Publications 2022

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1392 publications

PubMed DOI Crossref
Lipoic Acid Conjugated Boron Hybrids Enhance Wound Healing and Antimicrobial Processes.
Türkez H, Yıldırım ÖÇ, Öner S, ..., Yapça ÖE, Mardinoğlu A
Pharmaceutics 15 (1) - [2022-12-31; online 2022-12-31]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Label-Free Estimation of Sarcomere Orientation from Brightfield Microscopy Images of Induced Pluripotent Stem Cell Derived Cardiomyocyte Nuclei
Ahola ", Belay B, Wählby C, Hyttinen" J
- - (-) - [2022-12-31; online 2022-12-31]
PubMed DOI Crossref
Imaging of the Glucose-Dependent Insulinotropic Polypeptide Receptor Using a Novel Radiolabeled Peptide Rationally Designed Based on Endogenous GIP and Synthetic Exendin-4 Sequences.
Velikyan I, Bossart M, Haack T, ..., Wagner M, Eriksson O
Pharmaceuticals (Basel, Switzerland) 16 (1) - [2022-12-31; online 2022-12-31]
Olof Eriksson SciLifeLab Fellow
DOI Crossref
Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies
Osmanski AB, Paulat NS, Korstian J, ..., Karlsson EK, Ray DA
- - (-) - [2022-12-30; online 2022-12-30]
PubMed DOI Crossref
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.
Lagman D, Haines HJ, Abalo XM, Larhammar D
PLoS ONE 17 (12) e0279548 [2022-12-30; online 2022-12-30]
DOI Crossref
Molecular and spatial design of early skin development
Jacob T, Annusver K, Czarnewski P, ..., Björklund Å, Kasper M
- - (-) - [2022-12-29; online 2022-12-29]
DOI Crossref
Structure of plant Photosystem I in a native assembly state
Naschberger A, Fadeeva M, Klaiman D, ..., Nelson N, Amunts A
- - (-) - [2022-12-28; online 2022-12-28]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
Occurrence of late-apoptotic symptoms in porcine preimplantation embryos upon exposure of oocytes to perfluoroalkyl substances (PFASs) under in vitro meiotic maturation.
Leclercq A, Ranefall P, Sjunnesson YCB, Hallberg I
PLoS ONE 17 (12) e0279551 [2022-12-28; online 2022-12-28]
PubMed DOI Crossref
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
Kanoni S, Graham SE, Wang Y, ..., Assimes TL, Peloso GM
Genome Biol. 23 (1) 268 [2022-12-27; online 2022-12-27]
DOI Crossref
ISG15-modification of the Arp2/3 complex restricts pathogen spread
Zhang Y, Ripley B, Ouyang W, ..., Guerra S, Radoshevich L
- - (-) - [2022-12-27; online 2022-12-27]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening.
Tuerkova A, Bongers BJ, Norinder U, ..., van Westen GJP, Zdrazil B
J Chem Inf Model 62 (24) 6323-6335 [2022-12-26; online 2022-03-11]
PubMed DOI Crossref
Obesity-Associated Neurodegeneration Pattern Mimics Alzheimer's Disease in an Observational Cohort Study.
Morys F, Potvin O, Zeighami Y, ..., Dagher A, Alzheimer’s Disease Neuroimaging Initiative
J. Alzheimers Dis. 91 (3) 1059-1071 [2022-12-25; online 2022-12-25]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Detection of SARS-CoV-2 antibodies in serum and dried blood spot samples of vaccinated individuals using a sensitive homogeneous proximity extension assay.
Zhao H, Wang M, Muthelo P, ..., Mei YF, Landegren U
N Biotechnol 72 (-) 139-148 [2022-12-25; online 2022-11-21]
PubMed DOI Crossref
Allosteric Modulators of Dopamine D2 Receptors for Fine-Tuning of Dopaminergic Neurotransmission in CNS Diseases: Overview, Pharmacology, Structural Aspects and Synthesis.
Kaczor AA, Wróbel TM, Bartuzi D
Molecules 28 (1) - [2022-12-25; online 2022-12-25]
DOI Crossref
An annotated chromosome-scale reference genome for Eastern Black-eared Wheatear ( Oenanthe melanoleuca )
Peona V, Palacios-Gimenez OM, Lutgen D, ..., Suh A, Burri R
- - (-) - [2022-12-24; online 2022-12-24]
DOI Crossref
mapquik: Efficient low-divergence mapping of long reads in minimizer space
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R
- - (-) - [2022-12-23; online 2022-12-23]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Circulating Amino Acids and Risk of Peripheral Artery Disease in the PREDIMED Trial.
Razquin C, Ruiz-Canela M, Toledo E, ..., Hu FB, Martínez-González MA
Int J Mol Sci 24 (1) - [2022-12-23; online 2022-12-23]
Clemens Wittenbecher DDLS Fellow
DOI Crossref
C-ToMExO: Learning Cancer Progression Dynamics from Clonal Composition of Tumors
Neyshabouri MM, Dimitrakopoulou S, Lagergren J
- - (-) - [2022-12-23; online 2022-12-23]
PubMed DOI Crossref
Surface protein profiling of prostate-derived extracellular vesicles by mass spectrometry and proximity assays.
Manouchehri Doulabi E, Fredolini C, Gallini R, ..., Bergquist J, Kamali-Moghaddam M
Commun Biol 5 (1) 1402 [2022-12-22; online 2022-12-22]
PubMed DOI Crossref
STK4 protein expression pattern follows different trends in endometrioid and serous endometrial adenocarcinoma upon tumor progression.
Govorov I, Attarha S, Kovalevska L, ..., Kashuba E, Mints M
Sci Rep 12 (1) 22154 [2022-12-22; online 2022-12-22]
PubMed DOI Crossref
Role of ZNF143 and Its Association with Gene Expression Patterns, Noncoding Mutations, and the Immune System in Human Breast Cancer.
Saddeek S, Almassabi R, Mobashir M
Life (Basel) 13 (1) - [2022-12-22; online 2022-12-22]
PubMed DOI Crossref
Modulating glycosphingolipid metabolism and autophagy improves outcomes in pre-clinical models of myeloma bone disease.
Leng H, Zhang H, Li L, ..., Simon AK, Horwood NJ
Nat Commun 13 (1) 7868 [2022-12-22; online 2022-12-22]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Matched Analyses of Brain Metastases versus Primary Non-Small Cell Lung Cancer Reveal a Unique microRNA Signature.
Tsakonas G, Koulouris A, Kazmierczak D, ..., Hydbring P, Ekman S
Int J Mol Sci 24 (1) - [2022-12-22; online 2022-12-22]
PubMed DOI Crossref
Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes.
Milesi P, Claret JL, Unal S, Weill M, Labbé P
Parasit Vectors 15 (1) 484 [2022-12-22; online 2022-12-22]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
A brain atlas of synapse protein lifetime across the mouse lifespan.
Bulovaite E, Qiu Z, Kratschke M, ..., Fransén E, Grant SGN
Neuron 110 (24) 4057-4073.e8 [2022-12-21; online 2022-10-05]
PubMed DOI Crossref
UROSCAN and UROSCANSEQ: a large-scale multicenter effort towards translation of molecular bladder cancer subtypes into clinical practice - from biobank to RNA-sequencing in real time.
Liedberg F, Abrahamsson J, Bernardo C, ..., Sjödahl G, Eriksson P
Scand J Urol 57 (1-6) 2-9 [2022-12-20; online 2022-12-20]
DOI Crossref
Ghost admixture in eastern gorillas
Pawar H, Rymbekova A, Cuadros S, ..., Marques-Bonet T, Kuhlwilm M
- - (-) - [2022-12-19; online 2022-12-19]
DDLS Fellow Tom van der Valk
DOI Crossref
Genome-wide association study reveals loci with sex-specific effects on plasma bile acids
Landini A, Ghasemi-Semeskandeh D, Johansson Å, ..., Wilson JF, Klarić L
- - (-) - [2022-12-19; online 2022-12-19]
PubMed DOI Crossref
An Approach for Systems-Level Understanding of Prostate Cancer from High-Throughput Data Integration to Pathway Modeling and Simulation.
Mobashir M, Turunen SP, Izhari MA, ..., Helleday T, Lehti K
Cells 11 (24) - [2022-12-19; online 2022-12-19]
PubMed DOI Crossref
A conserved MTMR lipid phosphatase increasingly suppresses autophagy in brain neurons during aging.
Kovács T, Szinyákovics J, Billes V, ..., Maglóczky Z, Vellai T
Sci Rep 12 (1) 21817 [2022-12-17; online 2022-12-17]
PubMed DOI Crossref
Membrane Fusion Mediated by Non-covalent Binding of Re-engineered Cholera Toxin Assemblies to Glycolipids.
Wehrum S, Siukstaite L, Williamson DJ, ..., Römer W, Turnbull WB
ACS Synth. Biol. 11 (12) 3929-3938 [2022-12-16; online 2022-11-11]
PubMed DOI Crossref
Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma.
Borgenvik A, Holmberg KO, Bolin S, ..., Weishaupt H, Swartling FJ
Cancer Res. 82 (24) 4586-4603 [2022-12-16; online 2022-10-12]
PubMed DOI Crossref
Strobealign: flexible seed size enables ultra-fast and accurate read alignment.
Sahlin K
Genome Biol. 23 (1) 260 [2022-12-15; online 2022-12-15]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Linking Individual Differences in Personalized Functional Network Topography to Psychopathology in Youth.
Cui Z, Pines AR, Larsen B, ..., Fan Y, Satterthwaite TD
Biol. Psychiatry 92 (12) 973-983 [2022-12-15; online 2022-05-18]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Intrinsic Molecular Subtypes of Metastatic Castration-Resistant Prostate Cancer.
Feng E, Rydzewski NR, Zhang M, ..., Sjöström M, Zhao SG
Clin. Cancer Res. 28 (24) 5396-5404 [2022-12-15; online 2022-10-20]
Arian Lundberg DDLS Fellow
PubMed DOI Crossref
Influenza Virus Membrane Fusion Is Promoted by the Endosome-Resident Phospholipid Bis(monoacylglycero)phosphate.
Mannsverk S, Villamil Giraldo AM, Kasson PM
J Phys Chem B 126 (49) 10445-10451 [2022-12-15; online 2022-12-05]
DOI Crossref
Expression of substance P, NPY and their Receptors Is Altered in Major Depression
Barde S, Aguila J, Zhong W, ..., Hedlund E, Hökfelt T
- - (-) - [2022-12-15; online 2022-12-15]
PubMed DOI Crossref
Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction.
Olsson H, Kartasalo K, Mulliqi N, ..., Spjuth O, Eklund M
Nat Commun 13 (1) 7761 [2022-12-15; online 2022-12-15]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Loss of Y in leukocytes as a risk factor for critical COVID-19 in men.
Bruhn-Olszewska B, Davies H, Sarkisyan D, ..., Frithiof R, Dumanski JP
Genome Med 14 (1) 139 [2022-12-14; online 2022-12-14]
DOI Crossref
Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]
Hénin J, Lelièvre T, Shirts MR, Valsson O, Delemotte L
LiveCoMS 4 (1) 1583 [2022-12-14; online 2022-12-14]
Lucie Delemotte SciLifeLab Fellow
DOI Crossref
Deciphering the determinants of recombinant protein yield across the human secretome
Masson HO, Kuo CC, Malm M, ..., Rockberg J, Lewis NE
- - (-) - [2022-12-14; online 2022-12-14]
PubMed DOI Crossref
Targeting VEGF-A/VEGFR2 Y949 Signaling-Mediated Vascular Permeability Alleviates Hypoxic Pulmonary Hypertension.
Zhou W, Liu K, Zeng L, ..., Zhang F, Chen Y
Circulation 146 (24) 1855-1881 [2022-12-13; online 2022-11-17]
PubMed DOI Crossref
Metabolic reprogramming and membrane glycan remodeling as potential drivers of zebrafish heart regeneration.
Spelat R, Ferro F, Contessotto P, ..., Kilcoyne M, Pandit A
Commun Biol 5 (1) 1365 [2022-12-13; online 2022-12-13]
PubMed DOI Crossref
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel.
Lycksell M, Rovšnik U, Hanke A, ..., Howard RJ, Lindahl E
Proc. Natl. Acad. Sci. U.S.A. 119 (50) e2210669119 [2022-12-13; online 2022-12-08]
PubMed DOI Crossref
B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing.
Frede A, Czarnewski P, Monasterio G, ..., Das S, Villablanca EJ
Immunity 55 (12) 2336-2351.e12 [2022-12-13; online 2022-12-02]
Camilla Engblom SciLifeLab Fellow
DOI Crossref
dgram2dmap: Extraction, visualisation and formatting of distance constraints from AlphaFold distograms
Wallner B, Amunts A, Naschberger A, Nystedt B, Mirabello C
- - (-) - [2022-12-12; online 2022-12-12]
Alexey Amunts SciLifeLab Fellow
DOI Crossref
SpLitteR: Diploid genome assembly using TELL-Seq linked-reads and assembly graphs
Tolstoganov I, Chen Z, Pevzner PA, Korobeynikov A
- - (-) - [2022-12-12; online 2022-12-12]
PubMed DOI Crossref
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.
Voutilainen S, Heikkilä P, Bartkova J, ..., Bartek J, Mattson J
BMC Cancer 22 (1) 1298 [2022-12-12; online 2022-12-12]
DOI Crossref
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
Zhu W, Shenoy A, Kundrotas P, Elofsson A
- - (-) - [2022-12-12; online 2022-12-12]
DOI Crossref
Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
Andersson A, Behanova A, Avenel C, ..., Malmberg F, Wählby C
- - (-) - [2022-12-10; online 2022-12-10]
DOI Crossref
Therapeutic opportunity of phosphodiesterase 3A modulators in myxoid liposarcomas
Toivanen K, Kilpinen S, Ojala K, ..., Böhling T, Sihto H
- - (-) - [2022-12-09; online 2022-12-09]
PubMed DOI Crossref
Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ.
Al-Amin RA, Johansson L, Abdurakhmanov E, ..., Lundbäck T, Landegren U
Nucleic Acids Res. 50 (22) e129 [2022-12-09; online 2022-10-04]
PubMed DOI Crossref
Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.
Behle A, Dietsch M, Goldschmidt L, ..., Axmann IM, Machné R
Nucleic Acids Res. 50 (22) 12790-12808 [2022-12-09; online 2022-12-20]
Paul Hudson SciLifeLab Fellow
PubMed DOI Crossref
Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.
Fisher G, Corbella M, Alphey MS, ..., Kamerlin SCL, da Silva RG
Nat Commun 13 (1) 7607 [2022-12-09; online 2022-12-09]
PubMed DOI Crossref
Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.
Itoh Y, Singh V, Khawaja A, ..., Rorbach J, Amunts A
Elife 11 (-) - [2022-12-08; online 2022-12-08]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG.
Caceres M, Mumey B, Husic E, ..., Sahlin K, Tomescu AI
IEEE/ACM Trans Comput Biol Bioinform 19 (6) 3673-3684 [2022-12-08; online 2022-12-08]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Predicting the Influence of Fat Food Intake on the Absorption and Systemic Exposure of Small Drugs using ANDROMEDA by Prosilico Software
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O
- - (-) - [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation.
AKesson M, Singh P, Wrede F, Hellander A
IEEE/ACM Trans Comput Biol Bioinform 19 (6) 3353-3365 [2022-12-08; online 2022-12-08]
Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis.
Tengvall K, Sundström E, Wang C, ..., Andersson G, Lindblad-Toh K
Commun Biol 5 (1) 1348 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.
Rubanova Y, Shi R, Harrigan CF, ..., Morris QD, PCAWG Consortium
Nat Commun 13 (1) 7567 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes.
Reyna MA, Haan D, Paczkowska M, ..., Raphael BJ, PCAWG Consortium
Nat Commun 13 (1) 7566 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Integrative pathway enrichment analysis of multivariate omics data.
Paczkowska M, Barenboim J, Sintupisut N, ..., Reimand J, PCAWG Consortium
Nat Commun 13 (1) 7570 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Inferring structural variant cancer cell fraction.
Cmero M, Yuan K, Ong CS, ..., Macintyre G, PCAWG Consortium
Nat Commun 13 (1) 7568 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, ..., Creighton CJ, PCAWG Consortium
Nat Commun 13 (1) 7572 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer.
Sieverling L, Hong C, Koser SD, ..., Feuerbach L, PCAWG Consortium
Nat Commun 13 (1) 7574 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours.
Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium
Nat Commun 13 (1) 7569 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower.
Shuai S, PCAWG Drivers and Functional Interpretation Working Group , Gallinger S, Stein LD, PCAWG Consortium
Nat Commun 13 (1) 7571 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.
Carlevaro-Fita J, Lanzós A, Feuerbach L, ..., Johnson R, PCAWG Consortium
Commun Biol 5 (1) 1347 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.
Jiao W, Atwal G, Polak P, ..., Stein LD, PCAWG Consortium
Nat Commun 13 (1) 7573 [2022-12-08; online 2022-12-08]
PubMed DOI Crossref
Tyrosine-protein kinase Yes controls endothelial junctional plasticity and barrier integrity by regulating VE-cadherin phosphorylation and endocytosis.
Jin Y, Ding Y, Richards M, ..., Gerhardt H, Claesson-Welsh L
Nat Cardiovasc Res 1 (12) 1156-1173 [2022-12-07; online 2023-11-08]
DOI Crossref
The impact of genetically controlled splicing on exon inclusion and protein structure
Einson J, Minaeva M, Rafi F, Lappalainen T
- - (-) - [2022-12-07; online 2022-12-07]
PubMed DOI Crossref
SETD7 Expression Is Associated with Breast Cancer Survival Outcomes for Specific Molecular Subtypes: A Systematic Analysis of Publicly Available Datasets.
Monteiro FL, Stepanauskaite L, Williams C, Helguero LA
Cancers (Basel) 14 (24) - [2022-12-07; online 2022-12-07]
PubMed DOI Crossref
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
Sci Rep 12 (1) 21192 [2022-12-07; online 2022-12-07]
PubMed DOI Crossref
Aporphine and isoquinoline derivatives block glioblastoma cell stemness and enhance temozolomide cytotoxicity.
Rodrigues-Junior DM, Raminelli C, Hassanie H, ..., Moustakas A, Vettore AL
Sci Rep 12 (1) 21113 [2022-12-07; online 2022-12-07]
DOI Crossref
Role of interneuron subtypes in controlling trial-by-trial output variability in the neocortex
Guo L, Kumar A
- - (-) - [2022-12-06; online 2022-12-06]
PubMed DOI Crossref
Measuring single-virus fusion kinetics using an assay for nucleic acid exposure.
Villamil Giraldo AM, Mannsverk S, Kasson PM
Biophys. J. 121 (23) 4467-4475 [2022-12-06; online 2022-11-09]
DOI Crossref
Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
Vromman M, Anckaert J, Bortoluzzi S, ..., Vandesompele J, Volders PJ
- - (-) - [2022-12-06; online 2022-12-06]
DOI Crossref
Itch receptor MRGPRX4 interacts with the receptor activity-modifying proteins (RAMPs)
Kotliar IB, Ceraudo E, Kemelmakher-Liben K, ..., Schwenk JM, Sakmar TP
- - (-) - [2022-12-06; online 2022-12-06]
PubMed DOI Crossref
In Vitro Transcriptome Analysis of Cobalt Boride Nanoparticles on Human Pulmonary Alveolar Cells.
Arslan ME, Tatar A, Yıldırım ÖÇ, ..., Mardinoğlu A, Türkez H
Materials (Basel) 15 (23) - [2022-12-06; online 2022-12-06]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways
Pinheiro AS, Tsarouhas V, Senti K, Arefin B, Samakovlis C
- - (-) - [2022-12-05; online 2022-12-05]
DOI Crossref
Orthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkers
Johansson C, Hunt H, Signorelli M, ..., Uhlén M, Szigyarto CAK
- - (-) - [2022-12-05; online 2022-12-05]
DDLS Fellow Fredrik Edfors
DOI Crossref
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR
Obana N, Takada H, Crowe-McAuliffe C, ..., Wilson DN, Hauryliuk V
- - (-) - [2022-12-05; online 2022-12-05]
PubMed DOI Crossref
Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.
Moraitou M, Forsythe A, Fellows Yates JA, ..., Warinner C, Guschanski K
Mol. Biol. Evol. 39 (12) - [2022-12-05; online 2022-12-07]
PubMed DOI Crossref
Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3.
Parenti MD, Naldi M, Manoni E, ..., Bartolini M, Del Rio A
Eur J Med Chem 243 (-) 114683 [2022-12-05; online 2022-09-08]
PubMed DOI Crossref
Development of l-Dopa-containing diketopiperazines as blood-brain barrier shuttle.
Cornacchia C, Marinelli L, Di Rienzo A, ..., Di Stefano A, Cacciatore I
Eur J Med Chem 243 (-) 114746 [2022-12-05; online 2022-09-08]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Visualization & Quality Control Tools for Large-scale Multiplex Tissue Analysis in TissUUmaps 3
Behanova A, Avenel C, Andersson A, ..., Östman A, Wählby C
- - (-) - [2022-12-02; online 2022-12-02]
PubMed DOI Crossref
Personalized health risk assessment based on single-cell RNA sequencing analysis of a male with 45, X/48, XYYY karyotype.
Koczkowska M, Jąkalski M, Birkholz-Walerzak D, ..., Mieczkowski J, Piotrowski A
Sci Rep 12 (1) 20854 [2022-12-02; online 2022-12-02]
PubMed DOI Crossref
NF-kB in Signaling Patterns and Its Temporal Dynamics Encode/Decode Human Diseases.
Almowallad S, Alqahtani LS, Mobashir M
Life (Basel) 12 (12) - [2022-12-02; online 2022-12-02]
PubMed DOI Crossref
Madagascar's extraordinary biodiversity: Threats and opportunities.
Ralimanana H, Perrigo AL, Smith RJ, ..., Zizka A, Antonelli A
Science (New York, N.Y.) 378 (6623) eadf1466 [2022-12-02; online 2022-12-02]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
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
PubMed DOI Crossref
Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS.
Ilter M, Kasmer R, Jalalypour F, ..., Karakas N, Sensoy O
Elife 11 (-) - [2022-12-02; online 2022-12-02]
PubMed DOI Crossref
Editorial: Machine learning, epistasis, and protein engineering: From sequence-structure-function relationships to regulation of metabolic pathways.
Cadet F, Saavedra E, Syren PO, Gontero B
Front Mol Biosci 9 (-) 1098289 [2022-12-02; online 2022-12-02]
PubMed DOI Crossref
The structure of cellulose nanofibril networks at low concentrations and their stabilizing action on colloidal particles.
Nordenström M, Benselfelt T, Hollertz R, ..., Söderberg D, Wågberg L
Carbohydr Polym 297 (-) 120046 [2022-12-01; online 2022-09-01]
PubMed DOI Crossref
Hybrid immunity in immunocompromised patients with CLL after SARS-CoV-2 infection followed by booster mRNA vaccination.
Blixt L, Gao Y, Wullimann D, ..., Hansson L, Österborg A
Blood 140 (22) 2403-2407 [2022-12-01; online 2022-09-24]
DOI Crossref
High-efficiency transfection of Acanthamoeba castellanii using a cationic polymer
Moreno AB, Ek V, Eriksson J, Sellin ME, Guy L
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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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217P Characterization of immune cells in the tumor microenvironment of advanced bladder cancer
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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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Correction: Proof-of-principle studies on a strategy to enhance nucleotide imbalance specifically in cancer cells.
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Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells.
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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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Plasma protein biomarker profiling reveals major differences between acute leukaemia, lymphoma patients and controls.
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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.
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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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Camilla Engblom SciLifeLab Fellow
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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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METTL17 is an Fe-S cluster checkpoint for mitochondrial translation
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Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases.
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Choice of High-Throughput Proteomics Method Affects Data Integration with Transcriptomics and the Potential Use in Biomarker Discovery.
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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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Temporal Association of Total Serum Cholesterol and Pancreatic Cancer Incidence.
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Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight.
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Proteome Integral Solubility Alteration (PISA) Assay in Mammalian Cells for Deep, High-Confidence, and High-Throughput Target Deconvolution.
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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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Adil Mardinoglu SciLifeLab Fellow
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Platelet-leukocyte aggregate formation and inflammation in patients with pulmonary arterial hypertension and CTEPH.
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Integration of small RNAs from plasma and cerebrospinal fluid for classification of multiple sclerosis.
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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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The type II TGF-β receptor phosphorylates Tyr182 in the type I receptor to activate downstream Src signaling.
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The global groundwater resistome: core antibiotic resistance genes, their dynamics and drivers
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The Marine Product Elatol Is a Novel Inhibitor of Mitochondrial Translation Triggering the Integrated Stress Response and Apoptosis in Leukemia and Lymphoma Cells
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Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores.
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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
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Kristoffer Sahlin SciLifeLab Fellow
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Identification and Interpretation of Clinically Relevant Somatic Variants from Whole-Genome Sequencing Data
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Enhanced TLR3 responsiveness in hepatitis C virus resistant women from the Irish anti-D cohort.
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Data-Driven Molecular Hallmarks of Acute Myeloid Leukemia: Biological, Prognostic and Therapeutic Implications
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Comprehensive Exploration of NK Cell Education in ADCC Triggered By a Monoclonal Antibody or a Bispecific Killer Engager Molecule (BiKE)
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Comparison of Data from Fresh and Frozen AML Samples for Functional Drug Testing
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Affibody-Based BCMA x CD16 Dual Engagers for Activation of NK Cells Towards Multiple Myeloma
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Abstract A007: Pancreatic cancer comprises co-existing transcriptional states regulated by distinct master regulator programs
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A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint.
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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
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TMIC-70. HARMONIZED SINGLE-CELL LANDSCAPE, INTERCELLULAR CROSSTALK AND TUMOR ARCHITECTURE OF GLIOBLASTOMA
Ruiz-Moreno C, Salas SM, Samuelsson E, ..., Nilsson M, Stunnenberg H
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STEM-19. LIVE DETECTION OF NEURAL STEM AND GLIOBLASTOMA CELLS BY A LUMINESCENT CONJUGATED OLIGOTHIOPHENE DERIVATIVE
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Gating intermediates reveal inhibitory role of the voltage sensor in a cyclic nucleotide-modulated ion channel.
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Nat Commun 13 (1) 6919 [2022-11-14; online 2022-11-14]
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EPCO-21. THE SPATIAL ORGANIZATION OF H3-K27M MUTANT DIFFUSE MIDLINE GLIOMA
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Neuro-oncology 24 (Supplement_7) vii120-vii120 [2022-11-14; online 2022-11-14]
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EPCO-16. ESTIMATING THE DIFFERENTIATION POTENTIAL AND PLASTICITY OF GLIOBLASTOMA CELLS USING STATISTICAL MECHANICS
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Validation of predicted conformal intervals for prediction of human clinical pharmacokinetics
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Quantitative Transcriptome Analysis of Purified Equine Mast Cells Identifies a Dominant Mucosal Mast Cell Population with Possible Inflammatory Functions in Airways of Asthmatic Horses.
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Developmental disruption and restoration of brain synaptome architecture in the murine Pax6 neurodevelopmental disease model.
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Genomic trajectories of a near-extinction event in the Chatham Island black robin.
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BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]
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Super-Resolution Microscopy Opens New Doors to Life at the Nanoscale.
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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.
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Development of mesothelioma-specific oncolytic vaccine exploiting immunopeptidomic analysis of murine and human tumors
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Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level.
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A gene essentiality signature enables predicting the mechanism of action of drugs
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Systems Biology in ELIXIR: modelling in the spotlight
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Read-Based Phasing and Analysis of Phased Variants with WhatsHap.
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Case report: Two sisters with a germline CHEK2 variant and distinct endocrine neoplasias.
Vallera RD, Ding Y, Hatanpaa KJ, ..., Dahia PLM, Ghayee HK
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Xist ribonucleoproteins promote female sex-biased autoimmunity
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Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers
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DDLS Fellow Wei Ouyang
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]
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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
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Quantitative Phosphoproteomics and Acetylomics of Safranal Anticancer Effects in Triple-Negative Breast Cancer Cells.
Ashrafian S, Zarrineh M, Jensen P, ..., Ghassempour A, Larsen MR
J. Proteome Res. 21 (11) 2566-2585 [2022-11-04; online 2022-09-29]
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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
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Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.
Dyrhage K, Garcia-Montaner A, Tamarit D, ..., Webster MT, Andersson SGE
Genome Biol Evol 14 (11) - [2022-11-04; online 2022-10-21]
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An equine Endothelin 3 cis-regulatory variant links blood pressure modulation to elite racing performance
Fegraeus K, Rosengren MK, Naboulsi R, ..., Meadows JRS, Lindgren G
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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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The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.
Ament-Velásquez SL, Gilchrist C, Rêgo A, ..., Rafati N, Stelkens R
Mol. Biol. Evol. 39 (11) - [2022-11-03; online 2022-11-06]
PubMed DOI Crossref
Population dynamics and demographic history of Eurasian collared lemmings.
Lord E, Marangoni A, Baca M, ..., Fedorov VB, Dalén L
BMC Ecol Evol 22 (1) 126 [2022-11-03; online 2022-11-03]
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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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DAR 16-II Primes Endothelial Cells for Angiogenesis Improving Bone Ingrowth in 3D-Printed BCP Scaffolds and Regeneration of Critically Sized Bone Defects.
Alfayez E, Veschini L, Dettin M, ..., Coward T, Di Silvio L
Biomolecules 12 (11) - [2022-11-02; online 2022-11-02]
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Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides.
Gharibi H, Chernobrovkin AL, Saei AA, ..., Makarov AA, Zubarev RA
Anal. Chem. 94 (43) 15048-15056 [2022-11-01; online 2022-10-17]
DOI Crossref
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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Adil Mardinoglu DDLS Fellow Fredrik Edfors SciLifeLab Fellow
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Network analysis uncovers associations in the turnover of C1 molecules in a winter lake
Mondav R, Martin G, Peura S, Garcia SL
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Sarahi Garcia Sari Peura SciLifeLab Fellow
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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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Jens Carlsson SciLifeLab Fellow
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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]
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Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.
Sahraei SE, Sánchez-García M, Montoliu-Nerin M, ..., Rosendahl S, Rosling A
Mycorrhiza 32 (5-6) 361-371 [2022-11-00; online 2022-09-26]
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Translatome profiling in fatal familial insomnia implicates TOR signaling in somatostatin neurons.
Bauer S, Dittrich L, Kaczmarczyk L, ..., Benfeitas R, Jackson WS
Life Sci. Alliance 5 (11) - [2022-11-00; online 2022-10-03]
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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]
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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]
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Strong Association of Combined Genetic Deficiencies in the Classical Complement Pathway With Risk of Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.
Lundtoft C, Sjöwall C, Rantapää-Dahlqvist S, ..., Leonard D, Rönnblom L
Arthritis & rheumatology (Hoboken, N.J.) 74 (11) 1842-1850 [2022-11-00; online 2022-10-07]
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Stroke genetics informs drug discovery and risk prediction across ancestries.
Mishra A, Malik R, Hachiya T, ..., Dichgans M, Debette S
Nature 611 (7934) 115-123 [2022-11-00; online 2022-09-30]
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Spatial genomics maps the structure, nature and evolution of cancer clones.
Lomakin A, Svedlund J, Strell C, ..., Nilsson M, Yates LR
Nature 611 (7936) 594-602 [2022-11-00; online 2022-11-09]
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]
DDLS Fellow Wei Ouyang
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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]
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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
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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]
DOI Crossref
Organic Base-Mediated Carboxylation of (Hetero)aromatic Compounds Using Supercritical Carbon Dioxide (scCO2)
Govender T, Chetty LC, Kruger HG, Arvidsson PI, Naicker T
Synthesis 54 (21) 4827-4833 [2022-11-00; online 2022-08-16]
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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]
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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]
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Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.
Yavuz S, Pucholt P, Sandling JK, ..., Lindblad-Toh K, Rönnblom L
Lupus Sci Med 9 (1) - [2022-11-00; online 2022-11-05]
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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]
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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
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Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability.
Lindstrand A, Ek M, Kvarnung M, ..., Pettersson M, Nordgren A
Genet Med 24 (11) 2296-2307 [2022-11-00; online 2022-09-06]
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]
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Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.
Butler-Laporte G, Povysil G, Kosmicki JA, ..., Ferreira MAR, Richards JB
PLoS Genet 18 (11) e1010367 [2022-11-00; online 2022-11-03]
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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]
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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]
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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
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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]
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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]
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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
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Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.
Banijamali M, Höjer P, Nagy A, ..., Viktorsson K, Ahmadian A
J Extracell Vesicles 11 (11) e12277 [2022-11-00; online 2022-11-05]
DOI Crossref
Characterization of the Human Podocin Short Isoform In Vivo Using a New Mouse Model
Butt L, Unnersjö-Jess D, Rinschen MM, ..., Benzing T, Höhne M
J. Am. Soc. Nephrol. 33 (11S) 414-414 [2022-11-00; online 2022-11-00]
DOI Crossref
Caveolin-1 haplotypes as predictor for locoregional recurrence in breast cancer
Godina C, Tryggvadottir H, Bosch A, ..., Isaksson K, Jernström H
Eur. J. Cancer 175 (-) S85 [2022-11-00; online 2022-11-00]
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B-cell repopulation dynamics and drug pharmacokinetics impact SARS-CoV-2 vaccine efficacy in anti-CD20-treated multiple sclerosis patients.
Asplund Högelin K, Ruffin N, Pin E, ..., Piehl F, Al Nimer F
Eur J Neurol 29 (11) 3317-3328 [2022-11-00; online 2022-07-20]
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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]
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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]
DDLS Fellow Patrick Bryant
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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
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Lauterbur ME, Cavassim MIA, Gladstein AL, ..., Schrider DR, Gronau I
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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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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]
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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]
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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]
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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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Expansion Spatial Transcriptomics
Fan Y, Andrusivová Ž, Wu Y, ..., Lundeberg J, Wang B
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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]
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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
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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]
DOI Crossref
Comprehensive interrogation of a Drosophila embryonic patterning network reveals the impact of chromatin state on tissue-specific burst kinetics and RNA Polymerase II promoter-proximal pause release
Hunt G, Vaid R, Pirogov S, ..., Reimegård J, Mannervik M
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DOI Crossref
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
ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.
Schuster J, Klar J, Khalfallah A, ..., Birnir B, Dahl N
Front Mol Neurosci 15 (-) 988993 [2022-10-24; online 2022-10-24]
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The ACE-2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion
Cervantes M, Hess T, Morbioli GG, Sengar A, Kasson PM
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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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SciLifeLab Fellow
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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]
PubMed DOI Crossref
WASH activation controls endosomal recycling and EGFR and Hippo signaling during tumor-suppressive cell competition.
Liu D, Tsarouhas V, Samakovlis C
Nat Commun 13 (1) 6243 [2022-10-21; online 2022-10-21]
PubMed DOI Crossref
The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry.
Mohammed Taha H, Aalizadeh R, Alygizakis N, ..., Slobodnik J, Schymanski EL
Environ Sci Eur 34 (1) 104 [2022-10-21; online 2022-10-21]
PubMed DOI Crossref
Structure-Based Discovery of Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5.
Kampen S, Rodríguez D, Jørgensen M, ..., Lebon G, Carlsson J
ACS chemical biology 17 (10) 2744-2752 [2022-10-21; online 2022-09-23]
Jens Carlsson SciLifeLab Fellow
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PD-1 expression on mouse intratumoral NK cells and its effects on NK cell phenotype.
Wagner AK, Kadri N, Tibbitt C, ..., Kärre K, Chambers BJ
iScience 25 (10) 105137 [2022-10-21; online 2022-09-16]
DOI Crossref
Linking prokaryotic genome size variation to metabolic potential and environment
Rodríguez-Gijón A, Buck M, Andersson AF, ..., Nascimento FJA, Garcia SL
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Sarahi Garcia SciLifeLab Fellow
DOI Crossref
Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity
Li X, Lappalainen T, Bussemaker HJ
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PubMed DOI Crossref
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia.
Herbst SA, Vesterlund M, Helmboldt AJ, ..., Lehtiö J, Dietrich S
Nat Commun 13 (1) 6226 [2022-10-20; online 2022-10-20]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues.
Diamanti K, Cavalli M, Pereira MJ, ..., Eriksson JW, Wadelius C
Cell Rep Med 3 (10) 100763 [2022-10-18; online 2022-10-04]
PubMed DOI Crossref
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
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
DDLS Fellow Milka Doktorova
DOI Crossref
A new framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile R package for paralogs and CNVs detection
Karunarathne P, Zhou Q, Schliep K, Milesi P
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PubMed DOI Crossref
Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.
Tobiasson V, Berzina I, Amunts A
Nat Commun 13 (1) 6132 [2022-10-17; online 2022-10-17]
Alexey Amunts SciLifeLab Fellow
DOI Crossref
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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PubMed DOI Crossref
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]
PubMed DOI Crossref
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
RSC Adv. 12 (46) 29908-29914 [2022-10-17; online 2022-10-19]
DOI Crossref
Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult
Hellberg S, Ahmed O, Zhang Y, ..., Olofsson PS, Malin SG
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DOI Crossref
Entropy predicts sensitivity of pseudo-random seeds
Maier BD, Sahlin K
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Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Cell chirality exhibition of brain microvascular endothelial cells is dependent on micropattern width.
Porras Hernández AM, Tenje M, Antfolk M
RSC Adv. 12 (46) 30135-30144 [2022-10-17; online 2022-10-21]
PubMed DOI Crossref
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
DOI Crossref
Astrocyte 3D Culture and Bioprinting using Peptide Functionalized Hyaluronan Hydrogels
Matthiesen I, Jury M, Boroojeni FR, ..., Aili D, Herland A
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PubMed DOI Crossref
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]
PubMed DOI Crossref
Routine omics collection is a golden opportunity for European human research in space and analog environments.
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Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.
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Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo-endometrium interplay.
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Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.
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Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease.
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FAIR Points: From sdo:LearningResource to FAIR Digital Object
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Biospecimens in FDO world
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Scalable Constant pH Molecular Dynamics in GROMACS.
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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.
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Molecular tools to monitor health and disease - and lucky coincidences.
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Membrane-assisted assembly and selective secretory autophagy of enteroviruses.
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Metabolic Assessment of Human Induced Pluripotent Stem Cells-Derived Astrocytes and Fetal Primary Astrocytes: Lactate and Glucose Turnover.
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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
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PubMed DOI Crossref
Addressing the Protease Bias in Quantitative Proteomics.
Woessmann J, Kotol D, Hober A, Uhlén M, Edfors F
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DDLS Fellow Fredrik Edfors
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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.
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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
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bioRxiv - (-) - [2022-10-05; online 2022-10-05]
DDLS Fellow Tom van der Valk
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Youth with severe mental illness and complex non-somatic motor abnormalities: conflicting conceptualizations and unequal treatment.
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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
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Neglected, yet significant role of FOXP1 in T-cell quiescence, differentiation and exhaustion.
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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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Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity
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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.
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Cell. Mol. Life Sci. 79 (10) 535 [2022-10-01; online 2022-10-01]
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Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount.
Gaetani M, Zubarev RA
Methods in molecular biology (Clifton, N.J.) 2554 (-) 91-106 [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
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Asymmetry of wetting and de-wetting on high-friction surfaces originates from the same molecular physics
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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
PubMed DOI Crossref
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
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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]
Magda Bienko SciLifeLab Fellow
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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
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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
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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
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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
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Prostate cancer disease recurrence after radical prostatectomy is associated with HLA type and local cytomegalovirus immunity.
Classon J, Zamboni M, Engblom C, ..., Mold J, Frisén J
Mol Oncol 16 (19) 3452-3464 [2022-10-00; online 2022-08-31]
Camilla Engblom SciLifeLab Fellow
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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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Osteoclasts directly influence castration-resistant prostate cancer cells.
Huang J, Freyhult E, Buckland R, ..., Damber JE, Welén K
Clin Exp Metastasis 39 (5) 801-814 [2022-10-00; online 2022-08-16]
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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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
New regulators of the tetracycline-inducible gene expression system identified by chemical and genetic screens.
Colicchia V, Häggblad M, Sirozh O, ..., Hühn D, Fernandez-Capetillo O
FEBS Open Bio 12 (10) 1896-1908 [2022-10-00; online 2022-09-11]
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Mechanismen der Cristae-Biogenese in Humanparasiten
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Biospektrum 28 (6) 590-593 [2022-10-00; online 2022-10-11]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
PubMed DOI Crossref
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]
PubMed DOI Crossref
Implementing precision medicine in a regionally organized healthcare system in Sweden.
Fioretos T, Wirta V, Cavelier L, ..., Edsjö A, Rosenquist R
Nat. Med. 28 (10) 1980-1982 [2022-10-00; online 2022-09-20]
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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 Sari Peura SciLifeLab Fellow
PubMed DOI Crossref
Genome-wide association study of liver enzyme elevation in an extended cohort of rheumatoid arthritis patients starting low-dose methotrexate.
Cavalli M, Eriksson N, Sundbaum JK, ..., Hallberg P, Wadelius M
Pharmacogenomics 23 (15) 813-820 [2022-10-00; online 2022-09-07]
PubMed DOI Crossref
Generation of Human iPSC-Derived Astrocytes with a mature star-shaped phenotype for CNS modeling.
Voulgaris D, Nikolakopoulou P, Herland A
Stem Cell Rev Rep 18 (7) 2494-2512 [2022-10-00; online 2022-04-30]
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Familial platelet disorder due to germline exonic deletions in RUNX1: a diagnostic challenge with distinct alterations of the transcript isoform equilibrium.
Engvall M, Karlsson Y, Kuchinskaya E, ..., Cammenga J, Baliakas P
Leuk. Lymphoma 63 (10) 2311-2320 [2022-10-00; online 2022-05-09]
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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
PubMed DOI Crossref
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
Comparison of EM-seq and PBAT methylome library methods for low-input DNA.
Han Y, Zheleznyakova GY, Marincevic-Zuniga Y, ..., Needhamsen M, Jagodic M
Epigenetics 17 (10) 1195-1204 [2022-10-00; online 2021-11-17]
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
Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL3 domain in solution.
Han X, Levkovets M, Lesovoy D, ..., Agback P, Orekhov VY
Biomol NMR Assign 16 (2) 363-371 [2022-10-00; online 2022-09-12]
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]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
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]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
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
PubMed DOI Crossref
A Hitchhiker's guide through the bio-image analysis software universe.
Haase R, Fazeli E, Legland D, ..., Klemm A, Tischer C
FEBS Lett. 596 (19) 2472-2485 [2022-10-00; online 2022-07-29]
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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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PubMed DOI Crossref
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]
PubMed DOI Crossref
Anti-tumor effect of berberine on chronic lymphocytic leukemia cells.
Abdollahi M, Mohammadlou M, Hemati M, ..., Sarabi MA, Kokhaei P
Med. Oncol. 39 (12) 217 [2022-09-29; online 2022-09-29]
DOI Crossref
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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PubMed DOI Crossref
Proteome profiling of whole plasma and plasma-derived extracellular vesicles facilitates the detection of tissue biomarkers in the non-obese diabetic mouse.
Diaz Lozano IM, Sork H, Stone VM, ..., Gabrielsson S, Flodström-Tullberg M
Front Endocrinol (Lausanne) 13 (-) 971313 [2022-09-28; online 2022-09-28]
PubMed DOI Crossref
Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells.
Tsirigoti C, Ali MM, Maturi V, Heldin CH, Moustakas A
Cell Death Dis 13 (9) 832 [2022-09-28; online 2022-09-28]
PubMed DOI Crossref
Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.
Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S
Genome Res 32 (9) 1627-1641 [2022-09-27; online 2022-09-27]
PubMed DOI Crossref
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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Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
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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Author response: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
Leyhr J, Waldmann L, Filipek-Górniok B, ..., Allalou A, Haitina T
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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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Camilla Engblom SciLifeLab Fellow
DOI Crossref
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.
Dekkers KF, Sayols-Baixeras S, Baldanzi G, ..., Orho-Melander M, Fall T
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Author response: Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq
Vazquez SE, Mann SA, Bodansky A, ..., Anderson MS, DeRisi JL
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DOI Crossref
A conserved ribosomal protein has entirely dissimilar structures in different organisms
Schierholz L, Brown CR, Helena-Bueno K, ..., Barandun J, Melnikov SV
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Jonas Barandun SciLifeLab Fellow
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Deep learning-based tumor microenvironment segmentation is predictive of tumor mutations and patient survival in non-small-cell lung cancer.
Rączkowska A, Paśnik I, Kukiełka M, ..., Crosetto N, Szczurek E
BMC Cancer 22 (1) 1001 [2022-09-21; online 2022-09-21]
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Antibiotic perseverance increases the risk of resistance development
Brandis G, Larsson J, Elf J
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Synthesis of Silver Nano Particles Using Myricetin and the In-Vitro Assessment of Anti-Colorectal Cancer Activity: In-Silico Integration.
Anwer ST, Mobashir M, Fantoukh OI, ..., Naqvi IH, Rizvi MMA
Int J Mol Sci 23 (19) - [2022-09-20; online 2022-09-20]
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EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes
Richter DJ, Berney C, Strassert JFH, ..., Burki F, de Vargas C
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Fabien Burki SciLifeLab Fellow
DOI Crossref
Barcode-free prediction of cell lineages from scRNA-seq datasets
Eisele AS, Tarbier M, Dormann AA, Pelechano V, Suter DM
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DDLS Fellow Marcel Tarbier SciLifeLab Fellow
DOI Crossref
The genomic basis of hybrid male sterility in Ficedula flycatchers
Segami JC, Mugal CF, Cunha C, ..., Semon M, Qvarnström A
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In Vivo Imaging of the Pancreas and Gut Hormone Receptors
Eriksson O, Hulsart-Billström G, Mitran B, Puuvuori E, Velikyan I
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Olof Eriksson SciLifeLab Fellow
DOI Crossref
Coupling cellular drug-target engagement to downstream pharmacology with CeTEAM
Valerie NCK, Sanjiv K, Mortusewicz O, ..., Page BDG, Altun M
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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
Lagman D, Haines HJ, Abalo XM, Larhammar D
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Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.
Marklund M, Schultz N, Friedrich S, ..., Sonnhammer E, Lundeberg J
Nat Commun 13 (1) 5475 [2022-09-17; online 2022-09-17]
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New primer sets to detect recent human adenovirus F41 variants in wastewater: Is it linked to the new acute hepatitis?
Perez-Zabaleta M, Williams C, Cetecioglu Z
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Influenza virus membrane fusion is promoted by the endosome-resident phospholipid bis(monoacylglycero)phosphate
Mannsverk S, Villamil Giraldo AM, Kasson PM
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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
Eur J Cell Biol 101 (4) 151274 [2022-09-17; online 2022-09-17]
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Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis
Mastropasqua F, Oksanen M, Soldini C, ..., Bölte S, Tammimies K
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Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
The First Structure of Human MTHFD2L and Its Implications for the Development of Isoform-Selective Inhibitors.
Scaletti ER, Gustafsson Westergren R, Andersson Y, ..., Helleday T, Stenmark P
ChemMedChem 17 (18) e202200274 [2022-09-16; online 2022-07-06]
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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
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Retinol and Retinol Binding Protein 4 Levels and Cardiometabolic Disease Risk.
Schiborn C, Weber D, Grune T, ..., Schulze MB, Wittenbecher C
Circ. Res. 131 (7) 637-649 [2022-09-16; online 2022-08-26]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
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
ACS Synth. Biol. 11 (9) 3100-3113 [2022-09-16; online 2022-08-15]
Paul Hudson SciLifeLab Fellow
DOI Crossref
Front Cover: The First Structure of Human MTHFD2L and Its Implications for the Development of Isoform‐Selective Inhibitors (ChemMedChem 18/2022)
Scaletti ER, Gustafsson Westergren R, Andersson Y, ..., Helleday T, Stenmark P
ChemMedChem 17 (18) - [2022-09-16; online 2022-09-26]
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ERβ and Inflammation.
Hases L, Archer A, Williams C
Springer 1390 (-) 213-225 [2022-09-16; online 2022-09-16]
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Design, structure and plasma binding of ancestral β-CoV scaffold antigens
Syren PO, Hueting D, Schriever K, ..., Pan-Hammarstrom Q, Andrell J
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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
iScience 25 (9) 104868 [2022-09-16; online 2022-08-26]
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Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes
Younis S, Jouneau A, Larsson M, ..., Brochard V, Andersson L
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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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Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.
Peña-Pérez L, Frengen N, Hauenstein J, ..., Lindstrand A, Månsson R
Blood Adv 6 (17) 5009-5023 [2022-09-13; online 2022-06-09]
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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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Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals: An IMI DIRECT study
A WA, CA B, R B, ..., S B, Consortium I
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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
Plant Commun 3 (5) 100342 [2022-09-12; online 2022-05-27]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
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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Apoptosis Detection by Quantification of Cell Debris in Bright-Field Microscopy Images.
Ölander M, Artursson P
Methods in molecular biology (Clifton, N.J.) 2543 (-) 27-33 [2022-09-11; online 2022-09-11]
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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 & 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
Nat Commun 13 (1) 5303 [2022-09-09; online 2022-09-09]
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Author response: Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules
Itoh Y, Singh V, Khawaja A, ..., Rorbach J, Amunts A
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Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
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
From biomedical cloud platforms to microservices: next steps in FAIR data and analysis.
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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Colitis Induces Sex-Specific Intestinal Transcriptomic Responses in Mice.
Hases L, Birgersson M, Indukuri R, Archer A, Williams C
Int J Mol Sci 23 (18) - [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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Spatio-temporal predictions of COVID-19 test positivity in Uppsala County, Sweden: a comparative approach.
van Zoest V, Varotsis G, Menzel U, ..., Martinell M, Fall T
Sci Rep 12 (1) 15176 [2022-09-07; online 2022-09-07]
PubMed DOI Crossref
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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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]
PubMed DOI Crossref
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
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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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Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia.
Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T
Semin. Cancer Biol. 84 (-) 40-49 [2022-09-00; online 2021-10-01]
PubMed DOI Crossref
Trailblazing precision medicine in Europe: A joint view by Genomic Medicine Sweden and the Centers for Personalized Medicine, ZPM, in Germany.
Stenzinger A, Edsjö A, Ploeger C, ..., Rosenquist R, GMS working group and ZPM working group
Semin. Cancer Biol. 84 (-) 242-254 [2022-09-00; online 2021-05-24]
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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]
Paul Hudson SciLifeLab Fellow
PubMed DOI Crossref
The role of Gdf5 in the development of the zebrafish fin endoskeleton.
Waldmann L, Leyhr J, Zhang H, ..., Öhman-Mägi C, Haitina T
Dev. Dyn. 251 (9) 1535-1549 [2022-09-00; online 2021-07-29]
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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
J Pharm Sci 111 (9) 2645-2649 [2022-09-00; online 2022-07-03]
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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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Sir2 and Reb1 antagonistically regulate nucleosome occupancy in subtelomeric X-elements and repress TERRAs by distinct mechanisms.
Bauer SL, Grochalski TNT, Smialowska A, Åström SU
PLoS Genet 18 (9) e1010419 [2022-09-00; online 2022-09-22]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Plasma proteome profiling of healthy individuals across the life span in a Sicilian cohort with long-lived individuals.
Siino V, Ali A, Accardi G, ..., Levander F, Vasto S
Aging Cell 21 (9) e13684 [2022-09-00; online 2022-08-06]
DOI Crossref
P16-11 In search of sensitive safety biomarkers of peripheral neurotoxicity in the rat: a collaborative effort across industry and academia (IMI NeuroDeRisk project)
Di Cesare Mannelli L, Balayssac D, Busserolles J, ..., Penrrat K, Theil D
Toxicol. Lett. 368 (-) S222 [2022-09-00; online 2022-09-00]
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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]
Alexey Amunts SciLifeLab Fellow
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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]
Alexey Amunts SciLifeLab Fellow
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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]
DOI Crossref
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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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
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.
Wang Z, Emmerich A, Pillon NJ, ..., Loos RJF, Hoed MD
Nat. Genet. 54 (9) 1332-1344 [2022-09-00; online 2022-09-07]
PubMed DOI Crossref
Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection.
Ambikan AT, Svensson-Akusjärvi S, Krishnan S, ..., Benfeitas R, Neogi U
Life Sci. Alliance 5 (9) - [2022-09-00; online 2022-05-10]
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
Effect of perfluoroalkyl exposure in pregnancy and infancy on intrauterine and childhood growth and anthropometry. Sub study from COPSAC2010 birth cohort.
Sevelsted A, Gürdeniz G, Rago D, ..., Bisgaard H, Chawes B
EBioMedicine 83 (-) 104236 [2022-09-00; online 2022-08-26]
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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]
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EP16.04-001 The Role of Stromal PDGFRβ-activation in NSCLC
Lindberg A, Grandon A, Yu H, ..., Micke P, Strell C
Journal of Thoracic Oncology 17 (9) S610-S611 [2022-09-00; online 2022-09-00]
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
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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 DDLS Fellow Muhammad Arif SciLifeLab Fellow
PubMed DOI Crossref
Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting.
Wu M, Schmid M, Jensen TH, Sandelin A
NAR Genomics and Bioinformatics 4 (3) lqac071 [2022-09-00; online 2022-09-15]
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Automated detection of vascular remodeling in tumor-draining lymph nodes by the deep-learning tool HEV-finder.
Bekkhus T, Avenel C, Hanna S, ..., Wählby C, Ulvmar MH
J. Pathol. 258 (1) 4-11 [2022-09-00; online 2022-07-12]
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]
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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
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1668P Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction
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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.
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Integrative genomic and transcriptomic analyses illuminate the ontology of HER2-low breast carcinomas.
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Glioblastoma CD105+ cells define a SOX2- cancer stem cell-like subpopulation in the pre-invasive niche.
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Nucleic Acids Res. 50 (15) 8491-8511 [2022-08-26; online 2022-07-30]
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PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.
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Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
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Quantitative bile and serum proteomics for the screening and differential diagnosis of primary sclerosing cholangitis.
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Genomic and gene expression associations to morphology of a sexual ornament in the chicken.
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An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry.
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Mapping the GALNT1 substrate landscape with versatile proteomics tools
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Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates.
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Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection.
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Overexpressed C-Myc Sensitize Cells to TH1579, an Mitotic Arrest and Oxidative DNA Damage Inducer
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Multi-Omic Investigations of a 17-19 Translocation Links MINK1 Disruption to Autism, Epilepsy and Osteoporosis.
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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
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DDLS Fellow Tom van der Valk
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Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.
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Using the ANDROMEDA by Prosilico Software for Prediction of the Human Pharmacokinetics of 4 Compounds of Natural Origin - Colistin, Curucumin, UCN-01 and Voclosporin
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The origin and evolution of open habitats in North America inferred by Bayesian deep learning models.
Andermann T, Strömberg CAE, Antonelli A, Silvestro D
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Probe set selection for targeted spatial transcriptomics
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Multiomics characterization implicates PTK7 in ovarian cancer EMT and cell plasticity and offers strategies for therapeutic intervention.
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Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.
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Cell Syst 13 (8) 665-681.e4 [2022-08-17; online 2022-07-08]
Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow
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Zeitotox: Toxicology and the Rhythms of Life.
Xiao L, Antczak P, Rüegg J, Behrendt L
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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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nNOS-derived NO modulates force production and iNO-derived NO the excitability in C2C12-derived 3D tissue engineering skeletal muscle via different NO signaling pathways.
Mosqueira M, Scheid LM, Kiemel D, ..., Yildiz U, Porth I
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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.
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Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.
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Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models Using Similarity to Training Data
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A method for Boolean analysis of protein interactions at a molecular level.
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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.
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Selective Serotonin Reuptake Inhibitors Within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane
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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
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Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.
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Local molecular and global connectomic contributions to cross-disorder cortical abnormalities.
Hansen JY, Shafiei G, Vogel JW, ..., Dagher A, Misic B
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DDLS Fellow Jacob W Vogel
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Functional Characterization of Genetic Variant Effects on Expression.
Flynn ED, Lappalainen T
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Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.
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Ageing desexualizes the Drosophila brain transcriptome.
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Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition.
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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
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Bacterial type I signal peptidase inhibitors - Optimized hits from nature.
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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
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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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Adil Mardinoglu DDLS Fellow Fredrik Edfors SciLifeLab Fellow
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Editorial: Glycoconjugates in vaccines and immunotherapeutics.
Shivatare S, Sanjiv K, Kikkeri R, Adamo R
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Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing.
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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.
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Polymer Dots as Photoactive Membrane Vesicles for [FeFe]-Hydrogenase Self-Assembly and Solar-Driven Hydrogen Evolution.
Pavliuk MV, Lorenzi M, Morado DR, ..., Berggren G, Tian H
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Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.
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Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]
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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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Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms
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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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Simple and rapid quantification of cetirizine, venlafaxine, and O-desmethylvenlafaxine in human breast milk, and metformin in human milk and plasma with UHPLC-MS/MS.
Wegler C, Saleh A, Lindqvist A, ..., Smeraglia J, Baranczewski P
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Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects.
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Investigating the Effect of Estradiol Levels on the Risk of Breast, Endometrial, and Ovarian Cancer.
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Integrated cooling system for microfluidic PDMS devices used in biological microscopy studies
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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
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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
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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
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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
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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
Atherosclerosis 355 (-) 37 [2022-08-00; online 2022-08-00]
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The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.
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Mol Ecol Resour 22 (6) 2379-2395 [2022-08-00; online 2022-04-11]
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The evolutionary origin of host association in the Rickettsiales.
Schön ME, Martijn J, Vosseberg J, Köstlbacher S, Ettema TJG
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The discovAIR project: a roadmap towards the Human Lung Cell Atlas.
Luecken MD, Zaragosi LE, Madissoon E, ..., Meyer KB, Nawijn MC
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The biogenesis of β-lactamase enzymes.
Kaderabkova N, Bharathwaj M, Furniss RCD, ..., Palmer T, Mavridou DAI
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The anti-inflammatory peptide Catestatin blocks chemotaxis.
Muntjewerff EM, Parv K, Mahata SK, ..., Christoffersson G, van den Bogaart G
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Targeting the DNA repair enzymes MTH1 and OGG1 as a novel approach to treat inflammatory diseases.
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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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SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry.
Arslan T, Pan Y, Mermelekas G, ..., Orre LM, Lehtiö J
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Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J
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Single-cell and spatially resolved transcriptome analysis reveals cellular heterogeneities and novel regulators of atherosclerotic plaque destabilization
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Atherosclerosis 355 (-) 31-32 [2022-08-00; online 2022-08-00]
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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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IEEE J Biomed Health Inform 26 (8) 4079-4089 [2022-08-00; online 2022-08-11]
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Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.
Latz MAC, Grujcic V, Brugel S, ..., Andersson A, Andersson AF
Mol Ecol Resour 22 (6) 2304-2318 [2022-08-00; online 2022-05-06]
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SARS-CoV-2 air sampling: A systematic review on the methodologies for detection and infectivity.
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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
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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
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Phosphorylation of eIF4E in the stroma drives the production and spatial organisation of collagen type I in the mammary gland.
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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.
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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
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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]
PubMed DOI Crossref
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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Human adaptation to arsenic in Bolivians living in the Andes.
De Loma J, Vicente M, Tirado N, ..., Schlebusch CM, Broberg K
Chemosphere 301 (-) 134764 [2022-08-00; online 2022-04-28]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
Dihydroorotate dehydrogenase inhibition acts synergistically with tyrosine kinase inhibitors to induce apoptosis of mantle cell lymphoma cells.
Eriksen-Gjerstad M, Tveit Karlsen I, Fandalyuk Z, ..., Gelebart P, Mc Cormack E
EJHaem 3 (3) 913-918 [2022-08-00; online 2022-05-15]
PubMed DOI Crossref
Deep Visual Proteomics defines single-cell identity and heterogeneity.
Mund A, Coscia F, Kriston A, ..., Horvath P, Mann M
Nat. Biotechnol. 40 (8) 1231-1240 [2022-08-00; online 2022-05-19]
PubMed DOI Crossref
De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.
Marco Salas S, Yuan X, Sylven C, ..., Wählby C, Partel G
PLoS Comput Biol 18 (8) e1010366 [2022-08-00; online 2022-08-12]
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]
PubMed DOI Crossref
Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases.
Lundtoft C, Pucholt P, Martin M, ..., Svenungsson E, Rönnblom L
Arthritis & rheumatology (Hoboken, N.J.) 74 (8) 1440-1450 [2022-08-00; online 2022-06-27]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
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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]
PubMed DOI Crossref
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 DDLS Fellow Muhammad Arif 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]
PubMed DOI Crossref
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]
DOI Crossref
077 Identifying genetic factors that enable basal cell carcinoma to transition from microscopic to macroscopic disease
Trieu KG, Tsai S, Eberl M, ..., Dlugosz AA, Wong SY
J. Invest. Dermatol. 142 (8) S13 [2022-08-00; online 2022-08-00]
PubMed DOI Crossref
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
DOI Crossref
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]
PubMed DOI Crossref
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
DOI Crossref
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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DDLS Fellow Patrick Bryant
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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) 4287 [2022-07-27; online 2022-07-27]
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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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
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α-Synuclein-induced deformation of small unilamellar vesicles.
Makasewicz K, Wennmalm S, Linse S, Sparr E
QRB Discov 3 (-) e10 [2022-07-25; online 2022-07-25]
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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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Targeted Chromosome Conformation Capture (HiCap).
Zhigulev A, Sahlén P
Methods in molecular biology (Clifton, N.J.) 2532 (-) 75-94 [2022-07-23; online 2022-07-23]
DOI Crossref
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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DDLS Fellow Patrick Bryant
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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]
PubMed DOI Crossref
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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Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner.
Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L
Elife 11 (-) - [2022-07-21; online 2022-07-21]
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Vaccine-enhanced competition permits rational bacterial strain replacement in the gut
Lentsch V, Woller A, Rocker A, ..., Diard M, Slack E
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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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The Influence of Plant Stress Hormones and Biotic Elicitors on Cyclotide Production in Viola uliginosa Cell Suspension Cultures.
Slazak B, Jędrzejska A, Badyra B, ..., Andrén PE, Göransson U
Plants (Basel) 11 (14) - [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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Sanja Vickovic SciLifeLab Fellow
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Sensitive Protein Detection Using Site-Specifically Oligonucleotide-Conjugated Nanobodies.
Al-Amin RA, Muthelo PM, Abdurakhmanov E, ..., Danielson UH, Landegren U
Anal. Chem. 94 (28) 10054-10061 [2022-07-19; online 2022-07-05]
DOI Crossref
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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Prashant Singh SciLifeLab Fellow
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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]
PubMed DOI Crossref
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]
Patrick Sandoz SciLifeLab Fellow
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Resting State Neural Networks at Complex Visual Hallucinations in Charles Bonnet Syndrome
Hanoglu T, Velioglu HA, Salar BA, ..., Yulug B, Hanoglu L
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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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Daniel Globisch SciLifeLab Fellow
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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
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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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”Evolution of ipsilateral breast cancer decoded by proteogenomics”
Marchi TD, Pyl PT, Sjöström M, ..., Malmstöm J, Niméus E
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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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Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.
Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR
Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]
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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
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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]
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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, Af Klint E, ..., Ståhl PL, Malmström V
Sci Rep 12 (1) 11876 [2022-07-13; online 2022-07-13]
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Author response: Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner
Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L
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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]
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Ultra-sensitive monitoring of leukemia patients using superRCA mutation detection assays.
Chen L, Eriksson A, Weström S, ..., Cavelier L, Landegren U
Nat Commun 13 (1) 4033 [2022-07-12; online 2022-07-12]
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Reductive evolution in the structure of the microsporidian proteasome
Jespersen N, Ehrenbolger K, Winiger RR, ..., Vossbrinck CR, Barandun J
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Jonas Barandun SciLifeLab Fellow
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Recommendation: α-synuclein-induced Deformation of Small Unilamellar Vesicles — R1/PR4
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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]
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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
Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19
Yu M, Charles A, Cagigi A, ..., Loré K, Smed-Sörensen A
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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
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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]
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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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Daniel Fürth Erdinc Sezgin SciLifeLab Fellow
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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]
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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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PubMed DOI Crossref
High-throughput muscle fiber typing from RNA sequencing data.
Oskolkov N, Santel M, Parikh HM, ..., Pääbo S, Hansson O
Skelet Muscle 12 (1) 16 [2022-07-02; online 2022-07-02]
DOI Crossref
A new machine learning method for cancer mutation analysis
Habibi M, Taheri G
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DDLS Fellow Golnaz Taheri
PubMed DOI Crossref
Regulatory networks and 5' partner usage of miRNA host gene fusions in breast cancer.
Hafstað V, Søkilde R, Häkkinen J, ..., Rovira C, Persson H
Int. J. Cancer 151 (1) 95-106 [2022-07-01; online 2022-02-26]
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]
Paul Hudson SciLifeLab Fellow
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]
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New Views of Old Proteins: Clarifying the Enigmatic Proteome.
Burnum-Johnson KE, Conrads TP, Drake RR, ..., Walt DR, Kelleher NL
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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]
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Mercury–Selenium Accumulation Patterns in Muscle Tissue of Two Freshwater Fish Species, Eurasian Perch (Perca fluviatilis) and Vendace (Coregonus albula)
Regnell O, Tesson SVM, Oskolkov N, Nerentorp M
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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]
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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 DDLS Fellow Muhammad Arif SciLifeLab Fellow
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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]
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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]
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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]
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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]
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Identification of a novel compound that simultaneously impairs the ubiquitin-proteasome system and autophagy.
Giovannucci TA, Salomons FA, Stoy H, ..., Vallin M, Dantuma NP
Autophagy 18 (7) 1486-1502 [2022-07-00; online 2021-11-05]
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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]
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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]
DDLS Fellow Fredrik Edfors
PubMed DOI Crossref
HPA-axis dysregulation is not associated with accelerated epigenetic aging in patients with hypersexual disorder.
Boström ADE, Andersson P, Chatzittofis A, ..., Arver S, Jokinen J
Psychoneuroendocrinology 141 (-) 105765 [2022-07-00; online 2022-04-14]
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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
Genomic profile - a possible diagnostic and prognostic marker in upper tract urothelial carcinoma.
Grahn A, Eisfeldt J, Malm C, ..., Tham E, Brehmer M
BJU Int 130 (1) 92-101 [2022-07-00; online 2021-08-29]
PubMed DOI Crossref
Genomic dynamics of brown trout populations released to a novel environment.
Kurland S, Rafati N, Ryman N, Laikre L
Ecol Evol 12 (7) e9050 [2022-07-00; online 2022-07-03]
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
Coupling Lipid Nanoparticle Structure and Automated Single-Particle Composition Analysis to Design Phospholipase-Responsive Nanocarriers.
Barriga HMG, Pence IJ, Holme MN, ..., Carroni M, Stevens MM
Adv. Mater. Weinheim 34 (26) e2200839 [2022-07-00; online 2022-05-18]
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Clonal haematopoiesis as a risk factor for therapy-related myeloid neoplasms in patients with chronic lymphocytic leukaemia treated with chemo-(immuno)therapy.
Voso MT, Pandzic T, Falconi G, ..., Fabiani E, Baliakas P
Br. J. Haematol. 198 (1) 103-113 [2022-07-00; online 2022-03-11]
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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
DOI Crossref
An Adaptable Antibody‐Based Platform for Flexible Synthetic Peptide Delivery Built on Agonistic CD40 Antibodies
Eltahir M, Laurén I, Lord M, ..., Persson H, Mangsbo SM
Advanced Therapeutics 5 (7) - [2022-07-00; online 2022-06-14]
PubMed DOI Crossref
Age-dependent aneuploidy in mammalian oocytes instigated at the second meiotic division.
Kouznetsova A, Liu JG, Valentiniene S, Brismar H, Höög C
Aging Cell 21 (7) e13649 [2022-07-00; online 2022-06-03]
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
PubMed DOI Crossref
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.
Domenzain I, Sánchez B, Anton M, ..., Sonnenschein N, Nielsen J
Nat Commun 13 (1) 3766 [2022-06-30; online 2022-06-30]
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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Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Palidis: fast discovery of novel insertion sequences
Carr VR, Pissis SP, Mullany P, ..., Gomez-Cabrero D, Moyes DL
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Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
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
NPJ Breast Cancer 8 (1) 76 [2022-06-29; online 2022-06-29]
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]
DDLS Fellow José Cerca
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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PubMed DOI Crossref
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.
Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V
Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]
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
DOI Crossref
System-wide profiling by proteome integral solubility alteration assay of drug residence times for target characterization
Sabatier P, Beusch CM, Meng Z, Zubarev RA
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DOI Crossref
Multi-ancestry GWAS for venous thromboembolism identifies novel loci followed by experimental validation in zebrafish
Wolford BN, Zhao Y, Surakka I, ..., Shavit JA, Willer CJ
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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]
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Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex
Mühleip A, Flygaard RK, Haapanen O, ..., Sharma V, Amunts A
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Alexey Amunts SciLifeLab Fellow
DOI Crossref
A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats
Kakhki NA, Schweizer M, Lutgen D, ..., Schielzeth H, Burri R
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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]
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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]
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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
A qPCR-Based Method for Quantification of Replication Competent Adenovirus (RCA) in Conditionally Replicating Oncolytic Adenoviruses.
Yngve E, Gao M, Yu D
Methods in molecular biology (Clifton, N.J.) 2521 (-) 249-258 [2022-06-23; online 2022-06-23]
PubMed DOI Crossref
Ultrafast and selective labeling of endogenous proteins using affinity-based benzotriazole chemistry.
Xin X, Zhang Y, Gaetani M, ..., Corkery DP, Wu YW
Chem Sci 13 (24) 7240-7246 [2022-06-22; online 2022-05-30]
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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Lucie Delemotte SciLifeLab Fellow
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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Sarahi Garcia Sari Peura SciLifeLab Fellow
PubMed DOI Crossref
mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners.
Arnold H, Panara V, Hußmann M, ..., Schulte-Merker S, Koltowska K
Cell Reports 39 (12) 110982 [2022-06-21; online 2022-06-23]
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]
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MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.
Blixt MKE, Hellsand M, Konjusha D, ..., Ring H, Hallböök F
Oncogenesis 11 (1) 34 [2022-06-21; online 2022-06-21]
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
Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome
Singh V, Conor Moran J, Itoh Y, ..., Barrientos A, Amunts A
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Alexey Amunts SciLifeLab Fellow
DOI Crossref
Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5
McComas SE, Reichenbach T, Mitrovic D, ..., Delemotte L, Drew D
bioRxiv - (-) - [2022-06-18; online 2022-06-18]
Lucie Delemotte SciLifeLab Fellow
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Autoantigenic properties of the aminoacyl tRNA synthetase family in idiopathic inflammatory myopathies
Preger C, Notarnicola A, Hellström C, ..., Gräslund S, Jakobsson PJ
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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]
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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
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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
Review: α-synuclein-induced Deformation of Small Unilamellar Vesicles — R0/PR1
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DOI Crossref
Recommendation: α-synuclein-induced Deformation of Small Unilamellar Vesicles — R0/PR3
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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
Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells.
Saghaleyni R, Malm M, Moruzzi N, ..., Robinson JL, Rockberg J
Cell Reports 39 (11) 110936 [2022-06-14; online 2022-06-16]
Aleksej Zelezniak DDLS Fellow Fredrik Edfors SciLifeLab Fellow
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]
Adil Mardinoglu SciLifeLab Fellow
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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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Adil Mardinoglu SciLifeLab Fellow
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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Magda Bienko SciLifeLab Fellow
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
DOI Crossref
Deep thermal proteome profiling for detection of proteoforms and drug sensitivity biomarkers
Kurzawa N, Stahl M, Leo I, ..., Savitski MM, Jafari R
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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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Lucie Delemotte SciLifeLab Fellow
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]
Erdinc Sezgin SciLifeLab Fellow
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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DDLS Fellow Wei Ouyang
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
Ecology, not host phylogeny, shapes the oral microbiome in closely related species of gorillas
Moraitou M, Forsythe A, Fellows Yates JA, ..., Warinner C, Guschanski K
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PubMed DOI Crossref
Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis.
van Bruggen D, Pohl F, Langseth CM, ..., Sundström E, Castelo-Branco G
Dev. Cell 57 (11) 1421-1436.e5 [2022-06-06; online 2022-05-05]
DOI Crossref
Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression
Mattis KK, Krentz NA, Metzendorf C, ..., den Hoed M, Gloyn AL
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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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Erdinc Sezgin SciLifeLab Fellow
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LymphoTrack Is Equally Sensitive as PCR GeneScan and Sanger Sequencing for Detection of Clonal Rearrangements in ALL Patients.
Paulsen K, Marincevic M, Cavelier L, Hollander P, Amini RM
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Multi-staged gene expression profiling reveals potential genes and the critical pathways in kidney cancer.
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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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FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors.
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Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer.
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Genetic Landscape of the ACE2 Coronavirus Receptor.
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Basal cell carcinomas acquire secondary mutations to overcome dormancy and progress from microscopic to macroscopic disease.
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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
Trends Neurosci 45 (5) 342-345 [2022-05-00; online 2022-02-25]
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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
Nat. Med. 28 (5) 879-882 [2022-05-00; online 2022-04-07]
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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.
Arruda LCM, Gaballa A, Da Silva Rodrigues R, Makower B, Uhlin M
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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
The FASEB Journal 36 (S1) - [2022-05-00; online 2022-05-13]
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Re: Chen Dong, Sung-Lang Chen, and Wen-Wei Sung's Letter to the Editor re: Karin Welén, Ebba Rosendal, Magnus Gisslén, et al. A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data. Eur Urol. 2022;81:285-93.
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Proteomic profiles in cerebrospinal fluid predicted death and disability in term infants with perinatal asphyxia: A pilot study.
Leifsdottir K, Thelin EP, Lassarén P, ..., Eksborg S, Herlenius E
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Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: An epigenome-wide association study.
England-Mason G, Merrill SM, Gladish N, ..., Dewey D, APrON Study Team
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Polymorphisms in alpha 7 nicotinic acetylcholine receptor gene, CHRNA7, and its partially duplicated gene, CHRFAM7A, associate with increased inflammatory response in human peripheral mononuclear cells.
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NOX4 regulates TGFβ-induced proliferation and self-renewal in glioblastoma stem cells.
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MutT Homolog 1 Inhibitor Karonudib Attenuates Autoimmune Hepatitis by Inhibiting DNA Repair in Activated T Cells.
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Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate.
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Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation.
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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.
Tomczyk MM, Cheung KG, Xiang B, ..., Tong Q, Dolinsky VW
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Microbial functional genes influenced by short-term experimental drought across European agricultural fields
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Longitudinal analyses of development of the immune system during the first five years of life in relation to lifestyle.
Olin A, Acevedo N, Lakshmikanth T, ..., Scheynius A, Brodin P
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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.
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Author Correction: The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.
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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 starch- and sucrose-reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro-RNA levels.
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A motile doublet form of Salmonella Typhimurium diversifies target search behavior at the epithelial surface.
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Mol. Microbiol. 117 (5) 1156-1172 [2022-05-00; online 2022-04-12]
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"Randomized phase II study of azacitidine ± lenalidomide in higher-risk myelodysplastic syndromes and acute myeloid leukemia with a karyotype including Del(5q)".
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Understanding immune signaling using advanced imaging techniques.
Brameshuber M, Klotzsch E, Ponjavic A, Sezgin E
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.
Khadse A, Haakensen VD, Silwal-Pandit L, ..., Helland Å, Kure EH
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Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis.
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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
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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.
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Bioinformatics 38 (9) 2659-2660 [2022-04-28; online 2022-03-11]
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Fibroblast Growth Factor-23 and Risk of Cardiovascular Diseases: a Mendelian Randomisation study
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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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Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro.
Rojas L, Grüttner J, Ma'ayeh S, Xu F, Svärd SG
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Multiple Cortical to Striatal Accumulation Trajectories of β-Amyloid: Do All Roads Lead to Rome?
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Neurology 98 (17) 695-696 [2022-04-26; online 2022-03-25]
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Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.
Lu X, Maturi NP, Jarvius M, ..., Uhrbom L, Chen X
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward.
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The Carniolan Honeybee from Slovenia-A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies.
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Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment
Ezzamouri B, Rosario D, Bidkori G, ..., Uhlen M, Shoaie S
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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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App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden.
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Zeleznik OA, Wittenbecher C, Deik A, ..., Hu FB, Eliassen AH
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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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scAEGAN: Unification of Single-Cell Genomics Data by Adversarial Learning of Latent Space Correspondences
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The Role of Bio‐based Excipients in the Formulation of Lipophilic Nutraceuticals
Teleki A, Tsekou C, Connolly A
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Systems analysis shows a role of cytophilic antibodies in shaping innate tolerance to malaria.
Lautenbach MJ, Yman V, Silva CS, ..., Färnert A, Sundling C
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Silencing of STE20-type kinase STK25 in human aortic endothelial and smooth muscle cells is atheroprotective.
Cansby E, Kumari S, Caputo M, ..., Goncalves I, Mahlapuu M
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Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.
Neogi U, Elaldi N, Appelberg S, ..., Hewson R, Mirazimi A
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Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning.
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Impact of SARS-CoV-2 infection on vaccine-induced immune responses over time.
Havervall S, Marking U, Greilert-Norin N, ..., Åberg M, Thålin C
Clin Transl Immunology 11 (4) e1388 [2022-04-18; online 2022-04-18]
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An atlas of genetic scores to predict multi-omic traits
Xu Y, Ritchie SC, Liang Y, ..., Butterworth AS, Inouye M
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Phenotype assessment for neurodegenerative murine models with ataxia and application to Niemann-Pick disease, type C1.
Yerger J, Cougnoux AC, Abbott CB, ..., Porter FD, Davidson CD
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Associations of prenatal exposure to mixtures of organochlorine pesticides and smoking and drinking behaviors in adolescence.
Dickerson AS, Deng Z, Ransome Y, Factor-Litvak P, Karlsson O
Environ. Res. 206 (-) 112431 [2022-04-15; online 2021-11-27]
Oskar Karlsson SciLifeLab Fellow
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Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase.
Nain-Perez A, Foller Füchtbauer A, Håversen L, ..., Uhlen M, Grøtli M
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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Developmental disruption and restoration of brain synaptome architecture in the Pax6 neurodevelopmental disease model
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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
Brain Commun 4 (3) fcac085 [2022-04-13; online 2022-04-13]
DDLS Fellow Jacob W Vogel
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Basal ganglia neuropeptides show abnormal processing associated with L-DOPA-induced dyskinesia.
Hulme H, Fridjonsdottir E, Vallianatou T, ..., Bezard E, Andrén PE
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Supramolecular architecture of the ER-mitochondria encounter structure in its native environment
Wozny MR, Di Luca A, Morado DR, ..., Vanni S, Kukulski W
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Platelet-Derived PDGFB Promotes Recruitment of Cancer-Associated Fibroblasts, Deposition of Extracellular Matrix and Tgfβ Signaling in the Tumor Microenvironment.
Zhang Y, Manouchehri Doulabi E, Herre M, ..., Kamali-Moghaddam M, Olsson AK
Cancers (Basel) 14 (8) - [2022-04-12; online 2022-04-12]
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Fast and accurate gene regulatory network inference by normalized least squares regression.
Hillerton T, Seçilmiş D, Nelander S, Sonnhammer ELL
Bioinformatics 38 (8) 2263-2268 [2022-04-12; online 2022-02-18]
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Author Correction: Symptoms and syndromes associated with SARS-CoV-2 infection and severity in pregnant women from two community cohorts.
Molteni E, Astley CM, Ma W, ..., Chan AT, Modat M
Sci Rep 12 (1) 6083 [2022-04-12; online 2022-04-12]
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TEsorter: An accurate and fast method to classify LTR-retrotransposons in plant genomes.
Zhang RG, Li GY, Wang XL, ..., Ou S, Ma Y
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.
Schlebusch CM
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.
Pearce NM, Skyner R, Krojer T
Front Mol Biosci 9 (-) 861491 [2022-04-11; online 2022-04-11]
DDLS Fellow Nicholas Pearce
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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
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Peer Review Report For: ELIXIR and Toxicology: a community in development [version 1; peer review: 1 approved, 1 approved with reservations]
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PET-CT imaging of pulmonary inflammation using [68Ga]Ga-DOTA-TATE.
Puuvuori E, Liggieri F, Velikyan I, ..., Perchiazzi G, Eriksson O
EJNMMI Res 12 (1) 19 [2022-04-08; online 2022-04-08]
Olof Eriksson SciLifeLab Fellow
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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
Zhuang Y, Noviello CM, Hibbs RE, Howard RJ, Lindahl E
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Author response: Individualized discovery of rare cancer drivers in global network context
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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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Highly elevated systemic inflammation is a strong independent predictor of early mortality in advanced non-small cell lung cancer.
Isaksson J, Wennström L, Branden E, ..., Willén L, Botling J
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Comprehensive cancer-oriented biobanking resource of human samples for studies of post-zygotic genetic variation involved in cancer predisposition.
Filipowicz N, Drężek K, Horbacz M, ..., Piotrowski A, Dumanski JP
PLoS ONE 17 (4) e0266111 [2022-04-07; online 2022-04-07]
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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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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]
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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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Author Correction: The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.
Stjelja S, Fogelqvist J, Tellgren-Roth C, Dixelius C
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Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut
Mohammed M, Dziedziech A, Sekar V, ..., Rodriguez JV, Ankarklev J
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Marc Friedländer SciLifeLab Fellow
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SLC38A10 Regulate Glutamate Homeostasis and Modulate the AKT/TSC2/mTOR Pathway in Mouse Primary Cortex Cells.
Tripathi R, Aggarwal T, Lindberg FA, Klemm AH, Fredriksson R
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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
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Deadenylase-dependent mRNA decay of GDF15 and FGF21 orchestrates food intake and energy expenditure.
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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
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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
Mermans D, Nicolaus F, Fleisch K, von Heijne G
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Well-Plate μFASP for Proteomic Analysis of Single Pancreatic Islets.
Sandbaumhüter FA, Nezhyva M, Eriksson O, ..., Andrén PE, Jansson ET
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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
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The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host.
Krause S, Gfrerer S, von Kügelgen A, ..., Spang A, Gescher J
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Size matters - the impact of nucleus size on results from spatial transcriptomics
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Regular Use of Depot Medroxyprogesterone Acetate Causes Thinning of the Superficial Lining and Apical Distribution of Human Immunodeficiency Virus Target Cells in the Human Ectocervix.
Edfeldt G, Lajoie J, Röhl M, ..., Broliden K, Tjernlund A
J. Infect. Dis. 225 (7) 1151-1161 [2022-04-01; online 2020-08-12]
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Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
Plubell DL, Käll L, Webb-Robertson BJ, ..., Wu CC, MacCoss MJ
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Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.
LeDuc RD, Deutsch EW, Binz PA, ..., Thomas PM, Vizcaíno JA
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Metabolomics and Type 2 Diabetes Risk: An Updated Systematic Review and Meta-analysis of Prospective Cohort Studies.
Morze J, Wittenbecher C, Schwingshackl L, ..., Hu FB, Guasch-Ferré M
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.
Palmblad M, Böcker S, Degroeve S, ..., Noble WS, Wilhelm M
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Giant plasma membrane vesicles to study plasma membrane structure and dynamics.
Sezgin E
Biochim Biophys Acta Biomembr 1864 (4) 183857 [2022-04-01; online 2022-01-04]
Erdinc Sezgin SciLifeLab Fellow
DOI Crossref
Exploration of ultrasound-mediated microbubble-cell membrane interactions using novel protein-loaded microbubbles and their role in immunomodulation
Brans VA, Gray M, Sezgin E, Stride EP
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Erdinc Sezgin SciLifeLab Fellow
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Designing microplate layouts using artificial intelligence
Francisco Rodríguez MA, Puigvert JC, Spjuth O
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PubMed DOI Crossref
Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices.
Nicolaus F, Ibrahimi F, den Besten A, von Heijne G
FEBS Lett. 596 (8) 1004-1012 [2022-04-00; online 2022-01-31]
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Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment.
Antimycobacterial Susceptibility Testing Group
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]
DDLS Fellow Tobias Andermann
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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.
Bergenstråhle L, He B, Bergenstråhle J, ..., Lundeberg J, Maaskola J
Nat. Biotechnol. 40 (4) 476-479 [2022-04-00; online 2021-11-29]
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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]
PubMed DOI Crossref
Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach.
Li X, Shong K, Kim W, ..., Zhang C, Mardinoglu A
EBioMedicine 78 (-) 103963 [2022-04-00; online 2022-03-25]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
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 DDLS Fellow Muhammad Arif Saeed Shoaie SciLifeLab Fellow
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Molecular design of an electropolymerized copolymer with carboxylic and sulfonic acid functionalities
Gu M, Travaglini L, Hopkins J, ..., Officer DL, Mawad D
Synthetic Metals 285 (-) 117029 [2022-04-00; online 2022-04-00]
PubMed DOI Crossref
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
PubMed DOI Crossref
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 DDLS Fellow Muhammad Arif SciLifeLab Fellow
PubMed DOI Crossref
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]
PubMed DOI Crossref
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.
Pellegrinelli V, Rodriguez-Cuenca S, Rouault C, ..., Clément K, Vidal-Puig A
Nat Metab 4 (4) 476-494 [2022-04-00; online 2022-04-25]
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Cytogenetics in Chronic Lymphocytic Leukemia: ERIC Perspectives and Recommendations.
Baliakas P, Espinet B, Mellink C, ..., Haferlach C, Stamatopoulos K
Hemasphere 6 (4) e707 [2022-04-00; online 2022-03-25]
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Clonotypic analysis of protective influenza M2e-specific lung resident Th17 memory cells reveals extensive functional diversity.
Omokanye A, Ong LC, Lebrero-Fernandez C, ..., Czarnewski P, Lycke N
Mucosal Immunol 15 (4) 717-729 [2022-04-00; online 2022-03-08]
PubMed DOI Crossref
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.
Han L, Wei X, Liu C, ..., Esteban MA, Liu L
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.
Buchtova T, Skrott Z, Chroma K, ..., Bartek J, Mistrik M
Mol Oncol 16 (7) 1541-1554 [2022-04-00; online 2021-10-26]
PubMed DOI Crossref
Brain charts for the human lifespan.
Bethlehem RAI, Seidlitz J, White SR, ..., Bullmore ET, Alexander-Bloch AF
Nature 604 (7906) 525-533 [2022-04-00; online 2022-04-06]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro.
Hallberg I, Persson S, Olovsson M, ..., Rüegg J, Sjunnesson YCB
Reprod. Toxicol. 109 (-) 19-30 [2022-04-00; online 2022-02-24]
PubMed DOI Crossref
B cell-related gene signature and cancer immunotherapy response.
Lundberg A, Li B, Li R
Br. J. Cancer 126 (6) 899-906 [2022-04-00; online 2021-12-17]
Arian Lundberg DDLS Fellow
PubMed DOI Crossref
Associations between Listeria monocytogenes genomic characteristics and adhesion to polystyrene at 8 °C.
Mahoney DBJ, Falardeau J, Hingston P, ..., Jang SS, Wang S
Food Microbiol 102 (-) 103915 [2022-04-00; online 2021-09-23]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Anemoside B4 inhibits enterovirus 71 propagation in mice through upregulating 14-3-3 expression and type I interferon responses.
Kang NX, Zou Y, Liang QH, ..., Yang SL, Yu D
Acta Pharmacol Sin 43 (4) 977-991 [2022-04-00; online 2021-07-28]
PubMed DOI Crossref
An Open-Source Modular Framework for Automated Pipetting and Imaging Applications.
Ouyang W, Bowman RW, Wang H, ..., Carreras-Puigvert J, Diederich B
Adv Biol (Weinh) 6 (4) e2101063 [2022-04-00; online 2021-10-24]
DDLS Fellow Wei Ouyang
PubMed DOI Crossref
Acute sleep loss alters circulating fibroblast growth factor 21 levels in humans: A randomised crossover trial.
Mateus Brandão LE, Espes D, Westholm JO, ..., Benedict C, Cedernaes J
J Sleep Res 31 (2) e13472 [2022-04-00; online 2021-09-02]
Daniel Espes SciLifeLab Fellow
PubMed DOI Crossref
1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution.
Agback P, Lesovoy DM, Han X, ..., Achour A, Orekhov VY
Biomol NMR Assign 16 (1) 135-145 [2022-04-00; online 2022-02-12]
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Three-Dimensional Super-Resolved Imaging of Paraffin-Embedded Kidney Samples.
Unnersjö-Jess D, Ramdedovic A, Höhne M, ..., Schermer B, Benzing T
Kidney360 3 (3) 446-454 [2022-03-31; online 2021-12-01]
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Linear Epitope Binding Patterns of Grass Pollen-Specific Antibodies in Allergy and in Response to Allergen-Specific Immunotherapy.
Thörnqvist L, Sjöberg R, Greiff L, van Hage M, Ohlin M
Front Allergy 3 (-) 859126 [2022-03-31; online 2022-03-31]
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Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer.
Gyllensten U, Hedlund-Lindberg J, Svensson J, ..., Åberg M, Enroth S
Cancers (Basel) 14 (7) - [2022-03-30; online 2022-03-30]
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Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines.
Leo IR, Aswad L, Stahl M, ..., Vesterlund M, Jafari R
Nat Commun 13 (1) 1691 [2022-03-30; online 2022-03-30]
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Genomic dynamics of brown trout (Salmo trutta) populations released to a novel environment
Kurland S, Rafati N, Ryman N, Laikre L
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Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative
Butler-Laporte G, Povysil G, Kosmicki JA, ..., Ferreira MAR, Richards JB
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Reference-based cell type matching of spatial transcriptomics data
Zhang Y, Miller JA, Park J, ..., Lein ES, Scheuermann RH
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DOI Crossref
The dynamics of adaptation to stress from standing genetic variation and de novo mutations
Ament-Velásquez SL, Gilchrist C, Rêgo A, ..., Rafati N, Stelkens R
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Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches
Hill J, Lillie M, Pettersson ME, ..., Andersson L, Jern P
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Epigenetic modulators link mitochondrial redox homeostasis to cardiac function
Elbeck Z, Hossain MB, Siga H, ..., Végvári Á, Betsholtz C
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Translational profiling of neuronal subtypes in pre-symptomatic fatal familial insomnia mice reveals TOR signaling in somatostatin-expressing neurons
Bauer S, Dittrich L, Kaczmarczyk L, ..., Benfeitas R, Jackson WS
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The Fungal Endophyte Penicillium olsonii ML37 Reduces Fusarium Head Blight by Local Induced Resistance in Wheat Spikes.
Rojas EC, Jensen B, Jørgensen HJL, ..., Esteban P, Collinge DB
J Fungi (Basel) 8 (4) - [2022-03-25; online 2022-03-25]
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Peer Review Report For: Chanjo: Clincal grade sequence coverage analysis [version 1; peer review: 1 approved, 1 approved with reservations]
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PubMed DOI Crossref
Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq.
Vazquez SE, Mann SA, Bodansky A, ..., Anderson MS, DeRisi JL
bioRxiv - (-) - [2022-03-24; online 2022-03-24]
PubMed DOI Crossref
Author Correction: Improved prediction of protein-protein interactions using AlphaFold2.
Bryant P, Pozzati G, Elofsson A
Nat Commun 13 (1) 1694 [2022-03-24; online 2022-03-24]
DDLS Fellow Patrick Bryant
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Author Correction: 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) 5104 [2022-03-24; online 2022-03-24]
PubMed DOI Crossref
A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias.
Berglund E, Barbany G, Orsmark-Pietras C, ..., Fioretos T, Rosenquist R
Front Med (Lausanne) 9 (-) 842507 [2022-03-24; online 2022-03-24]
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The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design.
Krog MC, Madsen ME, Bliddal S, ..., Schuppe-Koistinen I, Nielsen HS
Hum Reprod Open 2022 (2) hoac015 [2022-03-23; online 2022-03-23]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Alkylating Agent-Induced Toxicity and Melatonin-Based Therapies.
Egea J, López-Muñoz F, Fernández-Capetillo O, Reiter RJ, Romero A
Front. Pharmacol. 13 (-) 873197 [2022-03-23; online 2022-03-23]
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l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics.
Ballabio F, Broggini L, Paissoni C, ..., Ricagno S, Camilloni C
ACS Omega 7 (11) 9622-9635 [2022-03-22; online 2022-03-07]
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The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis.
Wang J, Hao S, Gu J, Rudd SG, Wang Y
PeerJ 10 (-) e13141 [2022-03-22; online 2022-03-22]
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Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity
Garcia SL, Nuy JK, Mehrshad M, ..., Hawkes J, Bertilsson S
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Sarahi Garcia SciLifeLab Fellow
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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
Materials (Basel) 15 (7) - [2022-03-22; online 2022-03-22]
Adil Mardinoglu SciLifeLab Fellow
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Influence of Pre-treatment Saliva Microbial Diversity and Composition on Nasopharyngeal Carcinoma Prognosis.
Du Y, Feng R, Chang ET, ..., Cai Y, Ye W
Front. Cell. Infect. Microbiol. 12 (-) 831409 [2022-03-22; online 2022-03-22]
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A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines.
Feola S, Chiaro J, Martins B, ..., Lehtiö J, Cerullo V
Elife 11 (-) - [2022-03-22; online 2022-03-22]
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Peer Review Report For: ELIXIR and Toxicology: a community in development [version 1; peer review: 1 approved, 1 approved with reservations]
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Enabling automated and reproducible spatially resolved transcriptomics at scale
Stenbeck L, Taborsak-Lines F, Giacomello S
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Complementing machine learning-based structure predictions with native mass spectrometry
Allison TM, Degiacomi MT, Marklund EG, ..., Benesch JLP, Landreh M
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PubMed DOI Crossref
A Gene Co-Expression Network-Based Drug Repositioning Approach Identifies Candidates for Treatment of Hepatocellular Carcinoma.
Yuan M, Shong K, Li X, ..., Zhang C, Mardinoglu A
Cancers (Basel) 14 (6) - [2022-03-19; online 2022-03-19]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
Quantifying RNA synthesis at rate-limiting steps of transcription using nascent RNA-sequencing data.
Rabenius A, Chandrakumaran S, Sistonen L, Vihervaara A
STAR Protoc 3 (1) 101036 [2022-03-18; online 2022-01-05]
Anniina Vihervaara SciLifeLab Fellow
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Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates.
Cámara E, Olsson L, Zrimec J, ..., Geijer C, Nygård Y
Biotechnol Adv 57 (-) 107947 [2022-03-18; online 2022-03-18]
Aleksej Zelezniak SciLifeLab Fellow
DOI Crossref
Conformational Selection in Biocatalytic Plastic Degradation by PETase
Guo B, Vanga SR, Lopez-Lorenzo X, ..., Hakkarainen M, Syrén PO
ACS Catal 12 (6) 3397-3409 [2022-03-18; online 2022-03-01]
DOI Crossref
minute: A MINUTE-ChIP data analysis workflow
Navarro C, Martin M, Elsässer S
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SciLifeLab Fellow Simon Elsässer
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Sequence Diversification Screens with CRISPR‐Cas9‐Guided Base Editors
Persson J, Schmierer B
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PubMed DOI Crossref
Immune priming using DC- and T cell-targeting gene therapy sensitizes both treated and distant B16 tumors to checkpoint inhibition.
Wenthe J, Naseri S, Hellström AC, ..., Eriksson E, Loskog A
Mol Ther Oncolytics 24 (-) 429-442 [2022-03-17; online 2022-01-10]
PubMed DOI Crossref
Genome-wide association study on 13 167 individuals identifies regulators of blood CD34+cell levels.
Lopez de Lapuente Portilla A, Ekdahl L, Cafaro C, ..., Stefansson K, Nilsson B
Blood 139 (11) 1659-1669 [2022-03-17; online 2022-01-11]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Dual effect of TAT functionalized DHAH lipid nanoparticles with neurotrophic factors in human BBB and microglia cultures.
Hernando S, Nikolakopoulou P, Voulgaris D, ..., Igartua M, Herland A
Fluids Barriers CNS 19 (1) 22 [2022-03-17; online 2022-03-17]
PubMed DOI Crossref
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health.
Marabita F, James T, Karhu A, ..., Sallinen R, Kallioniemi O
Cell Syst 13 (3) 241-255.e7 [2022-03-16; online 2021-12-01]
PubMed DOI Crossref
Editorial: Tertiary Lymphoid Structures: From Basic Biology to Translational Impact in Cancer.
Sautès-Fridman C, Dimberg A, Verma V
Front Immunol 13 (-) 870862 [2022-03-16; online 2022-03-16]
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Claudin5 protects the peripheral endothelial barrier in an organ and vessel type-specific manner
Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L
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Chemical and genetic screens identify new regulators of tetracycline-inducible gene expression system in mammalian cells
Colicchia V, Häggblad M, Sirozh O, ..., Hühn D, Fernandez-Capetillo O
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PABP prevents the untimely decay of select mRNA populations in human cells.
Kajjo S, Sharma S, Chen S, ..., Larsson O, Fabian MR
EMBO J. 41 (6) e108650 [2022-03-15; online 2022-02-14]
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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
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DDLS Fellow Fredrik Edfors Paul Hudson SciLifeLab Fellow
PubMed DOI Crossref
Intra-Helical Salt Bridge Contribution to Membrane Protein Insertion.
Duart G, Lamb J, Ortiz-Mateu J, Elofsson A, Mingarro I
J. Mol. Biol. 434 (5) 167467 [2022-03-15; online 2022-01-29]
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Graph deep learning reveals multiple signal pathways activated in anti-citrullinated protein antibodies stimulated synoviocytes
Sun M, Chen Y, Brodin P, Catrina AI
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Dual spatially resolved transcriptomics for SARS-CoV-2 host-pathogen colocalization studies in humans
Sounart H, Lázár E, Masarapu Y, ..., Bergmann O, Giacomello S
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PubMed DOI Crossref
Salivary Microbiota and Host-Inflammatory Responses in Periodontitis Affected Individuals With and Without Rheumatoid Arthritis.
Eriksson K, Lundmark A, Delgado LF, ..., Andersson AF, Yucel-Lindberg T
Front. Cell. Infect. Microbiol. 12 (-) 841139 [2022-03-14; online 2022-03-14]
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Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Allen G, Weiss B, Panasenko O, ..., Pelechano V, Collart MA
bioRxiv - (-) - [2022-03-14; online 2022-03-14]
SciLifeLab Fellow
PubMed DOI Crossref
Norway spruce postglacial recolonization of Fennoscandia.
Nota K, Klaminder J, Milesi P, ..., Suyama Y, Parducci L
Nat Commun 13 (1) 1333 [2022-03-14; online 2022-03-14]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Neutrophil extracellular traps promote cancer-associated inflammation and myocardial stress.
Cedervall J, Herre M, Dragomir A, ..., Larsson A, Olsson AK
Oncoimmunology 11 (1) 2049487 [2022-03-14; online 2022-03-14]
PubMed DOI Crossref
N-terminome analyses underscore the prevalence of SPPL3-mediated intramembrane proteolysis among Golgi-resident enzymes and its role in Golgi enzyme secretion.
Hobohm L, Koudelka T, Bahr FH, ..., Tholey A, Voss M
Cell. Mol. Life Sci. 79 (3) 185 [2022-03-13; online 2022-03-13]
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Diversity and determinants of recombination landscapes in flowering plants
Brazier T, Glémin S
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PubMed DOI Crossref
Targeting Estrogen Signaling in the Radiation-induced Neurodegeneration: A Possible Role of Phytoestrogens.
Mitra S, Dash R, Sohel M, ..., Islam MT, Moon IS
Curr Neuropharmacol 21 (2) 353-379 [2022-03-12; online 2022-03-12]
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Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search
Bryant P, Pozzati G, Zhu W, ..., Kundrotas P, Elofsson A
bioRxiv - (-) - [2022-03-12; online 2022-03-12]
DDLS Fellow Patrick Bryant
DOI Crossref
Observation of a single protein by ultrafast X-ray diffraction
Ekeberg T, Assalauova D, Bielecki J, ..., Meyer M, Maia FRNC
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PubMed DOI Crossref
ELTD1 deletion reduces vascular abnormality and improves T-cell recruitment after PD-1 blockade in glioma.
Huang H, Georganaki M, Conze LL, ..., Lugano R, Dimberg A
Neuro-oncology 24 (3) 398-411 [2022-03-12; online 2021-08-05]
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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
Exposome 2 (1) - [2022-03-12; online 2022-10-12]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Synthesis and In Vitro Biological Evaluation of Quinolinyl Pyrimidines Targeting Type II NADH-Dehydrogenase (NDH-2).
Lu L, Åkerbladh L, Ahmad S, ..., Karlén A, Mowbray SL
ACS Infect Dis 8 (3) 482-498 [2022-03-11; online 2022-02-21]
PubMed DOI Crossref
OpenCell: Endogenous tagging for the cartography of human cellular organization.
Cho NH, Cheveralls KC, Brunner AD, ..., Mann M, Leonetti MD
Science (New York, N.Y.) 375 (6585) eabi6983 [2022-03-11; online 2022-03-11]
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Three adult cases of STAT1-gain-of-function with chronic mucocutaneous candidiasis treated with JAK inhibitors
Borgström EW, Edvinsson M, Perez LP, ..., Brodin P, Bergman P
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PubMed DOI Crossref
Improved prediction of protein-protein interactions using AlphaFold2.
Bryant P, Pozzati G, Elofsson A
Nat Commun 13 (1) 1265 [2022-03-10; online 2022-03-10]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
A Systematic Review to Define the Multi-Faceted Role of Lysine Methyltransferase SETD7 in Cancer.
Monteiro FL, Williams C, Helguero LA
Cancers (Basel) 14 (6) - [2022-03-10; online 2022-03-10]
PubMed DOI Crossref
Sirtuin-1 sensitive lysine-136 acetylation drives phase separation and pathological aggregation of TDP-43.
Garcia Morato J, Hans F, von Zweydorf F, ..., Neumann M, Kahle PJ
Nat Commun 13 (1) 1223 [2022-03-09; online 2022-03-09]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures.
Wood TM, Zeronian MR, Buijs N, ..., Janssen BJC, Martin NI
Chem Sci 13 (10) 2985-2991 [2022-03-09; online 2022-02-21]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Weakened resilience of benthic microbial communities in the face of climate change.
Seidel L, Ketzer M, Broman E, ..., Hylander S, Dopson M
ISME Commun 2 (1) 21 [2022-03-08; online 2022-03-08]
PubMed DOI Crossref
Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome.
Di Palma F, Decherchi S, Pardo-Avila F, ..., von Heijne G, Cavalli A
J Chem Theory Comput 18 (3) 1905-1914 [2022-03-08; online 2021-12-09]
PubMed DOI Crossref
Network Crosstalk as a Basis for Drug Repurposing.
Guala D, Sonnhammer ELL
Front Genet 13 (-) 792090 [2022-03-08; online 2022-03-08]
PubMed DOI Crossref
Mendelian randomization suggests a bidirectional, causal relationship between physical inactivity and adiposity.
Carrasquilla GD, García-Ureña M, Fall T, Sørensen TIA, Kilpeläinen TO
Elife 11 (-) - [2022-03-07; online 2022-03-07]
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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
bioRxiv - (-) - [2022-03-07; online 2022-03-07]
DDLS Fellow Tom van der Valk
DOI Crossref
Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan
Correia-Melo C, Kamrad S, Messner CB, ..., Papp B, Ralser M
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Aleksej Zelezniak SciLifeLab Fellow
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Four tumor micro-environmental niches explain a continuum of inter-patient variation in the macroscopic cellular composition of breast tumors
Marrahi AE, Lipreri F, Alber D, Hausser J
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Jean Hausser SciLifeLab Fellow
DOI Crossref
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
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DOI Crossref
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
Herbst SA, Vesterlund M, Helmboldt AJ, ..., Lehtiö J, Dietrich S
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DOI Crossref
Plasmonic Fiber Optic Absorbance Biosensor for MDR-Mtb detection using Padlock Probing
Saha U, Srinivasulu YG, M D, ..., Madaboosi N, Sai VVR
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PubMed DOI Crossref
A drug repurposing strategy for overcoming human multiple myeloma resistance to standard-of-care treatment.
Chroma K, Skrott Z, Gursky J, ..., Mistrik M, Bartek J
Cell Death Dis 13 (3) 203 [2022-03-04; online 2022-03-04]
PubMed DOI Crossref
A deep learning framework for characterization of genotype data.
Ausmees K, Nettelblad C
G3 12 (3) - [2022-03-04; online 2022-01-26]
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Critical role of PCYT2 in muscle health and aging
Cikes D, Elsayad K, Sezgin E, ..., Banka S, Penninger JM
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Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
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]
PubMed DOI Crossref
Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden.
Jönsson E, Ljung L, Norrman E, ..., Dahlqvist J, Rantapää-Dahlqvist S
Rheumatology (Oxford) 61 (3) 943-952 [2022-03-02; online 2021-05-17]
PubMed DOI Crossref
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.
Notarnicola A, Preger C, Lundström SL, ..., Lundberg IE, Fernandes-Cerqueira C
Arthritis Res Ther 24 (1) 62 [2022-03-02; online 2022-03-02]
DOI Crossref
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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Paul Hudson SciLifeLab Fellow
PubMed DOI Crossref
Host Adaptation in Legionellales Is 1.9 Ga, Coincident with Eukaryogenesis.
Hugoson E, Guliaev A, Ammunét T, Guy L
Mol. Biol. Evol. 39 (3) - [2022-03-02; online 2022-02-16]
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Author response: Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target
Neogi U, Elaldi N, Appelberg S, ..., Hewson R, Mirazimi A
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PubMed DOI Crossref
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]
PubMed DOI Crossref
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
Proc. Natl. Acad. Sci. U.S.A. 119 (9) - [2022-03-01; online 2022-02-27]
PubMed DOI Crossref
Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.
Stenudd M, Sabelström H, Llorens-Bobadilla E, ..., Barnabé-Heider F, Frisén J
Cell Reports 38 (9) 110440 [2022-03-01; online 2022-03-03]
DOI Crossref
High cardiomyocyte diversity in human early prenatal heart development
Sylvén C, Wärdell E, Månsson-Broberg A, ..., Björklund Å, Giacomello S
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PubMed DOI Crossref
Comparison of East-Asia and West-Europe cohorts explains disparities in survival outcomes and highlights predictive biomarkers of early gastric cancer aggressiveness.
Pereira C, Park JH, Campelos S, ..., Almeida GM, Oliveira C
Int. J. Cancer 150 (5) 868-880 [2022-03-01; online 2021-12-09]
PubMed DOI Crossref
Author Correction: 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 13 (1) 1200 [2022-03-01; online 2022-03-01]
PubMed DOI Crossref
The relationship between ageing and changes in the human blood and brain methylomes.
Bryant P, Elofsson A
NAR Genomics and Bioinformatics 4 (1) lqac001 [2022-03-00; online 2022-02-02]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA.
Gañez-Zapater A, Mackowiak SD, Guo Y, ..., Visa N, Östlund Farrants AK
Mol. Genet. Genomics 297 (2) 463-484 [2022-03-00; online 2022-02-20]
DDLS Fellow Marc Friedländer Marcel Tarbier SciLifeLab Fellow
PubMed DOI Crossref
Ten simple rules for making a software tool workflow-ready.
Brack P, Crowther P, Soiland-Reyes S, ..., Ewels P, Goble C
PLoS Comput Biol 18 (3) e1009823 [2022-03-00; online 2022-03-24]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.
Stsiapanava A, Xu C, Nishio S, ..., Wu B, Jovine L
Nat. Struct. Mol. Biol. 29 (3) 190-193 [2022-03-00; online 2022-03-10]
PubMed DOI Crossref
Stromal FAP Expression is Associated with MRI Visibility and Patient Survival in Prostate Cancer.
Pellinen T, Sandeman K, Blom S, ..., Rannikko A, Mirtti T
Cancer Res Commun 2 (3) 172-181 [2022-03-00; online 2022-03-21]
PubMed DOI Crossref
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.
Hickey JW, Neumann EK, Radtke AJ, ..., Kelleher NL, Saka SK
Nat. Methods 19 (3) 284-295 [2022-03-00; online 2021-11-22]
PubMed DOI Crossref
Sequence determinants of human gene regulatory elements.
Sahu B, Hartonen T, Pihlajamaa P, ..., Kivioja T, Taipale J
Nat. Genet. 54 (3) 283-294 [2022-03-00; online 2022-02-21]
PubMed DOI Crossref
Rare variants in the outcome of social skills group training for autism.
Li D, Choque Olsson N, Becker M, ..., Bölte S, Tammimies K
Autism Res 15 (3) 434-446 [2022-03-00; online 2021-12-30]
PubMed DOI Crossref
RNA-interference screen for p53 regulators unveils a role of WDR75 in ribosome biogenesis.
Moudry P, Chroma K, Bursac S, Volarevic S, Bartek J
Cell Death Differ. 29 (3) 687-696 [2022-03-00; online 2021-10-05]
PubMed DOI Crossref
Proteomics in thrombosis research.
Edfors F, Iglesias MJ, Butler LM, Odeberg J
Res Pract Thromb Haemost 6 (3) e12706 [2022-03-00; online 2022-04-25]
DDLS Fellow Fredrik Edfors
PubMed DOI Crossref
On the origin of TSAR: morphology, diversity and phylogeny of Telonemia.
Tikhonenkov DV, Jamy M, Borodina AS, ..., Burki F, Karpov SA
Open Biol 12 (3) 210325 [2022-03-00; online 2022-03-16]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
Loss of Y and clonal hematopoiesis in blood-two sides of the same coin?
Ljungström V, Mattisson J, Halvardson J, ..., Baliakas P, Forsberg LA
Leukemia 36 (3) 889-891 [2022-03-00; online 2021-11-01]
PubMed DOI Crossref
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
PubMed DOI Crossref
Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.
Mueller JC, Botero-Delgadillo E, Espíndola-Hernández P, ..., Gruselius J, Kempenaers B
Mol. Ecol. 31 (5) 1504-1514 [2022-03-00; online 2022-01-22]
PubMed DOI Crossref
Limited benefit in patients with MDS receiving venetoclax and azacitidine as a bridge to allogeneic stem cell transplantation.
Jädersten M, Boriskina K, Lindholm C, ..., Mielke S, Tobiasson M
Leuk. Lymphoma 63 (3) 755-758 [2022-03-00; online 2021-11-15]
PubMed DOI Crossref
Hypoxia induces radioresistance, epithelial‑mesenchymal transition, cancer stem cell‑like phenotype and changes in genes possessing multiple biological functions in head and neck squamous cell carcinoma.
Wiechec E, Matic N, Ali A, Roberg K
Oncol Rep 47 (3) - [2022-03-00; online 2022-01-21]
PubMed DOI Crossref
Human genetic and immunological determinants of critical COVID-19 pneumonia.
Zhang Q, Bastard P, COVID Human Genetic Effort , Cobat A, Casanova JL
Nature 603 (7902) 587-598 [2022-03-00; online 2022-01-28]
PubMed DOI Crossref
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]
DDLS Fellow Lisandro Milocco
PubMed DOI Crossref
Epigenetics in the Anthropocene: an interview with Oskar Karlsson.
Karlsson O
Epigenomics 14 (6) 315-318 [2022-03-00; online 2022-02-23]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Correction: GRK3 deficiency elicits brain immune activation and psychosis.
Sellgren CM, Imbeault S, Larsson MK, ..., Engberg G, Erhardt S
Mol. Psychiatry 27 (3) 1855 [2022-03-00; online 2021-11-09]
PubMed DOI Crossref
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]
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Circulating proteins reveal prior use of menopausal hormonal therapy and increased risk of breast cancer.
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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.
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J Biol Chem 298 (3) 101682 [2022-03-00; online 2022-02-03]
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A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data.
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Transition between conformational states of the TREK-1 K2P channel promoted by interaction with PIP 2
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Caecilian genomes reveal the molecular basis of adaptation, and convergent evolution of limblessness in snakes and caecilians
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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]
DDLS Fellow Patrick Bryant
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Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction.
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Andreas Luttens DDLS Fellow Jens Carlsson SciLifeLab Fellow
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Duration of SARS-CoV-2 Immune Responses Up to Six Months Following Homologous or Heterologous Primary Immunization with ChAdOx1 nCoV-19 and BNT162b2 mRNA Vaccines.
Marking U, Havervall S, Greilert-Norin N, ..., Åberg M, Thålin C
Vaccines (Basel) 10 (3) - [2022-02-24; online 2022-02-24]
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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
J Psychiatry Neurosci 47 (1) E67-E76 [2022-02-23; online 2022-02-23]
Erika Comasco SciLifeLab Fellow
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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
Journal of the American Chemical Society 144 (7) 2905-2920 [2022-02-23; online 2022-02-10]
Andreas Luttens DDLS Fellow Jens Carlsson SciLifeLab Fellow
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Thermodynamic limitations of metabolic strategies for PHB production from formate and fructose in Cupriavidus necator
Janasch M, Crang N, Bruch M, ..., Jahn M, Hudson EP
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Paul Hudson SciLifeLab Fellow
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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
Elife 11 (-) - [2022-02-23; online 2022-02-23]
Ilaria Testa Lucie Delemotte SciLifeLab Fellow
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Deep neural network prediction of genome-wide transcriptome signatures - beyond the Black-box.
Magnusson R, Tegnér JN, Gustafsson M
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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
mSystems 7 (1) e0000422 [2022-02-22; online 2022-02-08]
Adil Mardinoglu SciLifeLab Fellow
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Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis
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Genome-wide mapping of G-quadruplex structures with CUT&Tag.
Lyu J, Shao R, Kwong Yung PY, Elsässer SJ
Nucleic Acids Res. 50 (3) e13 [2022-02-22; online 2021-11-19]
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Early response evaluation by single cell signaling profiling in acute myeloid leukemia
Tislevoll B, Hellesøy M, Fagerholt O, ..., Blaser N, Gjertsen BT
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Author response: A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines
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An estimate of the deepest branches of the tree of life from ancient vertically evolving genes.
Moody ERR, Mahendrarajah TA, Dombrowski N, ..., Spang A, Williams TA
Elife 11 (-) - [2022-02-22; online 2022-02-22]
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Sequence-Based Analyses of the Goettingen Minipig Genome
Reimer C
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Investigation of the mitochondrial contact site and cristae organizing system and its role in cristae formation
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Tumorigenic activity of alternative per- and polyfluoroalkyl substances (PFAS): Mechanistic in vitro studies.
Pierozan P, Cattani D, Karlsson O
Sci. Total Environ. 808 (-) 151945 [2022-02-20; online 2021-11-27]
Oskar Karlsson SciLifeLab Fellow
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Reclassifying Cancer: Defining tumour cell cycle activity in terms of its tissue of origin in over 13,000 samples
Lundberg A, Yi JJJ, Lindström LS, Tobin NP
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Arian Lundberg DDLS Fellow
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Nontarget mass spectrometry and in silico molecular characterization of air pollution from the Indian subcontinent
Papazian S, D’Agostino LA, Sadiktsis I, ..., Gustafsson Ö, Martin JW
Commun Earth Environ 3 (1) - [2022-02-18; online 2022-02-18]
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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
iScience 25 (2) 103743 [2022-02-18; online 2022-01-07]
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The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling.
Noh HJ, Turner-Maier J, Schulberg SA, ..., Lindblad-Toh K, Hindle AG
Commun Biol 5 (1) 140 [2022-02-17; online 2022-02-17]
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots.
Huang Z, De O Furo I, Liu J, ..., de Oliveira EHC, Xu L
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Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment.
Garbulowski M, Smolinska K, Çabuk U, ..., Wadelius C, Komorowski J
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Longitudinal Serum Metabolomics in Extremely Premature Infants: Relationships With Gestational Age, Nutrition, and Morbidities.
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Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning
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Adil Mardinoglu DDLS Fellow Muhammad Arif SciLifeLab Fellow
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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
Nat Commun 13 (1) 936 [2022-02-17; online 2022-02-17]
Clemens Wittenbecher DDLS Fellow
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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
PLoS ONE 17 (2) e0264056 [2022-02-17; online 2022-02-17]
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Polygenic association with severity and long-term outcome in eating disorder cases.
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MicroRNAs are deeply linked to the emergence of the complex octopus brain
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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
Schagerholm C, Robertson S, Holm B, ..., Williams C, Hartman J
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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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J Chem Inf Model 62 (3) 577-590 [2022-02-14; online 2022-01-20]
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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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The spatial transcriptomic landscape of the healing mouse intestine following damage.
Parigi SM, Larsson L, Das S, ..., Lundeberg J, Villablanca EJ
Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]
Camilla Engblom SciLifeLab Fellow
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Salivary IgG to SARS-CoV-2 indicates seroconversion and correlates to serum neutralization in mRNA-vaccinated immunocompromised individuals.
Healy K, Pin E, Chen P, ..., Aleman S, Sällberg Chen M
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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]
Erika Comasco SciLifeLab Fellow
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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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Nat Commun 13 (1) 793 [2022-02-10; online 2022-02-10]
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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
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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.
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Exploring Non-orthosteric Interactions with a Series of Potent and Selective A3 Antagonists.
Miranda-Pastoriza D, Bernárdez R, Azuaje J, ..., Gutiérrez-de-Terán H, Sotelo E
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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
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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]
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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]
Jonas Barandun SciLifeLab Fellow
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Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.
Umer HM, Audain E, Zhu Y, ..., Branca RM, Perez-Riverol Y
Bioinformatics 38 (5) 1470-1472 [2022-02-07; online 2021-12-15]
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DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.
Bonet J, Chen M, Dabad M, ..., Lopez-Bigas N, Lagergren J
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.
Ristau J, Watt K, Oertlin C, Larsson O
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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
Methods in molecular biology (Clifton, N.J.) 2418 (-) 1-23 [2022-02-05; online 2022-02-05]
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Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation.
Oertlin C, Watt K, Ristau J, Larsson O
Methods in molecular biology (Clifton, N.J.) 2418 (-) 243-268 [2022-02-05; online 2022-02-05]
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An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta.
Indukuri R, Damdimopoulos A, Williams C
Methods in molecular biology (Clifton, N.J.) 2418 (-) 203-221 [2022-02-05; online 2022-02-05]
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Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.
Schuy J, Eisfeldt J, Pettersson M, ..., Falk A, Lindstrand A
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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.
Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T
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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 involvement of cyclotides in mutual interactions of violets and the two-spotted spider mite.
Slazak B, Jędrzejska A, Badyra B, ..., Göransson U, Kiełkiewicz M
Sci Rep 12 (1) 1914 [2022-02-03; online 2022-02-03]
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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.
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Author response: Identification of electroporation sites in the complex lipid organization of the plasma membrane
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Ilaria Testa Lucie Delemotte SciLifeLab Fellow
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Structural basis of streptomycin off-target binding to human mitoribosome
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Alexey Amunts SciLifeLab Fellow
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Possible Functional Roles of Patellamides in the Ascidian-Prochloron Symbiosis.
Baur P, Kühl M, Comba P, Behrendt L
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Lars Behrendt SciLifeLab Fellow
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Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
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Magda Bienko SciLifeLab Fellow
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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
Nat Commun 13 (1) 627 [2022-02-02; online 2022-02-02]
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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.
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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
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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
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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]
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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]
Gustaf Christoffersson SciLifeLab Fellow
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The antimicrobial drug pyrimethamine inhibits STAT3 transcriptional activity by targeting the enzyme dihydrofolate reductase.
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Molecular modeling investigation of proton coupling in XylE
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Covid-19 in patients with chronic lymphocytic leukemia: clinical outcome and B- and T-cell immunity during 13 months in consecutive patients.
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Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development.
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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
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Accurate and rapid microfluidic ELISA to monitor Infliximab titers in patients with inflammatory bowel diseases.
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VEGF-C expression in TAMs rewires the metastatic fate of breast cancer cells
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The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.
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Target 2035 - update on the quest for a probe for every protein.
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Confocal imaging dataset to assess endothelial cell orientation during extreme glucose conditions.
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The Earth BioGenome Project 2020: Starting the clock.
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Method To Visualize the Intratumor Distribution and Impact of Gemcitabine in Pancreatic Ductal Adenocarcinoma by Multimodal Imaging.
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Genetically Predicted Circulating Copper and Risk of Chronic Kidney Disease: A Mendelian Randomization Study.
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A cell-free high throughput assay for assessment of SARS-CoV-2 neutralizing antibodies.
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piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development.
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PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons
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BioRssay: an R package for analyses of bioassays and probit graphs.
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Single-Cell Transcriptomics reveals relaxed evolutionary constraint of spermatogenesis in two passerine birds as compared to mammals
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FOXO dictate initiation of B cell development and myeloid restriction in common lymphoid progenitors
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RET activation controlled by MAB21L4-CacyBP interaction drives squamous cell carcinoma
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Region-Specific and Age-Dependent Multitarget Effects of Acetylcholinesterase Inhibitor Tacrine on Comprehensive Neurotransmitter Systems.
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The new era of quantitative cell imaging-challenges and opportunities.
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Association of clonal hematopoiesis with chronic obstructive pulmonary disease.
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Loss of Y in leukocytes as a risk factor for critical COVID-19 in men
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Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort.
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Author response: Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae
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Accelerated Wound Healing in Minipigs by On-Site Production and Delivery of CXCL12 by Transformed Lactic Acid Bacteria.
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Radiotherapy transiently reduces the sensitivity of cancer cells to lymphocyte cytotoxicity.
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Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals: An IMI DIRECT study.
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Bacteria Detection at a Single-Cell Level through a Cyanotype-Based Photochemical Reaction.
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An Image-Analysis-Based Method for the Prediction of Recombinant Protein Fiber Tensile Strength.
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Activation of the Integrated Stress Response overcomes multidrug resistance in FBXW7-deficient cells
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Deciphering Biomarkers for Leptomeningeal Metastasis in Malignant Hemopathies (Lymphoma/Leukemia) Patients by Comprehensive Multipronged Proteomics Characterization of Cerebrospinal Fluid.
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Molecular Mechanisms Leading from Periodontal Disease to Cancer.
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Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2.
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CtIP-dependent nascent RNA expression flanking DNA breaks guides the choice of DNA repair pathway
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An essential function for autocrine Hedgehog signaling in epithelial proliferation and differentiation in the trachea
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First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016.
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Distinct roles for PARP-1 and PARP-2 in c-Myc-driven B-cell lymphoma in mice.
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Tuning Epithelial Cell-Cell Adhesion and Collective Dynamics with Functional DNA-E-Cadherin Hybrid Linkers.
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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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SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection.
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Integrative Lipidomics and Metabolomics for System-Level Understanding of the Metabolic Syndrome in Long-Term Treated HIV-Infected Individuals.
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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories
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Developmental origins of cell heterogeneity in the human lung
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Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides.
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CCT3-LINC00326 axis regulates hepatocarcinogenic lipid metabolism.
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Claudia Kutter SciLifeLab Fellow
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A multi-omics study of circulating phospholipid markers of blood pressure.
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Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.
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Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection.
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Sensitive protein detection using site-specifically oligonucleotide-conjugated nanobodies
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Experimental Characterization and Mathematical Modeling of the Adsorption of Proteins and Cells on Biomimetic Hydroxyapatite.
Atif AR, La Cis U, Engqvist H, ..., Bagheri S, Mestres G
ACS Omega 7 (1) 908-920 [2022-01-11; online 2021-12-22]
PubMed DOI Crossref
Functional dissection of inherited non-coding variation influencing multiple myeloma risk.
Ajore R, Niroula A, Pertesi M, ..., Houlston R, Nilsson B
Nat Commun 13 (1) 151 [2022-01-10; online 2022-01-10]
Abhishek Niroula DDLS Fellow
DOI Crossref
Autoantibodies in COVID-19 correlate with anti-viral humoral responses and distinct immune signatures
Taeschler P, Cervia C, Zurbuchen Y, ..., Probst-Müller E, Boyman O
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PubMed DOI Crossref
A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo.
Hanke L, Das H, Sheward DJ, ..., Murrell B, McInerney GM
Nat Commun 13 (1) 155 [2022-01-10; online 2022-01-10]
Erdinc Sezgin SciLifeLab Fellow
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MirGeneDB 2.1: toward a complete sampling of all major animal phyla.
Fromm B, Høye E, Domanska D, ..., Friedländer MR, Peterson KJ
Nucleic Acids Res. 50 (D1) D204-D210 [2022-01-07; online 2021-12-02]
DDLS Fellow Marc Friedländer Marcel Tarbier SciLifeLab Fellow
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
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DOI Crossref
Heparin-derived theranostic nanoprobes overcome the blood brain barrier and target glioma in murine model
Samanta S, Joncour VL, Wegrzyniak O, ..., Cabral H, Oommen OP
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Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.
Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T
Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.
Quaglia F, Mészáros B, Salladini E, ..., Tosatto SCE, Piovesan D
Nucleic Acids Res. 50 (D1) D480-D487 [2022-01-07; online 2021-12-02]
PubMed DOI Crossref
Controls for Phylogeny and Robust Analysis in Pareto Task Inference.
Adler M, Tendler A, Hausser J, ..., Mayo A, Alon U
Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-10-12]
Jean Hausser SciLifeLab Fellow
PubMed DOI Crossref
The Chinese pine genome and methylome unveil key features of conifer evolution.
Niu S, Li J, Bo W, ..., Wei H, Wu HX
Cell 185 (1) 204-217.e14 [2022-01-06; online 2021-12-28]
PubMed DOI Crossref
TRP channels: branching out into the fungal kingdom.
Hellmich UA, Delemotte L
Structure 30 (1) 2-4 [2022-01-06; online 2022-01-08]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets.
Prouteau A, Mottier S, Primot A, ..., Derrien T, Hedan B
Cancers (Basel) 14 (2) - [2022-01-06; online 2022-01-06]
DOI Crossref
Heterologous immunization with inactivated vaccine followed by mRNA booster elicits strong humoral and cellular immune responses against the SARS-CoV-2 Omicron variant
Zuo F, Abolhassani H, Du L, ..., Marcotte H, Pan-Hammarström Q
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DOI Crossref
Author response: Adverse childhood experiences and resilience among adult women: A population-based study
Daníelsdóttir HB, Aspelund T, Thordardottir EB, ..., Hauksdóttir A, Valdimarsdóttir UA
- - (-) - [2022-01-05; online 2022-01-05]
PubMed DOI Crossref
Author Correction: Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.
Halvorsen M, Huh R, Oskolkov N, ..., Sullivan PF, Szatkiewicz JP
Nat Commun 13 (1) 191 [2022-01-05; online 2022-01-05]
PubMed DOI Crossref
A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.
Rodríguez-Gijón A, Nuy JK, Mehrshad M, ..., Woyke T, Garcia SL
Front Microbiol 12 (-) 761869 [2022-01-05; online 2022-01-05]
Sarahi Garcia SciLifeLab Fellow
PubMed DOI Crossref
Evidence of Air and Surface Contamination with SARS-CoV-2 in a Major Hospital in Portugal.
Silva PGD, Gonçalves J, Lopes AIB, ..., Sousa SIV, Mesquita JR
Int J Environ Res Public Health 19 (1) - [2022-01-04; online 2022-01-04]
PubMed DOI Crossref
Effects on weight loss and glycemic control with SAR441255, a potent unimolecular peptide GLP-1/GIP/GCG receptor triagonist.
Bossart M, Wagner M, Elvert R, ..., Nitsche A, Konkar A
Cell Metab. 34 (1) 59-74.e10 [2022-01-04; online 2021-12-20]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine.
Choudhury K, Kasimova MA, McComas S, Howard RJ, Delemotte L
Biophys. J. 121 (1) 11-22 [2022-01-04; online 2021-12-08]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
APOBEC3 as a driver of genetic intratumor heterogeneity.
Venkatesan S, Angelova M, Bartkova J, ..., Kanu N, Swanton C
Mol Cell Oncol 10 (1) 2014734 [2022-01-03; online 2022-01-03]
DOI Crossref
The hidden structural variability in avian genomes
Peona V, Blom MPK, Frankl-Vilches C, ..., Irestedt M, Suh A
- - (-) - [2022-01-02; online 2022-01-02]
DOI Crossref
Zooplanktivore fish body growth responses to browning‐induced light limitation vary over ontogeny, but not with fish density
van Dorst RM, Gårdmark A, Svanbäck R, Huss M
Ecology of Freshwater Fish 31 (1) 17-28 [2022-01-00; online 2021-03-28]
PubMed DOI Crossref
Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.
Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L
Mol. Ecol. 31 (2) 498-511 [2022-01-00; online 2021-11-15]
PubMed DOI Crossref
Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology.
Skaftason A, Qu Y, Abdulla M, ..., Rosenquist R, Mansouri L
Genes Chromosomes Cancer 61 (1) 27-36 [2022-01-00; online 2021-10-23]
PubMed DOI Crossref
The ubiquitin-dependent ATPase p97 removes cytotoxic trapped PARP1 from chromatin.
Krastev DB, Li S, Sun Y, ..., Ramadan K, Lord CJ
Nat. Cell Biol. 24 (1) 62-73 [2022-01-00; online 2022-01-10]
PubMed DOI Crossref
The revolution evolution.
Amunts A
Nat Plants 8 (1) 14-17 [2022-01-00; online 2021-12-18]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
The protein kinase LKB1 promotes self-renewal and blocks invasiveness in glioblastoma.
Caja L, Dadras MS, Mezheyeuski A, ..., Heldin CH, Moustakas A
J. Cell. Physiol. 237 (1) 743-762 [2022-01-00; online 2021-08-05]
PubMed DOI Crossref
Super-Resolution Imaging of the Filtration Barrier Suggests a Role for Podocin R229Q in Genetic Predisposition to Glomerular Disease.
Butt L, Unnersjö-Jess D, Höhne M, ..., Schermer B, Benzing T
J. Am. Soc. Nephrol. 33 (1) 138-154 [2022-01-00; online 2021-12-01]
PubMed DOI Crossref
Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment.
Ruusuvuori P, Valkonen M, Kartasalo K, ..., Nykter M, Latonen L
Heliyon 8 (1) e08762 [2022-01-00; online 2022-01-14]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
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.
Kvitne KE, Robertsen I, Skovlund E, ..., Jansson-Löfmark R, Åsberg A
Clin Transl Sci 15 (1) 221-233 [2022-01-00; online 2021-08-26]
PubMed DOI Crossref
SARS-CoV-2-specific B- and T-cell immunity in a population-based study of young Swedish adults.
Björkander S, Du L, Zuo F, ..., Pan-Hammarström Q, BAMSE COVID-19 study group
J. Allergy Clin. Immunol. 149 (1) 65-75.e8 [2022-01-00; online 2021-10-23]
PubMed DOI Crossref
Robust humoral and cellular immune responses and low risk for reinfection at least 8 months following asymptomatic to mild COVID-19.
Havervall S, Ng H, Jernbom Falk A, ..., Hober S, Thålin C
J. Intern. Med. 291 (1) 72-80 [2022-01-00; online 2021-09-27]
PubMed DOI Crossref
Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins.
Schlesinger D, Elsässer SJ
FEBS J. 289 (1) 53-74 [2022-01-00; online 2021-02-24]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Regulation of gene expression via translational buffering.
Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L
Biochim Biophys Acta Mol Cell Res 1869 (1) 119140 [2022-01-00; online 2021-09-30]
DOI Crossref
Quantitative predictions from molecular simulations using explicit or implicit interactions
van der Spoel D, Zhang J, Zhang H
Wiley Interdiscip Rev Comput Mol Sci 12 (1) - [2022-01-00; online 2021-06-22]
PubMed DOI Crossref
Putative regulation of macrophage-mediated inflammation by catestatin.
Muntjewerff EM, Christoffersson G, Mahata SK, van den Bogaart G
Trends Immunol. 43 (1) 41-50 [2022-01-00; online 2021-11-27]
Gustaf Christoffersson SciLifeLab Fellow
PubMed DOI Crossref
Publisher Correction: A practical guide to large-scale docking.
Bender BJ, Gahbauer S, Luttens A, ..., Irwin JJ, Shoichet BK
Nat Protoc 17 (1) 177 [2022-01-00; online 2021-12-11]
Andreas Luttens DDLS Fellow Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells.
Hühn D, Martí-Rodrigo P, Mouron S, ..., Carreras-Puigvert J, Fernandez-Capetillo O
Mol Oncol 16 (1) 148-165 [2022-01-00; online 2021-08-29]
PubMed DOI Crossref
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.
Aasebø K, Bruun J, Bergsland CH, ..., Lothe RA, Sorbye H
Br. J. Cancer 126 (1) 48-56 [2022-01-00; online 2021-10-20]
PubMed DOI Crossref
Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples.
Zhang H, Polavarapu VK, Xing P, ..., Sjöblom T, Chen X
Genome Res 32 (1) 150-161 [2022-01-00; online 2021-07-14]
PubMed DOI Crossref
PRRX1 induced by BMP signaling decreases tumorigenesis by epigenetically regulating glioma-initiating cell properties via DNA methyltransferase 3A.
Tanabe R, Miyazono K, Todo T, ..., Westermark B, Heldin CH
Mol Oncol 16 (1) 269-288 [2022-01-00; online 2021-07-16]
PubMed DOI Crossref
Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma.
Yang M, Johnsson P, Bräutigam L, ..., Cao Y, Höiom V
Genet Med 24 (1) 157-169 [2022-01-00; online 2021-11-30]
PubMed DOI Crossref
MTH1 as a target to alleviate T cell driven diseases by selective suppression of activated T cells.
Karsten S, Fiskesund R, Zhang XM, ..., Helleday T, Warpman Berglund U
Cell Death Differ. 29 (1) 246-261 [2022-01-00; online 2021-08-29]
PubMed DOI Crossref
Improvement of the performance of anticancer peptides using a drug repositioning pipeline.
Mohammadi E, Tahmoorespur M, Benfeitas R, ..., Mardinoglu A, Sekhavati MH
Biotechnol J 17 (1) e2100417 [2022-01-00; online 2021-11-14]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Improved breast cancer histological grading using deep learning.
Wang Y, Acs B, Robertson S, ..., Hartman J, Rantalainen M
Ann. Oncol. 33 (1) 89-98 [2022-01-00; online 2021-09-29]
PubMed DOI Crossref
Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors.
Brem J, Panduwawala T, Hansen JU, ..., Walsh TR, Schofield CJ
Nat Chem 14 (1) 15-24 [2022-01-00; online 2021-12-13]
PubMed DOI Crossref
Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods.
Jiang R, Singh P, Wrede F, Hellander A, Petzold L
PLoS Comput Biol 18 (1) e1009830 [2022-01-00; online 2022-01-31]
Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
High-throughput ex vivo drug testing identifies potential drugs and drug combinations for NRAS-positive malignant melanoma.
Kohtamäki L, Arjama M, Mäkelä S, ..., Murumägi A, Hernberg M
Transl Oncol 15 (1) 101290 [2022-01-00; online 2021-11-24]
PubMed DOI Crossref
Distinct transcription kinetics of pluripotent cell states.
Shao R, Kumar B, Lidschreiber K, ..., Cramer P, Elsässer SJ
Mol Syst Biol 18 (1) e10407 [2022-01-00; online 2022-01-13]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Changes in metabolomics profiles over ten years and subsequent risk of developing type 2 diabetes: Results from the Nurses' Health Study.
Wittenbecher C, Guasch-Ferré M, Haslam DE, ..., Sun Q, Hu FB
EBioMedicine 75 (-) 103799 [2022-01-00; online 2021-12-31]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons.
Gao W, Gallardo-Dodd CJ, Kutter C
Genome Res 32 (1) 97-110 [2022-01-00; online 2021-12-02]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
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]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Allele frequency spectrum of known ankylosing spondylitis associated variants in a Swedish population.
Mathioudaki A, Nordin J, Kastbom A, ..., Lindblad-Toh K, Meadows J
Scand J Rheumatol 51 (1) 21-24 [2022-01-00; online 2021-06-25]
PubMed DOI Crossref
A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience.
Santos JPG, Pajo K, Trpevski D, ..., Hellgren Kotaleski J, Kramer A
Neuroinformatics 20 (1) 241-259 [2022-01-00; online 2021-10-28]
DOI Crossref
Transient Colonising Microbes Promote Gut Dysbiosis and Disease Pathology
Lee S, Meslier V, Bidkhori G, ..., Uhlen M, Shoaie S
- - (-) - [2022-00-00; online 2022-00-00]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
DOI Crossref
The Evolution of Blood Protein Profiles of Extremely Preterm Infants After Birth
Zhong W, Danielsson H, Brusselaers N, ..., Uhlen M, Hellstrom AK
SSRN Journal - (-) - [2022-00-00; online 2022-00-00]
DOI Crossref
Synthesis and in Vitro Toxicity Assessment of Different Nano-Calcium Phosphate Nanoparticles
Başak T, Hasan T, Feray B, ..., Di SA, Adil M
Braz. arch. biol. technol. 65 (-) - [2022-00-00; online 2022-00-00]
DOI Crossref
STED and RESOLFT Fluorescent Nanoscopy
Bodén A, Pennacchietti F, Testa I
- - (-) 201-232 [2022-00-00; online 2023-01-03]
Ilaria Testa SciLifeLab Fellow
DOI Crossref
Omics Technologies in Spaceflight: Challenges and Considerations for Applying Single-Cell and Spatially Resolved Gene Expression Technologies to Samples Collected In-Flight
Overbey E, Das S, Cope H, ..., Borg J, Giacomello S
- - (-) - [2022-00-00; online 2022-00-00]
DOI Crossref
Metabolic Rewiring and Cultivation Optimization for Photosynthetic Biofuel Production in Cyanobacteria
Xie H, Kukil K, Lindberg P, Miao R, Lindblad P
- - (-) 45-80 [2022-00-00; online 2022-05-31]
DOI Crossref
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
- - (-) - [2022-00-00; online 2022-00-00]
DOI Crossref
List of contributors
Alzahrani KJ, Bagh S, Barreiro C, ..., Zare A, Şeker UÖŞ
- - (-) xiii-xv [2022-00-00; online 2022-00-00]
DOI Crossref
Image Reconstruction for live 3D Multifocus Super-Resolution Microscopy
Bajor A, Hirata-Miyasaki E, Senftleben M, Abrahamsson S
- - (-) 3W1A.3 [2022-00-00; online 2022-00-00]
DOI Crossref
Drug Discovery Methods for Studying Brain Drug Delivery and Distribution
Loryan I, Hammarlund-Udenaes M
- - (-) 389-436 [2022-00-00; online 2022-05-25]
DOI Crossref
Dimensionality Reduction
Oskolkov N
- - (-) 151-167 [2022-00-00; online 2022-01-31]
DOI Crossref
Diffusion Measurements at the Nanoscale with STED-FCS
Schneider F, Sezgin E
- - (-) 323-336 [2022-00-00; online 2022-08-04]
Erdinc Sezgin SciLifeLab Fellow
DOI Crossref
Developments in the use of microfluidics in synthetic biology
Damiati LA, Damiati SA, Damiati S
- - (-) 423-435 [2022-00-00; online 2022-00-00]
DOI Crossref
Development of L-Dopa-Containing Diketopiperazines as Blood-Brain Barrier Shuttle
Cornacchia C, Marinelli L, Di Rienzo A, ..., Di Stefano A, Cacciatore I
- - (-) - [2022-00-00; online 2022-00-00]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Cholesterol stiffening of lipid membranes and drug interactions: Insights from neutron spin echo and deuterium NMR spectroscopy
Gupta S, Doole FT, Kumarage T, ..., Ashkar R, Brown MF
- - (-) 771-796 [2022-00-00; online 2022-00-00]
DDLS Fellow Milka Doktorova
DOI Crossref
Batch Processing Methods in ImageJ
Klemm A, Miura K
- - (-) 7-27 [2022-00-00; online 2022-09-29]
DOI Crossref
Association between single nucleotide polymorphisms in non-coding regions of the insulin gene and schizophrenia
Melkersson K, Persson B
Neuroscience Applied 1 (-) 100564 [2022-00-00; online 2022-00-00]
DOI Crossref
Acoustic Biosensors for Cell Research
Damiati S
- - (-) 537-568 [2022-00-00; online 2021-10-01]
SciLifeLab Data Centre
Publications 9.5.1