrophages for Photodynamic Therapy Using AGuIX®-Design Nanoparticles.
Lerouge L, Gries M, Chateau A, ..., Thomas N, Barberi-Heyob M
Pharmaceutics 15 (3) - [2023-03-20; online 2023-03-20]
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Amino acid usage and tRNA expression underlies proteome adaptation in Plasmodium falciparum
Li Q, Vetter L, Veith Y, ..., Larsson O, Chan SCL
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Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.
Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD
bioRxiv - (-) - [2023-03-18; online 2023-03-18]
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Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences.
Leal JL, Milesi P, Salojärvi J, Lascoux M
Syst. Biol. - (-) - [2023-03-18; online 2023-03-18]
Pascal Milesi SciLifeLab Fellow
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NDFIP1 limits cellular TAZ accumulation via exosomal sorting to inhibit NSCLC proliferation.
Cheng Y, Lu X, Li F, ..., Williams C, Xia W
Protein Cell 14 (2) 123-136 [2023-03-16; online 2023-03-18]
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What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds
Durairaj J, Waterhouse AM, Mets T, ..., Schwede T, Pereira J
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TASL Practice Guidance on the Clinical Assessment and Management of Patients with Nonalcoholic Fatty Liver Disease.
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A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea).
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Abstract PD4-01: PD4-01 Spatial transcriptomics reveals a substantial heterogeneity in TNBC tumor and stroma compartments with potential clinical implications
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Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.
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In silico tissue generation and power analysis for spatial omics.
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Exosomes: A missing link between chronic systemic inflammation and Alzheimer's disease?
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African Farmers, Not Stone Age Foragers: Reassessment of Human Remains from the Mumbwa Caves, Zambia
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A Microfluidic Contact Lens to Address Contact Lens-Induced Dry Eye.
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Magnetoresponsive fluorescent core-shell nanoclusters for biomedical applications.
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Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations.
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Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.
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Designed for Circularity: Chemically Recyclable and Enzymatically Degradable Biorenewable Schiff Base Polyester-Imines
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A 3D Bioprinted Gut Anaerobic Model for Studying Bacteria-Host Interactions.
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Statistical Analysis of SARS-CoV-2 Using Wastewater-Based Data of Stockholm, Sweden.
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Intraluminal neutrophils limit epithelium damage by reducing pathogen assault on intestinal epithelial cells during Salmonella gut infection
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A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31.
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Vaccine-induced correlate of protection against fatal COVID-19 in the old and frail during waves of neutralization resistant variants of concern
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Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.
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Nat Commun 14 (1) 982 [2023-02-22; online 2023-02-22]
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Prenylcysteine Oxidase 1 Is a Key Regulator of Adipogenesis.
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Modulation of lytic molecules restrain serial killing in γδ T lymphocytes
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Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.
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Genome Biol. 24 (1) 30 [2023-02-20; online 2023-02-20]
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Amyloid-β accumulation in human astrocytes induces mitochondrial disruption and changed energy metabolism.
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Antisecretory factor is safe to use as add-on treatment in newly diagnosed glioblastoma.
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BMC Neurol 23 (1) 76 [2023-02-18; online 2023-02-18]
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Systematic diet composition swap in a mouse genome-scale metabolic model reveals determinants of obesogenic diet metabolism in liver cancer.
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Phenotypic screening platform identifies statins as enhancers of immune cell-induced cancer cell death.
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Macrocyclic Pyrrolizidine Alkaloids and Silphiperfolanol Angelate Esters from Solanecio mannii
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Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.
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Nat Commun 14 (1) 910 [2023-02-17; online 2023-02-17]
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Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection.
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Generation of tumor spheroids in microwells to study NK cell cytotoxicity, infiltration and phenotype.
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Description of a novel subtype of acute myeloid leukemia defined by recurrent CBFB insertions.
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Blood 141 (7) 800-805 [2023-02-16; online 2022-10-01]
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Targeted proteomics using stable isotope labeled protein fragments enables precise and robust determination of total apolipoprotein(a) in human plasma.
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Population Genomics for Insect Conservation.
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When Two Become One: Conformational Changes in FXR/RXR Heterodimers Bound to Steroidal Antagonists.
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Genetic mechanisms of 184 neuro-related proteins in human plasma.
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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.
Bentley BP, Carrasco-Valenzuela T, Ramos EKS, ..., Mazzoni CJ, Komoroske LM
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Correction to: Persisting Salivary IgG Against SARS-CoV-2 at 9 Months After Mild COVID-19: A Complementary Approach to Population Surveys.
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Aptamer-Assisted Proximity Ligation Assay for Sensitive Detection of Infectious Bronchitis Coronavirus.
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CRISPR interference screens reveal tradeoffs between growth rate and robustness in Synechocystis sp. PCC 6803 across trophic conditions
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Loss of Y is associated with multi-omic changes in immune cells from Alzheimer’s disease patients
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Small-molecule-mediated OGG1 inhibition attenuates pulmonary inflammation and lung fibrosis in a murine lung fibrosis model.
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An α-π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb.
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PRO-IP-seq Tracks Molecular Modifications of Engaged Pol II Complexes at Nucleotide Resolution.
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scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences.
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Hybridization Mediated Range Expansion and Climate Change Resilience in Two Keystone Tree Species of Boreal Forests
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AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network.
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[18F]MK-7246 for Positron Emission Tomography Imaging of the Beta-Cell Surface Marker GPR44.
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Loci for insulin processing and secretion provide insight into type 2 diabetes risk.
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Feasibility of Co-Targeting HER3 and EpCAM Using Seribantumab and DARPin-Toxin Fusion in a Pancreatic Cancer Xenograft Model.
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Drug-Drug Interactions of Cannabidiol with Standard-of-Care Chemotherapeutics.
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Data-driven neuropathological staging and subtyping of TDP-43 proteinopathies.
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T cell receptor gene repertoire profiles in subgroups of patients with chronic lymphocytic leukemia bearing distinct genomic aberrations.
Vlachonikola E, Pechlivanis N, Karakatsoulis G, ..., Stamatopoulos K, Chatzidimitriou A
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Multiple Genetic Loci Associated with Pug Dog Thoracolumbar Myelopathy.
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Long-term SARS-CoV-2 surveillance in the wastewater of Stockholm: What lessons can be learned from the Swedish perspective?
Perez-Zabaleta M, Archer A, Khatami K, ..., Williams C, Cetecioglu Z
Sci. Total Environ. 858 (Pt 3) 160023 [2023-02-01; online 2022-11-08]
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Combined metabolic activators improve metabolic functions in the animal models of neurodegenerative diseases.
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Life Sci 314 (-) 121325 [2023-02-01; online 2022-12-26]
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Whole protein or long peptides in therapeutic vaccination strategies, does it make a difference?
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Expert Opin Biol Ther 23 (2) 115-117 [2023-02-00; online 2022-12-09]
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Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability
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Epiblast-like stem cells established by Wnt/β-catenin signaling manifest distinct features of formative pluripotency and germline competence.
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Enhanced translation expands the endo-lysosome size and promotes antigen presentation during phagocyte activation
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Astrocyte 3D culture and bioprinting using peptide functionalized hyaluronan hydrogels.
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Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues
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Novel analytical tools reveal that local synchronization of cilia coincides with tissue-scale metachronal waves in zebrafish multiciliated epithelia.
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Combined metabolic activators improve cognitive functions in Alzheimer's disease patients: a randomised, double-blinded, placebo-controlled phase-II trial.
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Metabolic stress-induced human beta-cell death is mediated by increased intracellular levels of adenosine.
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Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis.
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n-Type Organic Electrochemical Transistors with High Transconductance and Stability
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The swan genome and transcriptome, it is not all black and white.
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The development of blood protein profiles in extremely preterm infants follows a stereotypic evolution pattern
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Ellagic Acid and Its Metabolites as Potent and Selective Allosteric Inhibitors of Liver Pyruvate Kinase.
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Cortex-wide topography of 1/f-exponent in Parkinson’s disease
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Proline catabolism is key to facilitating Candida albicans pathogenicity
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TP53-mediated clonal hematopoiesis confers increased risk for incident atherosclerotic disease.
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scDual-Seq of Toxoplasma gondii -infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics
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Translating single-cell genomics into cell types
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A human stomach cell type transcriptome atlas
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Preclinical Characterisation of PSMA/GRPR-Targeting Heterodimer [68Ga]Ga-BQ7812 for PET Diagnostic Imaging of Prostate Cancer: A Step towards Clinical Translation.
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EvoBind: peptide binder design with inverse folding and protein structure prediction
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Simulation Reveals the Chameleonic Behavior of Macrocycles.
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Impaired thymic AIRE expression underlies autoantibodies against type I IFNs in humans with inborn errors of the alternative NF-kB pathway
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Synchronous effective population size changes and genetic stability of forest trees through glacial cycles
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Pascal Milesi SciLifeLab Fellow
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Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms.
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Drug repositioning for immunotherapy in breast cancer using single-cell analysis
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Author response: Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection
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Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase.
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Front Cover: Optimization of ‐Piperidinyl‐Benzimidazolone Derivatives as Potent and Selective Inhibitors of 8‐Oxo‐Guanine DNA Glycosylase 1 (ChemMedChem 1/2023)
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Exon-intron split analysis reveals posttranscriptional regulatory signals induced by high and low n-6/n-3 polyunsaturated fatty acid ratio diets in piglets.
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Cover Feature: Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase (ChemBioChem 1/2023)
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Proteoglycans: a common portal for SARS-CoV-2 and extracellular vesicle uptake.
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Neutrophil extracellular traps in the pathology of cancer and other inflammatory diseases.
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Fibroblast Growth Factor-23 and Risk of Cardiovascular Diseases: A Mendelian Randomization Study.
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Dimerization of the C-type lectin-like receptor CD93 promotes its binding to Multimerin-2 in endothelial cells.
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Unravelling the landscape of skin cancer through single-cell transcriptomics.
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Temporally and spatially regulated collagen XVIII isoforms are involved in ureteric tree development via the TSP1-like domain.
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Targeted proteomics identifies potential biomarkers of dysglycaemia, beta cell function and insulin sensitivity in Black African men and women.
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Diabetologia 66 (1) 174-189 [2023-01-00; online 2022-09-17]
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Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy.
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Leukemia 37 (1) 61-71 [2023-01-00; online 2022-11-15]
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Pharmacogenomics of GLP-1 receptor agonists: a genome-wide analysis of observational data and large randomised controlled trials.
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PatchDropout: Economizing Vision Transformers Using Patch Dropout
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Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain
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In Vivo Visualization and Quantification of Neutrophil Elastase in Lungs of COVID-19 Patients: A First-in-Humans PET Study with 11C-NES.
Antoni G, Lubberink M, Sörensen J, ..., Skorup P, Lipcsey M
Journal of nuclear medicine : official publication, Society of Nuclear Medicine 64 (1) 145-148 [2023-01-00; online 2022-06-09]
Olof Eriksson SciLifeLab Fellow
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In Silico Prediction of Human Clinical Pharmacokinetics with ANDROMEDA by Prosilico: Predictions for an Established Benchmarking Data Set, a Modern Small Drug Data Set, and a Comparison with Laboratory Methods.
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
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Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication.
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Elucidating the Interactome of G Protein-Coupled Receptors and Receptor Activity-Modifying Proteins.
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Divergent selection predating the Last Glacial Maximum mainly acted on macro-phenotypes in Norway spruce.
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Bioorthogonal azido-S1P works as substrate for S1PR1.
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The Role of Willpower in Major Depressive Disorder: An fMRI Study
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The MHC-E Peptide Ligand of Checkpoint NKG2A Is Governed by Inflammatory Signals and High Turnover
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Impaired Immuno-Metabolic Homeostasis and Microenvironmental Influence on Neuropsychiatric Risk in Treated HIV Infection
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Genome-Wide Annotation of the Human Protein-Coding Genes Using Co-Expression Clustering
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Genetically Incorporated Non-Canonical Amino Acids
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Engineered aldolases catalyzing stereoselective aldol reactions between aryl-substituted ketones and aldehydes
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Ruisheng Xiong SciLifeLab Fellow
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Distinct HLA Associations with Autoantibody-Defined Subgroups in Idiopathic Inflammatory Myopathies
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Ckap4 is Identified as a Therapeutic Target for the Treatment of Kidney Fibrosis
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Characterization of an &lt;i&gt;in vitro&lt;/i&gt; Steatosis Model for Modelling the Activated &lt;i&gt;de novo&lt;/i&gt; Lipogenesis in MAFLD Patients
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Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
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Brain sex classification in the limbic system as female-specific phenotype for depression
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Basic Concepts and Emergent Disease Mechanisms of Amyotrophic Lateral Sclerosis
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Associations between heredity, height, BMI, diabetes mellitus and gene variants in the insulin receptor gene in patients with schizophrenia
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A Surfactant Lipid Layer of Endosomal Membranes Empowers Airway Gas-Filling in &lt;i&gt;Drosophila&lt;/i&gt;
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A Risk Management Framework for Emergence of Novel Antibiotic Resistance Determinants
Heß S, Bengtsson-Palme J
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PubMed DOI Crossref
Lipoic Acid Conjugated Boron Hybrids Enhance Wound Healing and Antimicrobial Processes.
Türkez H, Yıldırım ÖÇ, Öner S, ..., Yapça ÖE, Mardinoğlu A
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Adil Mardinoglu SciLifeLab Fellow
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Label-Free Estimation of Sarcomere Orientation from Brightfield Microscopy Images of Induced Pluripotent Stem Cell Derived Cardiomyocyte Nuclei
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ISG15-modification of the Arp2/3 complex restricts pathogen spread
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Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening.
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Obesity-Associated Neurodegeneration Pattern Mimics Alzheimer's Disease in an Observational Cohort Study.
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Circulating Amino Acids and Risk of Peripheral Artery Disease in the PREDIMED Trial.
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C-ToMExO: Learning Cancer Progression Dynamics from Clonal Composition of Tumors
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Surface protein profiling of prostate-derived extracellular vesicles by mass spectrometry and proximity assays.
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STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression.
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Role of ZNF143 and Its Association with Gene Expression Patterns, Noncoding Mutations, and the Immune System in Human Breast Cancer.
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Modulating glycosphingolipid metabolism and autophagy improves outcomes in pre-clinical models of myeloma bone disease.
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Erdinc Sezgin SciLifeLab Fellow
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Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes.
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A brain atlas of synapse protein lifetime across the mouse lifespan.
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Ghost admixture in eastern gorillas
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Genome-wide association study reveals loci with sex-specific effects on plasma bile acids
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An Approach for Systems-Level Understanding of Prostate Cancer from High-Throughput Data Integration to Pathway Modeling and Simulation.
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The spectrum of tuberculosis described as differential DNA methylation patterns in alveolar macrophages and alveolar T cells.
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A conserved MTMR lipid phosphatase increasingly suppresses autophagy in brain neurons during aging.
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Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma.
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Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation
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PLoS Comput Biol 18 (12) e1010683 [2022-12-15; online 2022-12-15]
Prashant Singh SciLifeLab Fellow
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Strobealign: flexible seed size enables ultra-fast and accurate read alignment.
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Kristoffer Sahlin SciLifeLab Fellow
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Intrinsic Molecular Subtypes of Metastatic Castration-Resistant Prostate Cancer.
Feng E, Rydzewski NR, Zhang M, ..., Sjöström M, Zhao SG
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Arian Lundberg DDLS Fellow
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Influenza Virus Membrane Fusion Is Promoted by the Endosome-Resident Phospholipid Bis(monoacylglycero)phosphate.
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Expression of substance P, NPY and their Receptors Is Altered in Major Depression
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Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction.
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Deciphering the determinants of recombinant protein yield across the human secretome
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Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel.
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B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing.
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Markers associated with genomic instability, immunogenicity and immune therapy responsiveness in Metaplastic carcinoma of the breast: Expression of γH2AX, pRPA2, P53, PD-L1 and tumor infiltrating lymphocytes in 76 cases.
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Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
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Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
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Therapeutic opportunity of phosphodiesterase 3A modulators in myxoid liposarcomas
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Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.
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Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.
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Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.
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Predicting the Influence of Fat Food Intake on the Absorption and Systemic Exposure of Small Drugs using ANDROMEDA by Prosilico Software
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Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation.
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The impact of genetically controlled splicing on exon inclusion and protein structure
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SETD7 Expression Is Associated with Breast Cancer Survival Outcomes for Specific Molecular Subtypes: A Systematic Analysis of Publicly Available Datasets.
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Funnel metadynamics and behavioral studies reveal complex effect of D2AAK1 ligand on anxiety-like processes.
Bartuzi D, Kędzierska E, Targowska-Duda KM, ..., Poso A, Kaczor AA
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Aporphine and isoquinoline derivatives block glioblastoma cell stemness and enhance temozolomide cytotoxicity.
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Role of interneuron subtypes in controlling trial-by-trial output variability in the neocortex
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Measuring single-virus fusion kinetics using an assay for nucleic acid exposure.
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Itch receptor MRGPRX4 interacts with the receptor activity-modifying proteins (RAMPs)
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In Vitro Transcriptome Analysis of Cobalt Boride Nanoparticles on Human Pulmonary Alveolar Cells.
Arslan ME, Tatar A, Yıldırım ÖÇ, ..., Mardinoğlu A, Türkez H
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Adil Mardinoglu SciLifeLab Fellow
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Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways
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Orthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkers
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Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR
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Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.
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Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3.
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Development of l-Dopa-containing diketopiperazines as blood-brain barrier shuttle.
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Visualization &amp; Quality Control Tools for Large-scale Multiplex Tissue Analysis in TissUUmaps 3
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Personalized health risk assessment based on single-cell RNA sequencing analysis of a male with 45, X/48, XYYY karyotype.
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NF-kB in Signaling Patterns and Its Temporal Dynamics Encode/Decode Human Diseases.
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Madagascar's extraordinary biodiversity: Threats and opportunities.
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Science (New York, N.Y.) 378 (6623) eadf1466 [2022-12-02; online 2022-12-02]
DDLS Fellow Tobias Andermann
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Madagascar's extraordinary biodiversity: Evolution, distribution, and use.
Antonelli A, Smith RJ, Perrigo AL, ..., Zizka A, Ralimanana H
Science (New York, N.Y.) 378 (6623) eabf0869 [2022-12-02; online 2022-12-02]
DDLS Fellow Tobias Andermann
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Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS.
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Editorial: Machine learning, epistasis, and protein engineering: From sequence-structure-function relationships to regulation of metabolic pathways.
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Hybrid immunity in immunocompromised patients with CLL after SARS-CoV-2 infection followed by booster mRNA vaccination.
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High-efficiency transfection of<i>Acanthamoeba castellanii</i>using a cationic polymer
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Mikael Sellin SciLifeLab Fellow
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ToMExO: A probabilistic tree-structured model for cancer progression.
Mohaghegh Neyshabouri M, Lagergren J
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Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.
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Pascal Milesi SciLifeLab Fellow
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Targeting SAMHD1 with hydroxyurea in first-line cytarabine-based therapy of newly diagnosed acute myeloid leukaemia: Results from the HEAT-AML trial.
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TOPAS, a network-based approach to detect disease modules in a top-down fashion.
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Rapid TAURUS for Relaxation-Based Color Magnetic Particle Imaging.
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Plasma Metabolite Profiles Associated with the Amount and Source of Meat and Fish Consumption and the Risk of Type 2 Diabetes.
García-Gavilán J, Nishi SK, Paz-Graniel I, ..., Hu FB, Salas-Salvadó J
Mol Nutr Food Res 66 (23) e2200145 [2022-12-00; online 2022-10-26]
Clemens Wittenbecher DDLS Fellow
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Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact.
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Inorganic nanoparticles for oral drug delivery: opportunities, barriers, and future perspectives
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Alexandra Teleki SciLifeLab Fellow
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How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus.
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New Phytol. 236 (6) 2344-2357 [2022-12-00; online 2022-09-30]
Pascal Milesi SciLifeLab Fellow
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Grey matter morphology in women with premenstrual dysphoric disorder treated with a selective progesterone receptor modulator.
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Eur Neuropsychopharmacol 65 (-) 35-43 [2022-12-00; online 2022-11-04]
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Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases.
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Five commercially-available antibodies react differentially with allelic forms of human HLA-DR beta chain.
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Current challenges in understanding the role of enhancers in disease.
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A microfluidic-based approach to investigate the inflammatory response of macrophages to pristine and drug-loaded nanostructured hydroxyapatite.
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The Olfactomedin-4-Defined Human Neutrophil Subsets Differ in Proteomic Profile in Healthy Individuals and Patients with Septic Shock.
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Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle.
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DDLS Fellow Laura Carroll
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Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells.
Mathew NR, Jayanthan JK, Smirnov IV, ..., Bemark M, Angeletti D
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Overexpressed c-Myc Sensitizes Cells to TH1579, a Mitotic Arrest and Oxidative DNA Damage Inducer.
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Magnetic Bead Based Proximity Extension Assay for Sensitive Protein and Extracellular Vesicles Detection
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Predicting Gastrointestinal Absorption of Prodrugs and their Drugs with the ANDROMEDA by Prosilico Software
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Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale
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MicroRNAs are deeply linked to the emergence of the complex octopus brain.
Zolotarov G, Fromm B, Legnini I, ..., Peterson KJ, Rajewsky N
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Identification of a Small Molecule Inhibitor of Hyaluronan Synthesis, DDIT, Targeting Breast Cancer Cells.
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Gasdermin D is the only Gasdermin that provides non-redundant protection against acute Salmonella gut infection
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Editorial: Application of systems biology in molecular characterization and diagnosis of cancer, Volume II.
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Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue
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Proof-of-principle studies on a strategy to enhance nucleotide imbalance specifically in cancer cells.
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Multiplexed selectivity screening of anti-GPCR antibodies
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Finding Haplotypic Signatures in Proteins
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Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases.
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Caja L, Lonardo E, Sancho P
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Breast cancer spheroids can model phenotypic heterogeneity of cancer cells to evaluate targeted therapies.
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A Novel Machine Learning Method for Mutational Analysis to Identifying Driver Genes in Breast Cancer
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PubMed DOI Crossref
Temporal Association of Total Serum Cholesterol and Pancreatic Cancer Incidence.
Wang QL, Khil J, Hong S, ..., Kim HC, Giovannucci EL
Nutrients 14 (22) - [2022-11-21; online 2022-11-21]
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Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight.
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Toxicity of Glycyl-l-Prolyl-l-Glutamate Pseudotripeptides: Cytotoxic, Oxidative, Genotoxic, and Embryotoxic Perspectives.
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Biologic Evaluation of a Heterodimeric HER2-Albumin Targeted Affibody Molecule Produced by Chemo-Enzymatic Peptide Synthesis.
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Targeting myeloid suppressive cells revives cytotoxic anti-tumor responses in pancreatic cancer.
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Drug repositioning for immunotherapy in breast cancer using single-cell and spatial transcriptomics analysis
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Platelet-leukocyte aggregate formation and inflammation in patients with pulmonary arterial hypertension and CTEPH.
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Somatic Loss of the Y Chromosome and Alzheimer’s Disease Risk
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Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins
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CBP-HSF2 structural and functional interplay in Rubinstein-Taybi neurodevelopmental disorder.
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Anniina Vihervaara SciLifeLab Fellow
PubMed DOI Crossref
The type II TGF-β receptor phosphorylates Tyr182 in the type I receptor to activate downstream Src signaling.
Yakymovych I, Yakymovych M, Hamidi A, Landström M, Heldin CH
Sci Signal 15 (760) eabp9521 [2022-11-15; online 2022-11-15]
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The global groundwater resistome: core antibiotic resistance genes, their dynamics and drivers
Kampouris ID, Bengtsson-Palme J, Babin D, ..., Berendonk TU, Klümper U
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DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
The Marine Product Elatol Is a Novel Inhibitor of Mitochondrial Translation Triggering the Integrated Stress Response and Apoptosis in Leukemia and Lymphoma Cells
Cunningham TA, Maiti P, Manara P, ..., Barrientos A, Schatz JH
Blood 140 (Supplement 1) 7819-7819 [2022-11-15; online 2022-11-15]
PubMed DOI Crossref
Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores.
Jespersen N, Ehrenbolger K, Winiger RR, ..., Vossbrinck CR, Barandun J
Nat Commun 13 (1) 6962 [2022-11-15; online 2022-11-15]
Jonas Barandun SciLifeLab Fellow
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Nanopore sequencing enables multigenic family reconstruction despite highly frequent PCR-induced recombination
Namias A, Sahlin K, Makoundou P, ..., Belkhir K, Weill M
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Identification and Interpretation of Clinically Relevant Somatic Variants from Whole-Genome Sequencing Data
Maqbool K, Hassan Foroughi-Asl H, Ashwini Jeggari A, ..., Lohi O, Wirta V
Blood 140 (Supplement 1) 13003-13004 [2022-11-15; online 2022-11-15]
PubMed DOI Crossref
Enhanced TLR3 responsiveness in hepatitis C virus resistant women from the Irish anti-D cohort.
Sugrue JA, Posseme C, Tan Z, ..., Duffy D, O'Farrelly C
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Data-Driven Molecular Hallmarks of Acute Myeloid Leukemia: Biological, Prognostic and Therapeutic Implications
Erkers T, Marabita F, Struyf N, ..., Östling P, Kallioniemi O
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Comprehensive Exploration of NK Cell Education in ADCC Triggered By a Monoclonal Antibody or a Bispecific Killer Engager Molecule (BiKE)
Leijonhufvud C, Schlums H, Stikvoort A, ..., Bryceson YT, Carlsten M
Blood 140 (Supplement 1) 8350-8350 [2022-11-15; online 2022-11-15]
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Comparison of Data from Fresh and Frozen AML Samples for Functional Drug Testing
Struyf N, Arnroth C, Sunandar S, ..., Seashore-Ludlow B, Erkers T
Blood 140 (Supplement 1) 6290-6290 [2022-11-15; online 2022-11-15]
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Affibody-Based BCMA x CD16 Dual Engagers for Activation of NK Cells Towards Multiple Myeloma
Giang KA, Kanaya M, Boxaspen T, ..., Malmberg KJ, Nygren PÅ
Blood 140 (Supplement 1) 10699-10700 [2022-11-15; online 2022-11-15]
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A Comprehensive DNA Methylome Analysis of Stereotyped and Non-Stereotyped CLL Reveals an Epigenetic Signature with Strong Clinical Impact Encompassing IGHV Status, Stereotypes and IGLV3-21R110
Duran-Ferrer M, Mansouri L, Nadeu F, ..., Rosenquist R, Martín-Subero JI
Blood 140 (Supplement 1) 1800-1802 [2022-11-15; online 2022-11-15]
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STEM-19. LIVE DETECTION OF NEURAL STEM AND GLIOBLASTOMA CELLS BY A LUMINESCENT CONJUGATED OLIGOTHIOPHENE DERIVATIVE
Ilkhanizadeh S, Gracias A, Åslund AKO, ..., Nilsson KPR, Hermanson O
Neuro-oncology 24 (Supplement_7) vii35-vii35 [2022-11-14; online 2022-11-14]
PubMed DOI Crossref
Multi-foci parallelised RESOLFT nanoscopy in an extended field-of-view.
Casas Moreno X, Pennacchietti F, Minet G, ..., Barabas F, Testa I
J Microsc - (-) - [2022-11-14; online 2022-11-14]
Ilaria Testa SciLifeLab Fellow
PubMed DOI Crossref
Gating intermediates reveal inhibitory role of the voltage sensor in a cyclic nucleotide-modulated ion channel.
Gao X, Schmidpeter PAM, Berka V, ..., Jayaraman V, Nimigean CM
Nat Commun 13 (1) 6919 [2022-11-14; online 2022-11-14]
DOI Crossref
EPCO-16. ESTIMATING THE DIFFERENTIATION POTENTIAL AND PLASTICITY OF GLIOBLASTOMA CELLS USING STATISTICAL MECHANICS
Lång A, Larsson I, Jörnsten R, Nelander S
Neuro-oncology 24 (Supplement_7) vii119-vii119 [2022-11-14; online 2022-11-14]
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Validation of predicted conformal intervals for prediction of human clinical pharmacokinetics
Fagerholm U, Alvarsson J, Hellberg S, Spjuth O
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PubMed DOI Crossref
Quantitative Transcriptome Analysis of Purified Equine Mast Cells Identifies a Dominant Mucosal Mast Cell Population with Possible Inflammatory Functions in Airways of Asthmatic Horses.
Akula S, Riihimäki M, Waern I, ..., Hellman L, Wernersson S
Int J Mol Sci 23 (22) - [2022-11-12; online 2022-11-12]
PubMed DOI Crossref
Developmental disruption and restoration of brain synaptome architecture in the murine Pax6 neurodevelopmental disease model.
Tomas-Roca L, Qiu Z, Fransén E, ..., Komiyama NH, Grant SGN
Nat Commun 13 (1) 6836 [2022-11-11; online 2022-11-11]
PubMed DOI Crossref
Genomic trajectories of a near-extinction event in the Chatham Island black robin.
von Seth J, van der Valk T, Lord E, ..., Robertson BC, Dussex N
BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Super-Resolution Microscopy Opens New Doors to Life at the Nanoscale.
Fuhrmann M, Gockel N, Arizono M, ..., Testa I, Willig KI
J. Neurosci. 42 (45) 8488-8497 [2022-11-09; online 2022-11-10]
PubMed DOI Crossref
Comparative serum proteomic analysis of a selected protein panel in individuals with schizophrenia and bipolar disorder and the impact of genetic risk burden on serum proteomic profiles.
Oraki Kohshour M, Kannaiyan NR, Falk AJ, ..., Nilsson P, Schulze TG
Transl Psychiatry 12 (1) 471 [2022-11-09; online 2022-11-09]
DOI Crossref
Development of mesothelioma-specific oncolytic vaccine exploiting immunopeptidomic analysis of murine and human tumors
Chiaro J, Antignani G, Feola S, ..., Lehtiö J, Cerullo V
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PubMed DOI Crossref
Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level.
Wang F, Ding P, Liang X, ..., Lin L, Luo Y
Nat Commun 13 (1) 6748 [2022-11-08; online 2022-11-08]
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Xist ribonucleoproteins promote female sex-biased autoimmunity
Dou DR, Zhao Y, Belk JA, ..., Utz PJ, Chang HY
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Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers
King MR, Lin AZ, Ruff KM, ..., Lundberg E, Pappu RV
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PubMed DOI Crossref
The Understanding of the Potential Linkage between COVID-19, Type-2 Diabetes, and Cancer(s) Could Help in Better Drug Targets and Therapeutics.
Mobashir M
Comb Chem High Throughput Screen 25 (14) 2370-2371 [2022-11-05; online 2022-11-05]
PubMed DOI Crossref
FRET-FISH probes chromatin compaction at individual genomic loci in single cells.
Mota A, Berezicki S, Wernersson E, ..., Crosetto N, Bienko M
Nat Commun 13 (1) 6680 [2022-11-05; online 2022-11-05]
Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
Quantitative Phosphoproteomics and Acetylomics of Safranal Anticancer Effects in Triple-Negative Breast Cancer Cells.
Ashrafian S, Zarrineh M, Jensen P, ..., Ghassempour A, Larsen MR
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Lineage-specific targets of positive selection in three leaf beetles with different defence capacity against a parasitic wasp
Yang X, Wheat C, Slotte T, Hamback P
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SciLifeLab Fellow Tanja Slotte
DOI Crossref
Using evolutionary constraint to define novel candidate driver genes in medulloblastoma
Roy A, Sakthikumar S, Kozyrev SV, ..., Lindblad-Toh K, Forsberg-Nilsson K
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PubMed DOI Crossref
The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
Sjöström M, Zhao SG, Levy S, ..., Quigley DA, Feng FY
Cancer Res. 82 (21) 3888-3902 [2022-11-02; online 2022-10-18]
Arian Lundberg DDLS Fellow
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Next generation pan-cancer blood proteome profiling using proximity extension assay
Uhlen M, Álvez MB, Edfors F, ..., Pontén F, Fagerberg L
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Immunoglobulin G N-Glycosylation Signatures in Incident Type 2 Diabetes and Cardiovascular Disease.
Birukov A, Plavša B, Eichelmann F, ..., Lauc G, Wittenbecher C
Diabetes Care 45 (11) 2729-2736 [2022-11-01; online 2022-09-30]
Clemens Wittenbecher DDLS Fellow
DOI Crossref
Fungal infection drives metabolic reprogramming in epithelial cells via aerobic glycolysis and an alternative TCA cycle shunt
Pellon A, Nasab SDS, Bidkhori G, ..., Shoaie S, Moyes D
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Saeed Shoaie SciLifeLab Fellow
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Establishing mammalian GLUT kinetics and lipid preferences in a reconstituted-liposome system
Saudea A, Qureshi A, McComas S, ..., Carlsson J, Drew D
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PubMed DOI Crossref
Dynamic evolution of transient receptor potential vanilloid (TRPV) ion channel family with numerous gene duplications and losses.
Morini M, Bergqvist CA, Asturiano JF, Larhammar D, Dufour S
Front Endocrinol (Lausanne) 13 (-) 1013868 [2022-11-01; online 2022-11-01]
PubMed DOI Crossref
Targeting the DNA damage response and repair in cancer through nucleotide metabolism.
Helleday T, Rudd SG
Mol Oncol 16 (21) 3792-3810 [2022-11-00; online 2022-05-28]
PubMed DOI Crossref
Tailored Biocompatible Polyurethane-Poly(ethylene glycol) Hydrogels as a Versatile Nonfouling Biomaterial.
Speidel AT, Chivers PRA, Wood CS, ..., Olofsson PS, Stevens MM
Adv Healthc Mater 11 (21) e2201378 [2022-11-00; online 2022-08-29]
PubMed DOI Crossref
ShareLoc - an open platform for sharing localization microscopy data.
Ouyang W, Bai J, Singh MK, ..., Lelandais B, Zimmer C
Nat. Methods 19 (11) 1331-1333 [2022-11-00; online 2022-10-22]
PubMed DOI Crossref
Sex dimorphism in the tumor microenvironment - From bench to bedside and back.
He F, Furones AR, Landegren N, Fuxe J, Sarhan D
Semin. Cancer Biol. 86 (Pt 3) 166-179 [2022-11-00; online 2022-03-10]
PubMed DOI Crossref
Reply to: "Lack of hepatic autophagy promotes severity of liver injury but not steatosis": ATG7 genetic variants behave as fatty liver disease progression modifiers.
Baselli G, Romeo S, Valenti L
J Hepatol 77 (5) 1459-1461 [2022-11-00; online 2022-08-17]
PubMed DOI Crossref
Pregnancy induces pancreatic insulin secretion in women with long-standing type 1 diabetes.
Espes D, Magnusson L, Caballero-Corbalan J, ..., Casas R, Carlsson PO
BMJ Open Diabetes Res Care 10 (6) - [2022-11-00; online 2022-11-10]
Daniel Espes SciLifeLab Fellow
PubMed DOI Crossref
Pharmacological characterization of 5-iodo-A-85380, a β2-selective nicotinic receptor agonist, in mice.
Akinola LS, Bagdas D, Alkhlaif Y, ..., Papke RL, Damaj MI
J Psychopharmacol 36 (11) 1280-1293 [2022-11-00; online 2022-11-02]
PubMed DOI Crossref
NUDT1 promotes the accumulation and longevity of CD103+ TRM cells in primary biliary cholangitis.
Huang B, Lyu Z, Qian Q, ..., You Z, Ma X
J Hepatol 77 (5) 1311-1324 [2022-11-00; online 2022-06-23]
PubMed DOI Crossref
Multi-omics analysis reveals multiple mechanisms causing Prader-Willi like syndrome in a family with a X;15 translocation.
Eisfeldt J, Rezayee F, Pettersson M, ..., Grigelioniene G, Lindstrand A
Hum. Mutat. 43 (11) 1567-1575 [2022-11-00; online 2022-07-23]
PubMed DOI Crossref
Impact of type 2 diabetes on in vivo activities and protein expressions of cytochrome P450 in patients with obesity.
Kvitne KE, Åsberg A, Johnson LK, ..., Hjelmesaeth J, Robertsen I
Clin Transl Sci 15 (11) 2685-2696 [2022-11-00; online 2022-09-08]
PubMed DOI Crossref
Higher risk of severe hypoglycemia in children and adolescents with a rapid loss of C-peptide during the first 6 years after type 1 diabetes diagnosis.
Grönberg A, Espes D, Carlsson PO, Ludvigsson J
BMJ Open Diabetes Res Care 10 (6) e002991 [2022-11-00; online 2022-11-18]
Daniel Espes SciLifeLab Fellow
DOI Crossref
Functionalized silk promotes cell migration into calcium phosphate cements by providing macropores and cell adhesion motifs
Widhe M, Diez-Escudero A, Liu Y, ..., Hedhammar M, Mestres G
Ceramics International 48 (21) 31449-31460 [2022-11-00; online 2022-11-00]
PubMed DOI Crossref
Emerging concepts in drug discovery for cancer therapy.
Murga M, Fernandez-Capetillo O
Mol Oncol 16 (21) 3757-3760 [2022-11-00; online 2022-11-03]
PubMed DOI Crossref
Elucidation of the nematicidal mode of action of grammicin on Caenorhabditis elegans.
Nguyen VT, Park AR, Duraisamy K, Vo DD, Kim JC
Pestic Biochem Physiol 188 (-) 105244 [2022-11-00; online 2022-09-19]
PubMed DOI Crossref
Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets.
Covitz S, Tapera TM, Adebimpe A, ..., Cieslak M, Satterthwaite TD
NeuroImage 263 (-) 119609 [2022-11-00; online 2022-09-03]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Cryo-EM reveals the conformational epitope of human monoclonal antibody PAM1.4 broadly reacting with polymorphic malarial protein VAR2CSA.
Raghavan SSR, Dagil R, Lopez-Perez M, ..., Lavstsen T, Wang K
PLoS Pathog 18 (11) e1010924 [2022-11-00; online 2022-11-16]
PubMed DOI Crossref
Chemogenetic inhibition of MCH neurons does not alter memory performance in mice.
Mutlu-Burnaz O, Yulug B, Oncul M, ..., Hanoglu L, Velioglu HA
Biomed. Pharmacother. 155 (-) 113771 [2022-11-00; online 2022-10-01]
PubMed DOI Crossref
Chemical traits of cerebral amyloid angiopathy in familial British-, Danish-, and non-Alzheimer's dementias.
Michno W, Koutarapu S, Camacho R, ..., Lashley T, Hanrieder J
J. Neurochem. 163 (3) 233-246 [2022-11-00; online 2022-09-25]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Advances in plasma proteomics: Moving from technology to precision medicine.
Yu X, Schwenk JM, Xu P, LaBaer J
Proteomics Clin Appl 16 (6) e2200083 [2022-11-00; online 2022-11-16]
PubMed DOI Crossref
Adaptive single-KIR+NKG2C+ NK cells expanded from select superdonors show potent missing-self reactivity and efficiently control HLA-mismatched acute myeloid leukemia.
Haroun-Izquierdo A, Vincenti M, Netskar H, ..., Malmberg KJ, Sohlberg E
J Immunother Cancer 10 (11) - [2022-11-00; online 2022-11-02]
PubMed DOI Crossref
A structural biology community assessment of AlphaFold2 applications.
Akdel M, Pires DEV, Pardo EP, ..., Croll TI, Beltrao P
Nat. Struct. Mol. Biol. 29 (11) 1056-1067 [2022-11-00; online 2022-11-07]
PubMed DOI Crossref
Spatial and Quantitative Analysis of Tumor-Associated Macrophages: Intratumoral CD163-/PD-L1+ TAMs as a Marker of Favorable Clinical Outcomes in Triple-Negative Breast Cancer.
Shinohara H, Kobayashi M, Hayashi K, ..., Kitagawa M, Yamamoto K
Int J Mol Sci 23 (21) - [2022-10-31; online 2022-10-31]
DOI Crossref
Automated simulation-based membrane-protein refinement into cryo-EM data
Yvonnesdotter L, Rovšnik U, Blau C, ..., Howard RJ, Lindahl E
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PubMed DOI Crossref
Author Correction: Genome-wide association study identifies Sjögren's risk loci with functional implications in immune and glandular cells.
Khatri B, Tessneer KL, Rasmussen A, ..., Nordmark G, Lessard CJ
Nat Commun 13 (1) 6519 [2022-10-31; online 2022-10-31]
PubMed DOI Crossref
Integrating Identification and Quantification Uncertainty for Differential Protein Abundance Analysis with Triqler.
The M, Käll L
Methods in molecular biology (Clifton, N.J.) 2426 (-) 91-117 [2022-10-30; online 2022-10-30]
PubMed DOI Crossref
Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq.
Vazquez SE, Mann SA, Bodansky A, ..., Anderson MS, DeRisi JL
Elife 11 (-) - [2022-10-27; online 2022-10-27]
DOI Crossref
Genomic Changes During the Evolution of the Coxiella Genus Along the Parasitism-Mutualism Continuum
Santos-Garcia D, Morel O, Henri H, ..., Duron O, Vavre F
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DOI Crossref
Expansion Spatial Transcriptomics
Fan Y, Andrusivová Ž, Wu Y, ..., Lundeberg J, Wang B
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PubMed DOI Crossref
Crystal structure of the Na+/H+ antiporter NhaA at active pH reveals the mechanistic basis for pH sensing.
Winkelmann I, Uzdavinys P, Kenney IM, ..., Beckstein O, Drew D
Nat Commun 13 (1) 6383 [2022-10-26; online 2022-10-26]
PubMed DOI Crossref
Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) - assessing the dynamic associations between the microbiome and maternal and neonatal adverse events.
Fransson E, Gudnadottir U, Hugerth LW, ..., Brusselaers N, Engstrand L
BMJ Open 12 (10) e065825 [2022-10-26; online 2022-10-26]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators.
Zhuang Y, Noviello CM, Hibbs RE, Howard RJ, Lindahl E
Proc. Natl. Acad. Sci. U.S.A. 119 (43) e2208081119 [2022-10-25; online 2022-10-17]
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Comprehensive cell atlas of the first-trimester developing human brain
Braun E, Danan-Gotthold M, Borm LE, ..., Sundström E, Linnarsson S
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PubMed DOI Crossref
A Portable, Negative-Pressure Actuated, Dynamically Tunable Microfluidic Droplet Generator.
Trossbach M, de Lucas Sanz M, Seashore-Ludlow B, Joensson HN
Micromachines (Basel) 13 (11) - [2022-10-25; online 2022-10-25]
PubMed DOI Crossref
Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T
Curr. Biol. 32 (20) 4360-4371.e6 [2022-10-24; online 2022-09-09]
SciLifeLab Fellow Tanja Slotte
DOI Crossref
A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation
Altea-Manzano P, Doglioni G, Cuadros AM, ..., Malanchi I, Fendt SM
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PubMed DOI Crossref
Indirect 3D Bioprinting of a Robust Trilobular Hepatic Construct with Decellularized Liver Matrix Hydrogel.
Khati V, Turkki JA, Ramachandraiah H, ..., Gaudenzi G, Russom A
Bioengineering (Basel) 9 (11) - [2022-10-22; online 2022-10-22]
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WASH activation controls endosomal recycling and EGFR and Hippo signaling during tumor-suppressive cell competition.
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The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry.
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Environ Sci Eur 34 (1) 104 [2022-10-21; online 2022-10-21]
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Structure-Based Discovery of Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5.
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PD-1 expression on mouse intratumoral NK cells and its effects on NK cell phenotype.
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Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity
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Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.
Njoroge SM, Madé LF, von Mentzer A, ..., Woolhouse M, Kariuki S
Microbiol Resour Announc 11 (10) e0041622 [2022-10-20; online 2022-09-12]
Astrid von Mentzer DDLS Fellow
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Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates.
Lundborg M, Wennberg C, Lidmar J, ..., Lindahl E, Norlén L
Biophys. J. 121 (20) 3837-3849 [2022-10-18; online 2022-09-13]
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Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues.
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Influence of the extracellular domain size on the dynamic behavior of membrane proteins.
Gurdap CO, Wedemann L, Sych T, Sezgin E
Biophys. J. 121 (20) 3826-3836 [2022-10-18; online 2022-09-14]
Erdinc Sezgin SciLifeLab Fellow
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Hydrogen Peroxide Induced Toxicity Is Reversed by the Macrocyclic IRAP-Inhibitor HA08 in Primary Hippocampal Cell Cultures.
Stam F, Florén Lind S, Schroff A, ..., Larhed M, Hallberg M
Curr Issues Mol Biol 44 (10) 5000-5012 [2022-10-18; online 2022-10-18]
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Extracellular vesicles in heart failure - A study in patients with heart failure with preserved ejection fraction or heart failure with reduced ejection fraction characteristics undergoing elective coronary artery bypass grafting.
Matan D, Mobarrez F, Löfström U, ..., Persson H, Wallén H
Front Cardiovasc Med 9 (-) 952974 [2022-10-18; online 2022-10-18]
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Cholesterol's balancing act: Defying the status quo.
Doktorova M, Levental I
Biophys. J. 121 (20) 3771-3773 [2022-10-18; online 2022-08-30]
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Spatiotemporal dynamics of DNA repair proteins between the Golgi and nucleus maintain genomic stability
Galea G, Kuodyte K, Khan MM, ..., Lundberg E, Pepperkok R
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Pharmacological OGG1 inhibition decreases murine allergic airway inflammation.
Tanner L, Bergwik J, Bhongir RKV, ..., Adner M, Egesten A
Front. Pharmacol. 13 (-) 999180 [2022-10-17; online 2022-10-17]
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Partial peptide dissociation and binding groove plasticity in two major histocompatibility complex class I alleles - differences between alleles versus force field and sampling effects.
Wingbermühle S, Schäfer LV
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Entropy predicts sensitivity of pseudo-random seeds
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Cell chirality exhibition of brain microvascular endothelial cells is dependent on micropattern width.
Porras Hernández AM, Tenje M, Antfolk M
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In Vitro and In Vivo Neuroprotective Effects of Sarcosine.
Tanas A, Tozlu ÖÖ, Gezmiş T, ..., Mardinoğlu A, Türkez H
Biomed Res Int 2022 (-) 5467498 [2022-10-15; online 2022-10-15]
Adil Mardinoglu SciLifeLab Fellow
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Astrocyte 3D Culture and Bioprinting using Peptide Functionalized Hyaluronan Hydrogels
Matthiesen I, Jury M, Boroojeni FR, ..., Aili D, Herland A
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hCoCena: horizontal integration and analysis of transcriptomics datasets.
Oestreich M, Holsten L, Agrawal S, ..., Becker M, Ulas T
Bioinformatics 38 (20) 4727-4734 [2022-10-14; online 2022-08-27]
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Routine omics collection is a golden opportunity for European human research in space and analog environments.
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Far Red-Shifted CdTe Quantum Dots for Multicolour Stimulated Emission Depletion Nanoscopy.
Alvelid J, Bucci A, Testa I
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Ilaria Testa SciLifeLab Fellow
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Is brightfield all you need for mechanism of action prediction?
Gupta A, Harrison PJ, Wieslander H, ..., Spjuth O, Sintorn IM
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Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo-endometrium interplay.
Koel M, Krjutškov K, Saare M, ..., Salumets A, Altmäe S
Hum Reprod Open 2022 (4) hoac043 [2022-10-13; online 2022-10-13]
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Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.
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Scalable Constant pH Molecular Dynamics in GROMACS.
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An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.
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A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens
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The heat shock protein LarA activates the Lon protease at the onset of proteotoxic stress
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The Performance of FDA-Approved PET Imaging Agents in the Detection of Prostate Cancer.
Li M, Zelchan R, Orlova A
Biomedicines 10 (10) - [2022-10-10; online 2022-10-10]
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Molecular tools to monitor health and disease - and lucky coincidences.
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Extending fluorescence anisotropy to large complexes using reversibly switchable proteins.
Volpato A, Ollech D, Alvelid J, ..., Ingaramo M, Testa I
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Ilaria Testa SciLifeLab Fellow
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Metabolic Assessment of Human Induced Pluripotent Stem Cells-Derived Astrocytes and Fetal Primary Astrocytes: Lactate and Glucose Turnover.
Matthiesen I, Nasiri R, Tamashiro Orrego A, Winkler TE, Herland A
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Single-cell analysis of myeloid cells in HPV + tonsillar cancer
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Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt.
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Correlative Chemical Imaging Identifies Amyloid Peptide Signatures of Neuritic Plaques and Dystrophy in Human Sporadic Alzheimer's Disease.
Koutarapu S, Ge J, Jha D, ..., Michno W, Hanrieder J
Brain Connect - (-) - [2022-10-07; online 2022-10-07]
SciLifeLab Fellow Wojciech Michno
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Addressing the Protease Bias in Quantitative Proteomics.
Woessmann J, Kotol D, Hober A, Uhlén M, Edfors F
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ANDROMEDA by Prosilico Software Successfully Predicts Human Clinical Pharmacokinetics of 300 Drugs Out of Reach for In Vitro Methods
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A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
Gross SM, Dane MA, Smith RL, ..., Gray JW, Heiser LM
Commun Biol 5 (1) 1066 [2022-10-07; online 2022-10-07]
Cemal Erdem DDLS Fellow
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aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
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Three-dimensional genome re-wiring in loci with Human Accelerated Regions
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High-throughput cell spheroid production and assembly analysis by microfluidics and deep learning
Trossbach M, Åkerlund E, Langer K, Seashore-Ludlow B, Joensson HN
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Neglected, yet significant role of FOXP1 in T-cell quiescence, differentiation and exhaustion.
Kaminskiy Y, Kuznetsova V, Kudriaeva A, Zmievskaya E, Bulatov E
Front Immunol 13 (-) 971045 [2022-10-04; online 2022-10-04]
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Molecular programming modulates hepatic lipid metabolism and adult metabolic risk in the offspring of obese mothers in a sex-specific manner.
Savva C, Helguero LA, González-Granillo M, ..., Kutter C, Korach-André M
Commun Biol 5 (1) 1057 [2022-10-04; online 2022-10-04]
Claudia Kutter SciLifeLab Fellow
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Evolution of the ancestral mammalian karyotype and syntenic regions.
Damas J, Corbo M, Kim J, ..., Zoonomia Consortium , Lewin HA
Proc. Natl. Acad. Sci. U.S.A. 119 (40) e2209139119 [2022-10-04; online 2022-09-26]
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More than mcr : Canonical Plasmid- and Transposon-Encoded Mobilized Colistin Resistance ( mcr ) Genes Represent a Subset of Phosphoethanolamine Transferases
Gaballa A, Wiedmann M, Carroll LM
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Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity
Jurdzinski KT, Mehrshad M, Delgado LF, ..., Bertilsson S, Andersson AF
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Knowledge of the perturbation design is essential for accurate gene regulatory network inference.
Seçilmiş D, Hillerton T, Tjärnberg A, ..., Nordling TEM, Sonnhammer ELL
Sci Rep 12 (1) 16531 [2022-10-03; online 2022-10-03]
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A regression discontinuity analysis of the social distancing recommendations for older adults in Sweden during COVID-19.
Bonander C, Stranges D, Gustavsson J, ..., Björk J, COVID Symptom Study Sweden
Eur J Public Health 32 (5) 799-806 [2022-10-03; online 2022-08-14]
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p73 is required for vessel integrity controlling endothelial junctional dynamics through Angiomotin.
Maeso-Alonso L, Alonso-Olivares H, Martínez-García N, ..., Marques MM, Marin MC
Cell. Mol. Life Sci. 79 (10) 535 [2022-10-01; online 2022-10-01]
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Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium.
Mehregan A, Pérez-Conesa S, Zhuang Y, ..., Ulens C, Delemotte L
Biochim Biophys Acta Biomembr 1864 (10) 183994 [2022-10-01; online 2022-06-18]
Lucie Delemotte SciLifeLab Fellow
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Noncoding RNAs and RNA-binding proteins: emerging governors of liver physiology and metabolic diseases.
Sommerauer C, Kutter C
Am. J. Physiol., Cell Physiol. 323 (4) C1003-C1017 [2022-10-01; online 2022-08-15]
Claudia Kutter SciLifeLab Fellow
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Data-driven analysis of a validated risk score for ovarian cancer identifies clinically distinct patterns during follow-up and treatment.
Enroth S, Ivansson E, Lindberg JH, ..., Sundfeldt K, Gyllensten U
Commun Med (Lond) 2 (-) 124 [2022-10-01; online 2022-10-01]
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Asymmetry of wetting and de-wetting on high-friction surfaces originates from the same molecular physics
Pellegrino M, Hess B
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Unravelling the Phylogeny of a Common Intestinal Protist: Intrageneric Diversity of Endolimax.
Hocke EF, Jamy M, Burki F, Clark CG, Stensvold CR
Protist 173 (5) 125908 [2022-10-00; online 2022-09-07]
Fabien Burki SciLifeLab Fellow
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The mGlu5 Receptor Protomer-Mediated Dopamine D2 Receptor Trans-Inhibition Is Dependent on the Adenosine A2A Receptor Protomer: Implications for Parkinson's Disease.
Romero-Fernandez W, Taura JJ, Crans RAJ, ..., Fuxe K, Borroto-Escuela DO
Mol. Neurobiol. 59 (10) 5955-5969 [2022-10-00; online 2022-07-12]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
The era of 3D and spatial genomics.
Bouwman BAM, Crosetto N, Bienko M
Trends in Genetics 38 (10) 1062-1075 [2022-10-00; online 2022-06-06]
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The dynamic interplay of PIP2 and ATP in the regulation of the KATP channel.
Pipatpolkai T, Usher SG, Vedovato N, Ashcroft FM, Stansfeld PJ
J. Physiol. (Lond.) 600 (20) 4503-4519 [2022-10-00; online 2022-09-23]
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Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells.
Geng K, Merino LG, Wedemann L, ..., White RJ, Kutter C
Genome Res 32 (10) 1876-1891 [2022-10-00; online 2022-09-30]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Spatiotemporally controlled generation of NTPs for single-molecule studies.
Sabantsev A, Mao G, Aguirre Rivera J, ..., Khodorkovskiy M, Deindl S
Nat. Chem. Biol. 18 (10) 1144-1151 [2022-10-00; online 2022-09-21]
SciLifeLab Fellow Sebastian Deindl
PubMed DOI Crossref
Spatiotemporal characterization of cellular tau pathology in the human locus coeruleus-pericoerulear complex by three-dimensional imaging.
Gilvesy A, Husen E, Magloczky Z, ..., Kovacs GG, Adori C
Acta Neuropathol. 144 (4) 651-676 [2022-10-00; online 2022-08-30]
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Pro-oxidative priming but maintained cardiac function in a broad spectrum of murine models of chronic kidney disease.
Wollenhaupt J, Frisch J, Harlacher E, ..., Prates Roma L, Noels H
Redox Biol 56 (-) 102459 [2022-10-00; online 2022-08-30]
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Plasma RNA profiling unveils transcriptional signatures associated with resistance to osimertinib in EGFR T790M positive non-small cell lung cancer patients.
Alexeyenko A, Brustugun OT, Eide IJZ, ..., Hydbring P, Ekman S
Transl Lung Cancer Res 11 (10) 2064-2078 [2022-10-00; online 2022-11-18]
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P045: Plasma proteome profiling of cardiotoxicity in patients with Hodgkin lymphoma
Ulfstedt JM, Freyhult E, Christersson C, ..., Enblad G, Molin D
Hemasphere 6 (-) 20-21 [2022-10-00; online 2022-10-03]
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Oral Contraceptives, Hormone Replacement Therapy, and Stroke Risk.
Johansson T, Fowler P, Ek WE, ..., Karlsson T, Johansson Å
Stroke 53 (10) 3107-3115 [2022-10-00; online 2022-06-23]
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Obesity-associated metabolites in relation to type 2 diabetes risk: A prospective nested case-control study of the CARRS cohort.
Ali MK, Kadir MM, Gujral UP, ..., Narayan KMV, Ahmad S
Diabetes Obes Metab 24 (10) 2008-2016 [2022-10-00; online 2022-07-05]
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Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones.
Österlund N, Vosselman T, Leppert A, ..., Sahin C, Landreh M
Mol. Cell Proteomics 21 (10) 100413 [2022-10-00; online 2022-09-15]
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Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin.
Westerlund AM, Sridhar A, Dahl L, ..., Bodnar AY, Delemotte L
PLoS Comput Biol 18 (10) e1010583 [2022-10-00; online 2022-10-07]
Lucie Delemotte SciLifeLab Fellow
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Layer-by-Layer Cellulose Nanofibrils: A New Coating Strategy for Development and Characterization of Tumor Spheroids as a Model for In Vitro Anticancer Drug Screening.
Aljadi Z, Aval NA, Kumar T, ..., Pettersson T, Russom A
Macromol Biosci 22 (10) e2200137 [2022-10-00; online 2022-08-03]
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Global patterns and rates of habitat transitions across the eukaryotic tree of life.
Jamy M, Biwer C, Vaulot D, ..., Massana R, Burki F
Nat Ecol Evol 6 (10) 1458-1470 [2022-10-00; online 2022-08-04]
Fabien Burki SciLifeLab Fellow
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Event-triggered STED imaging.
Alvelid J, Damenti M, Sgattoni C, Testa I
Nat. Methods 19 (10) 1268-1275 [2022-10-00; online 2022-09-08]
Ilaria Testa SciLifeLab Fellow
PubMed DOI Crossref
Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic.
Rasmussen PU, Abrego N, Roslin T, ..., Hugerth LW, Tack AJM
New Phytol. 236 (2) 671-683 [2022-10-00; online 2022-07-15]
DDLS Fellow Luisa Hugerth
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Decoding the Human Genetic and Immunological Basis of COVID-19 mRNA Vaccine-Induced Myocarditis.
Bolze A, Mogensen TH, Zhang SY, ..., Casanova JL, Hsieh EWY
J Clin Immunol 42 (7) 1354-1359 [2022-10-00; online 2022-10-08]
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Correction to: Vaccination against galectin-1 promotes cytotoxic T-cell infiltration in melanoma and reduces tumor burden.
Femel J, van Hooren L, Herre M, ..., Dimberg A, Olsson AK
Cancer Immunol. Immunother. 71 (10) 2581 [2022-10-00; online 2022-03-01]
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Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method.
Taheri G, Habibi M
Appl Soft Comput 128 (-) 109510 [2022-10-00; online 2022-08-17]
DDLS Fellow Golnaz Taheri
PubMed DOI Crossref
Chronic hyperinsulinemia promotes human hepatocyte senescence.
Baboota RK, Spinelli R, Erlandsson MC, ..., Kahn CR, Smith U
Mol Metab 64 (-) 101558 [2022-10-00; online 2022-07-21]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.
Le T, Winsnes CF, Axelsson U, ..., Ouyang W, Lundberg E
Nat. Methods 19 (10) 1221-1229 [2022-10-00; online 2022-09-29]
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Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex.
Naschberger A, Mosebach L, Tobiasson V, ..., Hippler M, Amunts A
Nat Plants 8 (10) 1191-1201 [2022-10-00; online 2022-10-13]
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A new machine learning method for cancer mutation analysis.
Habibi M, Taheri G
PLoS Comput Biol 18 (10) e1010332 [2022-10-00; online 2022-10-17]
DDLS Fellow Golnaz Taheri
DOI Crossref
Prediction and Classification of the Uptake and Disposition of Antidepressants and New CNS-Active Drugs in the Human Brain using the ANDROMEDA by Prosilico Software and Brainavailability-Matrix
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
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Image recovery from unknown network mechanisms for DNA sequencing-based microscopy
Bonet DF, Hoffecker IT
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Transplantation of maternal intestinal flora to the newborn after elective cesarean section (SECFLOR): study protocol for a double blinded randomized controlled trial.
Carpén N, Brodin P, de Vos WM, ..., Andersson S, Helve O
BMC Pediatr 22 (1) 565 [2022-09-29; online 2022-09-29]
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Anti-tumor effect of berberine on chronic lymphocytic leukemia cells.
Abdollahi M, Mohammadlou M, Hemati M, ..., Sarabi MA, Kokhaei P
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A “grappling hook” interaction balances self-assembly and chaperone activity of Nucleophosmin 1
Saluri M, Leppert A, Gese GV, ..., Hällberg BM, Landreh M
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Spatial tumour gene signature discriminates neoplastic from non-neoplastic compartments in colon cancer: unravelling predictive biomarkers for relapse
Sallinger K, Gruber M, Müller CT, ..., Kroneis T, El-Heliebi A
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Single cell transcriptomics delineates the immune-cell landscape in equine lower airways and reveals upregulation of the FKBP5 gene in horses with asthma
Riihimäki M, Fegraeus K, Nordlund J, ..., Hellman L, Raine A
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance
Ren L, Duan X, Dong L, ..., Fang X, Zheng Y
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Di-n-Butyl Phthalate and Its Monoester Metabolite Impairs Steroid Hormone Biosynthesis in Human Cells: Mechanistic In Vitro Studies.
Källsten L, Pierozan P, Martin JW, Karlsson O
Cells 11 (19) - [2022-09-27; online 2022-09-27]
Oskar Karlsson SciLifeLab Fellow
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Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning
Mitrovic D, Comas SM, Alleva C, ..., Drew D, Delemotte L
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Integrative functional analysis uncovers metabolic differences between Candida species.
Begum N, Lee S, Portlock TJ, ..., Moyes DL, Shoaie S
Commun Biol 5 (1) 1013 [2022-09-26; online 2022-09-26]
Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
Host-mycobiome metabolic interactions in health and disease.
Begum N, Harzandi A, Lee S, ..., Moyes DL, Shoaie S
Gut Microbes 14 (1) 2121576 [2022-09-25; online 2022-09-25]
Saeed Shoaie SciLifeLab Fellow
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Omics and Multi-Omics Analysis for the Early Identification and Improved Outcome of Patients with Psoriatic Arthritis.
Gurke R, Bendes A, Bowes J, ..., Pennington SR, HIPPOCRATES Consortium
Biomedicines 10 (10) - [2022-09-24; online 2022-09-24]
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Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues
Shafighi SD, Geras A, Jurzysta B, ..., Lagergren J, Szczurek E
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Prediction of Biopharmaceutical Characteristics of PROTACs using the ANDROMEDA by Prosilico Software
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
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Lamin A/C impairments cause mitochondrial dysfunction by attenuating PGC1α and the NAMPT-NAD+ pathway.
Maynard S, Hall A, Galanos P, ..., Maya-Mendoza A, Bartek J
Nucleic Acids Res. 50 (17) 9948-9965 [2022-09-23; online 2022-09-14]
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An online atlas of human plasma metabolite signatures of gut microbiome composition.
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Deep learning-based tumor microenvironment segmentation is predictive of tumor mutations and patient survival in non-small-cell lung cancer.
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Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before re-expansion by whole genome duplications in vertebrates
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Epithelial cell cluster size affects force distribution in response to EGF-induced collective contractility.
Zambarda C, Pérez González C, Schoenit A, ..., Trepat X, Cavalcanti-Adam EA
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Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis
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The First Structure of Human MTHFD2L and Its Implications for the Development of Isoform-Selective Inhibitors.
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Retinol and Retinol Binding Protein 4 Levels and Cardiometabolic Disease Risk.
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Clemens Wittenbecher DDLS Fellow
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Inducible CRISPR/Cas9 Allows for Multiplexed and Rapidly Segregated Single-Target Genome Editing in Synechocystis Sp. PCC 6803.
Cengic I, Cañadas IC, Minton NP, Hudson EP
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Design, structure and plasma binding of ancestral β-CoV scaffold antigens
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Building the Space Omics Topical Team to boost European space researchers' role in the international consortia redefining spaceflight-generated datasets.
Herranz R, da Silveira W, Bezdan D, Giacomello S, Szewczyk N
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Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes
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Therapeutic potential of the Proprotein Convertase Subtilisin/Kexin family in vascular disease.
Suur BE, Chemaly M, Lindquist Liljeqvist M, ..., Nyberg M, Matic L
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Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
Mirzazadeh R, Andrusivova Z, Larsson L, ..., Boeckxstaens G, Lundeberg J
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Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe
Mattila T, Svensson E, Juras A, ..., Malmström H, Jakobsson M
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Cryo-EM structure and rRNA modification sites of a plant ribosome.
Cottilli P, Itoh Y, Nobe Y, ..., Taoka M, Amunts A
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Characterization of the T cell receptor repertoire and melanoma tumor microenvironment upon combined treatment with ipilimumab and hTERT vaccination.
Ellingsen EB, Bounova G, Kerzeli I, ..., Hovig E, Gaudernack G
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Single-cell transcriptomics of resected human traumatic brain injury tissues reveals acute activation of endogenous retroviruses in oligodendroglia
Garza R, Sharma Y, Atacho D, ..., Jakobsson J, Marklund N
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Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases.
Lentini A, Pereira A, Winqvist O, Reinius B
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Antonio Lentini DDLS Fellow
DOI Crossref
Image-based &amp; machine learning-guided multiplexed serology test for SARS-CoV-2
Pietiäinen V, Polso M, Migh E, ..., Horvath P, Hepojoki J
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Editorial: Systems biology approach for the mechanisms underlying chronic liver disease.
Liu Z, Zhu Y, Zhang C, Lee S
Front Med (Lausanne) 9 (-) 989976 [2022-09-09; online 2022-09-09]
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CtIP-dependent nascent RNA expression flanking DNA breaks guides the choice of DNA repair pathway.
Gómez-Cabello D, Pappas G, Aguilar-Morante D, Dinant C, Bartek J
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TET2-mutant clonal hematopoiesis and risk of gout.
Agrawal M, Niroula A, Cunin P, ..., Rao DA, Ebert BL
Blood 140 (10) 1094-1103 [2022-09-08; online 2022-06-18]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
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Sheffield NC, Bonazzi VR, Bourne PE, ..., Spjuth O, Yates AD
Sci Data 9 (1) 553 [2022-09-08; online 2022-09-08]
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Assessment of the neuroprotective potential of d-cycloserine and l-serine in aluminum chloride-induced experimental models of Alzheimer's disease: In vivo and in vitro studies.
Tozlu ÖÖ, Türkez H, Okkay U, ..., Hacımüftüoğlu A, Mardinoğlu A
Front Nutr 9 (-) 981889 [2022-09-08; online 2022-09-08]
Adil Mardinoglu SciLifeLab Fellow
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van Zoest V, Varotsis G, Menzel U, ..., Martinell M, Fall T
Sci Rep 12 (1) 15176 [2022-09-07; online 2022-09-07]
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Activation of the integrated stress response is a vulnerability for multidrug-resistant FBXW7-deficient cells.
Sanchez-Burgos L, Navarro-González B, García-Martín S, ..., Al-Shahrour F, Fernandez-Capetillo O
EMBO Mol Med 14 (9) e15855 [2022-09-07; online 2022-07-21]
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Quantitative high-throughput analysis of tumor infiltrating lymphocytes in breast cancer.
Hayashi K, Nogawa D, Kobayashi M, ..., Kitagawa M, Yamamoto K
Front Oncol 12 (-) 901591 [2022-09-05; online 2022-09-05]
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The airway microbiota in siblings with primary ciliary dyskinesia: related factors and correlation with clinical characteristics
Ademhan Tural D, Kasikci M, Altay O, ..., Diker KS, Ozcelik U
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Spatially resolved transcriptomics of human and mouse fibrotic lung
Franzén L, Olsson Lindvall M, Jackson S, ..., Ståhl P, Hornberg J
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Decoding spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E
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PubMed DOI Crossref
Selective transfer of maternal antibodies in preterm and fullterm children.
Dolatshahi S, Butler AL, Pou C, ..., Brodin P, Alter G
Sci Rep 12 (1) 14937 [2022-09-02; online 2022-09-02]
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Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds.
Ji Y, Feng S, Wu L, ..., Hackett SJ, Lei F
Sci Adv 8 (35) eabo0099 [2022-09-02; online 2022-08-31]
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MAB21L4 Deficiency Drives Squamous Cell Carcinoma via Activation of RET.
Srivastava A, Tommasi C, Sessions D, ..., Lopez-Pajares V, Lee CS
Cancer Res. 82 (17) 3143-3157 [2022-09-02; online 2022-06-16]
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Arginine catabolism metabolites and atrial fibrillation or heart failure risk: 2 case-control studies within the Prevención con Dieta Mediterránea (PREDIMED) trial.
Goni L, Razquin C, Toledo E, ..., Martínez-González MA, Ruiz-Canela M
Am. J. Clin. Nutr. 116 (3) 653-662 [2022-09-02; online 2022-05-17]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Viral infection-related gene upregulation in monocytes in children with signs of β-cell autoimmunity.
Valta M, Yoshihara M, Einarsdottir E, ..., Kere J, Lempainen J
Pediatr Diabetes 23 (6) 703-713 [2022-09-00; online 2022-04-25]
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Thermodynamic limitations of PHB production from formate and fructose in Cupriavidus necator.
Janasch M, Crang N, Asplund-Samuelsson J, ..., Jahn M, Hudson EP
Metab. Eng. 73 (-) 256-269 [2022-09-00; online 2022-08-18]
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The Impact of Reference Data Selection for the Prediction Accuracy of Intrinsic Hepatic Metabolic Clearance.
Fagerholm U, Spjuth O, Hellberg S
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Testing for association with rare variants in the coding and non-coding genome: RAVA-FIRST, a new approach based on CADD deleteriousness score.
Bocher O, Ludwig TE, Oglobinsky MS, ..., Perdry H, Génin E
PLoS Genet 18 (9) e1009923 [2022-09-00; online 2022-09-16]
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Short- and long-term effects of body weight, calorie restriction and gastric bypass on CYP1A2, CYP2C19 and CYP2C9 activity.
Kvitne KE, Krogstad V, Wegler C, ..., Christensen H, Robertsen I
Br J Clin Pharmacol 88 (9) 4121-4133 [2022-09-00; online 2022-04-25]
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Rare ATG7 genetic variants predispose patients to severe fatty liver disease.
Baselli GA, Jamialahmadi O, Pelusi S, ..., Valenti LV, EPIDEMIC Study Investigators
J Hepatol 77 (3) 596-606 [2022-09-00; online 2022-04-09]
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Randomized Versus Real-World Evidence on the Efficacy and Toxicity of Checkpoint Inhibitors in Cancer in Patients with Advanced Non-small Cell Lung Cancer or Melanoma: A Meta-analysis.
Digkas E, Tabiim AJ, Smith D, Valachis A
Target Oncol 17 (5) 507-515 [2022-09-00; online 2022-08-01]
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P16-11 In search of sensitive safety biomarkers of peripheral neurotoxicity in the rat: a collaborative effort across industry and academia (IMI NeuroDeRisk project)
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Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data.
Weiss MS, Wollenhaupt J, Correy GJ, ..., Thunissen M, Pearce NM
Protein Sci. 31 (9) e4391 [2022-09-00; online 2022-08-31]
DDLS Fellow Nicholas Pearce
DOI Crossref
New insights into a dimeric PSI structure, a high resolution model of PSI:plastocyanin complex and PSI dependent hydrogen production
Hippler M, Mosebach L, Ho TTH, ..., Nachberger A, Amunts A
Biochim Biophys Acta Bioenerg 1863 (-) 148829 [2022-09-00; online 2022-09-00]
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Myxovirus resistance protein A for discriminating between viral and bacterial lower respiratory tract infections in children - The TREND study.
Rhedin S, Eklundh A, Ryd-Rinder M, ..., Naucler P, Alfvén T
Clin. Microbiol. Infect. 28 (9) 1251-1257 [2022-09-00; online 2022-05-18]
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Mitochondrial ATP synthase of trypanosomes reveals the mechanism of oligomerization and its evolution
Gahura O, Mühleip A, Hierro-Yap C, ..., Zíková A, Amunts A
Biochim Biophys Acta Bioenerg 1863 (-) 148628 [2022-09-00; online 2022-09-00]
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Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery.
Wikström T, Abrahamsson S, Bengtsson-Palme J, ..., Valentin L, Hagberg H
Clin Transl Med 12 (9) e1023 [2022-09-00; online 2022-09-15]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Mendelian nightmares: the germline-restricted chromosome of songbirds.
Borodin P, Chen A, Forstmeier W, ..., Vontzou N, Suh A
Chromosome Res. 30 (2-3) 255-272 [2022-09-00; online 2022-04-13]
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Mast cell chymase has a negative impact on human osteoblasts.
Lind T, Melo FR, Gustafson AM, ..., Melhus H, Pejler G
Matrix Biol. 112 (-) 1-19 [2022-09-00; online 2022-07-29]
PubMed DOI Crossref
MNK2 deficiency potentiates β-cell regeneration via translational regulation.
Karampelias C, Watt K, Mattsson CL, ..., Larsson O, Andersson O
Nat. Chem. Biol. 18 (9) 942-953 [2022-09-00; online 2022-06-13]
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Laboratory Misidentifications Resulting from Taxonomic Changes to Bacillus cereus Group Species, 2018-2022.
Carroll LM, Matle I, Kovac J, Cheng RA, Wiedmann M
Emerg Infect Dis 28 (9) 1877-1881 [2022-09-00; online 2022-08-24]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
In Silico Predictions of the Gastrointestinal Uptake of Macrocycles in Man Using Conformal Prediction Methodology.
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
J Pharm Sci 111 (9) 2614-2619 [2022-09-00; online 2022-05-20]
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I11 High throughput screening reveal drugs to rescue polyQ induced toxicity in Huntington’s disease cell and animal models
Li X, Häggblad M, Bräutigam L, ..., Hühn D, Fernandez-Capetillo O
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PubMed DOI Crossref
Hit-and-run: a Swedish nationwide cohort study of serious transport accidents and convictions due to traffic offenses in obsessive-compulsive disorder.
Mataix-Cols D, Fernández de la Cruz L, Brander G, ..., Lichtenstein P, Sidorchuk A
Soc Psychiatry Psychiatr Epidemiol 57 (9) 1817-1827 [2022-09-00; online 2021-11-15]
PubMed DOI Crossref
Gaseous air pollutants and DNA methylation in a methylome-wide association study of an ethnically and environmentally diverse population of U.S. adults.
Holliday KM, Gondalia R, Baldassari A, ..., Baccarelli AA, Whitsel EA
Environ. Res. 212 (Pt C) 113360 [2022-09-00; online 2022-04-30]
PubMed DOI Crossref
Enhanced cytotoxicity of a novel family of ATPase inhibitors in colorectal cancer cells with high NAT2 activity.
Zhang X, Akcan E, Correia M, ..., Globisch D, Sjöblom T
Biochem. Pharmacol. 203 (-) 115184 [2022-09-00; online 2022-07-22]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Early divergence of translation initiation and elongation factors.
Fer E, McGrath KM, Guy L, Hockenberry AJ, Kaçar B
Protein Sci. 31 (9) e4393 [2022-09-00; online 2022-10-18]
PubMed DOI Crossref
Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties.
Ragaller F, Andronico L, Sykora J, ..., Vattulainen I, Sezgin E
Open Biol 12 (9) 220175 [2022-09-00; online 2022-09-14]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning.
Zhang C, Shi M, Kim W, ..., Boren J, Mardinoglu A
EBioMedicine 83 (-) 104214 [2022-09-00; online 2022-08-18]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Advances in spatial mass spectrometry enable in-depth neuropharmacodynamics.
Baijnath S, Kaya I, Nilsson A, Shariatgorji R, Andrén PE
Trends Pharmacol. Sci. 43 (9) 740-753 [2022-09-00; online 2022-07-05]
DOI Crossref
223P Gene expression profiles in endocrine-resistant breast cancer
Schagerholm C, Robertson S, Sifakis EG, ..., Williams C, Hartman J
Ann Oncol 33 (-) S640 [2022-09-00; online 2022-09-00]
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1711P Spatial transcriptomics reveals substantial heterogeneity in TNBC tumor and stroma compartments with potential clinical implications
Wang X, Venet D, Lifrange F, ..., Rothé F, Sotiriou C
Ann Oncol 33 (-) S1321-S1322 [2022-09-00; online 2022-09-00]
DOI Crossref
1668P Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction
Chen X, Sifakis EG, Robertson S, ..., Ma R, Hartman J
Ann Oncol 33 (-) S1306 [2022-09-00; online 2022-09-00]
PubMed DOI Crossref
Characterization of Selective and Potent JAK1 Inhibitors Intended for the Inhaled Treatment of Asthma.
Nilsson M, Rhedin M, Hendrickx R, ..., Birrell M, Borde A
Drug Des Devel Ther 16 (-) 2901-2917 [2022-08-31; online 2022-08-31]
PubMed DOI Crossref
Analysis of Growth Phases of Enterotoxigenic Escherichia coli Reveals a Distinct Transition Phase before Entry into Early Stationary Phase with Shifts in Tryptophan, Fucose, and Putrescine Metabolism and Degradation of Neurotransmitter Precursors.
Joffré E, Xiao X, Correia MSP, ..., Zhu B, Sjöling Å
Microbiol Spectr 10 (4) e0175521 [2022-08-31; online 2022-07-25]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Metastatic triple negative breast cancer adapts its metabolism to destination tissues while retaining key metabolic signatures.
Roshanzamir F, Robinson JL, Cook D, Karimi-Jafari MH, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 119 (35) e2205456119 [2022-08-30; online 2022-08-22]
PubMed DOI Crossref
Cotranslational folding and assembly of the dimeric Escherichia coli inner membrane protein EmrE.
Mermans D, Nicolaus F, Fleisch K, von Heijne G
Proc. Natl. Acad. Sci. U.S.A. 119 (35) e2205810119 [2022-08-30; online 2022-08-22]
PubMed DOI Crossref
RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases.
Magnusson R, Rundquist O, Kim MJ, ..., Kim MS, Gustafsson M
Front Mol Biosci 9 (-) 916128 [2022-08-29; online 2022-08-29]
PubMed DOI Crossref
Integrative genomic and transcriptomic analyses illuminate the ontology of HER2-low breast carcinomas.
Berrino E, Annaratone L, Bellomo SE, ..., Sapino A, Marchiò C
Genome Med 14 (1) 98 [2022-08-29; online 2022-08-29]
DOI Crossref
Eurasian back-migrations into Northeast Africa was a complex and multifaceted process
Hammarén R, Goldstein ST, Schlebusch CM
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DOI Crossref
Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma
Ruiz-Moreno C, Salas SM, Samuelsson E, ..., Nilsson M, Stunnenberg HG
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PubMed DOI Crossref
TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation.
Stolz P, Mantero AS, Tvardovskiy A, ..., Elsässer SJ, Bultmann S
Nucleic Acids Res. 50 (15) 8491-8511 [2022-08-26; online 2022-07-30]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
Amselem E, Broadwater B, Havermark T, Johansson M, Elf J
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Quantitative bile and serum proteomics for the screening and differential diagnosis of primary sclerosing cholangitis.
Holm M, Joenväärä S, Saraswat M, ..., Renkonen R, Färkkilä M
PLoS ONE 17 (8) e0272810 [2022-08-25; online 2022-08-25]
PubMed DOI Crossref
An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry.
Koelmel JP, Xie H, Price EJ, ..., Martin JW, Godri Pollitt KJ
Exposome 2 (1) osac007 [2022-08-25; online 2022-08-25]
PubMed DOI Crossref
Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates.
Zadeh CO, Huggins JR, Sarmah D, ..., Erdem C, Birtwistle MR
ACS Omega 7 (33) 28912-28923 [2022-08-23; online 2022-08-11]
Cemal Erdem DDLS Fellow
PubMed DOI Crossref
Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection.
Seal S, Carreras-Puigvert J, Trapotsi MA, ..., Spjuth O, Bender A
Commun Biol 5 (1) 858 [2022-08-23; online 2022-08-23]
DOI Crossref
Overexpressed C-Myc Sensitize Cells to TH1579, an Mitotic Arrest and Oxidative DNA Damage Inducer
Henriksson S, Calderón-Montaño JM, Solvie D, Warpman Berglund U, Helleday T
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PubMed DOI Crossref
Reclassifying tumour cell cycle activity in terms of its tissue of origin.
Lundberg A, Yi JJJ, Lindström LS, Tobin NP
NPJ Precis Oncol 6 (1) 59 [2022-08-20; online 2022-08-20]
Arian Lundberg DDLS Fellow
PubMed DOI Crossref
Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
DDLS Fellow Tom van der Valk
DOI Crossref
Using the ANDROMEDA by Prosilico Software for Prediction of the Human Pharmacokinetics of 4 Compounds of Natural Origin - Colistin, Curucumin, UCN-01 and Voclosporin
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
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PubMed DOI Crossref
The origin and evolution of open habitats in North America inferred by Bayesian deep learning models.
Andermann T, Strömberg CAE, Antonelli A, Silvestro D
Nat Commun 13 (1) 4833 [2022-08-17; online 2022-08-17]
DDLS Fellow Tobias Andermann
DOI Crossref
Probe set selection for targeted spatial transcriptomics
Kuemmerle LB, Luecken MD, Firsova AB, ..., Samakovlis C, Theis FJ
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PubMed DOI Crossref
Multiomics characterization implicates PTK7 in ovarian cancer EMT and cell plasticity and offers strategies for therapeutic intervention.
Raivola J, Dini A, Karvonen H, ..., Murumägi A, Ungureanu D
Cell Death Dis 13 (8) 714 [2022-08-17; online 2022-08-17]
PubMed DOI Crossref
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.
Ambikan AT, Yang H, Krishnan S, ..., Benfeitas R, Neogi U
Cell Syst 13 (8) 665-681.e4 [2022-08-17; online 2022-07-08]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Zeitotox: Toxicology and the Rhythms of Life.
Xiao L, Antczak P, Rüegg J, Behrendt L
Environ. Sci. Technol. 56 (16) 11100-11102 [2022-08-16; online 2022-07-27]
Lars Behrendt SciLifeLab Fellow
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The neuropeptide landscape of human prefrontal cortex.
Zhong W, Barde S, Mitsios N, ..., Mulder J, Hökfelt T
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Unexpected short- and long-term effects of chronic adolescent HU-210 exposure on emotional behavior.
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The Acid Ceramidase Is a SARS-CoV-2 Host Factor.
Geiger N, Kersting L, Schlegel J, ..., Seibel J, Bodem J
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Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.
Broman E, Izabel-Shen D, Rodríguez-Gijón A, ..., Garcia SL, Nascimento FJA
Microbiome 10 (1) 126 [2022-08-15; online 2022-08-15]
Sarahi Garcia SciLifeLab Fellow
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Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models Using Similarity to Training Data
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The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes.
Porcellato E, González-Sánchez JC, Ahlmann-Eltze C, ..., Wieland FT, Metzendorf C
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agoTRIBE detects miRNA-target interactions transcriptome-wide in single cells
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PTEN inhibits AMPK to control collective migration.
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nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.
Dang CC, Minh BQ, McShea H, ..., Vinh LS, Lanfear R
Syst. Biol. 71 (5) 1110-1123 [2022-08-10; online 2022-02-10]
DDLS Fellow Jennifer James
PubMed DOI Crossref
Local molecular and global connectomic contributions to cross-disorder cortical abnormalities.
Hansen JY, Shafiei G, Vogel JW, ..., Dagher A, Misic B
Nat Commun 13 (1) 4682 [2022-08-10; online 2022-08-10]
DDLS Fellow Jacob W Vogel
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Functional Characterization of Genetic Variant Effects on Expression.
Flynn ED, Lappalainen T
Annu Rev Biomed Data Sci 5 (-) 119-139 [2022-08-10; online 2022-04-28]
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Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition.
Sandalova T, Sala BM, Achour A
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Cotranslational folding of human growth hormone in vitro and in Escherichia coli
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A Universal Language for Finding Mass Spectrometry Data Patterns
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Daniel Globisch SciLifeLab Fellow
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Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities.
Zhu S, Sridhar A, Teng J, ..., Lindahl E, Hibbs RE
Nat Commun 13 (1) 4582 [2022-08-06; online 2022-08-06]
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Bacterial type I signal peptidase inhibitors - Optimized hits from nature.
Szałaj N, Benediktsdottir A, Rusin D, ..., Mowbray SL, Więckowska A
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Ameliorative Effects by Hexagonal Boron Nitride Nanoparticles against Beta Amyloid Induced Neurotoxicity.
Aydin N, Turkez H, Tozlu OO, ..., Di Stefano A, Mardinoglu A
Nanomaterials (Basel) 12 (15) - [2022-08-05; online 2022-08-05]
Adil Mardinoglu SciLifeLab Fellow
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Adult Exposure to Di-N-Butyl Phthalate (DBP) Induces Persistent Effects on Testicular Cell Markers and Testosterone Biosynthesis in Mice.
Källsten L, Almamoun R, Pierozan P, ..., Martin JW, Karlsson O
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Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Recombination of repeat elements generates somatic complexity in human genomes.
Pascarella G, Hon CC, Hashimoto K, ..., Frith M, Carninci P
Cell 185 (16) 3025-3040.e6 [2022-08-04; online 2022-07-25]
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Genome-wide single cell annotation of the human protein-coding genes
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Editorial: Glycoconjugates in vaccines and immunotherapeutics.
Shivatare S, Sanjiv K, Kikkeri R, Adamo R
Front Immunol 13 (-) 941474 [2022-08-04; online 2022-08-04]
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Correction: Mutant p53-reactivating compound APR-246 synergizes with asparaginase in inducing growth suppression in acute lymphoblastic leukemia cells.
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Cell Death Dis 13 (8) 672 [2022-08-03; online 2022-08-03]
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The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and Worldwide Collaboration on Suspect Screening in High Resolution Mass Spectrometry
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Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects.
Rietdijk J, Aggarwal T, Georgieva P, ..., Carreras-Puigvert J, Spjuth O
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Investigating the Effect of Estradiol Levels on the Risk of Breast, Endometrial, and Ovarian Cancer.
Johansson Å, Schmitz D, Höglund J, ..., Karlsson T, Ek WE
J Endocr Soc 6 (8) bvac100 [2022-08-01; online 2022-06-29]
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Integrated cooling system for microfluidic PDMS devices used in biological microscopy studies
Khaji Z, Tenje M
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A novel CD34-specific T-cell engager efficiently depletes acute myeloid leukemia and leukemic stem cells in vitro and in vivo.
Arruda LCM, Stikvoort A, Lambert M, ..., Carlsten M, Uhlin M
Haematologica 107 (8) 1786-1795 [2022-08-01; online 2022-08-01]
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miR-378a regulates keratinocyte responsiveness to interleukin-17A in psoriasis.
Xia P, Pasquali L, Gao C, ..., Pivarcsi A, Sonkoly E
Br. J. Dermatol. 187 (2) 211-222 [2022-08-00; online 2022-05-25]
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What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?
Birkeland S, Slotte T, Krag Brysting A, ..., Brochmann C, Nowak MD
Mol. Ecol. 31 (16) 4271-4285 [2022-08-00; online 2022-07-15]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Vaccination against galectin-1 promotes cytotoxic T-cell infiltration in melanoma and reduces tumor burden.
Femel J, van Hooren L, Herre M, ..., Dimberg A, Olsson AK
Cancer Immunol. Immunother. 71 (8) 2029-2040 [2022-08-00; online 2022-01-11]
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Tricalbin proteins regulate plasma membrane phospholipid homeostasis.
Thomas FB, Omnus DJ, Bader JM, ..., Kono N, Stefan CJ
Life Sci. Alliance 5 (8) - [2022-08-00; online 2022-04-19]
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Transcriptome variation in human tissues revealed by long-read sequencing.
Glinos DA, Garborcauskas G, Hoffman P, ..., Lappalainen T, Cummings BB
Nature 608 (7922) 353-359 [2022-08-00; online 2022-08-03]
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The ubiquitin-ligase TRAF6 and TGFβ type I receptor form a complex with Aurora kinase B contributing to mitotic progression and cytokinesis in cancer cells.
Song J, Zhou Y, Yakymovych I, ..., Heldin CH, Landström M
EBioMedicine 82 (-) 104155 [2022-08-00; online 2022-07-16]
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The role of rare enhancer variants in bicuspid aortic valve pathology
Zhigulev A, Lång K, Pradhananga S, ..., Eriksson P, Sahlén P
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The evolutionary origin of host association in the Rickettsiales.
Schön ME, Martijn J, Vosseberg J, Köstlbacher S, Ettema TJG
Nat. Microbiol 7 (8) 1189-1199 [2022-08-00; online 2022-07-07]
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The biogenesis of β-lactamase enzymes.
Kaderabkova N, Bharathwaj M, Furniss RCD, ..., Palmer T, Mavridou DAI
Microbiology (Reading, Engl.) 168 (8) - [2022-08-00; online 2022-08-10]
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The anti-inflammatory peptide Catestatin blocks chemotaxis.
Muntjewerff EM, Parv K, Mahata SK, ..., Christoffersson G, van den Bogaart G
J Leukoc Biol 112 (2) 273-278 [2022-08-00; online 2021-12-22]
Gustaf Christoffersson SciLifeLab Fellow
PubMed DOI Crossref
Targeting the DNA repair enzymes MTH1 and OGG1 as a novel approach to treat inflammatory diseases.
Karsten S
Basic Clin. Pharmacol. Toxicol. 131 (2) 95-103 [2022-08-00; online 2022-06-24]
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Synthetic switches of OGG1 control initiation of base excision repair and offer new treatment strategies.
Benitéz-Buelga C, Helleday T, Michel M
Clin Transl Med 12 (8) e1035 [2022-08-00; online 2022-08-30]
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SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images.
Gupta A, Sabirsh A, Wahlby C, Sintorn IM
IEEE J Biomed Health Inform 26 (8) 4079-4089 [2022-08-00; online 2022-08-11]
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SARS-CoV-2 air sampling: A systematic review on the methodologies for detection and infectivity.
Silva PG, Branco PTBS, Soares RRG, Mesquita JR, Sousa SIV
Indoor Air 32 (8) e13083 [2022-08-00; online 2022-08-31]
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Recent and local diversification of Central American understorey palms
Cano Á, Stauffer FW, Andermann T, ..., Perret M, Antonelli A
Global Ecol. Biogeogr. 31 (8) 1513-1525 [2022-08-00; online 2022-05-11]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Photophysiological response of Symbiodiniaceae single cells to temperature stress.
Xiao L, Johansson S, Rughöft S, ..., Tenje M, Behrendt L
ISME J 16 (8) 2060-2064 [2022-08-00; online 2022-04-26]
Fabien Burki Lars Behrendt SciLifeLab Fellow
PubMed DOI Crossref
Phosphorylation of eIF4E in the stroma drives the production and spatial organisation of collagen type I in the mammary gland.
Preston SEJ, Bartish M, Richard VR, ..., Miller WH, Del Rincón SV
Matrix Biol. 111 (-) 264-288 [2022-08-00; online 2022-07-14]
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Nudix hydrolase 18 catalyzes the hydrolysis of active triphosphate metabolites of the antivirals remdesivir, ribavirin, and molnupiravir.
Jemth AS, Scaletti ER, Homan E, ..., Helleday T, Michel M
J Biol Chem 298 (8) 102169 [2022-08-00; online 2022-06-19]
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Mutation accumulation opposes polymorphism: supergenes and the curious case of balanced lethals.
Berdan EL, Blanckaert A, Butlin RK, ..., Slotte T, Wielstra B
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 377 (1856) 20210199 [2022-08-00; online 2022-06-13]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Key Modulators of the Stress Granule Response TIA1, TDP-43, and G3BP1 Are Altered by Polyglutamine-Expanded ATXN7.
Niss F, Piñero-Paez L, Zaidi W, Hallberg E, Ström AL
Mol. Neurobiol. 59 (8) 5236-5251 [2022-08-00; online 2022-06-10]
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Interplay between Caveolin-1 and body and tumor size affects clinical outcomes in breast cancer.
Godina C, Indira Chandran V, Barbachowska M, ..., Belting M, Jernström H
Transl Oncol 22 (-) 101464 [2022-08-00; online 2022-06-01]
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Imaging cell biology.
Andrews B, Chang JB, Collinson L, ..., Wu T', Zaritsky A
Nat. Cell Biol. 24 (8) 1180-1185 [2022-08-00; online 2022-07-28]
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Human cytomegalovirus hijacks host stress response fueling replication stress and genome instability.
Merchut-Maya JM, Bartek J, Bartkova J, ..., Maya-Mendoza A, Söderberg-Naucler C
Cell Death Differ. 29 (8) 1639-1653 [2022-08-00; online 2022-02-22]
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Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus).
Prost S, Machado AP, Zumbroich J, ..., Kotze A, Burger PA
Mol. Ecol. 31 (16) 4208-4223 [2022-08-00; online 2022-07-17]
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Five Percent Variant Allele Frequency Is a Reliable Reporting Threshold for TP53 Variants Detected by Next Generation Sequencing in Chronic Lymphocytic Leukemia in the Clinical Setting.
Pandzic T, Ladenvall C, Engvall M, ..., Ljungström V, Baliakas P
Hemasphere 6 (8) e761 [2022-08-00; online 2022-08-02]
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Diversity and determinants of recombination landscapes in flowering plants.
Brazier T, Glémin S
PLoS Genet 18 (8) e1010141 [2022-08-00; online 2022-08-30]
PubMed DOI Crossref
Correlations between 4β-hydroxycholesterol and hepatic and intestinal CYP3A4: protein expression, microsomal ex vivo activity, and in vivo activity in patients with a wide body weight range.
Eide Kvitne K, Hole K, Krogstad V, ..., Molden E, Robertsen I
European journal of clinical pharmacology 78 (8) 1289-1299 [2022-08-00; online 2022-06-01]
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Baseline characteristics of 547 new onset heart failure patients in the PREFERS heart failure study.
Linde C, Ekström M, Eriksson MJ, ..., Hage C, Stockholm County/Karolinska Institutet 4D heart failure investigators
ESC Heart Fail 9 (4) 2125-2138 [2022-08-00; online 2022-04-10]
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BMP4 and Gremlin 1 regulate hepatic cell senescence during clinical progression of NAFLD/NASH.
Baboota RK, Rawshani A, Bonnet L, ..., Blüher M, Smith U
Nat Metab 4 (8) 1007-1021 [2022-08-00; online 2022-08-22]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Autoantibodies in COVID-19 correlate with antiviral humoral responses and distinct immune signatures.
Taeschler P, Cervia C, Zurbuchen Y, ..., Probst-Müller E, Boyman O
Allergy 77 (8) 2415-2430 [2022-08-00; online 2022-04-08]
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Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
Mahdessian D, Cesnik AJ, Gnann C, ..., Sullivan DP, Lundberg E
Nature 608 (7924) E32 [2022-08-00; online 2022-08-06]
Adil Mardinoglu SciLifeLab Fellow
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Application of precision medicine in clinical routine in haematology-Challenges and opportunities.
Wästerlid T, Cavelier L, Haferlach C, ..., Fioretos T, Smedby KE
J. Intern. Med. 292 (2) 243-261 [2022-08-00; online 2022-06-04]
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Antibacterial peptide CyclomarinA creates toxicity by deregulating the Mycobacterium tuberculosis ClpC1-ClpP1P2 protease.
Taylor G, Frommherz Y, Katikaridis P, ..., Weber-Ban E, Mogk A
J Biol Chem 298 (8) 102202 [2022-08-00; online 2022-06-26]
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Strains Associated with Two 2020 Welder Anthrax Cases in the United States Belong to Separate Lineages within Bacillus cereus sensu lato.
Carroll LM, Marston CK, Kolton CB, ..., Weiner ZP, Kovac J
Pathogens 11 (8) - [2022-07-29; online 2022-07-29]
DDLS Fellow Laura Carroll
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Community-driven ELIXIR activities in single-cell omics
Czarnewski P, Mahfouz A, Calogero RA, ..., Ishaque N, Korpelainen E
F1000Res 11 (-) 869 [2022-07-29; online 2022-07-29]
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Chromatin accessibility profiling in tissue sections by spatial ATAC
Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL
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Markers of neutrophil activation and neutrophil extracellular traps in diagnosing patients with acute venous thromboembolism: A feasibility study based on two VTE cohorts.
Smith P, Rosell A, Farm M, ..., Odeberg J, Thålin C
PLoS ONE 17 (7) e0270865 [2022-07-28; online 2022-07-28]
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Boron Compounds Exhibit Protective Effects against Aluminum-Induced Neurotoxicity and Genotoxicity: In Vitro and In Vivo Study.
Turkez H, Yıldırım S, Sahin E, ..., Saruhan F, Mardinoglu A
Toxics 10 (8) - [2022-07-28; online 2022-07-28]
Adil Mardinoglu SciLifeLab Fellow
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Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.
Elofsson A, Bryant P, Pozzati G, ..., Shenoy A, Kundrotas P
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Superresolution microscopy localizes endogenous Dvl2 to Wnt signaling-responsive biomolecular condensates.
Schubert A, Voloshanenko O, Ragaller F, ..., Engel U, Boutros M
Proc. Natl. Acad. Sci. U.S.A. 119 (30) e2122476119 [2022-07-26; online 2022-07-22]
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SimVec: predicting polypharmacy side effects for new drugs.
Lukashina N, Kartysheva E, Spjuth O, Virko E, Shpilman A
J Cheminform 14 (1) 49 [2022-07-26; online 2022-07-26]
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Boron Nitride Nanoparticles Loaded with a Boron-Based Hybrid as a Promising Drug Carrier System for Alzheimer's Disease Treatment.
Yıldırım ÖÇ, Arslan ME, Öner S, ..., Mardinoglu A, Turkez H
Int J Mol Sci 23 (15) - [2022-07-26; online 2022-07-26]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Issues and recommendations for the residual approach to quantifying cognitive resilience and reserve.
Elman JA, Vogel JW, Bocancea DI, ..., Kremen WS, Alzheimer’s Disease Neuroimaging Initiative
Alzheimers Res Ther 14 (1) 102 [2022-07-25; online 2022-07-25]
DDLS Fellow Jacob W Vogel
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PD-L1 ATTAC mice reveal the potential of targeting PD-L1 expressing cells in cancer therapy
Fueyo-Marcos E, Fustero-Torre C, Lopez G, ..., Fernández-Capetillo O, Murga M
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EvoBind: in silico directed evolution of peptide binders with AlphaFold
Bryant P, Elofsson A
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Gene-Based Variant Analysis of Whole-Exome Sequencing in Relation to Eosinophil Count.
Höglund J, Hadizadeh F, Ek WE, Karlsson T, Johansson Å
Front Immunol 13 (-) 862255 [2022-07-22; online 2022-07-22]
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SnapShot: Spatial transcriptomics.
Larsson L, Bergenstråhle L, He M, Andrusivova Z, Lundeberg J
Cell 185 (15) 2840-2840.e1 [2022-07-21; online 2022-07-23]
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Multiset correlation and factor analysis enables exploration of multi-omic data
Brown BC, Wang C, Kasela S, ..., Knowles DA, Lappalainen T
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The cerebrospinal fluid proteome of preterm infants predicts neurodevelopmental outcome.
Leifsdottir K, Jost K, Siljehav V, ..., Eksborg S, Herlenius E
Front Pediatr 10 (-) 921444 [2022-07-19; online 2022-07-19]
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Stress-induced perturbations in intracellular amino acids reprogram mRNA translation in osmoadaptation independently of the ISR.
Krokowski D, Jobava R, Szkop KJ, ..., Larsson O, Hatzoglou M
Cell Reports 40 (3) 111092 [2022-07-19; online 2022-07-21]
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Spatial host-microbiome sequencing
Lötstedt B, Stražar M, Xavier R, Regev A, Vickovic S
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Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics
Saarenpää S, Shalev O, Ashkenazy H, ..., Weigel D, Giacomello S
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Robust and integrative Bayesian neural networks for likelihood-free parameter inference
Wrede F, Eriksson R, Jiang R, ..., Hellander A, Singh P
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Molecular Genetic Screening in Patients With ACE Inhibitor/Angiotensin Receptor Blocker-Induced Angioedema to Explore the Role of Hereditary Angioedema Genes.
Mathey CM, Maj C, Scheer AB, ..., Nöthen MM, Forstner AJ
Front Genet 13 (-) 914376 [2022-07-18; online 2022-07-18]
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Miniaturized and multiplexed high-content screening of drug and immune sensitivity in a multichambered microwell chip.
Sandström N, Carannante V, Olofsson K, ..., Östling P, Önfelt B
Cell Rep Methods 2 (7) 100256 [2022-07-18; online 2022-07-18]
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A broad, exposome-type evaluation of xenobiotic phase II biotransformation in human biofluids by LC-MS/MS
Fareed Y, Braun D, Flasch M, Globisch D, Warth B
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Hematopoietic loss of Y chromosome leads to cardiac fibrosis and heart failure mortality.
Sano S, Horitani K, Ogawa H, ..., Forsberg LA, Walsh K
Science (New York, N.Y.) 377 (6603) 292-297 [2022-07-15; online 2022-07-14]
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Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders.
Proffitt C, Bidkhori G, Lee S, ..., Moyes DL, Shoaie S
iScience 25 (7) 104513 [2022-07-15; online 2022-06-02]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
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Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain.
Chi G, Liang Q, Sridhar A, ..., Covarrubias M, Dürr KL
Nat Commun 13 (1) 4087 [2022-07-15; online 2022-07-15]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
2-Alkyl substituted benzimidazoles as a new class of selective AT2 receptor ligands.
Roy T, Petersen NN, Gopalan G, ..., Hallberg M, Larhed M
Bioorg. Med. Chem. 66 (-) 116804 [2022-07-15; online 2022-05-07]
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Lokatt: A hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network
Xu X, Bhalla N, Ståhl P, Jaldén J
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Galectin-9 and Interferon-Gamma Are Released by Natural Killer Cells upon Activation with Interferon-Alpha and Orchestrate the Suppression of Hepatitis C Virus Infection.
Carreca AP, Gaetani M, Busà R, ..., Conaldi PG, Badami E
Viruses 14 (7) - [2022-07-14; online 2022-07-14]
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Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference.
Seçilmiş D, Nelander S, Sonnhammer ELL
Front Genet 13 (-) 855770 [2022-07-13; online 2022-07-13]
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Neoadjuvant Chemoradiotherapy and Surgery for Esophageal Squamous Cell Carcinoma Versus Definitive Chemoradiotherapy With Salvage Surgery as Needed: The Study Protocol for the Randomized Controlled NEEDS Trial.
Nilsson M, Olafsdottir H, Alexandersson von Döbeln G, ..., de Manzoni G, Lordick F
Front Oncol 12 (-) 917961 [2022-07-13; online 2022-07-13]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Intratumoral administration of pro-inflammatory allogeneic dendritic cells improved the anti-tumor response of systemic anti-CTLA-4 treatment via unleashing a T cell-dependent response.
Jin C, Ali A, Iskantar A, ..., Karlsson-Parra A, Yu D
Oncoimmunology 11 (1) 2099642 [2022-07-13; online 2022-07-13]
PubMed DOI Crossref
3D Bioprinting of Multi-Material Decellularized Liver Matrix Hydrogel at Physiological Temperatures.
Khati V, Ramachandraiah H, Pati F, ..., Gaudenzi G, Russom A
Biosensors (Basel) 12 (7) - [2022-07-13; online 2022-07-13]
PubMed DOI Crossref
Multi-Omics Interdisciplinary Research Integration to Accelerate Dementia Biomarker Development (MIRIADE).
Mavrina E, Kimble L, Waury K, ..., Teunissen C, MIRIADE consortium
Front Neurol 13 (-) 890638 [2022-07-12; online 2022-07-12]
PubMed DOI Crossref
Fibrin protofibril packing and clot stability are enhanced by extended knob-hole interactions and catch-slip bonds.
Asquith NL, Duval C, Zhmurov A, ..., Barsegov V, Ariëns RAS
Blood Adv 6 (13) 4015-4027 [2022-07-12; online 2022-05-14]
DOI Crossref
Autocrine Sfrp1 inhibits lung fibroblast invasion during transition to injury induced myofibroblasts
Mayr CH, Sengupta A, Ansari M, ..., Burgstaller G, Schiller HB
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PubMed DOI Crossref
An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.
Ballarino R, Bouwman BAM, Agostini F, ..., Bienko M, Crosetto N
Sci Data 9 (1) 400 [2022-07-12; online 2022-07-12]
Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
A method to predict the response to directional selection using a Kalman filter.
Milocco L, Salazar-Ciudad I
Proc. Natl. Acad. Sci. U.S.A. 119 (28) e2117916119 [2022-07-12; online 2022-07-06]
DDLS Fellow Lisandro Milocco
PubMed DOI Crossref
A human adipose tissue cell-type transcriptome atlas.
Norreen-Thorsen M, Struck EC, Öling S, ..., Dusart PJ, Butler LM
Cell Reports 40 (2) 111046 [2022-07-12; online 2022-07-14]
DOI Crossref
Single particle profiler for measuring content and properties of nano-sized bioparticles
Sych T, Schlegel J, Barriga HMG, ..., Stevens MM, Sezgin E
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PubMed DOI Crossref
Survivin Inhibition by Piperine Sensitizes Glioblastoma Cancer Stem Cells and Leads to Better Drug Response.
Warrier NM, Krishnan RK, Prabhu V, ..., Agarwal P, Kumar P
Int J Mol Sci 23 (14) - [2022-07-09; online 2022-07-09]
PubMed DOI Crossref
In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures.
Abrahamsson D, Siddharth A, Young TM, ..., Martin JW, Woodruff TJ
J. Am. Soc. Mass Spectrom. 33 (7) 1134-1147 [2022-07-06; online 2022-06-01]
PubMed DOI Crossref
ERα and ERβ Homodimers in the Same Cellular Context Regulate Distinct Transcriptomes and Functions.
Song D, He H, Indukuri R, ..., Zhao C, Williams C
Front Endocrinol (Lausanne) 13 (-) 930227 [2022-07-06; online 2022-07-06]
PubMed DOI Crossref
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.
Eriksson O, Bhalla US, Blackwell KT, ..., Wade RC, Hellgren Kotaleski J
Elife 11 (-) - [2022-07-06; online 2022-07-06]
PubMed DOI Crossref
The Quest for Orthologs orthology benchmark service in 2022.
Nevers Y, Jones TEM, Jyothi D, ..., Dessimoz C, Altenhoff A
Nucleic Acids Res. 50 (W1) W623-W632 [2022-07-05; online 2022-05-14]
PubMed DOI Crossref
Myeloid cell-specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation.
Zhu K, Wang Y, Sarlus H, ..., Högberg B, Harris RA
EMBO Rep. 23 (7) e54499 [2022-07-05; online 2022-05-20]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.
Seçilmiş D, Hillerton T, Sonnhammer ELL
Nucleic Acids Res. 50 (W1) W398-W404 [2022-07-05; online 2022-05-25]
PubMed DOI Crossref
Deep Lipidomics in Human Plasma: Cardiometabolic Disease Risk and Effect of Dietary Fat Modulation.
Eichelmann F, Sellem L, Wittenbecher C, ..., Lovegrove JA, Schulze MB
Circulation 146 (1) 21-35 [2022-07-05; online 2022-04-15]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Regeneration in the Auditory Organ in Cuban and African Dwarf Crocodiles (Crocodylus rhombifer and Osteolaemus tetraspis) Can We Learn From the Crocodile How to Restore Our Hearing?
Li H, Staxäng K, Hodik M, ..., Rask-Andersen M, Rask-Andersen H
Front Cell Dev Biol 10 (-) 934571 [2022-07-04; online 2022-07-04]
DOI Crossref
Pathway Analysis Through Mutual Information
Jeuken GS, Käll L
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DOI Crossref
A new machine learning method for cancer mutation analysis
Habibi M, Taheri G
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PubMed DOI Crossref
Angiotensin II AT2 receptor ligands with phenylthiazole scaffolds.
Gopalan G, Palo-Nieto C, Petersen NN, Hallberg M, Larhed M
Bioorg. Med. Chem. 65 (-) 116790 [2022-07-01; online 2022-05-04]
PubMed DOI Crossref
Understudied proteins: opportunities and challenges for functional proteomics.
Kustatscher G, Collins T, Gingras AC, ..., Ralser M, Rappsilber J
Nat. Methods 19 (7) 774-779 [2022-07-00; online 2022-05-10]
PubMed DOI Crossref
The age-dependent association of risk factors with pancreatic cancer.
Yuan C, Kim J, Wang QL, ..., Kraft P, Wolpin BM
Ann. Oncol. 33 (7) 693-701 [2022-07-00; online 2022-04-06]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria.
Yunus IS, Anfelt J, Sporre E, ..., Hudson EP, Jones PR
Metab. Eng. 72 (-) 14-23 [2022-07-00; online 2022-02-05]
PubMed DOI Crossref
SignalP 6.0 predicts all five types of signal peptides using protein language models.
Teufel F, Almagro Armenteros JJ, Johansen AR, ..., von Heijne G, Nielsen H
Nat. Biotechnol. 40 (7) 1023-1025 [2022-07-00; online 2022-01-03]
PubMed DOI Crossref
Scoring of protein-protein docking models utilizing predicted interface residues.
Pozzati G, Kundrotas P, Elofsson A
Proteins 90 (7) 1493-1505 [2022-07-00; online 2022-03-14]
PubMed DOI Crossref
New Views of Old Proteins: Clarifying the Enigmatic Proteome.
Burnum-Johnson KE, Conrads TP, Drake RR, ..., Walt DR, Kelleher NL
Mol. Cell Proteomics 21 (7) 100254 [2022-07-00; online 2022-05-30]
PubMed DOI Crossref
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic D, Hörtenhuber M, Balwierz PJ, ..., Lenhard B, Müller F
Nat. Genet. 54 (7) 1037-1050 [2022-07-00; online 2022-07-04]
PubMed DOI Crossref
Maternal and child biomonitoring strategies and levels of exposure in western Canada during the past seventeen years: The Alberta Biomonitoring Program: 2005-2021.
MacDonald AM, Gabos S, Braakman S, ..., Bennett MJ, Kinniburgh DW
Int J Hyg Environ Health 244 (-) 113990 [2022-07-00; online 2022-06-14]
PubMed DOI Crossref
MRI characterization of skeletal muscle size and fatty infiltration in long-term trained and untrained individuals.
Emanuelsson EB, Berry DB, Reitzner SM, ..., Sundberg CJ, Chapman MA
Physiol Rep 10 (14) e15398 [2022-07-00; online 2022-07-21]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Investigation of multiple populations highlight VEGFA polymorphisms to modulate anterior cruciate ligament injury.
Feldmann DC, Rahim M, Suijkerbuijk MAM, ..., Collins M, September AV
J Orthop Res 40 (7) 1604-1612 [2022-07-00; online 2021-10-18]
PubMed DOI Crossref
In vitro activity of ceragenins against Burkholderia cepacia complex.
Demir ES, Oyardi O, Savage PB, Altay HO, Bozkurt-Guzel C
J Antibiot (Tokyo) 75 (7) 403-409 [2022-07-00; online 2022-05-13]
PubMed DOI Crossref
Immune responses after omicron infection in triple-vaccinated health-care workers with and without previous SARS-CoV-2 infection.
Blom K, Marking U, Havervall S, ..., Klingström J, Thålin C
Lancet Infect Dis 22 (7) 943-945 [2022-07-00; online 2022-06-09]
PubMed DOI Crossref
Identification of early neurodegenerative pathways in progressive multiple sclerosis.
Kaufmann M, Schaupp AL, Sun R, ..., Mann M, Fugger L
Nat. Neurosci. 25 (7) 944-955 [2022-07-00; online 2022-06-20]
PubMed DOI Crossref
High Throughput Screening of a Prescription Drug Library for Inhibitors of Organic Cation Transporter 3, OCT3.
Chen EC, Matsson P, Azimi M, ..., Artursson P, Giacomini KM
Pharm. Res. 39 (7) 1599-1613 [2022-07-00; online 2022-01-28]
PubMed DOI Crossref
Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins.
Malm M, Kuo CC, Barzadd MM, ..., Hatton D, Rockberg J
Metab. Eng. 72 (-) 171-187 [2022-07-00; online 2022-03-14]
PubMed DOI Crossref
Giardia duodenalis.
Rojas-López L, Marques RC, Svärd SG
Trends Parasitol. 38 (7) 605-606 [2022-07-00; online 2022-01-21]
PubMed DOI Crossref
Detection of perineural invasion in prostate needle biopsies with deep neural networks.
Kartasalo K, Ström P, Ruusuvuori P, ..., Eklund M, Egevad L
Virchows Arch. 481 (1) 73-82 [2022-07-00; online 2022-04-21]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
CAR T cells expressing a bacterial virulence factor trigger potent bystander antitumour responses in solid cancers.
Jin C, Ma J, Ramachandran M, Yu D, Essand M
Nat Biomed Eng 6 (7) 830-841 [2022-07-00; online 2022-04-04]
PubMed DOI Crossref
Biosynthetic potential of the global ocean microbiome.
Paoli L, Ruscheweyh HJ, Forneris CC, ..., Piel J, Sunagawa S
Nature 607 (7917) 111-118 [2022-07-00; online 2022-06-22]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Adenosine A2A receptor antagonists: from caffeine to selective non-xanthines.
Jacobson KA, Gao ZG, Matricon P, Eddy MT, Carlsson J
Br J Pharmacol 179 (14) 3496-3511 [2022-07-00; online 2020-06-19]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses.
Tamarit D, Caceres EF, Krupovic M, ..., Robinson NP, Ettema TJG
Nat. Microbiol 7 (7) 948-952 [2022-07-00; online 2022-06-27]
PubMed DOI Crossref
The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle.
Krog MC, Hugerth LW, Fransson E, ..., Schuppe-Koistinen I, Nielsen HS
Hum. Reprod. 37 (7) 1525-1543 [2022-06-30; online 2022-05-14]
DDLS Fellow Luisa Hugerth
DOI Crossref
Hexokinase 1b is a novel target for Non–small-cell lung cancer
Yozgat Y, Karakoc E, Sahin O, ..., Ozturk G, Cevher MA
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PubMed DOI Crossref
Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking.
Carroll LM, Pierneef R, Mathole A, Atanda A, Matle I
Microbiol Spectr 10 (3) e0070022 [2022-06-29; online 2022-04-27]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
The genomic basis of the plant island syndrome in Darwin's giant daisies.
Cerca J, Petersen B, Lazaro-Guevara JM, ..., Rieseberg LH, Martin MD
Nat Commun 13 (1) 3729 [2022-06-28; online 2022-06-28]
PubMed DOI Crossref
Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections.
Rosendal E, Mihai IS, Becker M, ..., Överby AK, Lenman A
MBio 13 (3) e0089222 [2022-06-28; online 2022-05-09]
DOI Crossref
Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics
Arora A, Becker M, Marques C, ..., Lanekoff I, Tammimies K
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DOI Crossref
From biomedical cloud platforms to microservices: next steps in FAIR data and analysis
Sheffield NC, Bonazzi V, Bourne PE, ..., Spjuth O, Yates AD
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PubMed DOI Crossref
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks.
Weitz P, Wang Y, Kartasalo K, ..., Eklund M, Rantalainen M
Bioinformatics 38 (13) 3462-3469 [2022-06-27; online 2022-05-21]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Heparanase Expression Propagates Liver Damage in CCL4-Induced Mouse Model.
Cheng X, Jia J, Zhang T, ..., Vlodavsky I, Li JP
Cells 11 (13) - [2022-06-27; online 2022-06-27]
PubMed DOI Crossref
THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1.
Kamp JA, Lemmens BBLG, Romeijn RJ, ..., van Schendel R, Tijsterman M
Nucleic Acids Res. 50 (11) 6235-6250 [2022-06-24; online 2022-06-08]
PubMed DOI Crossref
Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function.
Michel M, Benítez-Buelga C, Calvo PA, ..., de Vega M, Helleday T
Science (New York, N.Y.) 376 (6600) 1471-1476 [2022-06-24; online 2022-06-23]
PubMed DOI Crossref
HSFs drive transcription of distinct genes and enhancers during oxidative stress and heat shock.
Himanen SV, Puustinen MC, Da Silva AJ, Vihervaara A, Sistonen L
Nucleic Acids Res. 50 (11) 6102-6115 [2022-06-24; online 2022-06-11]
Anniina Vihervaara SciLifeLab Fellow
PubMed DOI Crossref
Estrogen Receptor β (ESR2) Transcriptome and Chromatin Binding in a Mantle Cell Lymphoma Tumor Model Reveal the Tumor-Suppressing Mechanisms of Estrogens.
Huang D, Huang Z, Indukuri R, ..., Williams C, Okret S
Cancers (Basel) 14 (13) - [2022-06-24; online 2022-06-24]
PubMed DOI Crossref
Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level.
Wang F, Ding P, Liang X, ..., Lin L, Luo Y
Nat Commun 13 (1) 3620 [2022-06-24; online 2022-06-24]
PubMed DOI Crossref
The VirF21:VirF30 protein ratio is affected by temperature and impacts Shigella flexneri host cell invasion.
Skovajsová E, Colonna B, Prosseda G, Sellin ME, Di Martino ML
FEMS Microbiol. Lett. 369 (1) - [2022-06-22; online 2022-05-07]
Mikael Sellin SciLifeLab Fellow
DOI Crossref
Optimizing insect metabarcoding using replicated mock communities
Iwaszkiewicz-Eggebrecht E, Granqvist E, Buczek M, ..., Ronquist F, Łukasik P
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DOI Crossref
An α-π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb
Choudhury K, Howard RJ, Delemotte L
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DOI Crossref
A metagenomic view on fungal diversity in freshwater lakes
Sanyal A, Kluge M, Redondo MA, ..., Bertilsson S, Peura S
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PubMed DOI Crossref
Transition between conformational states of the TREK-1 K2P channel promoted by interaction with PIP2.
Panasawatwong A, Pipatpolkai T, Tucker SJ
Biophys. J. 121 (12) 2380-2388 [2022-06-21; online 2022-05-19]
PubMed DOI Crossref
Expansion of a retrovirus lineage in the koala genome.
Lillie M, Hill J, Pettersson ME, Jern P
Proc. Natl. Acad. Sci. U.S.A. 119 (25) e2201844119 [2022-06-21; online 2022-06-13]
PubMed DOI Crossref
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.
Erdem C, Mutsuddy A, Bensman EM, ..., Feltus FA, Birtwistle MR
Nat Commun 13 (1) 3555 [2022-06-21; online 2022-06-21]
Cemal Erdem DDLS Fellow
DOI Crossref
Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5
McComas SE, Reichenbach T, Mitrovic D, ..., Delemotte L, Drew D
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PubMed DOI Crossref
T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles.
Céspedes PF, Jainarayanan A, Fernández-Messina L, ..., Sánchez-Madrid F, Dustin ML
Nat Commun 13 (1) 3460 [2022-06-16; online 2022-06-16]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
EviCor: Interactive Web Platform for Exploration of Molecular Features and Response to Anti-cancer Drugs.
Petrov I, Alexeyenko A
J. Mol. Biol. 434 (11) 167528 [2022-06-15; online 2022-03-05]
PubMed DOI Crossref
Differential grey matter structure in women with premenstrual dysphoric disorder: evidence from brain morphometry and data-driven classification.
Dubol M, Stiernman L, Wikström J, ..., Bixo M, Comasco E
Transl Psychiatry 12 (1) 250 [2022-06-15; online 2022-06-15]
Erika Comasco SciLifeLab Fellow
DOI Crossref
Abstract 2171: The spatial landscape of clonal somatic mutations in benign and malignant tissue
Erickson A, Berglund E, He M, ..., Lamb AD, Lundenberg J
Cancer Res. 82 (12_Supplement) 2171-2171 [2022-06-15; online 2022-06-15]
DOI Crossref
Abstract 1890: Development of the drug efficacy testing in ex vivo 3D cultures (DETECT) platform and its application to functional precision medicine in ovarian cancer
Åkerlund E, Gudoityte G, Lamodiere EM, ..., Joneborg U, Seashore-Ludlow B
Cancer Res. 82 (12_Supplement) 1890-1890 [2022-06-15; online 2022-06-15]
DOI Crossref
A GPU-based computational framework that bridges Neuron simulation and Artificial Intelligence
Zhang Y, He G, Liu X, ..., Du K, Huang T
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DOI Crossref
A GPU-based computational framework that bridges Neuron simulation and Artificial Intelligence
Zhang Y, He G, Liu X, ..., Du K, Huang T
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DOI Crossref
Obstructive sleep apnea is associated with specific gut microbiota species and functions in the population-based Swedish CardioPulmonary bioImage Study (SCAPIS)
Baldanzi G, Sayols-Baixeras S, Theorell-Haglöw J, ..., Lindberg E, Fall T
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PubMed DOI Crossref
Repositioning of Anti-Inflammatory Drugs for the Treatment of Cervical Cancer Sub-Types.
Kori M, Arga KY, Mardinoglu A, Turanli B
Front. Pharmacol. 13 (-) 884548 [2022-06-13; online 2022-06-13]
DOI Crossref
Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection
Mikaeloff F, Gelpi M, Benfeitas R, ..., Nielsen SD, Neogi U
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PubMed DOI Crossref
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.
Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-Del-Molino D
BMC Bioinformatics 23 (1) 228 [2022-06-13; online 2022-06-13]
DDLS Fellow Tom van der Valk
DOI Crossref
Separation of transcriptional repressor and activator functions in HDAC3
Tang M, Regadas I, Belikov S, ..., Bienko M, Mannervik M
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DOI Crossref
Nanoscale sheared droplet: volume-of-fluid, phase-field and no-slip molecular dynamics
Lācis U, Pellegrino M, Sundin J, ..., Hess B, Bagheri S
J. Fluid Mech. 940 (-) - [2022-06-10; online 2022-04-06]
PubMed DOI Crossref
Microfluidics platform for studies of peptide - polyelectrolyte interaction.
Wanselius M, Searle S, Rodler A, ..., Abrahmsén-Alami S, Hansson P
Int J Pharm 621 (-) 121785 [2022-06-10; online 2022-04-30]
Incidensen av levercancer ökar över hela världen
Kutter C
Onkologi i Sverige - (-) - [2022-06-10; online 2022-06-10]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Trade-offs predicted by metabolic network structure give rise to evolutionary specialization and phenotypic diversification.
Ekkers DM, Tusso S, Moreno-Gamez S, ..., Kuipers OP, van Doorn GS
Mol. Biol. Evol. 39 (6) - [2022-06-09; online 2022-06-09]
DOI Crossref
Markov State Modelling Reveals Heterogeneous Drug-Inhibition Mechanism of Calmodulin
Westerlund AM, Sridhar A, Dahl L, ..., Bodnar AY, Delemotte L
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PubMed DOI Crossref
FOXO1 and FOXO3 Cooperatively Regulate Innate Lymphoid Cell Development.
Luu TT, Søndergaard JN, Peña-Pérez L, ..., Månsson R, Kadri N
Front Immunol 13 (-) 854312 [2022-06-09; online 2022-06-09]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5.
Galiani S, Reglinski K, Carravilla P, ..., Erdmann R, Eggeling C
Biophys Rep (N Y) 2 (2) None [2022-06-08; online 2022-06-08]
PubMed DOI Crossref
Correction to "Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases".
Crean RM, Biler M, Corbella M, ..., Hengge AC, Kamerlin SCL
Journal of the American Chemical Society 144 (22) 10091-10093 [2022-06-08; online 2022-05-24]
DOI Crossref
BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
Ouyang W, Beuttenmueller F, Gómez-de-Mariscal E, ..., Jug F, Kreshuk A
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PubMed DOI Crossref
Sugar-sweetened beverage and sugar consumption and colorectal cancer incidence and mortality according to anatomic subsite.
Yuan C, Joh HK, Wang QL, ..., Giovannucci EL, Wu K
Am. J. Clin. Nutr. 115 (6) 1481-1489 [2022-06-07; online 2022-04-27]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
Probing the Link between Pancratistatin and Mitochondrial Apoptosis through Changes in the Membrane Dynamics on the Nanoscale.
Castillo SR, Rickeard BW, DiPasquale M, ..., Kelley EG, Marquardt D
Mol. Pharm. 19 (6) 1839-1852 [2022-06-06; online 2022-05-13]
DDLS Fellow Milka Doktorova
DOI Crossref
Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties
Ragaller F, Andronico L, Sykora J, ..., Vattulainen I, Sezgin E
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DOI Crossref
PATH-04. Array-based global DNA Methylation profiling of mouse brain tumors allows comparison to human tumors
Schoof M, Spohn M, Dorostkar M, ..., Kerl K, Schüller U
Neuro-oncology 24 (Supplement_1) i158-i159 [2022-06-03; online 2022-06-03]
PubMed DOI Crossref
Identification of cerebrospinal fluid and serum metabolomic biomarkers in first episode psychosis patients.
Shang P, Ho AM, Tufvesson-Alm M, ..., Erhardt S, Choi DS
Transl Psychiatry 12 (1) 229 [2022-06-03; online 2022-06-03]
PubMed DOI Crossref
Chemotherapeutic Activities of Dietary Phytoestrogens against Prostate Cancer: From Observational to Clinical Studies.
Sohel M, Sultana H, Sultana T, ..., Mitra S, Dash R
Curr. Pharm. Des. 28 (19) 1561-1580 [2022-06-03; online 2022-06-03]
PubMed DOI Crossref
A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.
Luo X, Bittremieux W, Griss J, ..., Käll L, Perez-Riverol Y
J. Proteome Res. 21 (6) 1566-1574 [2022-06-03; online 2022-05-13]
PubMed DOI Crossref
Thermoadaptation in an Ancestral Diterpene Cyclase by Altered Loop Stability.
Hueting DA, Vanga SR, Syrén PO
J Phys Chem B 126 (21) 3809-3821 [2022-06-02; online 2022-05-18]
PubMed DOI Crossref
Secondary resistance to idelalisib is characterized by upregulation of IGF1R rather than by MAPK/ERK pathway mutations.
Tausch E, Ljungström V, Agathangelidis A, ..., Rosenquist R, Stilgenbauer S
Blood 139 (22) 3340-3344 [2022-06-02; online 2022-04-05]
PubMed DOI Crossref
Artificial neural networks enable genome-scale simulations of intracellular signaling.
Nilsson A, Peters JM, Meimetis N, Bryson B, Lauffenburger DA
Nat Commun 13 (1) 3069 [2022-06-02; online 2022-06-02]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Subtype-specific responses of hKv7.4 and hKv7.5 channels to polyunsaturated fatty acids reveal an unconventional modulatory site and mechanism.
Frampton DJA, Choudhury K, Nikesjö J, Delemotte L, Liin SI
Elife 11 (-) - [2022-06-01; online 2022-06-01]
DOI Crossref
What Makes Transfer Learning Work for Medical Images: Feature Reuse &amp; Other Factors
Matsoukas C, Haslum JF, Sorkhei M, Soderberg M, Smith K
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PubMed DOI Crossref
The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe.
Cornille A, Tiret M, Salcedo A, ..., Wright SI, Lascoux M
AoB Plants 14 (3) plac011 [2022-06-00; online 2022-04-02]
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Potato genomes pave the way to crop improvement.
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OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.
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Heparin‐Derived Theranostic Nanoprobes Overcome the Blood–Brain Barrier and Target Glioma in Murine Model
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Genomic associations with poxvirus across divergent island populations in Berthelot's pipit.
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E-cadherin is a robust prognostic biomarker in colorectal cancer and low expression is associated with sensitivity to inhibitors of topoisomerase, aurora, and HSP90 in preclinical models.
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Complementing machine learning-based structure predictions with native mass spectrometry.
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Checkpoint CD47 expression in classical Hodgkin lymphoma.
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Bioorthogonally Cross-Linked Hyaluronan-Laminin Hydrogels for 3D Neuronal Cell Culture and Biofabrication.
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An open invitation to the Understudied Proteins Initiative.
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Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface.
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A D-peptide ligand of neuropeptide Y receptor Y1 serves as nanocarrier traversing of the blood brain barrier and targets glioma
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Targeting Tumor Cells Overexpressing the Human Epidermal Growth Factor Receptor 3 with Potent Drug Conjugates Based on Affibody Molecules.
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Machine Learning Analysis Reveals Biomarkers for the Detection of Neurological Diseases.
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Live single cell imaging assays in glass microwells produced by laser-induced deep etching.
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Integration of single-cell RNA and protein data identifies novel clinically-relevant lymphocyte phenotypes in breast cancers
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Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.
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Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.
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Streptococcus species abundance in the gut is linked to subclinical coronary atherosclerosis in 8973 participants from the SCAPIS cohort
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Simultaneous visualization of flow fields and oxygen concentrations to unravel transport and metabolic processes in biological systems.
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Rapid, in-patient adaptations of Legionella pneumophila to the human host
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A qPCR-Based Method for Quantification of RCA Contaminants in Oncolytic Adenovirus Products.
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A dominant negative splice variant of the heparan sulfate biosynthesis enzyme NDST1 reduces heparan sulfate sulfation.
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Interplay between VSD, pore and membrane lipids in electromechanical coupling in HCN channels
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Individualized discovery of rare cancer drivers in global network context.
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Design, Synthesis, and Evaluation of Linker-Optimised PSMA-Targeting Radioligands.
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Phylogenetic Analysis of Small Hive Beetles From Native to Introduced Populations.
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OGG1 inhibitor TH5487 alleviates allergic airway inflammation in mice
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Dangerous RNA links pave the way to glioblastoma.
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Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method
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Using unsupervised learning algorithms to identify essential genes associated with SARS-CoV-2 as potential therapeutic targets for COVID-19
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Hyperthermia-Induced In Situ Drug Amorphization by Superparamagnetic Nanoparticles in Oral Dosage Forms.
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Molecular Analysis of SARS-CoV-2 Lineages in Armenia.
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The origin and evolution of mitochondrial tropism in Midichloria bacteria
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The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis.
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Quantitative glycoproteomics of human milk and association with atopic disease.
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PLoS ONE 17 (5) e0267967 [2022-05-13; online 2022-05-13]
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Heterologous immunization with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant.
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Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.
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Patatin-like phospholipase CapV in Escherichia coli - morphological and physiological effects of one amino acid substitution.
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Data-Driven Model of Postsynaptic Currents Mediated by NMDA or AMPA Receptors in Striatal Neurons.
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Upregulation of PKN1 as a Prognosis Biomarker for Endometrial Cancer.
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OGG1 Inhibition Triggers Synthetic Lethality and Enhances The Effect of PARP Inhibitor Olaparib in BRCA1-Deficient TNBC Cells.
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Integrative multi-omics analysis reveals molecular subtypes and tumor evolution of synovial sarcoma
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Cohort profile: the Swedish study of SUDden cardiac Death in the Young (SUDDY) 2000-2010: a complete nationwide cohort of SCDs.
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Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.
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Lipid-Protein Interactions in Plasma Membrane Organization and Function.
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Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities.
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Potential and Therapeutic Roles of Diosmin in Human Diseases.
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Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data.
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Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
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Author response: Subtype-specific responses of hKv7.4 and hKv7.5 channels to polyunsaturated fatty acids reveal an unconventional modulatory site and mechanism
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Maternal prenatal depressive symptoms and toddler behavior: an umbilical cord blood epigenome-wide association study.
Kallak TK, Fransson E, Bränn E, ..., Lyle R, Skalkidou A
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Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation
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Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression.
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Multi-staged gene expression profiling reveals potential genes and the critical pathways in kidney cancer.
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Sci Rep 12 (1) 7240 [2022-05-04; online 2022-05-04]
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Inhibition of Oxidized Nucleotide Sanitation By TH1579 and Conventional Chemotherapy Cooperatively Enhance Oxidative DNA Damage and Survival in AML.
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Genetics of smoking and risk of clonal hematopoiesis.
Levin MG, Nakao T, Zekavat SM, ..., Damrauer SM, Natarajan P
Sci Rep 12 (1) 7248 [2022-05-04; online 2022-05-04]
Abhishek Niroula DDLS Fellow
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Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer.
Vega PN, Nilsson A, Kumar MP, ..., Lauffenburger DA, Lau KS
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Avlant Nilsson DDLS Fellow
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Basal cell carcinomas acquire secondary mutations to overcome dormancy and progress from microscopic to macroscopic disease.
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Cell Reports 39 (5) 110779 [2022-05-03; online 2022-05-05]
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The right bug in the right place: opportunities for bacterial vaginosis treatment.
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Influence of T-Bar on Calcium Concentration Impacting Release Probability.
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Tissue ischemia induces mobilization of pro-angiogenic neutrophils from the spleen
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AGPAT1 as a Novel Colonic Biomarker for Discriminating Between Ulcerative Colitis With and Without Primary Sclerosing Cholangitis.
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p53 at the crossroad of DNA replication and ribosome biogenesis stress pathways.
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The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin-Associated Musculoskeletal Symptoms.
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Subtypes of Alzheimer's disease: questions, controversy, and meaning.
Vogel JW, Hansson O
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Studying severe long COVID to understand post-infectious disorders beyond COVID-19.
Brodin P, Casari G, Townsend L, ..., Casanova JL, COVID Human Genetic Effort
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Scalable federated machine learning with FEDn
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Prashant Singh SciLifeLab Fellow
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SARS-CoV-2 (COVID-19)-specific T cell and B cell responses in convalescent rheumatoid arthritis: Monozygotic twins pair case observation.
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Reverting Colitis Symptoms by Oral Administration of L. reuteri Expressing CXCL12 Acting Through Novel Pathway Demonstrated in Two Experimental Animal Models
Öhnstedt E, Donas Cuadra C, Lofton Tomenius H, ..., Roos S, Phillipson M
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MutT Homolog 1 Inhibitor Karonudib Attenuates Autoimmune Hepatitis by Inhibiting DNA Repair in Activated T Cells.
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Mitoribosomal defects aggravate liver cancer via aberrant glycolytic flux and T cell exhaustion.
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Mitochondrial Sirtuin-3 (SIRT3) Prevents Doxorubicin-Induced Dilated Cardiomyopathy by Modulating Protein Acetylation and Oxidative Stress.
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Liver stromal cells restrict macrophage maturation and stromal IL-6 limits the differentiation of cirrhosis-linked macrophages.
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International validation of the EORTC QLQ-CLL17 questionnaire for assessment of health-related quality of life for patients with chronic lymphocytic leukaemia.
Oerlemans S, Efficace F, Kieffer JM, ..., van de Poll-Franse L, EORTC Quality of Life Group
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Glucagonlike Peptide-1 Receptor Imaging in Individuals with Type 2 Diabetes.
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Durable and dynamic hTERT immune responses following vaccination with the long-peptide cancer vaccine UV1: long-term follow-up of three phase I clinical trials.
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Direct Observation of Na,K‐ATPase Oligomers in The Plasma Membrane of Living Cells by FRET‐FCS
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Clonal Hematopoiesis and CKD Progression.
Niroula A, Belizaire R
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Association between menopausal hormone therapy use and mortality risk: a Swedish population-based matched cohort study.
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A2B adenosine receptor antagonists rescue lymphocyte activity in adenosine-producing patient-derived cancer models.
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A motile doublet form of Salmonella Typhimurium diversifies target search behavior at the epithelial surface.
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Understanding immune signaling using advanced imaging techniques.
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Biochem. Soc. Trans. 50 (2) 853-866 [2022-04-29; online 2022-03-29]
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Prognostic Significance of the Loss of Heterozygosity of KRAS in Early-Stage Lung Adenocarcinoma.
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Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence.
Silva SV, Andermann T, Zizka A, Kozlowski G, Silvestro D
Front Plant Sci 13 (-) 839792 [2022-04-29; online 2022-04-29]
DDLS Fellow Tobias Andermann
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Cancer cells use self-inflicted DNA breaks to evade growth limits imposed by genotoxic stress.
Larsen BD, Benada J, Yung PYK, ..., Bartek J, Sørensen CS
Science (New York, N.Y.) 376 (6592) 476-483 [2022-04-29; online 2022-04-28]
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Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation.
Liu Z, Xu J, Que S, ..., Mardinoglu A, Zheng S
J Clin Transl Hepatol 10 (2) 363-373 [2022-04-28; online 2022-01-04]
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PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk.
Ogris C, Castresana-Aguirre M, Sonnhammer ELL
Bioinformatics 38 (9) 2659-2660 [2022-04-28; online 2022-03-11]
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Author Correction: Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability.
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Using genotyping and whole-exome sequencing data to improve genetic risk prediction in deep venous thrombosis
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Implications of Heparanase on Heparin Synthesis and Metabolism in Mast Cells.
Maccarana M, Jia J, Li H, ..., Vlodavsky I, Li JP
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Multiple Cortical to Striatal Accumulation Trajectories of β-Amyloid: Do All Roads Lead to Rome?
Vogel JW, Tosun D
Neurology 98 (17) 695-696 [2022-04-26; online 2022-03-25]
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward.
Zisi A, Bartek J, Lindström MS
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Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment
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Elevated plasma Complement Factor H Regulating Protein 5 is associated with venous thromboembolism and COVID-19 severity
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Intrapersonal Stability of Plasma Metabolomic Profiles over 10 Years among Women.
Zeleznik OA, Wittenbecher C, Deik A, ..., Hu FB, Eliassen AH
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Clemens Wittenbecher DDLS Fellow
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A DNA molecular printer capable of programmable positioning and patterning in two dimensions.
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Sci Robot 7 (65) eabn5459 [2022-04-20; online 2022-04-20]
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The Role of Bio‐based Excipients in the Formulation of Lipophilic Nutraceuticals
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Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.
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Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning.
Andermann T, Antonelli A, Barrett RL, Silvestro D
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An atlas of genetic scores to predict multi-omic traits
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Phenotype assessment for neurodegenerative murine models with ataxia and application to Niemann-Pick disease, type C1.
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Associations of prenatal exposure to mixtures of organochlorine pesticides and smoking and drinking behaviors in adolescence.
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Oskar Karlsson SciLifeLab Fellow
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Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase.
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Eur J Med Chem 234 (-) 114270 [2022-04-15; online 2022-03-08]
Adil Mardinoglu SciLifeLab Fellow
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Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021).
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Differentiating amyloid beta spread in autosomal dominant and sporadic Alzheimer's disease.
Levitis E, Vogel JW, Funck T, ..., Dominantly Inherited Alzheimer Network , Alzheimer’s Disease Neuroimaging Initiative
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DDLS Fellow Jacob W Vogel
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Platelet-Derived PDGFB Promotes Recruitment of Cancer-Associated Fibroblasts, Deposition of Extracellular Matrix and Tgfβ Signaling in the Tumor Microenvironment.
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Fast and accurate gene regulatory network inference by normalized least squares regression.
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TEsorter: An accurate and fast method to classify LTR-retrotransposons in plant genomes.
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Hortic Res 9 (-) uhac017 [2022-04-11; online 2022-04-11]
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Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions.
Ghaffari P, Shoaie S, Nielsen LK
J Transl Med 20 (1) 173 [2022-04-11; online 2022-04-11]
Saeed Shoaie SciLifeLab Fellow
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Genomics: Testing the limits of de-extinction.
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Curr. Biol. 32 (7) R324-R327 [2022-04-11; online 2022-04-13]
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Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.
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Front Mol Biosci 9 (-) 861491 [2022-04-11; online 2022-04-11]
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Grey matter correlates of affective and somatic symptoms of premenstrual dysphoric disorder.
Dubol M, Wikström J, Lanzenberger R, ..., Sundström-Poromaa I, Comasco E
Sci Rep 12 (1) 5996 [2022-04-09; online 2022-04-09]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
PET-CT imaging of pulmonary inflammation using [68Ga]Ga-DOTA-TATE.
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EJNMMI Res 12 (1) 19 [2022-04-08; online 2022-04-08]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential.
Nakao T, Bick AG, Taub MA, ..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium , Natarajan P
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Abhishek Niroula DDLS Fellow
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Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators
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SimSearch: A Human-in-the-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images
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Comprehensive cancer-oriented biobanking resource of human samples for studies of post-zygotic genetic variation involved in cancer predisposition.
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Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics.
Crowe-McAuliffe C, Murina V, Turnbull KJ, ..., Wilson DN, Hauryliuk V
Nat Commun 13 (1) 1860 [2022-04-06; online 2022-04-06]
SciLifeLab Fellow Vicente Pelechano
PubMed DOI Crossref
Elastic dosage compensation by X-chromosome upregulation.
Lentini A, Cheng H, Noble JC, ..., Enge M, Reinius B
Nat Commun 13 (1) 1854 [2022-04-06; online 2022-04-06]
Antonio Lentini DDLS Fellow
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Editorial: Role of Sex Steroids and Their Receptor in Cancers.
Giovannelli P, Ramaraj P, Williams C
Front Endocrinol (Lausanne) 13 (-) 883229 [2022-04-06; online 2022-04-06]
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Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut
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MutSβ regulates G4-associated telomeric R-loops to maintain telomere integrity in ALT cancer cells.
Sakellariou D, Bak ST, Isik E, ..., Janscak P, Peña-Diaz J
Cell Reports 39 (1) 110602 [2022-04-05; online 2022-04-07]
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Deadenylase-dependent mRNA decay of GDF15 and FGF21 orchestrates food intake and energy expenditure.
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Cell Metab. 34 (4) 564-580.e8 [2022-04-05; online 2022-04-07]
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Correlates of protection, viral load trajectories and symptoms in BA.1, BA.1.1 and BA.2 breakthrough infections in triple vaccinated healthcare workers
Marking U, Havervall S, Greilert Norin N, ..., Klingström J, Thålin C
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The relationship of major diseases with childlessness: a sibling matched case-control and population register study in Finland and Sweden
Liu A, Akimova ET, Ding X, ..., Mills MC, Ganna A
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Cotranslational folding and assembly of the dimeric E. coli inner membrane protein EmrE
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Uniting diversity to create a more inclusive academic environment.
Delemotte L, Garcia SL, Rodríguez-Gijón A, Sezgin E, Vihervaara A
J. Cell. Sci. 135 (7) - [2022-04-01; online 2022-04-12]
Anniina Vihervaara Erdinc Sezgin Lucie Delemotte Sarahi Garcia SciLifeLab Fellow
PubMed DOI Crossref
The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host.
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Size matters - the impact of nucleus size on results from spatial transcriptomics
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Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
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Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.
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Metabolomics and Type 2 Diabetes Risk: An Updated Systematic Review and Meta-analysis of Prospective Cohort Studies.
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Diabetes Care 45 (4) 1013-1024 [2022-04-01; online 2022-03-30]
Clemens Wittenbecher DDLS Fellow
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Is heparan sulfate a target for inhibition of RNA virus infection?
Ling J, Li J, Khan A, Lundkvist Å, Li JP
Am. J. Physiol., Cell Physiol. 322 (4) C605-C613 [2022-04-01; online 2022-02-23]
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Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics.
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Giant plasma membrane vesicles to study plasma membrane structure and dynamics.
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Biochim Biophys Acta Biomembr 1864 (4) 183857 [2022-04-01; online 2022-01-04]
Erdinc Sezgin SciLifeLab Fellow
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Exploration of ultrasound-mediated microbubble-cell membrane interactions using novel protein-loaded microbubbles and their role in immunomodulation
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Designing microplate layouts using artificial intelligence
Francisco Rodríguez MA, Puigvert JC, Spjuth O
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Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices.
Nicolaus F, Ibrahimi F, den Besten A, von Heijne G
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Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment.
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Eur. Respir. J. 59 (4) - [2022-04-00; online 2022-04-14]
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Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
Ferreira PL, Batista R, Andermann T, ..., Bacon CD, Antonelli A
Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]
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TP53 mutations at codon 234 are associated with chlorambucil treatment in chronic lymphocytic leukemia.
Lazarian G, Theves F, Hormi M, ..., Soussi T, French Innovative Leukemia Organisation (FILO)
Am. J. Hematol. 97 (4) E159-E162 [2022-04-00; online 2022-02-01]
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Super-resolved spatial transcriptomics by deep data fusion.
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Pulmonary and blood dendritic cells from sarcoidosis patients more potently induce IFNγ-producing Th1 cells compared with monocytes.
Lepzien R, Nie M, Czarnewski P, ..., Grunewald J, Smed-Sörensen A
J Leukoc Biol 111 (4) 857-866 [2022-04-00; online 2021-08-25]
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Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach.
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EBioMedicine 78 (-) 103963 [2022-04-00; online 2022-03-25]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
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Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.
Zeybel M, Arif M, Li X, ..., Borén J, Mardinoglu A
Adv Sci (Weinh) 9 (11) e2104373 [2022-04-00; online 2022-02-07]
Adil Mardinoglu SciLifeLab Fellow
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Molecular design of an electropolymerized copolymer with carboxylic and sulfonic acid functionalities
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Synthetic Metals 285 (-) 117029 [2022-04-00; online 2022-04-00]
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Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology.
Laurén I, Havervall S, Ng H, ..., Thålin C, Mangsbo S
Immun Inflamm Dis 10 (4) e595 [2022-04-00; online 2022-03-30]
Gustaf Christoffersson SciLifeLab Fellow
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Integrative study of diet-induced mouse models of NAFLD identifies PPARα as a sexually dimorphic drug target.
Smati S, Polizzi A, Fougerat A, ..., Gourdy P, Guillou H
Gut 71 (4) 807-821 [2022-04-00; online 2021-04-26]
Adil Mardinoglu SciLifeLab Fellow
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IgE cross-linking induces activation of human and mouse mast cell progenitors.
Méndez-Enríquez E, Salomonsson M, Eriksson J, ..., Sellin ME, Hallgren J
J. Allergy Clin. Immunol. 149 (4) 1458-1463 [2022-04-00; online 2021-09-04]
Mikael Sellin SciLifeLab Fellow
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Identification of a New Cholesterol-Binding Site within the IFN-γ Receptor that is Required for Signal Transduction.
Morana O, Nieto-Garai JA, Björkholm P, ..., Lorizate M, Contreras FX
Adv Sci (Weinh) 9 (11) e2105170 [2022-04-00; online 2022-02-15]
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Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging.
Mishra K, Fuenzalida-Werner JP, Pennacchietti F, ..., Ntziachristos V, Stiel AC
Nat. Biotechnol. 40 (4) 598-605 [2022-04-00; online 2021-11-29]
Ilaria Testa SciLifeLab Fellow
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Generation of a human iPSC line (UUIGPi015-A) from a patient with Dravet syndrome and a 2.9 Mb deletion spanning SCN1A on chromosome 2.
Schuster J, de Guidi C, Tripathi R, Klar J, Dahl N
Stem Cell Res 60 (-) 102712 [2022-04-00; online 2022-02-16]
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Dysregulation of macrophage PEPD in obesity determines adipose tissue fibro-inflammation and insulin resistance.
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Cytogenetics in Chronic Lymphocytic Leukemia: ERIC Perspectives and Recommendations.
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Hemasphere 6 (4) e707 [2022-04-00; online 2022-03-25]
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Circulating tumor DNA (ctDNA) in adjuvant therapy of early stage colon cancer: current status and future perspectives.
Merk C, Martling A, Lindberg J, ..., Taieb J, Lind P
Acta Oncol 61 (4) 523-530 [2022-04-00; online 2022-02-09]
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Cell transcriptomic atlas of the non-human primate Macaca fascicularis.
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Nature 604 (7907) 723-731 [2022-04-00; online 2022-04-13]
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Cannabidiol-induced activation of the metallothionein pathway impedes anticancer effects of disulfiram and its metabolite CuET.
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The Fungal Endophyte Penicillium olsonii ML37 Reduces Fusarium Head Blight by Local Induced Resistance in Wheat Spikes.
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Molecular Genetics and Cytotoxic Responses to Titanium Diboride and Zinc Borate Nanoparticles on Cultured Human Primary Alveolar Epithelial Cells.
Türkez H, Arslan ME, Tatar A, ..., Tatar A, Mardinoglu A
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A Gene Co-Expression Network-Based Drug Repositioning Approach Identifies Candidates for Treatment of Hepatocellular Carcinoma.
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Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
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Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates.
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Conformational Selection in Biocatalytic Plastic Degradation by PETase
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Editorial: Tertiary Lymphoid Structures: From Basic Biology to Translational Impact in Cancer.
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Dual spatially resolved transcriptomics for SARS-CoV-2 host-pathogen colocalization studies in humans
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Norway spruce postglacial recolonization of Fennoscandia.
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Pascal Milesi SciLifeLab Fellow
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Neutrophil extracellular traps promote cancer-associated inflammation and myocardial stress.
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N-terminome analyses underscore the prevalence of SPPL3-mediated intramembrane proteolysis among Golgi-resident enzymes and its role in Golgi enzyme secretion.
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Targeting Estrogen Signaling in the Radiation-induced Neurodegeneration: A Possible Role of Phytoestrogens.
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Observation of a single protein by ultrafast X-ray diffraction
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ELTD1 deletion reduces vascular abnormality and improves T-cell recruitment after PD-1 blockade in glioma.
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Daniel Globisch SciLifeLab Fellow
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Synthesis and In Vitro Biological Evaluation of Quinolinyl Pyrimidines Targeting Type II NADH-Dehydrogenase (NDH-2).
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OpenCell: Endogenous tagging for the cartography of human cellular organization.
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Improved prediction of protein-protein interactions using AlphaFold2.
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A Systematic Review to Define the Multi-Faceted Role of Lysine Methyltransferase SETD7 in Cancer.
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Sirtuin-1 sensitive lysine-136 acetylation drives phase separation and pathological aggregation of TDP-43.
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Nat Commun 13 (1) 1223 [2022-03-09; online 2022-03-09]
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Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures.
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Chem Sci 13 (10) 2985-2991 [2022-03-09; online 2022-02-21]
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Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome.
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Network Crosstalk as a Basis for Drug Repurposing.
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Mendelian randomization suggests a bidirectional, causal relationship between physical inactivity and adiposity.
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GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
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Four tumor micro-environmental niches explain a continuum of inter-patient variation in the macroscopic cellular composition of breast tumors
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Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
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Plasmonic Fiber Optic Absorbance Biosensor for MDR-Mtb detection using Padlock Probing
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A drug repurposing strategy for overcoming human multiple myeloma resistance to standard-of-care treatment.
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A deep learning framework for characterization of genotype data.
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Critical role of PCYT2 in muscle health and aging
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A Lab-in-a-Fiber optofluidic device using droplet microfluidics and laser-induced fluorescence for virus detection.
Parker HE, Sengupta S, Harish AV, ..., Russom A, Laurell F
Sci Rep 12 (1) 3539 [2022-03-03; online 2022-03-03]
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Longitudinal assessment of reactivity and affinity profile of anti-Jo1 autoantibodies to distinct HisRS domains and a splice variant in a cohort of patients with myositis and anti-synthetase syndrome.
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Inducible CRISPR/Cas9 allows for multiplexed and rapidly segregated single target genome editing in Synechocystis sp. PCC 6803
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Host Adaptation in Legionellales Is 1.9 Ga, Coincident with Eukaryogenesis.
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Use of Antibiotics and Risk of Psychiatric Disorders in Newly Diagnosed Cancer Patients: A Population-Based Cohort Study in Sweden.
Hu K, Smedby KE, Sjölander A, ..., Fang F, Fall K
Cancer Epidemiol Biomarkers Prev 31 (3) 528-535 [2022-03-01; online 2022-01-15]
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Landscape of surfaceome and endocytome in human glioma is divergent and depends on cellular spatial organization.
Governa V, Talbot H, Gonçalves de Oliveira K, ..., Welinder C, Belting M
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High cardiomyocyte diversity in human early prenatal heart development
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Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
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The relationship between ageing and changes in the human blood and brain methylomes.
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The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA.
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Mol. Genet. Genomics 297 (2) 463-484 [2022-03-00; online 2022-02-20]
DDLS Fellow Marc Friedländer Marcel Tarbier SciLifeLab Fellow
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Brack P, Crowther P, Soiland-Reyes S, ..., Ewels P, Goble C
PLoS Comput Biol 18 (3) e1009823 [2022-03-00; online 2022-03-24]
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Survival analysis of pathway activity as a prognostic determinant in breast cancer.
Jeuken GS, Tobin NP, Käll L
PLoS Comput Biol 18 (3) e1010020 [2022-03-00; online 2022-03-28]
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Stromal FAP Expression is Associated with MRI Visibility and Patient Survival in Prostate Cancer.
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Cancer Res Commun 2 (3) 172-181 [2022-03-00; online 2022-03-21]
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Sequence determinants of human gene regulatory elements.
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Rare variants in the outcome of social skills group training for autism.
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RNA-interference screen for p53 regulators unveils a role of WDR75 in ribosome biogenesis.
Moudry P, Chroma K, Bursac S, Volarevic S, Bartek J
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Proteomics in thrombosis research.
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On the origin of TSAR: morphology, diversity and phylogeny of Telonemia.
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Open Biol 12 (3) 210325 [2022-03-00; online 2022-03-16]
Fabien Burki SciLifeLab Fellow
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MYCMI-7: A Small MYC-Binding Compound that Inhibits MYC: MAX Interaction and Tumor Growth in a MYC-Dependent Manner.
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Longitudinal trajectories of lifetime body shape and prostate cancer angiogenesis.
Wang QL, Song M, Clinton SK, ..., Lagergren J, Giovannucci EL
Eur. J. Epidemiol. 37 (3) 261-270 [2022-03-00; online 2022-01-13]
DDLS Fellow Qiaoli Wang
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Evolution of the G Matrix under Nonlinear Genotype-Phenotype Maps.
Milocco L, Salazar-Ciudad I
Am Nat 199 (3) 420-435 [2022-03-00; online 2022-01-11]
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Epigenetics in the Anthropocene: an interview with Oskar Karlsson.
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Oskar Karlsson SciLifeLab Fellow
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Correction to: Toxicogenomics directory of chemically exposed human hepatocytes.
Grinberg M, Stöber RM, Edlund K, ..., Rahnenführer J, Hengstler JG
Arch. Toxicol. 96 (3) 945-946 [2022-03-00; online 2022-02-01]
Adil Mardinoglu SciLifeLab Fellow
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Comparison Between Portal Vein Perfusion Chemotherapy and Neoadjuvant Hepatic Arterial Infusion Chemotherapy for Resectable Intermediate to Advanced Stage Hepatocellular Carcinoma.
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Coexpression of MTH1 and PMS2 Is Associated with Advanced Disease and Disease Progression after Therapy in Melanoma.
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Clonal Hematopoiesis Is Associated With Higher Risk of Stroke.
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Stroke 53 (3) 788-797 [2022-03-00; online 2021-11-08]
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Autoantibodies and SARS-CoV2 infection: The spectrum from association to clinical implication: Report of the 15th Dresden Symposium on Autoantibodies.
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Abstract 016: Artificially Sweetened Beverage Consumption, Plasma Metabolomics, And Risk Of Type 2 Diabetes Among US Adults
Haslam DE, Wang B, Li J, ..., Hu FB, Bhupathiraju SN
Circulation 145 (Suppl_1) - [2022-03-00; online 2022-03-00]
Clemens Wittenbecher DDLS Fellow
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ASO Visual Abstract: Comparison between Portal Vein Perfusion Chemotherapy and Neoadjuvant Hepatic Arterial Infusion Chemotherapy for Resectable Intermediate/Advanced-Stage Hepatocellular Carcinoma
Pan Y, Mei J, Chen J, ..., Guo R, Xu L
Ann Surg Oncol 29 (3) 2032-2033 [2022-03-00; online 2021-10-21]
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ASO Author Reflections: Neoadjuvant Hepatic Arterial Infusion Chemotherapy with Oxaliplatin, Fluorouracil, and Leucovorin Is an Incredible Helper in Curing Patients with Intermediate-Advanced-Stage and Technically Resectable Hepatocellular Carcinoma.
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ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.
Widmark A, Sagredo EA, Karlström V, ..., Daniel C, Öhman M
J Biol Chem 298 (3) 101682 [2022-03-00; online 2022-02-03]
Marc Friedländer SciLifeLab Fellow
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A Swedish Genome-Wide Haplotype Association Analysis Identifies a Novel Breast Cancer Susceptibility Locus in 8p21.2 and Characterizes Three Loci on Chromosomes 10, 11 and 16.
Barnekow E, Liu W, Helgadottir HT, ..., Margolin S, Lindblom A
Cancers (Basel) 14 (5) - [2022-02-25; online 2022-02-25]
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Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction.
Begnini F, Geschwindner S, Johansson P, ..., Schiesser S, Kihlberg J
J Med Chem 65 (4) 3473-3517 [2022-02-24; online 2022-02-02]
Jens Carlsson SciLifeLab Fellow
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White matter microstructure and volume correlates of premenstrual dysphoric disorder.
Gu X, Dubol M, Stiernman L, ..., Sundström-Poromaa I, Comasco E
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Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.
Luttens A, Gullberg H, Abdurakhmanov E, ..., Danielson UH, Carlsson J
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Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort
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Early response evaluation by single cell signaling profiling in acute myeloid leukemia
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An estimate of the deepest branches of the tree of life from ancient vertically evolving genes.
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Tumorigenic activity of alternative per- and polyfluoroalkyl substances (PFAS): Mechanistic in vitro studies.
Pierozan P, Cattani D, Karlsson O
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Reclassifying Cancer: Defining tumour cell cycle activity in terms of its tissue of origin in over 13,000 samples
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Immunity to SARS-CoV-2 up to 15 months after infection.
Marcotte H, Piralla A, Zuo F, ..., Baldanti F, Pan-Hammarström Q
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The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling.
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots.
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Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment.
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Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning
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Dihydroceramide- and ceramide-profiling provides insights into human cardiometabolic disease etiology.
Wittenbecher C, Cuadrat R, Johnston L, ..., Hu FB, Schulze MB
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A retrospective two centre study of Birt-Hogg-Dubé syndrome reveals a pathogenic founder mutation in FLCN in the Swedish population.
Lagerstedt-Robinson K, Baranowska Körberg I, Tsiaprazis S, ..., Johansson-Soller M, Aravidis C
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Polygenic association with severity and long-term outcome in eating disorder cases.
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Clonally heritable gene expression imparts a layer of diversity within cell types
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Balanced chromosomal rearrangements offer insights into coding and noncoding genomic features associated with developmental disorders
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A genome-wide association study in a large community-based cohort identifies multiple loci associated with susceptibility to bacterial and viral infections.
Tängdén T, Gustafsson S, Rao AS, Ingelsson E
Sci Rep 12 (1) 2582 [2022-02-16; online 2022-02-16]
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Potentiating Vγ9Vδ2 T cell proliferation and assessing their cytotoxicity towards adherent cancer cells at the single cell level.
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Machine learning analysis reveals biomarkers for the detection of neurodegenerative diseases
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Abstract P1-07-07: Endoresist: Prognostic and predictive gene profiles in endocrine-resistant breast cancers
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Structure and mechanism of the tripartite ATP-independent periplasmic (TRAP) transporter
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Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA.
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Evening chronotype is associated with elevated biomarkers of cardiometabolic risk in the EpiHealth cohort: a cross-sectional study.
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Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.
Vickovic S, Schapiro D, Carlberg K, ..., Regev A, Ståhl PL
Commun Biol 5 (1) 129 [2022-02-11; online 2022-02-11]
Sanja Vickovic SciLifeLab Fellow
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Prevalence and correlates of current suicidal ideation in women with premenstrual dysphoric disorder.
Wikman A, Sacher J, Bixo M, ..., Comasco E, Sundström Poromaa I
BMC Womens Health 22 (1) 35 [2022-02-11; online 2022-02-11]
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Tree of Mutually Exclusive Oncogenes
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Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor.
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Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.
Mota A, Schweitzer M, Wernersson E, Crosetto N, Bienko M
Sci Data 9 (1) 47 [2022-02-10; online 2022-02-10]
Magda Bienko SciLifeLab Fellow
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SM-Omics is an automated platform for high-throughput spatial multi-omics.
Vickovic S, Lötstedt B, Klughammer J, ..., Rozenblatt-Rosen O, Regev A
Nat Commun 13 (1) 795 [2022-02-10; online 2022-02-10]
Sanja Vickovic SciLifeLab Fellow
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Predictions of Skin Permeability Using Molecular Dynamics Simulation from Two-Dimensional Sampling of Spatial and Alchemical Perturbation Reaction Coordinates
Lundborg M, Wennberg C, Lidmar J, ..., Lindahl E, Norlén L
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Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
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Glioblastoma stem cells express non-canonical proteins and exclusive mesenchymal-like or non-mesenchymal-like protein signatures
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Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops.
Zhivkoplias EK, Vavulov O, Hillerton T, Sonnhammer ELL
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Exploring Non-orthosteric Interactions with a Series of Potent and Selective A3 Antagonists.
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Characterization of Metronidazole-Resistant Giardia intestinalis Lines by Comparative Transcriptomics and Proteomics.
Krakovka S, Ribacke U, Miyamoto Y, Eckmann L, Svärd S
Front Microbiol 13 (-) 834008 [2022-02-10; online 2022-02-10]
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Genomics and adaptation in forest ecosystems.
Neophytou C, Heer K, Milesi P, ..., Rellstab C, Gugerli F
Tree Genet Genomes 18 (2) 12 [2022-02-09; online 2022-02-09]
Pascal Milesi SciLifeLab Fellow
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Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae.
Nadeem A, Berg A, Pace H, ..., Uhlin BE, Wai SN
Elife 11 (-) - [2022-02-08; online 2022-02-08]
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DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.
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Bioinformatics 38 (5) 1235-1243 [2022-02-07; online 2021-11-01]
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Polysome Fractionation for Transcriptome-Wide Studies of mRNA Translation.
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Expression Profiles of Estrogen-Regulated MicroRNAs in Cancer Cells.
Archer A, Kutter C, Williams C
Methods in molecular biology (Clifton, N.J.) 2418 (-) 313-343 [2022-02-05; online 2022-02-05]
Claudia Kutter SciLifeLab Fellow
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Antibody Validation for Estrogen Receptor Beta.
Birgersson M, Katona B, Lindskog C, Pontén F, Williams C
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Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation.
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An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta.
Indukuri R, Damdimopoulos A, Williams C
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ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export.
Malla S, Prasad Bhattarai D, Groza P, ..., Kutter C, Aguilo F
EMBO Rep. 23 (3) e53191 [2022-02-03; online 2022-01-17]
Claudia Kutter SciLifeLab Fellow
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The Evolution of Oxytocin and Vasotocin Receptor Genes in Jawed Vertebrates: A Clear Case for Gene Duplications Through Ancestral Whole-Genome Duplications.
Ocampo Daza D, Bergqvist CA, Larhammar D
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Author response: Identification of electroporation sites in the complex lipid organization of the plasma membrane
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Possible Functional Roles of Patellamides in the Ascidian-Prochloron Symbiosis.
Baur P, Kühl M, Comba P, Behrendt L
Mar Drugs 20 (2) - [2022-02-02; online 2022-02-02]
Lars Behrendt SciLifeLab Fellow
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Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
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ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the lamprey central canal.
Jalalvand E, Alvelid J, Coceano G, ..., Grillner S, Testa I
Elife 11 (-) - [2022-02-01; online 2022-02-01]
Ilaria Testa SciLifeLab Fellow
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Effect of General Adiposity and Central Body Fat Distribution on the Circulating Metabolome: A Multicohort Nontargeted Metabolomics Observational and Mendelian Randomization Study.
Ahmad S, Hammar U, Kennedy B, ..., Larsson SC, Fall T
Diabetes 71 (2) 329-339 [2022-02-01; online 2021-11-18]
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Correction: MEIS-WNT5A axis regulates development of fourth ventricle choroid plexus.
Kaiser K, Jang A, Kompanikova P, ..., Lehtinen MK, Bryja V
Development 149 (3) - [2022-02-01; online 2022-02-04]
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Biomarker-Based Prediction of Longitudinal Tau Positron Emission Tomography in Alzheimer Disease.
Leuzy A, Smith R, Cullen NC, ..., Stomrud E, Hansson O
JAMA Neurol 79 (2) 149-158 [2022-02-01; online 2021-12-21]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
An essential function for autocrine hedgehog signaling in epithelial proliferation and differentiation in the trachea.
Yin W, Liontos A, Koepke J, ..., Stainier DYR, Samakovlis C
Development 149 (3) - [2022-02-01; online 2022-02-07]
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Adverse childhood experiences and resilience among adult women: A population-based study.
Daníelsdóttir HB, Aspelund T, Thordardottir EB, ..., Hauksdóttir A, Valdimarsdóttir UA
Elife 11 (-) - [2022-02-01; online 2022-02-01]
PubMed DOI Crossref
gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.
Irrgang ME, Davis C, Kasson PM
PLoS Comput Biol 18 (2) e1009835 [2022-02-00; online 2022-02-14]
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Towards effective beta-cell replacement through understanding and targeting of the autoreactive immune response during onset of type 1 diabetes
Christoffersson G
Journal of Immunology and Regenerative Medicine 15 (-) 100057 [2022-02-00; online 2022-02-00]
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The Skin's Barrier: A Cryo-EM Based Overview of its Architecture and Stepwise Formation.
Norlén L, Lundborg M, Wennberg C, Narangifard A, Daneholt B
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Structural amyloid plaque polymorphism is associated with distinct lipid accumulations revealed by trapped ion mobility mass spectrometry imaging.
Michno W, Wehrli PM, Koutarapu S, ..., Hopf C, Hanrieder J
J. Neurochem. 160 (4) 482-498 [2022-02-00; online 2021-12-26]
SciLifeLab Fellow Wojciech Michno
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Rifaximin-α reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial.
Patel VC, Lee S, McPhail MJW, ..., Shoaie S, Shawcross DL
J Hepatol 76 (2) 332-342 [2022-02-00; online 2021-09-24]
Saeed Shoaie SciLifeLab Fellow
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Regulation of pentameric ligand-gated ion channels by a semiconserved cation-pi interaction site
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Biophysical Journal 121 (3) 370a [2022-02-00; online 2022-02-00]
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RNA gradients: Shapers of 3D genome architecture.
Bouwman BAM, Crosetto N, Bienko M
Curr Opin Cell Biol 74 (-) 7-12 [2022-02-00; online 2022-01-05]
Magda Bienko SciLifeLab Fellow
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Population-based study of multisystem inflammatory syndrome associated with COVID-19 found that 36% of children had persistent symptoms.
Kahn R, Berg S, Berntson L, ..., Säve-Söderbergh E, Altman M
Acta Paediatr 111 (2) 354-362 [2022-02-00; online 2021-12-01]
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Peroxiredoxin 6 protects irradiated cells from oxidative stress and shapes their senescence-associated cytokine landscape.
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Nociceptin/orphanin FQ opioid receptor (NOP) selective ligand MCOPPB links anxiolytic and senolytic effects.
Raffaele M, Kovacovicova K, Biagini T, ..., Curran SP, Vinciguerra M
Geroscience 44 (1) 463-483 [2022-02-00; online 2021-11-24]
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Multiplex protein screening of biomarkers associated with major bleeding in patients with atrial fibrillation treated with oral anticoagulation: Response to Luo and Bu.
Siegbahn A
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Molecular modeling investigation of proton coupling in XylE
Alleva C, Drew D, Delemotte L
Biophysical Journal 121 (3) 468a [2022-02-00; online 2022-02-00]
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Inhibition of prolyl oligopeptidase: A promising pathway to prevent the progression of age-related macular degeneration.
Hellinen L, Koskela A, Vattulainen E, ..., Artursson P, Urtti A
Biomed. Pharmacother. 146 (-) 112501 [2022-02-00; online 2021-12-07]
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In silico predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology.
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
Xenobiotica 52 (2) 113-118 [2022-02-00; online 2022-03-16]
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Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia.
Malani D, Kumar A, Brück O, ..., Kallioniemi O, Porkka K
Cancer Discov 12 (2) 388-401 [2022-02-00; online 2021-11-17]
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Image-based assessment of extracellular mucin-to-tumor area predicts consensus molecular subtypes (CMS) in colorectal cancer.
Nguyen HG, Lundström O, Blank A, ..., Anisimova M, Zlobec I
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IUCNN – Deep learning approaches to approximate species' extinction risk
Zizka A, Andermann T, Silvestro D
Diversity and Distributions 28 (2) 227-241 [2022-02-00; online 2021-12-16]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
IL-22 Downregulates Peptidylarginine Deiminase-1 in Human Keratinocytes: Adding Another Piece to the IL-22 Puzzle in Epidermal Barrier Formation.
Padhi A, Srivastava A, Ramesh A, ..., Bergman P, Lysell J
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How can we optimize the development of drugs for wound healing?
Vågesjö E, Grigoleit P, Fasth A, Phillipson M
Expert Opin Drug Discov 17 (2) 93-96 [2022-02-00; online 2021-10-20]
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Glutaredoxin 2 promotes SP-1-dependent CSPG4 transcription and migration of wound healing NG2 glia and glioma cells: Enzymatic Taoism.
Wilms C, Lepka K, Häberlein F, ..., Odermatt B, Berndt C
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Details of G-protein coupled receptor activation via data-driven molecular modeling
Delemotte L, Fleetwood O, Chen Y, Pérez Conesa S
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Constant-Ph molecular dynamics simulations of a proton-gated ion channel
Jansen A, Bauer P, Howard RJ, Lindahl E, Hess B
Biophysical Journal 121 (3) 309a [2022-02-00; online 2022-02-00]
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A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection.
Andreakos E, Abel L, Vinh DC, ..., Casanova JL, Spaan AN
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Protocol: A Multiplexed Reporter Assay to Study Effects of Chromatin Context on DNA Double-Strand Break Repair.
Schep R, Leemans C, Brinkman EK, van Schaik T, van Steensel B
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An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection.
Sanchez-Burgos L, Gómez-López G, Al-Shahrour F, Fernandez-Capetillo O
Sci Rep 12 (1) 1626 [2022-01-31; online 2022-01-31]
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Accurate and rapid microfluidic ELISA to monitor Infliximab titers in patients with inflammatory bowel diseases.
Iria I, Soares RRG, Brás EJS, ..., Gonçalves J, Conde JP
Analyst 147 (3) 480-488 [2022-01-31; online 2022-01-31]
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A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments
Abramova A, Berendonk TU, Bengtsson-Palme J
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TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data
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The genomic basis of the plant island syndrome in Darwin’s giant daisies
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The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.
Melani RD, Gerbasi VR, Anderson LC, ..., Levitsky J, Kelleher NL
Science (New York, N.Y.) 375 (6579) 411-418 [2022-01-28; online 2022-01-27]
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Sequence specificity in DNA binding is mainly governed by association.
Marklund E, Mao G, Yuan J, ..., Deindl S, Elf J
Science (New York, N.Y.) 375 (6579) 442-445 [2022-01-28; online 2022-01-27]
Emil Marklund SciLifeLab Fellow Sebastian Deindl
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Role of Cellular Metabolism during Candida-Host Interactions.
Pellon A, Begum N, Sadeghi Nasab SD, ..., Shoaie S, Moyes DL
Pathogens 11 (2) - [2022-01-28; online 2022-01-28]
Saeed Shoaie SciLifeLab Fellow
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Target 2035 - update on the quest for a probe for every protein.
Müller S, Ackloo S, Al Chawaf A, ..., Workman P, Arrowsmith CH
RSC Med Chem 13 (1) 13-21 [2022-01-27; online 2021-12-03]
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Limits and potential of combined folding and docking.
Pozzati G, Zhu W, Bassot C, ..., Kundrotas P, Elofsson A
Bioinformatics 38 (4) 954-961 [2022-01-27; online 2021-11-18]
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Confocal imaging dataset to assess endothelial cell orientation during extreme glucose conditions.
Porras Hernández AM, Barbe L, Pohlit H, Tenje M, Antfolk M
Sci Data 9 (1) 26 [2022-01-27; online 2022-01-27]
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A comprehensive evaluation of consensus spectrum generation methods in proteomics
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Why sequence all eukaryotes?
Blaxter M, Archibald JM, Childers AK, ..., Zhang G, Lewin HA
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Evidence of Air and Surface Contamination with SARS-CoV-2 in a Major Hospital in Portugal.
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Heliyon 8 (1) e08762 [2022-01-00; online 2022-01-14]
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Short- and long-term effects of body weight loss following calorie restriction and gastric bypass on CYP3A-activity - a non-randomized three-armed controlled trial.
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SARS-CoV-2-specific B- and T-cell immunity in a population-based study of young Swedish adults.
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Prognostic role of tumour-infiltrating lymphocytes and macrophages in relation to MSI, CDX2 and BRAF status: a population-based study of metastatic colorectal cancer patients.
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Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples.
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PRRX1 induced by BMP signaling decreases tumorigenesis by epigenetically regulating glioma-initiating cell properties via DNA methyltransferase 3A.
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MTH1 as a target to alleviate T cell driven diseases by selective suppression of activated T cells.
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Improvement of the performance of anticancer peptides using a drug repositioning pipeline.
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Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods.
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PLoS Comput Biol 18 (1) e1009830 [2022-01-00; online 2022-01-31]
Prashant Singh SciLifeLab Fellow
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High-throughput ex vivo drug testing identifies potential drugs and drug combinations for NRAS-positive malignant melanoma.
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Distinct transcription kinetics of pluripotent cell states.
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Changes in metabolomics profiles over ten years and subsequent risk of developing type 2 diabetes: Results from the Nurses' Health Study.
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EBioMedicine 75 (-) 103799 [2022-01-00; online 2021-12-31]
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Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons.
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Genome Res 32 (1) 97-110 [2022-01-00; online 2021-12-02]
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Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge.
Bulten W, Kartasalo K, Chen PC, ..., Eklund M, PANDA challenge consortium
Nat. Med. 28 (1) 154-163 [2022-01-00; online 2022-01-13]
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Allele frequency spectrum of known ankylosing spondylitis associated variants in a Swedish population.
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A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience.
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Transient Colonising Microbes Promote Gut Dysbiosis and Disease Pathology
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The Evolution of Blood Protein Profiles of Extremely Preterm Infants After Birth
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Synthesis and in Vitro Toxicity Assessment of Different Nano-Calcium Phosphate Nanoparticles
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STED and RESOLFT Fluorescent Nanoscopy
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Long-Term SARS-CoV-2 Surveillance in the Wastewater of Stockholm: What Lessons Can Be Learned from the Swedish Perspective?
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Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]
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Diffusion Measurements at the Nanoscale with STED-FCS
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Development of L-Dopa-Containing Diketopiperazines as Blood-Brain Barrier Shuttle
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Cholesterol stiffening of lipid membranes and drug interactions: Insights from neutron spin echo and deuterium NMR spectroscopy
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Association between single nucleotide polymorphisms in non-coding regions of the insulin gene and schizophrenia
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Therapeutic Potential of Ferulic Acid in Alzheimer's Disease.
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An online atlas of human plasma metabolite signatures of gut microbiome composition
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Potential of [11C]UCB-J as a PET tracer for islets of Langerhans.
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Regional Brain Analysis of Modified Amino Acids and Dipeptides during the Sleep/Wake Cycle.
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Influenza A H1N1–mediated pre-existing immunity to SARS-CoV-2 predicts COVID-19 outbreak dynamics
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Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices
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Amino Acid Sensing and Assimilation by the Fungal Pathogen Candida albicans in the Human Host.
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A gene-centric approach to biomarker discovery identifies transglutaminase 1 as an epidermal autoantigen.
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Author response: ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the lamprey central canal
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Analysis of blood group antigens on MUC5AC in mucinous ovarian cancer tissues using in situ proximity ligation assay.
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FRET-FISH probes chromatin compaction at individual genomic loci in single cells
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Proactive autoscaling for edge computing systems with kubernetes
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Monitoring Drug-Target Interactions through Target Engagement-Mediated Amplification on Arrays and in situ
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The Current State of Beta-Cell-Mass PET Imaging for Diabetes Research and Therapies.
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Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cells
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A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization.
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Syndromic RNA polymerase II insufficiency: Generation of a human induced pluripotent stem cell line (UUIGPi002A-5) with a heterozygous disruption of POLR2A.
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Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms.
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Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.
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Identification of a novel variant in GPR56/ADGRG1 gene through whole exome sequencing in a consanguineous Pakistani family.
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High resolution and rapid separation of bacteria from blood using elasto-inertial microfluidics.
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COVID-19 severity and mortality in patients with CLL: an update of the international ERIC and Campus CLL study.
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Leukemia 35 (12) 3444-3454 [2021-12-00; online 2021-11-01]
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Safety in multi-assembly via paths appearing in all path covers of a DAG.
Caceres M, Mumey B, Husic E, ..., Sahlin K, Tomescu AII
IEEE/ACM Trans Comput Biol Bioinform PP (-) - [2021-11-30; online 2021-11-30]
Kristoffer Sahlin SciLifeLab Fellow
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Interleukin-35 Prevents Development of Autoimmune Diabetes Possibly by Maintaining the Phenotype of Regulatory B Cells.
Luo Z, Lundin S, Mejia-Cordova M, ..., Sandler S, Singh K
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A Detailed Gene Expression Map of Giardia Encystation.
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Genomic and niche divergence in an Amazonian palm species complex
Bacon CD, Roncal J, Andermann T, ..., Tunarosa N, Antonelli A
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Editorial: Methanotrophs: Diversity, Environmental Relevance and Applications.
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Biology and Treatment of High-Risk CLL: Significance of Complex Karyotype.
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Training algorithm matters for the performance of neural network potential: A case study of Adam and the Kalman filter optimizers.
Shao Y, Dietrich FM, Nettelblad C, Zhang C
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A panel of CSF proteins separates genetic frontotemporal dementia from presymptomatic mutation carriers: a GENFI study.
Bergström S, Öijerstedt L, Remnestål J, ..., Nilsson P, Genetic Frontotemporal Dementia Initiative (GENFI)
Mol Neurodegener 16 (1) 79 [2021-11-27; online 2021-11-27]
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Point-of-care testing in a high-income country paediatric emergency department: a qualitative study in Sweden.
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HSFs drive stress type-specific transcription of genes and enhancers
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STK11 pathway in vitro validation
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Pinene-Based Oxidative Synthetic Toolbox for Scalable Polyester Synthesis.
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Mass spectrometry-based proteomic analysis of NSCLC tumor and biopsy samples
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Immune landscape evaluation of NSCLC clinical samples
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Bioinformatics analysis of NSCLC multi-omics data
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The Influence of Domain Permutations of an Albumin-Binding Domain-Fused HER2-Targeting Affibody-Based Drug Conjugate on Tumor Cell Proliferation and Therapy Efficacy.
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Pharmaceutics 13 (11) - [2021-11-21; online 2021-11-21]
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High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue
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Fragment-based design of selective GPCR ligands guided by free energy simulations.
Matricon P, Vo DD, Gao ZG, ..., Jacobson KA, Carlsson J
Chem. Commun. (Camb.) 57 (92) 12305-12308 [2021-11-19; online 2021-11-19]
Jens Carlsson SciLifeLab Fellow
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FOXP3+ T cells in uterine sarcomas are associated with favorable prognosis, low extracellular matrix expression and reduced YAP activation.
Gultekin O, Gonzalez-Molina J, Hardell E, ..., Lehti K, Carlson JW
NPJ Precis Oncol 5 (1) 97 [2021-11-19; online 2021-11-19]
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A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease.
Yang H, Arif M, Yuan M, ..., Zhang C, Mardinoglu A
iScience 24 (11) 103222 [2021-11-19; online 2021-10-05]
Adil Mardinoglu SciLifeLab Fellow
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Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps.
Paes Dias M, Tripathi V, van der Heijden I, ..., Ray Chaudhuri A, Jonkers J
Mol. Cell 81 (22) 4692-4708.e9 [2021-11-18; online 2021-09-22]
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Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.
Schön ME, Zlatogursky VV, Singh RP, ..., Wideman JG, Burki F
Nat Commun 12 (1) 6651 [2021-11-17; online 2021-11-17]
Fabien Burki SciLifeLab Fellow
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NUDT18 catalyzes the hydrolysis of active metabolites of the antivirals Remdesivir, Ribavirin and Molnupiravir
Jemth AS, Scaletti ER, Homan E, ..., Helleday T, Michel M
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CD93 Signaling via Rho Proteins Drives Cytoskeletal Remodeling in Spreading Endothelial Cells.
Barbera S, Raucci L, Lugano R, ..., Galvagni F, Orlandini M
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Boron-based hybrids as novel scaffolds for the development of drugs with neuroprotective properties.
Cacciatore I, Turkez H, Di Rienzo A, ..., Mardinoglu A, Di Stefano A
RSC Med Chem 12 (11) 1944-1949 [2021-11-17; online 2021-08-13]
Adil Mardinoglu SciLifeLab Fellow
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Using High-Sensitivity Lipidomics To Assess Microscale Heterogeneity in Oceanic Sinking Particles and Single Phytoplankton Cells.
Hunter JE, Fredricks HF, Behrendt L, ..., Stocker R, Van Mooy BAS
Environ. Sci. Technol. 55 (22) 15456-15465 [2021-11-16; online 2021-11-01]
Lars Behrendt SciLifeLab Fellow
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Precise blood proteome profiling in an undiagnosed population with COVID-19
Fredolini C, Dodig-Crnković T, Bendes A, ..., Roxhed N, Schwenk JM
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MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.
Kang W, Fromm B, Houben AJ, ..., Biryukova I, Friedländer MR
Cell Reports 37 (7) 110015 [2021-11-16; online 2021-11-18]
Marc Friedländer SciLifeLab Fellow
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Influence of the extracellular domain size on the dynamic behavior of membrane proteins
Gurdap CO, Wedemann L, Sych T, Sezgin E
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Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids.
van Husen LS, Katsori AM, Meineke B, ..., Schedin-Weiss S, Elsässer SJ
Chembiochem 22 (22) 3208-3213 [2021-11-16; online 2021-09-13]
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Cover Feature: Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids (ChemBioChem 22/2021)
van Husen LS, Katsori A, Meineke B, ..., Schedin‐Weiss S, Elsässer SJ
Chembiochem 22 (22) 3108-3108 [2021-11-16; online 2021-09-28]
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Antibacterial sulfonimidamide-based oligopeptides as type I signal peptidase inhibitors: Synthesis and biological evaluation.
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Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor.
Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L
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Lucie Delemotte SciLifeLab Fellow
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Glucosylceramide synthase deficiency in the heart compromises β1-adrenergic receptor trafficking.
Andersson L, Cinato M, Mardani I, ..., Borén J, Levin MC
Eur. Heart J. 42 (43) 4481-4492 [2021-11-14; online 2021-07-24]
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A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data
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Image-based high-throughput mapping of TGF-β-induced phosphocomplexes at a single-cell level.
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Commun Biol 4 (1) 1284 [2021-11-12; online 2021-11-12]
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GutMicroNet: an interactive platform for gut microbiome interaction exploration
Arif M, Portlock T, Güngör C, ..., Mardinoglu A, Shoaie S
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A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling.
Meineke B, Heimgärtner J, Craig AJ, ..., Moodie LWK, Elsässer SJ
Front Chem 9 (-) 768535 [2021-11-11; online 2021-11-11]
SciLifeLab Fellow Simon Elsässer
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Association between proton-pump inhibitors and the risk of gastric cancer: a systematic review with meta-analysis.
Segna D, Brusselaers N, Glaus D, Krupka N, Misselwitz B
Ther Adv Gastroenterol 14 (-) 17562848211051463 [2021-11-10; online 2021-11-10]
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Annotation of pituitary neuroendocrine tumors with genome-wide expression analysis.
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Towards a structurally resolved human protein interaction network
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Reprogrammed transsulfuration promotes basal-like breast tumor progression via realigning cellular cysteine persulfidation.
Erdélyi K, Ditrói T, Johansson HJ, ..., Lehtiö J, Nagy P
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Large-scale identification of RBP-RNA interactions by RAPseq refines essentials of post-transcriptional gene regulation
Atanasoai I, Papavasileiou S, Preiß N, Kutter C
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Claudia Kutter SciLifeLab Fellow
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Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis.
Hober A, Tran-Minh KH, Foley D, ..., Engstrand L, Edfors F
Elife 10 (-) - [2021-11-08; online 2021-11-08]
PubMed DOI Crossref
NETs decorated with bioactive IL-33 infiltrate inflamed tissues and induce IFN-α production in patients with SLE.
Georgakis S, Gkirtzimanaki K, Papadaki G, ..., Verginis P, Bertsias G
JCI Insight 6 (21) - [2021-11-08; online 2021-11-08]
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ELIXIR and Toxicology: a community in development
Martens M, Stierum R, Schymanski EL, ..., Županič A, Willighagen EL
F1000Res 10 (-) 1129 [2021-11-08; online 2021-11-08]
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CRISPRi as a Tool to Repress Multiple Copies of Extracellular Polymeric Substances (EPS)-Related Genes in the Cyanobacterium Synechocystis sp. PCC 6803.
Santos M, Pacheco CC, Yao L, Hudson EP, Tamagnini P
Life (Basel) 11 (11) - [2021-11-06; online 2021-11-06]
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pyconsFold: a fast and easy tool for modeling and docking using distance predictions.
Lamb J, Elofsson A
Bioinformatics 37 (21) 3959-3960 [2021-11-05; online 2021-07-10]
DOI Crossref
Specific T Cell Receptor Gene Repertoire Profiles in Subgroups of CLL Patients with Distinct Genomic Aberrations
Vlachonikola E, Sofou E, Gkoliou G, ..., Baliakas P, Chatzidimitriou A
Blood 138 (Supplement 1) 3749-3749 [2021-11-05; online 2021-11-05]
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OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology.
Mulliqi N, Kartasalo K, Olsson H, ..., Eklund M, Ruusuvuori P
Bioinformatics 37 (21) 3995-3997 [2021-11-05; online 2021-08-07]
DDLS Fellow Kimmo Kartasalo
DOI Crossref
Different Prognostic Impact of Recurrent Gene Mutations in IGHV-Mutated and IGHV-Unmutated Chronic Lymphocytic Leukemia: A Retrospective, Multi-Center Cohort Study By Eric, the European Research Initiative on CLL, in Harmony
Mansouri L, Thorvaldsdottir B, Sutton LA, ..., Stamatopoulos K, Rosenquist R
Blood 138 (Supplement 1) 2617-2617 [2021-11-05; online 2021-11-05]
PubMed DOI Crossref
Adaptation to Chronic-Cycling Hypoxia Renders Cancer Cells Resistant to MTH1-Inhibitor Treatment Which Can Be Counteracted by Glutathione Depletion.
Hansel C, Hlouschek J, Xiang K, ..., Jendrossek V, Matschke J
Cells 10 (11) - [2021-11-05; online 2021-11-05]
DOI Crossref
A Novel CD34-Specific T-Cell Engager Efficiently Depletes Stem Cells and Acute Myeloid Leukemia Cells in Vitro and In Vivo
Arruda LCM, Jin L, Lambert M, ..., Carlsten M, Uhlin M
Blood 138 (Supplement 1) 2861-2861 [2021-11-05; online 2021-11-05]
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Testing for association with rare variants in the coding and non-coding genome: RAVA-FIRST, a new approach based on CADD deleteriousness score
Bocher O, Ludwig TE, Marenne G, ..., Perdry H, Génin E
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PubMed DOI Crossref
Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles.
Lewis-Laurent A, Doktorova M, Heberle FA, Marquardt D
Biophys. J. 120 (21) 4639-4648 [2021-11-02; online 2021-09-24]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping.
Soares RRG, Madaboosi N, Nilsson M
Acc. Chem. Res. 54 (21) 3979-3990 [2021-11-02; online 2021-10-12]
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Regulatory T cell differentiation is controlled by αKG-induced alterations in mitochondrial metabolism and lipid homeostasis.
Matias MI, Yong CS, Foroushani A, ..., Taylor N, Dardalhon V
Cell Reports 37 (5) 109911 [2021-11-02; online 2021-11-04]
PubMed DOI Crossref
Mining the Protein Data Bank to improve prediction of changes in protein-protein binding.
Flores SC, Alexiou A, Glaros A
PLoS ONE 16 (11) e0257614 [2021-11-02; online 2021-11-02]
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Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator.
Jahn M, Crang N, Janasch M, ..., Asplund-Samuelsson J, Hudson EP
Elife 10 (-) - [2021-11-01; online 2021-11-01]
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Intercrypt sentinel macrophages tune antibacterial NF-κB responses in gut epithelial cells via TNF.
Hausmann A, Felmy B, Kunz L, ..., Sellin ME, Hardt WD
J. Exp. Med. 218 (11) - [2021-11-01; online 2021-09-16]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Improving sampling of crystallographic disorder in ensemble refinement.
Ploscariu N, Burnley T, Gros P, Pearce NM
Acta Crystallogr D Struct Biol 77 (Pt 11) 1357-1364 [2021-11-01; online 2021-10-20]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Characterization of the human ABO genotypes and their association to common inflammatory and cardiovascular diseases in the UK Biobank.
Höglund J, Karlsson T, Johansson T, Ek WE, Johansson Å
Am. J. Hematol. 96 (11) 1350-1362 [2021-11-01; online 2021-08-18]
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The stress-immunity axis in shellfish.
Coates CJ, Söderhäll K
J Invertebr Pathol 186 (-) 107492 [2021-11-00; online 2020-10-18]
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The role of CDHR3 in susceptibility to otitis media.
Hirsch SD, Elling CL, Bootpetch TC, ..., Ryan AF, Santos-Cortez RLP
J. Mol. Med. 99 (11) 1571-1583 [2021-11-00; online 2021-07-28]
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The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus.
Schwochow D, Bornelöv S, Jiang T, ..., Tixier-Boichard M, Andersson L
Pigment Cell Melanoma Res 34 (6) 1015-1028 [2021-11-00; online 2021-05-04]
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Single cell and spatial transcriptomics in human tendon disease indicate dysregulated immune homeostasis.
Akbar M, MacDonald L, Crowe LAN, ..., McInnes IB, Millar NL
Ann. Rheum. Dis. 80 (11) 1494-1497 [2021-11-00; online 2021-05-17]
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Safety and Efficacy Assessments to Take Antioxidants in Glioblastoma Therapy: From In Vitro Experiences to Animal and Clinical Studies.
Turkez H, Tozlu OO, Arslan ME, Mardinoglu A
Neurochem Int 150 (-) 105168 [2021-11-00; online 2021-08-25]
Adil Mardinoglu SciLifeLab Fellow
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SOX9 Defines Distinct Populations of Cells in SHH Medulloblastoma but Is Not Required for Math1-Driven Tumor Formation.
Adolphe C, Millar A, Kojic M, ..., Genovesi LA, Wainwright BJ
Mol. Cancer Res. 19 (11) 1831-1839 [2021-11-00; online 2021-07-30]
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Protein kinase C family evolution in jawed vertebrates.
Garcia-Concejo A, Larhammar D
Dev. Biol. 479 (-) 77-90 [2021-11-00; online 2021-07-28]
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Intratumoral immunostimulatory AdCD40L gene therapy in patients with advanced solid tumors.
Irenaeus S, Hellström V, Wenthe J, ..., Loskog A, Ullenhag GJ
Cancer Gene Ther. 28 (10-11) 1188-1197 [2021-11-00; online 2020-12-14]
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GRK3 deficiency elicits brain immune activation and psychosis.
Sellgren CM, Imbeault S, Larsson MK, ..., Engberg G, Erhardt S
Mol. Psychiatry 26 (11) 6820-6832 [2021-11-00; online 2021-05-12]
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Effective sequence similarity detection with strobemers
Sahlin K
Genome Res. 31 (11) 2080-2094 [2021-11-00; online 2021-10-19]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Distinction of lymphoid and myeloid clonal hematopoiesis.
Niroula A, Sekar A, Murakami MA, ..., Natarajan P, Ebert BL
Nat. Med. 27 (11) 1921-1927 [2021-11-00; online 2021-10-18]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Discordant Reporting of a Previously Undescribed Pathogenic Germline BRCA2 Variant in Blood and Tumor Tissue in a Patient With Pancreatic Adenocarcinoma.
Kordes M, Tamborero D, Lagerstedt-Robinson K, ..., Löhr JM, Gustafsson Liljefors M
JCO Precis Oncol 5 (-) 974-980 [2021-11-00; online 2022-01-08]
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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.
Biancalani T, Scalia G, Buffoni L, ..., Macosko EZ, Regev A
Nat. Methods 18 (11) 1352-1362 [2021-11-00; online 2021-10-28]
Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations.
Jespers W, Heitman LH, IJzerman AP, ..., Åqvist J, Gutiérrez-de-Terán H
PLoS Comput Biol 17 (11) e1009152 [2021-11-00; online 2021-11-24]
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Cycling between growth and production phases increases cyanobacteria bioproduction of lactate.
Shabestary K, Hernández HP, Miao R, ..., Branco Dos Santos F, Hudson EP
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Correction to: IL‑15 superagonist N‑803 improves IFNγ production and killing of leukemia and ovarian cancer cells by CD34+ progenitor‑derived NK cells.
Van der Meer JMR, Maas RJA, Guldevall K, ..., Hobo W, Dolstra H
Cancer Immunol. Immunother. 70 (11) 3367 [2021-11-00; online 2021-09-16]
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Combined RNA/tissue profiling identifies novel Cancer/testis genes.
Jamin SP, Hikmet F, Mathieu R, ..., Chalmel F, Primig M
Mol Oncol 15 (11) 3003-3023 [2021-11-00; online 2021-06-23]
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Colistin resistance in Escherichia coli confers protection of the cytoplasmic but not outer membrane from the polymyxin antibiotic.
Humphrey M, Larrouy-Maumus GJ, Furniss RCD, ..., Sabnis A, Edwards AM
Microbiology (Reading, Engl.) 167 (11) - [2021-11-00; online 2021-11-02]
PubMed DOI Crossref
Author Correction: Selective inhibitors of mTORC1 activate 4EBP1 and suppress tumor growth.
Lee BJ, Boyer JA, Burnett GL, ..., Smith JAM, Rosen N
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Advances in plasma proteomics: Call for papers for an upcoming special issue.
Yu X, Schwenk J, Xu P, LaBaer J
Proteomics Clin Appl 15 (6) e2100084 [2021-11-00; online 2021-11-12]
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Stratification of the Gut Microbiota Composition Landscape Across the Alzheimer’s Disease Continuum in a Turkish Cohort
Yıldırım S, Nalbantoğlu ÖU, Bayraktar A, ..., Köseoğlu E, Hanoğlu L
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Gene Expression Profiling of Early Acute Febrile Stage of Dengue Infection and Its Comparative Analysis With Streptococcus pneumoniae Infection.
Bajrai LH, Sohrab SS, Alandijany TA, ..., Parveen S, Azhar EI
Front. Cell. Infect. Microbiol. 11 (-) 707905 [2021-10-28; online 2021-10-28]
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Event-triggered STED imaging
Alvelid J, Damenti M, Testa I
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Comprehensive analysis of chemical and biological problems associated with browning agents used in aquatic studies
Scharnweber K, Peura S, Attermeyer K, ..., Tranvik LJ, Székely AJ
Limnol Oceanogr Methods - (-) - [2021-10-28; online 2021-10-28]
Sarahi Garcia SciLifeLab Fellow
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Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis.
Bayraktar A, Lam S, Altay O, ..., Shoaie S, Mardinoglu A
Int J Mol Sci 22 (21) 11556 [2021-10-26; online 2021-10-26]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
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Europe and the world: boosting international academic cooperation in a time of geopolitical tension and polarization.
Vallin M, Gaunt A, Tomson G, Ottersen OP
Eur J Public Health 31 (5) 929-930 [2021-10-26; online 2021-08-27]
PubMed DOI Crossref
The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle.
Omnus DJ, Fink MJ, Szwedo K, Jonas K
Elife 10 (-) - [2021-10-25; online 2021-10-25]
PubMed DOI Crossref
Inferring the experimental design for accurate gene regulatory network inference.
Seçilmiş D, Hillerton T, Nelander S, Sonnhammer ELL
Bioinformatics 37 (20) 3553-3559 [2021-10-25; online 2021-05-13]
PubMed DOI Crossref
Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration.
Liimatainen K, Latonen L, Valkonen M, Kartasalo K, Ruusuvuori P
BMC Cancer 21 (1) 1133 [2021-10-22; online 2021-10-22]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Genome-wide Association Study of Estradiol Levels and the Causal Effect of Estradiol on Bone Mineral Density.
Schmitz D, Ek WE, Berggren E, ..., Karlsson T, Johansson Å
J. Clin. Endocrinol. Metab. 106 (11) e4471-e4486 [2021-10-21; online 2021-07-14]
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Dopaminergic and Cholinergic Modulation of Large Scale Networks in silico Using Snudda.
Frost Nylen J, Hjorth JJJ, Grillner S, Hellgren Kotaleski J
Front Neural Circuits 15 (-) 748989 [2021-10-21; online 2021-10-21]
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Simulation of jet printing of solder paste for surface mounted technology
Mårtensson GE, Göhl J, Mark A
SSMT 33 (5) 266-273 [2021-10-19; online 2021-05-13]
DOI Crossref
Impact of SARS-CoV-2 infection on vaccine-induced immune responses over time
Havervall S, Marking U, Greilert-Norin N, ..., Åberg M, Thålin C
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PubMed DOI Crossref
Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19.
Rivero-García I, Castresana-Aguirre M, Guglielmo L, Guala D, Sonnhammer ELL
Sci Rep 11 (1) 20687 [2021-10-19; online 2021-10-19]
DOI Crossref
Author response: Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis
Hober A, Tran-Minh KH, Foley D, ..., Engstrand L, Edfors F
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PubMed DOI Crossref
Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing.
Carroll LM, Buehler AJ, Gaballa A, ..., Cheng RA, Wiedmann M
Front Microbiol 12 (-) 763669 [2021-10-18; online 2021-10-18]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Chemoselective and Highly Sensitive Quantification of Gut Microbiome and Human Metabolites.
Lin W, Conway LP, Vujasinovic M, Löhr JM, Globisch D
Angew. Chem. Int. Ed. Engl. 60 (43) 23232-23240 [2021-10-18; online 2021-09-17]
Daniel Globisch SciLifeLab Fellow
DOI Crossref
Revisiting the demographic history of Central African populations from a genetic perspective
Breton G, Fortes-Lima C, Schlebusch CM
Hum Popul Genet Genom - (-) 1-29 [2021-10-16; online 2021-10-16]
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Identification of electroporation sites in the complex lipid organization of the plasma membrane
Rems L, Tang X, Zhao F, ..., Testa I, Delemotte L
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scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
Raine A, Lundmark A, Annett A, ..., Bergin C, Nordlund J
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PubMed DOI Crossref
Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel.
Bergh C, Heusser SA, Howard R, Lindahl E
Elife 10 (-) - [2021-10-15; online 2021-10-15]
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Integrative Analysis to Identify Genes Associated with Stemness and Immune Infiltration in Glioblastoma.
Warrier NM, Agarwal P, Kumar P
Cells 10 (10) - [2021-10-15; online 2021-10-15]
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Functional Proteomic Profiling of Triple-Negative Breast Cancer.
Gromova I, Espinoza JA, Grauslund M, ..., van Oostrum J, Moreira JMA
Cells 10 (10) - [2021-10-15; online 2021-10-15]
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Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil.
Kipper D, Orsi RH, Carroll LM, ..., Wiedmann M, Lunge VR
Applied and environmental microbiology 87 (21) e0103621 [2021-10-14; online 2021-08-18]
DDLS Fellow Laura Carroll
DOI Crossref
PoSTcode: Probabilistic image-based spatial transcriptomics decoder
Gataric M, Park JS, Li T, ..., Bayraktar O, Gerstung M
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Imatinib protects against human beta-cell death via inhibition of mitochondrial respiration and activation of AMPK.
Elksnis A, Schiffer TA, Palm F, ..., Welsh N, Wang X
Clin. Sci. 135 (19) 2243-2263 [2021-10-14; online 2021-09-28]
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Herpes Simplex Virus 1 and 2 Infections during Differentiation of Human Cortical Neurons.
Bergström P, Trybala E, Eriksson CE, ..., Zetterberg H, Bergström T
Viruses 13 (10) - [2021-10-14; online 2021-10-14]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
The Assessment of Selected miRNA Profile in Familial Mediterranean Fever.
Kahraman CY, Egin ME, Tatar A, Turkez H, Mardinoglu A
Biomed Res Int 2021 (-) 6495700 [2021-10-13; online 2021-10-13]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars.
Cohn AR, Orsi RH, Carroll LM, ..., Wiedmann M, Cheng RA
Front Microbiol 12 (-) 730411 [2021-10-13; online 2021-10-13]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
USP7 and VCPFAF1 define the SUMO/Ubiquitin landscape at the DNA replication fork.
Franz A, Valledor P, Ubieto-Capella P, ..., Fernandez-Capetillo O, Lecona E
Cell Reports 37 (2) 109819 [2021-10-12; online 2021-10-14]
PubMed DOI Crossref
The polarity protein Par3 coordinates positively self-renewal and negatively invasiveness in glioblastoma.
Dadras MS, Caja L, Mezheyeuski A, ..., Heldin CH, Moustakas A
Cell Death Dis 12 (10) 932 [2021-10-12; online 2021-10-12]
PubMed DOI Crossref
Defining the Scope of Exposome Studies and Research Needs from a Multidisciplinary Perspective.
Zhang P, Carlsten C, Chaleckis R, ..., Wright RO, Wheelock CE
Environ Sci Technol Lett 8 (10) 839-852 [2021-10-12; online 2021-09-07]
DOI Crossref
The coordination of replication initiation with growth rate in Escherichia coli
Knöppel A, Broström O, Gras K, Fange D, Elf J
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Diversity and ecology of protists revealed by metabarcoding.
Burki F, Sandin MM, Jamy M
Curr. Biol. 31 (19) R1267-R1280 [2021-10-11; online 2021-10-13]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet.
Yang H, Mayneris-Perxachs J, Boqué N, ..., Mardinoglu A, Caimari A
Biomedicines 9 (10) - [2021-10-11; online 2021-10-11]
Adil Mardinoglu SciLifeLab Fellow
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Squaric acid as a new chemoselective moiety for mass spectrometry-based metabolomics analysis of amines.
Lin W, Yang Z, Kaur A, ..., Löhr JM, Globisch D
RSC Chem Biol 2 (5) 1479-1483 [2021-10-07; online 2021-08-12]
Daniel Globisch SciLifeLab Fellow
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PatientMatcher: a customizable Python-based open-source tool for matching undiagnosed rare disease patients via the MatchMaker Exchange network
Rasi C, Nilsson D, Magnusson M, ..., Wirta V, Stranneheim H
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Membrane-assisted assembly and selective autophagy of enteroviruses
Dahmane S, Kerviel A, Morado DR, ..., Altan-Bonnet N, Carlson LA
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AKAP79 enables calcineurin to directly suppress protein kinase A activity.
Church TW, Tewatia P, Hannan S, ..., Hellgren Kotaleski J, Gold MG
Elife 10 (-) - [2021-10-06; online 2021-10-06]
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Progress and Future Directions with Peptide-Drug Conjugates for Targeted Cancer Therapy.
Lindberg J, Nilvebrant J, Nygren PÅ, Lehmann F
Molecules 26 (19) - [2021-10-05; online 2021-10-05]
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CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations
Höijer I, Emmanouilidou A, Östlund R, ..., den Hoed M, Ameur A
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Biocatalysis in the Recycling Landscape for Synthetic Polymers and Plastics towards Circular Textiles.
Jönsson C, Wei R, Biundo A, ..., Bornscheuer UT, Syrén PO
ChemSusChem 14 (19) 4028-4040 [2021-10-05; online 2021-02-12]
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Nanoengineered DNA origami with repurposed TOP1 inhibitors targeting myeloid cells for the mitigation of neuroinflammation
Zhu K, Wang Y, Sarlus H, ..., Högberg B, Harris RA
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Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.
Carroll LM, Pierneef R, Mathole M, Matle I
Front Microbiol 12 (-) 748611 [2021-10-04; online 2021-10-04]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Brain microvasculature endothelial cell orientation on micropatterned hydrogels is affected by glucose level variations.
Porras Hernández AM, Barbe L, Pohlit H, Tenje M, Antfolk M
Sci Rep 11 (1) 19608 [2021-10-04; online 2021-10-04]
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Appearance of IgG to SARS-CoV-2 in saliva effectively indicates seroconversion in mRNA vaccinated immunocompromised individuals
Healy K, Pin E, Chen P, ..., Aleman S, Sällberg Chen M
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PubMed DOI Crossref
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning.
Norinder U, Spjuth O, Svensson F
J Cheminform 13 (1) 77 [2021-10-02; online 2021-10-02]
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Evaluating metagenomic assembly approaches for biome-specific gene catalogues
Delgado LF, Andersson AF
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A reassessment of archaeological human remains recovered from rock shelters in Cathkin Peak, South Africa
Meyer A, Peyroteo-Stjerna R, Jolly C, Schlebusch CM, Steyn M
Azania: Archaeological Research in Africa 56 (4) 508-538 [2021-10-02; online 2022-02-08]
PubMed DOI Crossref
Understanding the role of potential pathways and its components including hypoxia and immune system in case of oral cancer.
Bajrai LH, Sohrab SS, Mobashir M, ..., Rizvi MA, Azhar EI
Sci Rep 11 (1) 19576 [2021-10-01; online 2021-10-01]
PubMed DOI Crossref
Predicting Molecular Phenotypes from Histopathology Images: A Transcriptome-Wide Expression-Morphology Analysis in Breast Cancer.
Wang Y, Kartasalo K, Weitz P, ..., Hartman J, Rantalainen M
Cancer Res. 81 (19) 5115-5126 [2021-10-01; online 2021-08-02]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Differential susceptibility of rat primary neurons and neural stem cells to PFOS and PFOA toxicity.
Pierozan P, Karlsson O
Toxicol. Lett. 349 (-) 61-68 [2021-10-01; online 2021-06-11]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Cold-Active Shewanella glacialimarina TZS-4T nov. Features a Temperature-Dependent Fatty Acid Profile and Putative Sialic Acid Metabolism.
Qasim MS, Lampi M, Heinonen MK, ..., Roine E, Sarin LP
Front Microbiol 12 (-) 737641 [2021-10-01; online 2021-10-01]
PubMed DOI Crossref
Clinical Experience of Proteasome Inhibitor Bortezomib Regarding Efficacy and Safety in Severe Systemic Lupus Erythematosus: A Nationwide Study.
Walhelm T, Gunnarsson I, Heijke R, ..., Eriksson P, Sjöwall C
Front Immunol 12 (-) 756941 [2021-10-01; online 2021-10-01]
DOI Crossref
Author response: Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel
Bergh C, Heusser SA, Howard R, Lindahl E
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PubMed DOI Crossref
ZBED6 counteracts high-fat diet-induced glucose intolerance by maintaining beta cell area and reducing excess mitochondrial activation.
Wang X, Younis S, Cen J, ..., Andersson L, Welsh N
Diabetologia 64 (10) 2292-2305 [2021-10-00; online 2021-07-22]
PubMed DOI Crossref
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection.
Lu H, Li F, Yuan L, ..., Kerkhoven EJ, Nielsen J
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Eur Neuropsychopharmacol 51 (-) e165-e166 [2021-10-00; online 2021-10-00]
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The Thioesterase ACOT1 as a Regulator of Lipid Metabolism in Type 2 Diabetes Detected in a Multi-Omics Study of Human Liver.
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Kohshour MO, Papiol S, Just D, ..., Nilsson P, Schulze TG
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Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You?
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Jens Carlsson SciLifeLab Fellow
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Lars Behrendt SciLifeLab Fellow
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Michno W, Blennow K, Zetterberg H, Brinkmalm G
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
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DDLS Fellow Johan Bengtsson-Palme
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Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and valnemulin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06858 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
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Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides: lincomycin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
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DDLS Fellow Johan Bengtsson-Palme
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06855 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06854 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
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EFSA Panel on Biological Hazards (BIOHAZ) , Allende A, Koutsoumanis K, ..., Stella P, Peixe L
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DDLS Fellow Johan Bengtsson-Palme
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
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DDLS Fellow Johan Bengtsson-Palme
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
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DDLS Fellow Johan Bengtsson-Palme
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EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06864 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
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Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 11: Sulfonamides.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06863 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
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Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 10: Quinolones: flumequine and oxolinic acid.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06862 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
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Knowing more from less: miniaturization of ligand-binding assays and electrophoresis as new paradigms for at-line monitoring and control of mammalian cell bioprocesses.
Pinto IF, Mikkonen S, Josefsson L, ..., Emmer Å, Chotteau V
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Interaction of prenatal bisphenols, maternal nutrients, and toxic metal exposures on neurodevelopment of 2-year-olds in the APrON cohort.
Liu J, Martin LJ, Dinu I, ..., Dewey D, Martin JW
Environ Int 155 (-) 106601 [2021-10-00; online 2021-05-04]
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Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution.
Venkatesan S, Angelova M, Puttick C, ..., Swanton C, TRACERx Consortium
Cancer Discov 11 (10) 2456-2473 [2021-10-00; online 2021-05-04]
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Immune‐Modulating Mucin Hydrogel Microdroplets for the Encapsulation of Cell and Microtissue
Yan H, Melin M, Jiang K, ..., Joensson HN, Crouzier T
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Genome-Wide Association Study of Peripheral Artery Disease.
van Zuydam NR, Stiby A, Abdalla M, ..., Kullo IJ, GoLEAD Consortium, SUMMIT Consortium†
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GABA induces a hormonal counter-regulatory response in subjects with long-standing type 1 diabetes.
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Fecal Microbiota in Untreated Children With Juvenile Idiopathic Arthritis: A Comparison With Healthy Children and Healthy Siblings.
Öman A, Dicksved J, Engstrand L, Berntson L
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FP16.04 A Nationwide Population-Based Mapping of Mutations and Gene Fusions in Lung Cancer Among Never-Smokers
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Dog colour patterns explained by modular promoters of ancient canid origin.
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DeepImageJ: A user-friendly environment to run deep learning models in ImageJ.
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Nat. Methods 18 (10) 1192-1195 [2021-10-00; online 2021-09-30]
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Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients.
Fernandes SJ, Ericsson M, Khademi M, ..., Kockum I, Tegnér J
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Corrigendum: Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene.
Fromm B, Tarbier M, Smith O, ..., Gilbert MTP, Friedländer MR
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Marc Friedländer SciLifeLab Fellow
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Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma.
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Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.
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Boosting CAR T-cell responses in lymphoma by simultaneous targeting of CD40/4-1BB using oncolytic viral gene therapy.
Wenthe J, Naseri S, Labani-Motlagh A, ..., Loskog A, Lövgren T
Cancer Immunol. Immunother. 70 (10) 2851-2865 [2021-10-00; online 2021-03-05]
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Association of levonorgestrel intrauterine devices with stress reactivity, mental health, quality of life and sexual functioning: A systematic review.
Bürger Z, Bucher AM, Comasco E, ..., Kogler L, Derntl B
Front Neuroendocrinol 63 (-) 100943 [2021-10-00; online 2021-08-20]
Erika Comasco SciLifeLab Fellow
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A practical guide to large-scale docking.
Bender BJ, Gahbauer S, Luttens A, ..., Irwin JJ, Shoichet BK
Nat Protoc 16 (10) 4799-4832 [2021-10-00; online 2021-09-24]
Jens Carlsson SciLifeLab Fellow
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A microfluidic chip carrier including temperature control and perfusion system for long-term cell imaging.
Cantoni F, Werr G, Barbe L, Porras AM, Tenje M
HardwareX 10 (-) e00245 [2021-10-00; online 2021-11-06]
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An evaluation of a FluoroSpot assay as a diagnostic tool to determine SARS-CoV-2 specific T cell responses.
Mangsbo SM, Havervall S, Laurén I, ..., Klingström J, Thålin C
PLoS ONE 16 (9) e0258041 [2021-09-30; online 2021-09-30]
Gustaf Christoffersson SciLifeLab Fellow
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Machine Learning Predicts the Presence of 2,4,6-Trinitrotoluene in Sediments of a Baltic Sea Munitions Dumpsite Using Microbial Community Compositions.
Janßen R, Beck AJ, Werner J, ..., Andersson AF, Labrenz M
Front Microbiol 12 (-) 626048 [2021-09-29; online 2021-09-29]
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Church TW, Tewatia P, Hannan S, ..., Hellgren Kotaleski J, Gold MG
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Separable Microneedle Patch to Protect and Deliver DNA Nanovaccines Against COVID-19.
Yin Y, Su W, Zhang J, ..., Nie G, Wang H
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Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.
Chelebian E, Avenel C, Kartasalo K, ..., Lundeberg J, Wählby C
Cancers (Basel) 13 (19) - [2021-09-28; online 2021-09-28]
DDLS Fellow Kimmo Kartasalo
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Improved Radiolytic Stability of a 68Ga-labelled Collagelin Analogue for the Imaging of Fibrosis.
Velikyan I, Rosenström U, Rosestedt M, Eriksson O, Antoni G
Pharmaceuticals (Basel, Switzerland) 14 (10) - [2021-09-28; online 2021-09-28]
Olof Eriksson SciLifeLab Fellow
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Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel.
Zayni S, Damiati S, Moreno-Flores S, ..., Jin D, Ehmoser EK
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Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.
Huang X, Fortier AL, Coffman AJ, ..., Ragsdale AP, Gutenkunst RN
Mol. Biol. Evol. 38 (10) 4588-4602 [2021-09-27; online 2021-05-28]
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High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing
Kostecka A, Nowikiewicz T, Olszewski P, ..., Dumanski JP, Piotrowski A
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Discovery, optimization and biodistribution of an Affibody molecule for imaging of CD69.
Persson J, Puuvuori E, Zhang B, ..., Eriksson O, Löfblom J
Sci Rep 11 (1) 19151 [2021-09-27; online 2021-09-27]
Olof Eriksson SciLifeLab Fellow
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A Chromosome-Level Assembly of Blunt Snout Bream (Megalobrama amblycephala) Genome Reveals an Expansion of Olfactory Receptor Genes in Freshwater Fish.
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A structural biology community assessment of AlphaFold 2 applications
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Toward Rapid Detection of Viable Bacteria in Whole Blood for Early Sepsis Diagnostics and Susceptibility Testing.
Narayana Iyengar S, Dietvorst J, Ferrer-Vilanova A, ..., Muñoz-Berbel X, Russom A
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Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
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Adil Mardinoglu SciLifeLab Fellow
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HER3 PET Imaging: 68Ga-Labeled Affibody Molecules Provide Superior HER3 Contrast to 89Zr-Labeled Antibody and Antibody-Fragment-Based Tracers.
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From variant to function in human disease genetics.
Lappalainen T, MacArthur DG
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Editorial: The Role of Biomembranes and Biophysics in Immune Cell Signaling.
Shi Y, Sezgin E, Chen W
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Optimization of an Imidazo[1,2-a]pyridine Series to Afford Highly Selective Type I1/2 Dual Mer/Axl Kinase Inhibitors with In Vivo Efficacy.
McCoull W, Boyd S, Brown MR, ..., Zhu Q, Smith PD
J Med Chem 64 (18) 13524-13539 [2021-09-23; online 2021-09-03]
SciLifeLab Fellow Yumeng Mao
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Microfluidic Synthesis of Indomethacin-Loaded PLGA Microparticles Optimized by Machine Learning.
Damiati SA, Damiati S
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Using informative features in machine learning based method for COVID-19 drug repurposing.
Aghdam R, Habibi M, Taheri G
J Cheminform 13 (1) 70 [2021-09-20; online 2021-09-20]
DDLS Fellow Golnaz Taheri
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Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide.
Su T, Kudva R, Becker T, ..., Cheng J, Beckmann R
Nucleic Acids Res. 49 (16) 9539-9547 [2021-09-20; online 2021-08-18]
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A method for intuitively extracting macromolecular dynamics from structural disorder
Pearce NM, Gros P
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The shared risk of diabetes between dog and cat owners and their pets: register based cohort study
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Secondary ossification center induces and protects growth plate structure
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Purkinje cells located in the adult zebrafish valvula cerebelli exhibit variable functional responses.
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Potential of brain mast cells for therapeutic application in the immune response to bacterial and viral infections.
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Improved prediction of protein-protein interactions using AlphaFold2
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A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability.
Felletti M, Romilly C, Wagner EGH, Jonas K
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Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering.
Lycksell M, Rovšnik U, Bergh C, ..., Howard RJ, Lindahl E
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Glucose and Amino Acid Metabolic Dependencies Linked to Stemness and Metastasis in Different Aggressive Cancer Types.
Chisari A, Golán I, Campisano S, ..., Sancho P, Caja L
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Safety and efficacy of the mRNA BNT162b2 vaccine against SARS-CoV-2 in five groups of immunocompromised patients and healthy controls in a prospective open-label clinical trial
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Protein-lipid interaction at low pH induces oligomerisation of the MakA cytotoxin from Vibrio cholerae
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ShareLoc – an open platform for sharing localization microscopy data
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Re-expression of glucuronyl C5-epimerase in the mutant MEF cells increases heparan sulfate epimerization but has no influence on the Golgi localization and enzymatic activity of 2-O-sulfotransferase.
Cui H, Wang Z, Zhang T, Li JP, Fang J
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Selection on accessible chromatin regions in Capsella grandiflora.
Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T
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Vision, challenges and opportunities for a Plant Cell Atlas.
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Dynamin inhibition causes context-dependent cell death of leukemia and lymphoma cells.
von Beek C, Alriksson L, Palle J, ..., Sellin ME, Pejler G
PLoS ONE 16 (9) e0256708 [2021-09-07; online 2021-09-07]
Mikael Sellin SciLifeLab Fellow
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Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma.
van den Boogaard ML, Oka R, Hakkert A, ..., Koster J, Molenaar JJ
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Correction to 'Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue'.
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Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome.
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Foxm1 regulates neural progenitor fate during spinal cord regeneration.
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Comprehensive cancer-oriented biobanking resource of human samples for studies of post-zygotic genetic variation involved in cancer predisposition
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Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina
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Multi-omics approaches for revealing the complexity of cardiovascular disease.
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ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing.
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Blood Cancer Discov 2 (5) 500-517 [2021-09-00; online 2021-07-14]
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The long-time orphan protist Meringosphaera mediterranea Lohmann, 1902 [1903] is a centrohelid heliozoan.
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Wiktor J, Gynnå AH, Leroy P, ..., Testa I, Elf J
Nature 597 (7876) 426-429 [2021-09-00; online 2021-09-01]
Ilaria Testa SciLifeLab Fellow
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Profiles of Glucose Metabolism in Different Prediabetes Phenotypes, Classified by Fasting Glycemia, 2-Hour OGTT, Glycated Hemoglobin, and 1-Hour OGTT: An IMI DIRECT Study.
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Potential for improved retention rate by personalized antiseizure medication selection: A register-based analysis.
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Jens Carlsson SciLifeLab Fellow
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Phosphorus Regulation of Methane Oxidation in Water From Ice‐Covered Lakes
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PharmVar GeneFocus: CYP2C9.
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Killing two enemies with one stone? Genomics of resistance to two sympatric pathogens in Norway spruce.
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Pascal Milesi SciLifeLab Fellow
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Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells.
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Hereditary palmoplantar keratoderma - phenotypes and mutations in 64 patients.
Harjama L, Karvonen V, Kettunen K, ..., Kere J, Hannula-Jouppi K
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Genes in human obesity loci are causal obesity genes in C. elegans.
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Umer HM, Smolinska K, Komorowski J, Wadelius C
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Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19.
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Cell morphology descriptors and gene ontology profiles improve prediction for mitochondrial toxicity
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A single-cell and spatially resolved atlas of human breast cancers.
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A highly multiplexed quantitative phosphosite assay for biology and preclinical studies.
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Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies.
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A brief review of vertebrate sex evolution with a pledge for integrative research: towards 'sexomics'.
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Enterotoxigenic Escherichia coli display a distinct growth phase before entry into stationary phase with shifts in tryptophan- fucose- and putrescine metabolism and degradation of neurotransmitter precursors
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Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics.
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TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia.
Bensberg M, Rundquist O, Selimović A, ..., Lentini A, Nestor CE
Proc. Natl. Acad. Sci. U.S.A. 118 (34) - [2021-08-24; online 2021-08-21]
Antonio Lentini DDLS Fellow
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High definition DIC imaging uncovers transient stages of pathogen infection cycles on the surface of human adult stem cell-derived intestinal epithelium
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Single cell organization and cell cycle characterization of DNA stained multicellular tumor spheroids.
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Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly.
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Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm differentiation
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Structure and Sequence-based Computational Approaches to Allosteric Signal Transduction: Application to Electromechanical Coupling in Voltage-gated Ion Channels.
Elbahnsi A, Delemotte L
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Lucie Delemotte SciLifeLab Fellow
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Ion Channels: Intersection of Structure, Function, and Pharmacology.
Moiseenkova-Bell V, Delemotte L, Minor DL
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Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models.
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The ABCC4 gene is associated with pyometra in golden retriever dogs.
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NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1.
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Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins
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Functional cross-talk between phosphorylation and disease-causing mutations in the cardiac sodium channel Nav1.5.
Galleano I, Harms H, Choudhury K, ..., Delemotte L, Pless SA
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Lucie Delemotte SciLifeLab Fellow
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ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the central canal
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Coordinating DNA Replication and Mitosis through Ubiquitin/SUMO and CDK1.
Galarreta A, Valledor P, Fernandez-Capetillo O, Lecona E
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Advances in the Relationships Between Cow's Milk Protein Allergy and Gut Microbiota in Infants.
Yang Y, Li X, Yang Y, ..., Ji B, Wei Y
Front Microbiol 12 (-) 716667 [2021-08-16; online 2021-08-16]
Saeed Shoaie SciLifeLab Fellow
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ImSwitch: Generalizing microscope control in Python
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JOSS 6 (64) 3394 [2021-08-14; online 2021-08-14]
Ilaria Testa SciLifeLab Fellow
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Neutralization of VOCs including Delta one year post COVID-19 or vaccine
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Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.
Martin G, Rissanen AJ, Garcia SL, ..., Buck M, Peura S
Front Microbiol 12 (-) 669937 [2021-08-12; online 2021-08-12]
Sarahi Garcia SciLifeLab Fellow
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The Uppsala APP deletion causes early onset autosomal dominant Alzheimer's disease by altering APP processing and increasing amyloid β fibril formation.
Pagnon de la Vega M, Giedraitis V, Michno W, ..., Sehlin D, Ingelsson M
Sci Transl Med 13 (606) - [2021-08-11; online 2021-08-13]
SciLifeLab Fellow Wojciech Michno
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Neuronal mimicry generates an ecosystem critical for brain metastatic growth of SCLC
Qu F, Cao S, Michno W, ..., Paşca AM, Sage J
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SciLifeLab Fellow Wojciech Michno
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Structure‐Guided Design of G‐Protein‐Coupled Receptor Polypharmacology
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Angewandte Chemie 133 (33) 18170-18178 [2021-08-09; online 2021-07-16]
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Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology.
Kampen S, Duy Vo D, Zhang X, ..., Kihlberg J, Carlsson J
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Jens Carlsson SciLifeLab Fellow
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Key molecular alterations in endothelial cells in human glioblastoma uncovered through single-cell RNA sequencing.
Xie Y, He L, Lugano R, ..., Dimberg A, Zhang L
JCI Insight 6 (15) - [2021-08-09; online 2021-08-09]
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Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Baranasic D, Hörtenhuber M, Balwierz P, ..., Lenhard B, Müller F
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Integrated Single Cell and Spatial Transcriptomics Reveal Autoreactive Differentiated B Cells in Joints of Early Rheumatoid Arthritis
Hardt U, Carlberg K, Klint Ea, ..., Ståhl PL, Malmström V
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Author response: A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability
Felletti M, Romilly C, Wagner EGH, Jonas K
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Sample-to-answer COVID-19 nucleic acid testing using a low-cost centrifugal microfluidic platform with bead-based signal enhancement and smartphone read-out.
Soares RRG, Akhtar AS, Pinto IF, ..., Pelechano V, Russom A
Lab Chip 21 (15) 2932-2944 [2021-08-07; online 2021-06-11]
SciLifeLab Fellow Vicente Pelechano
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Genome assemblies of three closely related leaf beetle species (Galerucella spp.).
Yang X, Slotte T, Dainat J, Hambäck PA
G3 11 (8) - [2021-08-07; online 2021-12-02]
SciLifeLab Fellow Tanja Slotte
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Quantifying RNA Synthesis at Rate-Limiting Steps of Transcription Using Nascent RNA-Sequencing Data
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Canine oral melanoma genomic and transcriptomic study defines two molecular subgroups with different therapeutical targets
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MapToCleave: high-throughput profiling of microRNA biogenesis in living cells
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Lysine demethylase LSD1 delivered via small extracellular vesicles promotes gastric cancer cell stemness.
Zhao LJ, Li YY, Zhang YT, ..., Zheng YC, Liu HM
EMBO Rep. 22 (8) e50922 [2021-08-04; online 2021-05-31]
Adil Mardinoglu SciLifeLab Fellow
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Imaging-Guided Therapy Simultaneously Targeting HER2 and EpCAM with Trastuzumab and EpCAM-Directed Toxin Provides Additive Effect in Ovarian Cancer Model.
Xu T, Vorobyeva A, Schulga A, ..., Tolmachev V, Deyev SM
Cancers (Basel) 13 (16) - [2021-08-04; online 2021-08-04]
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Combined Metabolic Activators Improve Cognitive Functions without Altering Motor Scores in Parkinson’s Disease
Yulug B, Altay O, Li X, ..., Uhlén M, Mardinoglu A
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Microbial retention and resistances in stormwater quality improvement devices treating road runoff
Liguori R, Rommel SH, Bengtsson-Palme J, Helmreich B, Wurzbacher C
FEMS Microbes 2 (-) - [2021-08-03; online 2021-07-22]
DDLS Fellow Johan Bengtsson-Palme
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A phenomics approach for antiviral drug discovery.
Rietdijk J, Tampere M, Pettke A, ..., Puumalainen MR, Carreras-Puigvert J
BMC Biol. 19 (1) 156 [2021-08-02; online 2021-08-02]
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Response to Lai.
Wang QL, Lagergren J
Am J Gastroenterol 116 (8) 1758 [2021-08-01; online 2021-05-25]
DDLS Fellow Qiaoli Wang
PubMed DOI Crossref
NEIL3 Prevents Senescence in Hepatocellular Carcinoma by Repairing Oxidative Lesions at Telomeres during Mitosis.
Zhao Z, Gad H, Benitez-Buelga C, ..., Xia Q, Helleday T
Cancer Res. 81 (15) 4079-4093 [2021-08-01; online 2021-05-27]
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Co-occurrence of cohesin complex and Ras signaling mutations during progression from myelodysplastic syndromes to secondary acute myeloid leukemia.
Martín-Izquierdo M, Abáigar M, Hernández-Sánchez JM, ..., Díez-Campelo M, Hernández-Rivas JM
Haematologica 106 (8) 2215-2223 [2021-08-01; online 2021-08-01]
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Theoretical studies on 1,4-dihydropyridine derivatives as P-glycoprotein allosteric inhibitors: insights on symmetry and stereochemistry.
Mollazadeh S, Hadizadeh F, Ferreira RJ
J Biomol Struct Dyn 39 (13) 4752-4763 [2021-08-00; online 2020-06-23]
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The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.
Kanellis DC, Espinoza JA, Zisi A, ..., Lindström MS, Bartek J
Sci Adv 7 (32) - [2021-08-00; online 2021-08-04]
SciLifeLab Fellow Simon Elsässer
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The evolutionary history of topological variations in the CPA/AT transporters.
Sudha G, Bassot C, Lamb J, ..., Huang Y, Elofsson A
PLoS Comput Biol 17 (8) e1009278 [2021-08-00; online 2021-08-17]
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The emerging role of artificial intelligence in the reporting of prostate pathology.
Egevad L, Delahunt B, Samaratunga H, ..., Kartasalo K, Eklund M
Pathology 53 (5) 565-567 [2021-08-00; online 2021-06-06]
DDLS Fellow Kimmo Kartasalo
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Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase.
Frewein MPK, Doktorova M, Heberle FA, ..., Porcar L, Pabst G
Symmetry (Basel) 13 (8) - [2021-08-00; online 2021-08-05]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.
Garrido-Godino AI, Gupta I, Gutiérrez-Santiago F, ..., Pelechano V, Navarro F
RNA Biol 18 (8) 1206-1220 [2021-08-00; online 2020-11-01]
SciLifeLab Fellow Vicente Pelechano
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Regulation of a pentameric ligand-gated ion channel by a semiconserved cationic lipid-binding site.
Sridhar A, Lummis SCR, Pasini D, ..., Howard RJ, Ulens C
J Biol Chem 297 (2) 100899 [2021-08-00; online 2021-06-19]
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Prognostic and Predictive Implications of Cytogenetics and Genomics.
Ljungström V, Baliakas P
Hematol Oncol Clin North Am 35 (4) 703-713 [2021-08-00; online 2021-05-28]
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Polymorphisms rs55710213 and rs56334587 regulate SCD1 expression by modulating HNF4A binding.
Pan G, Cavalli M, Wadelius C
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1864 (8) 194724 [2021-08-00; online 2021-06-22]
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Phylogenomics and evolutionary history of Oreobates (Anura: Craugastoridae) Neotropical frogs along elevational gradients.
Montero-Mendieta S, De la Riva I, Irisarri I, ..., Webster MT, Vilà C
Mol. Phylogenet. Evol. 161 (-) 107167 [2021-08-00; online 2021-03-30]
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PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.
Tice AK, Žihala D, Pánek T, ..., Kolísko M, Brown MW
PLoS Biol. 19 (8) e3001365 [2021-08-00; online 2021-08-06]
Fabien Burki SciLifeLab Fellow
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Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry.
Scott HL, Kennison KB, Enoki TA, ..., Heberle FA, Katsaras J
Symmetry (Basel) 13 (8) - [2021-08-00; online 2021-07-26]
DDLS Fellow Milka Doktorova
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MTH1 Inhibitors for the Treatment of Psoriasis.
Bivik Eding C, Köhler I, Verma D, ..., Warpman Berglund U, Enerbäck C
J. Invest. Dermatol. 141 (8) 2037-2048.e4 [2021-08-00; online 2021-03-05]
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Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica.
Powers TR, Haeberle AL, Predeus AV, ..., Hinton JCD, Knodler LA
PLoS Pathog 17 (8) e1009280 [2021-08-00; online 2021-08-30]
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In vitro neuroprotective effects of farnesene sesquiterpene on alzheimer's disease model of differentiated neuroblastoma cell line.
Arslan ME, Türkez H, Mardinoğlu A
Int J Neurosci 131 (8) 745-754 [2021-08-00; online 2020-04-19]
Adil Mardinoglu SciLifeLab Fellow
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Hepatocyte size fractionation allows dissection of human liver zonation.
Ölander M, Wegler C, Flörkemeier I, ..., Urdzik J, Artursson P
J. Cell. Physiol. 236 (8) 5885-5894 [2021-08-00; online 2021-01-16]
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Getting a grip with kirigami.
Teleki A, Artursson P
Nat Mater 20 (8) 1043-1044 [2021-08-00; online 2021-07-30]
Alexandra Teleki SciLifeLab Fellow
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PFKFB3 Inhibition Sensitizes DNA Crosslinking Chemotherapies by Suppressing Fanconi Anemia Repair.
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The Healthy Female Microbiome Across Body Sites: Effect of Hormonal Contraceptives and the Menstrual Cycle
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Recent Progress in the Molecular Imaging of Nonalcoholic Fatty Liver Disease.
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Circadian Genes as Exploratory Biomarkers in DMD: Results From Both the mdx Mouse Model and Patients.
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Wide-Ranging Effects on the Brain Proteome in a Transgenic Mouse Model of Alzheimer's Disease Following Treatment with a Brain-Targeting Somatostatin Peptide.
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Interpretable Machine Learning Identifies Paediatric Systemic Lupus Erythematosus Subtypes Based On Gene Expression Data
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A Novel mRNA-Mediated and MicroRNA-Guided Approach to Specifically Eradicate Drug-Resistant Hepatocellular Carcinoma Cell Lines by Se-Methylselenocysteine.
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Genome-Wide Association Study of Estradiol Levels, and the Causal Effect of Estradiol on Bone Mineral Density
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Agonistic CD40 therapy induces tertiary lymphoid structures but impairs responses to checkpoint blockade in glioma.
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The spatial transcriptomic landscape of the healing intestine following damage
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DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics.
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The Effect of the Molecular Weight of Polyvinylpyrrolidone and the Model Drug on Laser-Induced In Situ Amorphization.
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Tafazzin Deficiency Reduces Basal Insulin Secretion and Mitochondrial Function in Pancreatic Islets From Male Mice.
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PathBIX-a web server for network-based pathway annotation with adaptive null models.
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CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells
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The emerging role of radionuclide molecular imaging of HER2 expression in breast cancer.
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Simultaneous detection of SARS-CoV-2 and pandemic (H1N1) 2009 virus with real-time isothermal platform.
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Same data, different conclusions: Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis
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Safety Assessments of Nickel Boride Nanoparticles on the Human Pulmonary Alveolar Cells by Using Cell Viability and Gene Expression Analyses.
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Biol Trace Elem Res 199 (7) 2602-2611 [2021-07-00; online 2020-09-09]
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STED and parallelized RESOLFT optical nanoscopy of the tubular endoplasmic reticulum and its mitochondrial contacts in neuronal cells.
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Reconditioning the Neurogenic Niche of Adult Non-human Primates by Antisense Oligonucleotide-Mediated Attenuation of TGFβ Signaling.
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Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.
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Prediagnostic use of estrogen-only therapy is associated with improved colorectal cancer survival in menopausal women: a Swedish population-based cohort study.
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On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).
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Multifaceted regulation of hepatic lipid metabolism by YY1.
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Multi-cohort profiling reveals elevated CSF levels of brain-enriched proteins in Alzheimer's disease.
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Molecular Dynamics Simulations of Ion Channels.
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Modification of Heritability for Educational Attainment and Fluid Intelligence by Socioeconomic Deprivation in the UK Biobank.
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Metabolic control of nitrogen fixation in rhizobium-legume symbioses.
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Increased levels of inflammatory markers in the subscapularis tendon and joint capsule in patients with subacromial impingement.
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Identification and characterisation of tertiary lymphoid organs in human type 1 diabetes.
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Diabetes Obes Metab 23 (7) 1505-1517 [2021-07-00; online 2021-03-12]
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Environ Int 152 (-) 106488 [2021-07-00; online 2021-03-10]
Oskar Karlsson SciLifeLab Fellow
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Neuropsychopharmacology 46 (8) 1460-1467 [2021-07-00; online 2021-04-29]
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Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer in Biopsies-Current Status and Next Steps.
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Eur Urol Focus 7 (4) 687-691 [2021-07-00; online 2021-08-12]
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Analogue tuning of particle focusing in elasto-inertial flow
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Developing an Electrochemical Biosensor for the Detection of Hemagglutinin Protein of Influenza A Virus Subtype H1N1 in Artificial Saliva
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Kristina Jonas SciLifeLab Fellow
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A Multi-omics Study of Circulating Phospholipid Markers of Blood Pressure
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The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle
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DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data
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Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides.
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Analysis at single-cell resolution identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons
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Cisplatin inhibits frequency and suppressive activity of monocytic myeloid-derived suppressor cells in cancer patients.
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Pesticide-induced multigenerational effects on amphibian reproduction and metabolism.
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Oskar Karlsson SciLifeLab Fellow
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Concurrent expression of HP-NAP enhances antitumor efficacy of oncolytic vaccinia virus but not for Semliki Forest virus.
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Chemical mapping exposes the importance of active site interactions in governing the temperature dependence of enzyme turnover
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The human nucleoporin Tpr protects cells from RNA-mediated replication stress.
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Engineered human induced pluripotent cells enable genetic code expansion in brain organoids
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An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
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COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.
Simonetti M, Zhang N, Harbers L, ..., Ghisetti V, Crosetto N
Nat Commun 12 (1) 3903 [2021-06-23; online 2021-06-23]
Magda Bienko SciLifeLab Fellow
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Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators.
Jiang RM, Wrede F, Singh P, Hellander A, Petzold LR
BMC Bioinformatics 22 (1) 339 [2021-06-23; online 2021-06-23]
Prashant Singh SciLifeLab Fellow
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Probing interplays between human XBP1u translational arrest peptide and 80S ribosome
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Plasma Proteomic Analysis in Non-Small Cell Lung Cancer Patients Treated with PD-1/PD-L1 Blockade.
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Intra-vessel heterogeneity establishes enhanced sites of macromolecular leakage downstream of laminin α5.
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A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells
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The contribution of rare whole genome sequencing variants to plasma protein levels and to the missing heritability
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The Influence of Drug–Polymer Solubility on Laser-Induced In Situ Drug Amorphization Using Photothermal Plasmonic Nanoparticles
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Digital droplet microfluidic integrated Lab-in-a-fiber detection of SARS-CoV2 viral RNA
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CLEO®/Europe-EQEC 2021, One Page Summary Template Volumetric RESOLFT fluorescence nanoscopy
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Mendelian randomization suggests a bidirectional, causal relationship between physical inactivity and obesity
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Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome
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Stable IgG-antibody levels in patients with mild SARS-CoV-2 infection
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Application of high-throughput 5'P sequencing for the study of co-translational mRNA decay.
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A combination of genetic and phenotypic characterization of spring- and autumn-spawning herring suggests gene flow between populations
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Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.
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flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data.
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Means, Motive, and Opportunity: Do Non-Islet-Reactive Infiltrating T Cells Contribute to Autoimmunity in Type 1 Diabetes?
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Front Immunol 12 (-) 683091 [2021-06-16; online 2021-06-16]
Gustaf Christoffersson SciLifeLab Fellow
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Early Changes in Crayfish Hemocyte Proteins after Injection with a β-1,3-glucan, Compared to Saline Injected and Naive Animals.
Ekblom C, Söderhäll K, Söderhäll I
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Cooperativity of α-Synuclein Binding to Lipid Membranes.
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Insights into the Role of the Discontinuous TM7 Helix of Human Ferroportin through the Prism of the Asp325 Residue.
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Flex Printed Circuit Board Implemented Graphene-Based DNA Sensor for Detection of SARS-CoV-2.
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Comparison of vaginal self-sampling and cervical sampling by medical professionals for the detection of HPV and CIN2+: A randomized study.
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Cell scientist to watch – Alexey Amunts
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Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology.
Shakur R, Ochoa JP, Robinson AJ, ..., Vihinen M, Monserrat L
NPJ Genom Med 6 (1) 47 [2021-06-14; online 2021-06-14]
Abhishek Niroula DDLS Fellow
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Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling.
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Angew. Chem. Int. Ed. Engl. 60 (25) 13937-13944 [2021-06-14; online 2021-05-05]
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Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.
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Genome Biol. 22 (1) 179 [2021-06-13; online 2021-06-13]
Pascal Milesi SciLifeLab Fellow
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Affinity Proteomics Assays for Cardiovascular and Atherosclerotic Disease Biomarkers.
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Author response: NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
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A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics.
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Systems analysis reveals ageing-related perturbations in retinoids and sex hormones in Alzheimer’s and Parkinson’s diseases
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SignalP 6.0 achieves signal peptide prediction across all types using protein language models
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Learning the Regulatory Code of Gene Expression.
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A porcine brain-wide RNA editing landscape.
Huang J, Lin L, Dong Z, ..., Bolund L, Luo Y
Commun Biol 4 (1) 717 [2021-06-10; online 2021-06-10]
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Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
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A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines
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New Perspectives on the Evolution of Within-Individual Genome Variation and Germline/Soma Distinction.
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Utilizing Laser Activation of Photothermal Plasmonic Nanoparticles to Induce On-Demand Drug Amorphization inside a Tablet
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Mol. Pharmaceutics 18 (6) 2254-2262 [2021-06-07; online 2021-05-05]
Alexandra Teleki SciLifeLab Fellow
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SARS-CoV-2-related MIS-C: A key to the viral and genetic causes of Kawasaki disease?
Sancho-Shimizu V, Brodin P, Cobat A, ..., Casanova JL, Zhang SY
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Limits and potential of combined folding and docking using PconsDock
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Spatial cell type mapping of the oligodendrocyte lineage in the mouse juvenile and adult CNS with in situ sequencing
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STED super-resolution imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes
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Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data
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Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment LC-MS Analysis
Hober A, Hua TMK, Foley D, ..., Engstrand L, Edfors F
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The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function.
Oftedal BE, Maio S, Handel AE, ..., Maizels RM, Holländer GA
Commun Biol 4 (1) 681 [2021-06-03; online 2021-06-03]
Erdinc Sezgin SciLifeLab Fellow
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Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data
Younes S, Annett A, Stoll P, ..., Meadows J, Komorowski J
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte M, Saraswat M, Bessière C, ..., Bréhélin L, Lecellier CH
Nat Commun 12 (1) 3297 [2021-06-02; online 2021-06-02]
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USP7 limits CDK1 activity throughout the cell cycle.
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Imaging of the Glucagon Receptor in Subjects with Type 2 Diabetes.
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Journal of nuclear medicine : official publication, Society of Nuclear Medicine 62 (6) 833-838 [2021-06-01; online 2020-10-23]
Olof Eriksson SciLifeLab Fellow
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EMBR-07. MYC BUT NOT MYCN GENERATES AGGRESSIVE GROUP 3 MEDULLOBLASTOMA BY ARF PATHWAY SUPPRESSION
Mainwaring O, Weishaupt H, Hutter S, ..., Kasper M, Swartling F
Neuro-oncology 23 (Supplement_1) i7-i7 [2021-06-01; online 2021-06-01]
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Unboxing mutations: Connecting mutation types with evolutionary consequences.
Berdan EL, Blanckaert A, Slotte T, ..., Westram AM, Fragata I
Mol. Ecol. 30 (12) 2710-2723 [2021-06-00; online 2021-05-19]
SciLifeLab Fellow Tanja Slotte
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Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being.
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Biol Futur 72 (2) 119-125 [2021-06-00; online 2020-09-07]
SciLifeLab Fellow Simon Elsässer
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Nat Cancer 2 (6) 581-583 [2021-06-00; online 2022-02-06]
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POS0392 PRESENCE OF FOUR SERUM AUTOANTIBODIES ASSOCIATES WITH THE ACPA STATUS IN EARLY RHEUMATOID ARTHRITIS
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Ann Rheum Dis 80 (-) 425-426 [2021-06-00; online 2021-06-00]
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POS0008 IDENTIFICATION AND CHARACTERIZATION OF HISRS+ CD4+ T CELLS PATIENTS WITH IDIOPATHIC INFLAMMATORY MYOPATHIES
Horuluoglu B, Galindo-Feria AS, Chemin K, ..., Malmström V, Lundberg IE
Ann Rheum Dis 80 (-) 206 [2021-06-00; online 2021-06-00]
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More Than Just Letters and Chemistry: Genomics Goes Mechanics.
Deindl S, Elf J
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SciLifeLab Fellow Sebastian Deindl
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Lynch syndrome and Muir-Torre phenotype associated with a recurrent variant in the 3'UTR of the MSH6 gene.
Cini G, Carnevali I, Sahnane N, ..., Viel A, Tibiletti MG
Cancer Genet 254-255 (-) 1-10 [2021-06-00; online 2021-01-19]
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Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies.
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Virchows Arch. 478 (6) 1109-1116 [2021-06-00; online 2021-02-03]
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Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells.
Erdem C, Lee AV, Taylor DL, Lezon TR
PLoS Comput Biol 17 (6) e1009125 [2021-06-00; online 2021-06-30]
Cemal Erdem DDLS Fellow
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Human origins in Southern African palaeo-wetlands? Strong claims from weak evidence
Schlebusch CM, Loog L, Groucutt HS, ..., Brierley C, Thomas MG
Journal of Archaeological Science 130 (-) 105374 [2021-06-00; online 2021-06-00]
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GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction.
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From Prehistory to Precision Medicine: Are Genetic Risk Scores Our Next Step?
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Following spatial Aβ aggregation dynamics in evolving Alzheimer's disease pathology by imaging stable isotope labeling kinetics.
Michno W, Stringer KM, Enzlein T, ..., Edwards FA, Hanrieder J
Sci Adv 7 (25) - [2021-06-00; online 2021-06-16]
SciLifeLab Fellow Wojciech Michno
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Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV-CATCHER): A customizable purification assay designed for small-RNA biomarker identification and evaluation of circulating small-EVs.
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Diversity in immunogenomics: the value and the challenge.
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Nat. Methods 18 (6) 588-591 [2021-06-00; online 2021-05-19]
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Digest: Population genomics reveals convergence toward melanism in different island populations.
Robert A, Peona V, Ottenburghs J
Evolution 75 (6) 1582-1584 [2021-06-00; online 2021-05-05]
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Correction to: Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being.
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Biol Futur 72 (2) 127 [2021-06-00; online 2021-09-24]
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Circle-to-circle amplification coupled with microfluidic affinity chromatography enrichment for in vitro molecular diagnostics of Zika fever and analysis of anti-flaviviral drug efficacy
Soares RRG, Pettke A, Robles-Remacho A, ..., Nilsson M, Madaboosi N
Sensors and Actuators B: Chemical 336 (-) 129723 [2021-06-00; online 2021-06-00]
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Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides.
Muntjewerff EM, Tang K, Lutter L, ..., van den Bogaart G, Mahata SK
Acta Physiol 232 (2) e13655 [2021-06-00; online 2021-05-06]
Gustaf Christoffersson SciLifeLab Fellow
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A microfluidics-based method for culturing osteoblasts on biomimetic hydroxyapatite.
Atif AR, Pujari-Palmer M, Tenje M, Mestres G
Acta Biomater 127 (-) 327-337 [2021-06-00; online 2021-03-27]
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Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents.
Rezaei Somee M, Dastgheib SMM, Shavandi M, ..., Amoozegar MA, Mehrshad M
Sci Rep 11 (1) 11316 [2021-05-31; online 2021-05-31]
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Synthetic antigen-presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses
Céspedes PF, Jainarayanan A, Fernández-Messina L, ..., Sánchez-Madrid F, Dustin ML
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Revisiting the Role of γδ T Cells in Anti-CMV Immune Response after Transplantation.
Gaballa A, Alagrafi F, Uhlin M, Stikvoort A
Viruses 13 (6) - [2021-05-29; online 2021-05-29]
PubMed DOI Crossref
Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source.
Douangamath A, Powell A, Fearon D, ..., Gorrie-Stone T, von Delft F
J Vis Exp - (171) - [2021-05-29; online 2021-05-29]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Using TIF-Seq2 to investigate association between 5´ and 3´mRNA ends.
Li B, Marques S, Wang J, Pelechano V
Meth. Enzymol. 655 (-) 85-118 [2021-05-28; online 2021-05-28]
SciLifeLab Fellow Vicente Pelechano
PubMed DOI Crossref
The accelerated weight histogram method for alchemical free energy calculations.
Lundborg M, Lidmar J, Hess B
J Chem Phys 154 (20) 204103 [2021-05-28; online 2021-07-10]
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Perivascular Macrophages Regulate Blood Flow Following Tissue Damage.
Vågesjö E, Parv K, Ahl D, ..., Christoffersson G, Phillipson M
Circ. Res. 128 (11) 1694-1707 [2021-05-28; online 2021-04-21]
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Multi-Parametric Field Experiment Links Explosive Activity and Persistent Degassing at Stromboli
Thivet S, Harris AJL, Gurioli L, ..., Bombrun M, Marchetti E
Front. Earth Sci. 9 (-) - [2021-05-28; online 2021-05-28]
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Integration of the Microbiome, Metabolome and Transcriptomics Data Identified Novel Metabolic Pathway Regulation in Colorectal Cancer.
Bisht V, Nash K, Xu Y, ..., Gkoutos GV, Acharjee A
Int J Mol Sci 22 (11) - [2021-05-28; online 2021-05-28]
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FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity.
Persson E, Castresana-Aguirre M, Buzzao D, Guala D, Sonnhammer ELL
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Editorial: Application of Systems Biology in Molecular Characterization and Diagnosis of Cancer.
Zhang C, Wei Y, Mardinoglu A, Zhang P
Front Mol Biosci 8 (-) 668146 [2021-05-28; online 2021-05-28]
Adil Mardinoglu SciLifeLab Fellow
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Blocking Fra-1 sensitizes triple-negative breast cancer to PARP inhibitor.
Song D, He H, Sinha I, ..., Zhao C, Williams C
Cancer Lett. 506 (-) 23-34 [2021-05-28; online 2021-02-27]
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3D genomics across the tree of life reveals condensin II as a determinant of architecture type.
Hoencamp C, Dudchenko O, Elbatsh AMO, ..., Lieberman Aiden E, Rowland BD
Science (New York, N.Y.) 372 (6545) 984-989 [2021-05-28; online 2021-05-29]
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Small molecule inhibitors of the mitochondrial ClpXP protease possess cytostatic potential and re-sensitize chemo-resistant cancers.
Meßner M, Mandl MM, Hackl MW, ..., Sieber SA, Pachmayr J
Sci Rep 11 (1) 11185 [2021-05-27; online 2021-05-27]
DOI Crossref
Molecular programming in utero modulates hepatic lipid metabolism and adult metabolic risk in obese mother offspring in a sex-specific manner
Savva C, Helguero LA, González-Granillo M, ..., Kutter C, Korach-André M
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Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5
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COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance
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Author response: Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation
Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith RC
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Phagocytosis and Efferocytosis by Resident Macrophages in the Mouse Pancreas.
Parv K, Westerlund N, Merchant K, ..., Lindsay RS, Christoffersson G
Front Endocrinol (Lausanne) 12 (-) 606175 [2021-05-25; online 2021-05-25]
Gustaf Christoffersson SciLifeLab Fellow
DOI Crossref
Integrative functional analysis uncovers metabolic differences between Candida species
Begum N, Lee S, Pellon A, ..., Moyes D, Shoaie S
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Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.
Bohutínská M, Vlček J, Yair S, ..., Slotte T, Kolář F
Proc. Natl. Acad. Sci. U.S.A. 118 (21) - [2021-05-25; online 2021-05-19]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
A combined approach for single-cell mRNA and intracellular protein expression analysis.
Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ
Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]
DDLS Fellow Marc Friedländer Marcel Tarbier SciLifeLab Fellow
PubMed DOI Crossref
Digging into bivalve miRNAomes: between conservation and innovation.
Rosani U, Bortoletto E, Bai CM, ..., Venier P, Fromm B
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 376 (1825) 20200165 [2021-05-24; online 2021-04-05]
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Multi-omics analysis reveals the impact of microbiota on host metabolism in hepatic steatosis
Zeybel M, Arif M, Li X, ..., Borén J, Mardinoglu A
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Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients
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Circulating proteins reveal prior use of menopausal hormonal therapy and increased risk of breast cancer
Thomas CE, Dahl L, Byström S, ..., Schwenk JM, Gabrielson M
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What Is Abnormal in Normal Karyotype Acute Myeloid Leukemia in Children? Analysis of the Mutational Landscape and Prognosis of the TARGET-AML Cohort.
Herlin MK, Yones SA, Kjeldsen E, Holmfeldt L, Hasle H
Genes (Basel) 12 (6) - [2021-05-21; online 2021-05-21]
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Systemic administration of monovalent follistatin-like 3-Fc-fusion protein increases muscle mass in mice.
Ozawa T, Morikawa M, Morishita Y, ..., Nygren PÅ, Miyazono K
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Microbial Community Interactions Are Sensitive to Small Changes in Temperature.
Burman E, Bengtsson-Palme J
Front Microbiol 12 (-) 672910 [2021-05-21; online 2021-05-21]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Faculty Opinions recommendation of Replication timing maintains the global epigenetic state in human cells.
Elsässer S, Lafranchi L
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DHODH inhibition modulates glucose metabolism and circulating GDF15, and improves metabolic balance.
Zhang J, Terán G, Popa M, ..., Laín S, Darekar S
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Survival analysis of pathway activity as a prognostic determinant in breast cancer
Jeuken GS, Tobin NP, Käll L
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Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.
Schep R, Brinkman EK, Leemans C, ..., Medema RH, van Steensel B
Mol. Cell 81 (10) 2216-2230.e10 [2021-05-20; online 2021-04-12]
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Integration of Mass Spectrometry Imaging and Machine Learning Visualizes Region-Specific Age-Induced and Drug-Target Metabolic Perturbations in the Brain.
Vallianatou T, Shariatgorji R, Nilsson A, ..., Svenningsson P, Andrén PE
ACS Chem Neurosci 12 (10) 1811-1823 [2021-05-19; online 2021-05-03]
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The evolution and changing ecology of the African hominid oral microbiome.
Fellows Yates JA, Velsko IM, Aron F, ..., Herbig A, Warinner C
Proc. Natl. Acad. Sci. U.S.A. 118 (20) - [2021-05-18; online 2021-05-12]
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The Effect of Chemical Structure of OEG Ligand Shells with Quaternary Ammonium Moiety on the Colloidal Stabilization, Cellular Uptake and Photothermal Stability of Gold Nanorods.
Salajkova S, Havel F, Sramek M, ..., Zarska M, Hodny Z
Int J Nanomedicine 16 (-) 3407-3427 [2021-05-18; online 2021-05-18]
PubMed DOI Crossref
Reply to Nagle et al.: The universal stiffening effects of cholesterol on lipid membranes.
Ashkar R, Doktorova M, Heberle FA, ..., Khelashvili G, Brown MF
Proc. Natl. Acad. Sci. U.S.A. 118 (20) - [2021-05-18; online 2021-05-07]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
The human exposome and health in the Anthropocene.
Karlsson O, Rocklöv J, Lehoux AP, ..., Blunt MJ, Birnbaum LS
Int J Epidemiol 50 (2) 378-389 [2021-05-17; online 2020-12-23]
Oskar Karlsson SciLifeLab Fellow
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MEIS-WNT5A axis regulates development of fourth ventricle choroid plexus.
Kaiser K, Jang A, Kompanikova P, ..., Lehtinen MK, Bryja V
Development 148 (10) - [2021-05-15; online 2021-05-25]
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Phylogenomic Insights into the Origin of Primary Plastids.
Irisarri I, Strassert JFH, Burki F
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Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.
Buck M, Garcia SL, Fernandez L, ..., Bertilsson S, Peura S
Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]
Sarahi Garcia SciLifeLab Fellow
PubMed DOI Crossref
Using patients' own knowledge of early sensations and symptoms to develop an interactive, individualized e-questionnaire to facilitate early diagnosis of lung cancer.
Levitsky A, Bernhardson BM, Henoch I, ..., Tishelman C, Eriksson LE
BMC Cancer 21 (1) 544 [2021-05-13; online 2021-05-13]
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Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden.
Karlsson PA, Tano E, Jernberg C, ..., Järhult JD, Wang H
Front Microbiol 12 (-) 664665 [2021-05-13; online 2021-05-13]
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Informing Pharmacokinetic Models With Physiological Data: Oral Population Modeling of L-Serine in Humans.
Bosley JR, Björnson E, Zhang C, ..., Borén J, Mardinoglu A
Front. Pharmacol. 12 (-) 643179 [2021-05-13; online 2021-05-13]
Adil Mardinoglu SciLifeLab Fellow
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Correcting for Naturally Occurring Mass Isotopologue Abundances in Stable-Isotope Tracing Experiments with PolyMID.
Jeong H, Yu Y, Johansson HJ, ..., Lehtiö J, Vacanti NM
Metabolites 11 (5) - [2021-05-12; online 2021-05-12]
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Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
Kang D, Shoaie S, Jacquiod S, Sørensen SJ, Ledesma-Amaro R
Microorganisms 9 (5) 1042 [2021-05-12; online 2021-05-12]
Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction.
Arif M, Klevstig M, Benfeitas R, ..., Mardinoglu A, Boren J
Elife 10 (-) - [2021-05-11; online 2021-05-11]
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Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.
Garcia SL, Mehrshad M, Buck M, ..., Greening C, Peura S
mSystems 6 (3) - [2021-05-11; online 2021-05-11]
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Antibody Responses After a Single Dose of ChAdOx1 nCoV-19 Vaccine in Healthcare Workers Previously Infected with SARS-CoV-2
Havervall S, Marking U, Greilert-Norin N, ..., Nilsson P, Thålin C
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Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches.
Gapsys V, Yildirim A, Aldeghi M, ..., van der Spoel D, de Groot BL
Commun Chem 4 (1) 61 [2021-05-11; online 2021-05-11]
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Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes and normal tissues
Diamanti K, Cavalli M, Pereira MJ, ..., Eriksson JW, Wadelius C
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High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3.
Söderhäll C, Reinius LE, Salmenperä P, ..., Myllykangas S, Kere J
Clin Epigenetics 13 (1) 106 [2021-05-10; online 2021-05-10]
PubMed DOI Crossref
Heparanase overexpression impedes perivascular clearance of amyloid-β from murine brain: relevance to Alzheimer's disease.
Zhang X, O'Callaghan P, Li H, ..., Lindahl U, Li JP
Acta Neuropathol Commun 9 (1) 84 [2021-05-10; online 2021-05-10]
PubMed DOI Crossref
The Genomic Architecture and Evolutionary Fates of Supergenes.
Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-20]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
The ribosome modulates folding inside the ribosomal exit tunnel.
Wruck F, Tian P, Kudva R, ..., Tans SJ, Katranidis A
Commun Biol 4 (1) 523 [2021-05-05; online 2021-05-05]
PubMed DOI Crossref
Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition.
Espeso-Gil S, Holik AZ, Bonnin S, ..., Hor CN, Ossowski S
Front Mol Neurosci 14 (-) 664912 [2021-05-05; online 2021-05-05]
Marc Friedländer SciLifeLab Fellow
PubMed DOI Crossref
Correction to: A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence.
Komseli ES, Pateras IS, Krejsgaard T, ..., Bartek J, Gorgoulis VG
BMC Genomics 22 (1) 327 [2021-05-05; online 2021-05-05]
PubMed DOI Crossref
The Chaperonin GroESL Facilitates Caulobacter crescentus Cell Division by Supporting the Functions of the Z-Ring Regulators FtsA and FzlA.
Schroeder K, Heinrich K, Neuwirth I, Jonas K
MBio 12 (3) - [2021-05-04; online 2021-05-04]
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Accuratede novoidentification of biosynthetic gene clusters with GECCO
Carroll LM, Larralde M, Fleck JS, ..., Cappio E, Zeller G
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DDLS Fellow Laura Carroll
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A microscopy-compatible temperature regulation system for single-cell phenotype analysis - demonstrated by thermoresponse mapping of microalgae.
Andersson M, Johansson S, Bergman H, ..., Behrendt L, Tenje M
Lab Chip 21 (9) 1694-1705 [2021-05-04; online 2021-05-06]
Lars Behrendt SciLifeLab Fellow
PubMed DOI Crossref
A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition.
Cheng L, Kaźmierczak D, Norenhag J, ..., Hydbring P, Du J
mSystems 6 (3) - [2021-05-04; online 2021-05-04]
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Synthetic Biology in Cyanobacteria and Applications for Biotechnology
Hudson EP
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Next generation plasma proteome profiling to monitor health and disease.
Zhong W, Edfors F, Gummesson A, ..., Fagerberg L, Uhlén M
Nat Commun 12 (1) 2493 [2021-05-03; online 2021-05-03]
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Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond.
Carroll LM, Cheng RA, Wiedmann M, Kovac J
Crit Rev Food Sci Nutr 62 (28) 7677-7702 [2021-05-03; online 2021-05-03]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Cannabidiol inhibits the skeletal muscle Nav1.4 by blocking its pore and by altering membrane elasticity.
Ghovanloo MR, Choudhury K, Bandaru TS, ..., Goodchild SJ, Ruben PC
J. Gen. Physiol. 153 (5) - [2021-05-03; online 2021-04-10]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Inflammation and Apolipoproteins Are Potential Biomarkers for Stratification of Cutaneous Melanoma Patients for Immunotherapy and Targeted Therapy.
Karlsson MJ, Costa Svedman F, Tebani A, ..., Egyhazi Brage S, Maddalo G
Cancer Res. 81 (9) 2545-2555 [2021-05-01; online 2021-02-11]
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Volumetric live cell imaging with three-dimensional parallelized RESOLFT microscopy.
Bodén A, Pennacchietti F, Coceano G, ..., Ratz M, Testa I
Nat. Biotechnol. 39 (5) 609-618 [2021-05-00; online 2021-01-11]
Ilaria Testa SciLifeLab Fellow
PubMed DOI Crossref
The noncoding MIR100HG RNA enhances the autocrine function of transforming growth factor β signaling.
Papoutsoglou P, Rodrigues-Junior DM, Morén A, ..., Heldin CH, Moustakas A
Oncogene 40 (21) 3748-3765 [2021-05-00; online 2021-05-04]
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The C-type lectin CD93 controls endothelial cell migration via activation of the Rho family of small GTPases.
Barbera S, Lugano R, Pedalina A, ..., Galvagni F, Orlandini M
Matrix Biol. 99 (-) 1-17 [2021-05-00; online 2021-05-29]
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Stromal FAP is an independent poor prognosis marker in non-small cell lung adenocarcinoma and associated with p53 mutation.
Moreno-Ruiz P, Corvigno S, Te Grootenhuis NC, ..., Micke P, Östman A
Lung Cancer 155 (-) 10-19 [2021-05-00; online 2021-02-25]
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Strategies for Constructing and Operating DNA Origami Linear Actuators.
Benson E, Carrascosa Marzo R, Bath J, Turberfield AJ
Small 17 (20) e2007704 [2021-05-00; online 2021-05-04]
Erik Benson SciLifeLab Fellow
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Quick Systemic Lupus Activity Questionnaire (Q-SLAQ): a simplified version of SLAQ for patient-reported disease activity.
Svenungsson E, Gunnarsson I, Illescas-Bäckelin V, ..., Sjöwall C, Pettersson S
Lupus Sci Med 8 (1) - [2021-05-00; online 2021-05-12]
PubMed DOI Crossref
Pancreatic cancer cachexia: three dimensions of a complex syndrome.
Kordes M, Larsson L, Engstrand L, Löhr JM
Br. J. Cancer 124 (10) 1623-1636 [2021-05-00; online 2021-03-19]
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Molecular Reorganization during the Formation of the Human Skin Barrier Studied In Situ.
Narangifard A, Wennberg CL, den Hollander L, ..., Daneholt B, Norlén L
J. Invest. Dermatol. 141 (5) 1243-1253.e6 [2021-05-00; online 2020-10-22]
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Involvement of Autophagy in Levodopa-Induced Dyskinesia.
Feyder M, Plewnia C, Lieberman OJ, ..., Borgkvist A, Fisone G
Mov Disord 36 (5) 1137-1146 [2021-05-00; online 2021-01-18]
PubMed DOI Crossref
IL-15 superagonist N-803 improves IFNγ production and killing of leukemia and ovarian cancer cells by CD34+ progenitor-derived NK cells.
Van der Meer JMR, Maas RJA, Guldevall K, ..., Hobo W, Dolstra H
Cancer Immunol. Immunother. 70 (5) 1305-1321 [2021-05-00; online 2020-11-03]
PubMed DOI Crossref
High-throughput 5′P sequencing enables the study of degradation-associated ribosome stalls
Zhang Y, Pelechano V
Cell Rep Methods 1 (1) 100001 [2021-05-00; online 2021-05-00]
SciLifeLab Fellow Vicente Pelechano
PubMed DOI Crossref
Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions.
Kim JH, Megquier K, Thomas R, ..., Lindblad-Toh K, Modiano JF
Mol. Cancer Res. 19 (5) 847-861 [2021-05-00; online 2021-03-01]
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Epithelium-autonomous NAIP/NLRC4 prevents TNF-driven inflammatory destruction of the gut epithelial barrier in Salmonella-infected mice.
Fattinger SA, Geiser P, Samperio Ventayol P, ..., Hardt WD, Sellin ME
Mucosal Immunol 14 (3) 615-629 [2021-05-00; online 2021-03-17]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Distinct whole-blood transcriptome profile of children with metabolic healthy overweight/obesity compared to metabolic unhealthy overweight/obesity.
Plaza-Florido A, Altmäe S, Esteban FJ, ..., Radom-Aizik S, Ortega FB
Pediatr. Res. 89 (7) 1687-1694 [2021-05-00; online 2020-11-23]
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DLG4-related synaptopathy: a new rare brain disorder.
Rodríguez-Palmero A, Boerrigter MM, Gómez-Andrés D, ..., Pujol A, Tümer Z
Genet Med 23 (5) 888-899 [2021-05-00; online 2021-02-17]
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Critical assessment of protein intrinsic disorder prediction.
Necci M, Piovesan D, CAID Predictors , DisProt Curators , Tosatto SCE
Nat. Methods 18 (5) 472-481 [2021-05-00; online 2021-04-19]
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Cerebrospinal Fluid Proteins Altered in Corticobasal Degeneration.
Paslawski W, Bergström S, Zhang X, ..., Nilsson P, Svenningsson P
Mov Disord 36 (5) 1278-1280 [2021-05-00; online 2021-03-04]
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Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
Kapla J, Rodríguez-Espigares I, Ballante F, Selent J, Carlsson J
PLoS Comput Biol 17 (5) e1008936 [2021-05-00; online 2021-05-13]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR.
Kaspar S, Oertlin C, Szczepanowska K, ..., Topisirovic I, Trifunovic A
Sci Adv 7 (22) - [2021-05-00; online 2021-05-26]
PubMed DOI Crossref
A droplet acoustofluidic platform for time-controlled microbead-based reactions.
Liu Z, Fornell A, Tenje M
Biomicrofluidics 15 (3) 034103 [2021-05-00; online 2021-05-17]
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093 Dissecting intercellular communication in adult human skin with single-cell and spatial transcriptomics
Ji A, Thrane K, Guo M, ..., Lundeberg J, Khavari P
J. Invest. Dermatol. 141 (5) S17 [2021-05-00; online 2021-05-00]
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The Protein Quality Control Network in Caulobacter crescentus.
Schroeder K, Jonas K
Front Mol Biosci 8 (-) 682967 [2021-04-30; online 2021-04-30]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing.
Habibi M, Taheri G, Aghdam R
Sci Rep 11 (1) 9378 [2021-04-30; online 2021-04-30]
DDLS Fellow Golnaz Taheri
PubMed DOI Crossref
Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time.
von Mentzer A, Blackwell GA, Pickard D, ..., Dougan G, Sjöling Å
Sci Rep 11 (1) 9256 [2021-04-29; online 2021-04-29]
Astrid von Mentzer DDLS Fellow
PubMed DOI Crossref
Assessing the calibration in toxicological in vitro models with conformal prediction.
Morger A, Svensson F, Arvidsson McShane S, ..., Spjuth O, Volkamer A
J Cheminform 13 (1) 35 [2021-04-29; online 2021-04-29]
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Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel.
Pérez-Conesa S, Keeler EG, Zhang D, Delemotte L, McDermott AE
J Chem Phys 154 (16) 165102 [2021-04-28; online 2021-05-05]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
How Does Liquid-Liquid Phase Separation in Model Membranes Reflect Cell Membrane Heterogeneity?
Sych T, Gurdap CO, Wedemann L, Sezgin E
Membranes (Basel) 11 (5) - [2021-04-28; online 2021-04-28]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology.
Fagerholm U, Hellberg S, Spjuth O
Molecules 26 (9) - [2021-04-28; online 2021-04-28]
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NEIL1 and NEIL2 Are Recruited as Potential Backup for OGG1 upon OGG1 Depletion or Inhibition by TH5487.
Hanna BMF, Michel M, Helleday T, Mortusewicz O
Int J Mol Sci 22 (9) - [2021-04-27; online 2021-04-27]
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Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth.
Sighel D, Notarangelo M, Aibara S, ..., Modelska A, Quattrone A
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Prashant Singh SciLifeLab Fellow
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High throughput viscoelastic particle focusing and separation in spiral microchannels.
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The evolving landscape of biomarker testing for non-small cell lung cancer in Europe.
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The International Association for the Study of Lung Cancer Global Survey on Programmed Death-Ligand 1 Testing for NSCLC.
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STRN-ALK rearranged pediatric malignant peritoneal mesothelioma - Functional testing of 527 cancer drugs in patient-derived cancer cells.
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PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS.
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Exploring the GLP-1-GLP-1R axis in porcine pancreas and gastrointestinal tract in vivo by ex vivo autoradiography.
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Effects of prenatal exposure and co-exposure to metallic or metalloid elements on early infant neurodevelopmental outcomes in areas with small-scale gold mining activities in Northern Tanzania.
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Drug Occupancy Assessment at the Glucose-Dependent Insulinotropic Polypeptide Receptor by Positron Emission Tomography.
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Olof Eriksson SciLifeLab Fellow
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Differential expression of microRNAs and tRNA fragments mediate the adaptation of the liver fluke Fasciola gigantica to its intermediate snail and definitive mammalian hosts.
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Development and Validation of a Risk Prediction Model for Esophageal Squamous Cell Carcinoma Using Cohort Studies.
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Colorimetric isothermal nucleic acid detection of SARS-CoV-2 with dye combination.
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Autoantibody profiles are associated with specific clinical features in psychotic disorders
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Apoptotic effect of berberine via Bcl-2, ROR1, and mir-21 in patients with B-chronic lymphocytic leukemia.
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Accurate detection of Newcastle disease virus using proximity-dependent DNA aptamer ligation assays.
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FEBS Open Bio 11 (4) 1122-1131 [2021-04-00; online 2021-03-11]
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AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity.
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A new era for plant science: spatial single-cell transcriptomics.
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A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability
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PD-1 expression on NK cells can be related to cytokine stimulation and tissue residency
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Increased Pathway Complexity Is a Prognostic Biomarker in Metastatic Castration-Resistant Prostate Cancer.
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A FOXN1 mutation competitively displaces wild-type FOXN1 from higher-order nuclear condensates to cause immunodeficiency
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Systemic immunity upon local oncolytic virotherapy armed with immunostimulatory genes may be supported by tumor-derived exosomes.
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Graphene FET Sensors for Alzheimer's Disease Protein Biomarker Clusterin Detection.
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Symptoms and syndromes associated with SARS-CoV-2 infection and severity in pregnant women from two community cohorts.
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Ulipristal Acetate for Treatment of Premenstrual Dysphoric Disorder: A Proof-of-Concept Randomized Controlled Trial.
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The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe
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Global Ecol. Biogeogr. 30 (3) 590-597 [2021-03-00; online 2021-01-06]
Pascal Milesi SciLifeLab Fellow
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Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease
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Revisiting old lessons from classic literature on persistent global pollutants : This article belongs to Ambio's 50th Anniversary Collection. Theme: Environmental contaminants.
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Assembly of a Rieske non-heme iron oxygenase multicomponent system from Phenylobacterium immobile E DSM 1986 enables pyrazon cis-dihydroxylation in E. coli.
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A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits.
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Small-molecule-mediated OGG1 inhibition attenuates pulmonary inflammation and lung fibrosis
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Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study
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Machine learning for cell classification and neighborhood analysis in glioma tissue
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