Publications 2021

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255 publications

PubMed DOI Crossref
Therapeutic Potential of Ferulic Acid in Alzheimer's Disease.
Turkez H, Arslan ME, Barboza JN, ..., de Sousa DP, Mardinoğlu A
Curr Drug Deliv 19 (8) 860-873 [2021-12-30; online 2021-12-30]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Potential of [11C]UCB-J as a PET tracer for islets of Langerhans.
Puuvuori E, Rokka J, Carlsson PO, ..., Eriksson J, Eriksson O
Sci Rep 11 (1) 24466 [2021-12-28; online 2021-12-28]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Regional Brain Analysis of Modified Amino Acids and Dipeptides during the Sleep/Wake Cycle.
Vallianatou T, Bèchet NB, Correia MSP, Lundgaard I, Globisch D
Metabolites 12 (1) - [2021-12-27; online 2021-12-27]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Accurate spliced alignment of long RNA sequencing reads
Sahlin K, Mäkinen V
Bioinformatics 37 (24) 4643-4651 [2021-12-11; online 2021-07-24]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Systems Biology Approaches to Decipher the Underlying Molecular Mechanisms of Glioblastoma Multiforme.
Kaynar A, Altay O, Li X, ..., Shoaie S, Mardinoglu A
Int J Mol Sci 22 (24) 13213 [2021-12-08; online 2021-12-08]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes.
Carravilla P, Dasgupta A, Zhurgenbayeva G, ..., Sezgin E, Eggeling C
Biophys Rep (N Y) 1 (2) None [2021-12-08; online 2021-12-08]
Erdinc Sezgin 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. - (-) - [2021-12-08; online 2021-12-08]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach.
Bengtsson-Palme J, Jonsson V, Heß S
Environ. Sci. Technol. 55 (23) 15734-15743 [2021-12-07; online 2021-11-18]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Proactive autoscaling for edge computing systems with kubernetes
Ju L, Singh P, Toor S
- - (-) - [2021-12-06; online 2022-02-07]
Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis.
Kim PG, Niroula A, Shkolnik V, ..., Natarajan P, Ebert BL
J. Exp. Med. 218 (12) - [2021-12-06; online 2021-10-26]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
The Current State of Beta-Cell-Mass PET Imaging for Diabetes Research and Therapies.
Cheung P, Eriksson O
Biomedicines 9 (12) - [2021-12-03; online 2021-12-03]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Salmonella effector driven invasion of the gut epithelium: breaking in and setting the house on fire.
Fattinger SA, Sellin ME, Hardt WD
Curr Opin Microbiol 64 (-) 9-18 [2021-12-00; online 2021-09-06]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms.
Zhong W, Altay O, Arif M, ..., Uhlen M, Fagerberg L
EBioMedicine 74 (-) 103723 [2021-12-00; online 2021-11-27]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
In vitro transcriptome response to propolis in differentiated SH-SY5Y neurons.
Turkez H, Arslan ME, Yilmaz A, ..., Abd El-Aty AM, Mardinoglu A
J Food Biochem 45 (12) e13990 [2021-12-00; online 2021-11-03]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.
G Ribeiro P, Torres Jiménez MF, Andermann T, ..., Bacon CD, Matos-Maraví P
Mol. Ecol. 30 (23) 6021-6035 [2021-12-00; online 2021-10-31]
DDLS Fellow Tobias Andermann
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 AII
IEEE/ACM Trans Comput Biol Bioinform PP (-) - [2021-11-30; online 2021-11-30]
Kristoffer Sahlin SciLifeLab Fellow
DOI Crossref
Genomic and niche divergence in an Amazonian palm species complex
Bacon CD, Roncal J, Andermann T, ..., Tunarosa N, Antonelli A
- 197 (4) 498-512 [2021-11-29; online 2021-05-10]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Fragment-based design of selective GPCR ligands guided by free energy simulations.
Matricon P, Vo DD, Gao ZG, ..., Jacobson KA, Carlsson J
Chem. Commun. (Camb.) 57 (92) 12305-12308 [2021-11-19; online 2021-11-19]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease.
Yang H, Arif M, Yuan M, ..., Zhang C, Mardinoglu A
iScience 24 (11) 103222 [2021-11-19; online 2021-10-05]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.
Schön ME, Zlatogursky VV, Singh RP, ..., Wideman JG, Burki F
Nat Commun 12 (1) 6651 [2021-11-17; online 2021-11-17]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
Boron-based hybrids as novel scaffolds for the development of drugs with neuroprotective properties.
Cacciatore I, Turkez H, Di Rienzo A, ..., Mardinoglu A, Di Stefano A
RSC Med Chem 12 (11) 1944-1949 [2021-11-17; online 2021-08-13]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Using High-Sensitivity Lipidomics To Assess Microscale Heterogeneity in Oceanic Sinking Particles and Single Phytoplankton Cells.
Hunter JE, Fredricks HF, Behrendt L, ..., Stocker R, Van Mooy BAS
Environ. Sci. Technol. 55 (22) 15456-15465 [2021-11-16; online 2021-11-01]
Lars Behrendt SciLifeLab Fellow
PubMed DOI Crossref
MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.
Kang W, Fromm B, Houben AJ, ..., Biryukova I, Friedländer MR
Cell Reports 37 (7) 110015 [2021-11-16; online 2021-11-18]
Marc Friedländer SciLifeLab Fellow
PubMed DOI Crossref
Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids.
van Husen LS, Katsori AM, Meineke B, ..., Schedin-Weiss S, Elsässer SJ
Chembiochem 22 (22) 3208-3213 [2021-11-16; online 2021-09-13]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor.
Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L
J Chem Inf Model - (-) - [2021-11-15; online 2021-11-15]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Glucosylceramide synthase deficiency in the heart compromises β1-adrenergic receptor trafficking.
Andersson L, Cinato M, Mardani I, ..., Borén J, Levin MC
Eur. Heart J. 42 (43) 4481-4492 [2021-11-14; online 2021-07-24]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling.
Meineke B, Heimgärtner J, Craig AJ, ..., Moodie LWK, Elsässer SJ
Front Chem 9 (-) 768535 [2021-11-11; online 2021-11-11]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Large-scale identification of RBP-RNA interactions by RAPseq refines essentials of post-transcriptional gene regulation
Atanasoai I, Papavasileiou S, Preiß N, Kutter C
- - (-) - [2021-11-09; online 2021-11-09]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology.
Mulliqi N, Kartasalo K, Olsson H, ..., Eklund M, Ruusuvuori P
Bioinformatics 37 (21) 3995-3997 [2021-11-05; online 2021-08-07]
Kimmo Kartasalo
PubMed DOI Crossref
Intercrypt sentinel macrophages tune antibacterial NF-κB responses in gut epithelial cells via TNF.
Hausmann A, Felmy B, Kunz L, ..., Sellin ME, Hardt WD
J. Exp. Med. 218 (11) - [2021-11-01; online 2021-09-16]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Improving sampling of crystallographic disorder in ensemble refinement.
Ploscariu N, Burnley T, Gros P, Pearce NM
Acta Crystallogr D Struct Biol 77 (Pt 11) 1357-1364 [2021-11-01; online 2021-10-20]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Safety and Efficacy Assessments to Take Antioxidants in Glioblastoma Therapy: From In Vitro Experiences to Animal and Clinical Studies.
Turkez H, Tozlu OO, Arslan ME, Mardinoglu A
Neurochem Int 150 (-) 105168 [2021-11-00; online 2021-08-25]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Effective sequence similarity detection with strobemers
Sahlin K
Genome Res. 31 (11) 2080-2094 [2021-11-00; online 2021-10-19]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Distinction of lymphoid and myeloid clonal hematopoiesis.
Niroula A, Sekar A, Murakami MA, ..., Natarajan P, Ebert BL
Nat. Med. 27 (11) 1921-1927 [2021-11-00; online 2021-10-18]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.
Biancalani T, Scalia G, Buffoni L, ..., Macosko EZ, Regev A
Nat. Methods 18 (11) 1352-1362 [2021-11-00; online 2021-10-28]
Sanja Vickovic SciLifeLab Fellow
DOI Crossref
Comprehensive analysis of chemical and biological problems associated with browning agents used in aquatic studies
Scharnweber K, Peura S, Attermeyer K, ..., Tranvik LJ, Székely AJ
Limnol Oceanogr Methods - (-) - [2021-10-28; online 2021-10-28]
Sarahi Garcia SciLifeLab Fellow
PubMed DOI Crossref
Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis.
Bayraktar A, Lam S, Altay O, ..., Shoaie S, Mardinoglu A
Int J Mol Sci 22 (21) 11556 [2021-10-26; online 2021-10-26]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle.
Omnus DJ, Fink MJ, Szwedo K, Jonas K
Elife 10 (-) - [2021-10-25; online 2021-10-25]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration.
Liimatainen K, Latonen L, Valkonen M, Kartasalo K, Ruusuvuori P
BMC Cancer 21 (1) 1133 [2021-10-22; online 2021-10-22]
Kimmo Kartasalo
PubMed DOI Crossref
Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing.
Carroll LM, Buehler AJ, Gaballa A, ..., Cheng RA, Wiedmann M
Front Microbiol 12 (-) 763669 [2021-10-18; online 2021-10-18]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Chemoselective and Highly Sensitive Quantification of Gut Microbiome and Human Metabolites.
Lin W, Conway LP, Vujasinovic M, Löhr JM, Globisch D
Angew. Chem. Int. Ed. Engl. 60 (43) 23232-23240 [2021-10-18; online 2021-09-17]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Herpes Simplex Virus 1 and 2 Infections during Differentiation of Human Cortical Neurons.
Bergström P, Trybala E, Eriksson CE, ..., Zetterberg H, Bergström T
Viruses 13 (10) - [2021-10-14; online 2021-10-14]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
The Assessment of Selected miRNA Profile in Familial Mediterranean Fever.
Kahraman CY, Egin ME, Tatar A, Turkez H, Mardinoglu A
Biomed Res Int 2021 (-) 6495700 [2021-10-13; online 2021-10-13]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars.
Cohn AR, Orsi RH, Carroll LM, ..., Wiedmann M, Cheng RA
Front Microbiol 12 (-) 730411 [2021-10-13; online 2021-10-13]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Diversity and ecology of protists revealed by metabarcoding.
Burki F, Sandin MM, Jamy M
Curr. Biol. 31 (19) R1267-R1280 [2021-10-11; online 2021-10-13]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet.
Yang H, Mayneris-Perxachs J, Boqué N, ..., Mardinoglu A, Caimari A
Biomedicines 9 (10) - [2021-10-11; online 2021-10-11]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Squaric acid as a new chemoselective moiety for mass spectrometry-based metabolomics analysis of amines.
Lin W, Yang Z, Kaur A, ..., Löhr JM, Globisch D
RSC Chem Biol 2 (5) 1479-1483 [2021-10-07; online 2021-08-12]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.
Carroll LM, Pierneef R, Mathole M, Matle I
Front Microbiol 12 (-) 748611 [2021-10-04; online 2021-10-04]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Predicting Molecular Phenotypes from Histopathology Images: A Transcriptome-Wide Expression-Morphology Analysis in Breast Cancer.
Wang Y, Kartasalo K, Weitz P, ..., Hartman J, Rantalainen M
Cancer Res. 81 (19) 5115-5126 [2021-10-01; online 2021-08-02]
Kimmo Kartasalo
PubMed DOI Crossref
Differential susceptibility of rat primary neurons and neural stem cells to PFOS and PFOA toxicity.
Pierozan P, Karlsson O
Toxicol. Lett. 349 (-) 61-68 [2021-10-01; online 2021-06-11]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You?
Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J
Pharmacol Rev 73 (4) 527-565 [2021-10-00; online 2021-12-16]
Jens Carlsson SciLifeLab Fellow
DOI Crossref
Sinking enhances the degradation of organic particles by marine bacteria
Alcolombri U, Peaudecerf FJ, Fernandez VI, ..., Lee KS, Stocker R
Nat. Geosci. 14 (10) 775-780 [2021-10-00; online 2021-09-23]
Lars Behrendt SciLifeLab Fellow
PubMed DOI Crossref
Refining the amyloid β peptide and oligomer fingerprint ambiguities in Alzheimer's disease: Mass spectrometric molecular characterization in brain, cerebrospinal fluid, blood, and plasma.
Michno W, Blennow K, Zetterberg H, Brinkmalm G
J. Neurochem. 159 (2) 234-257 [2021-10-00; online 2021-07-27]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Promising potential of boron compounds against Glioblastoma: In Vitro antioxidant, anti-inflammatory and anticancer studies.
Turkez H, Arslan ME, Tatar A, Mardinoglu A
Neurochem Int 149 (-) 105137 [2021-10-00; online 2021-07-19]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 9: Polymyxins: colistin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06861 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and valnemulin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06860 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7: Amphenicols: florfenicol and thiamphenicol.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06859 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 6: Macrolides: tilmicosin, tylosin and tylvalosin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06858 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides: lincomycin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06856 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 4: β-Lactams: amoxicillin and penicillin V.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06855 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 3: Amprolium.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06854 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 2: Aminoglycosides/aminocyclitols: apramycin, paromomycin, neomycin and spectinomycin.
EFSA Panel on Biological Hazards (BIOHAZ) , Allende A, Koutsoumanis K, ..., Stella P, Peixe L
EFSA J 19 (10) e06853 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 1: Methodology, general data gaps and uncertainties.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06852 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 13: Diaminopyrimidines: trimethoprim.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06865 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and doxycycline.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06864 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 11: Sulfonamides.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06863 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 10: Quinolones: flumequine and oxolinic acid.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06862 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Corrigendum: Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene.
Fromm B, Tarbier M, Smith O, ..., Gilbert MTP, Friedländer MR
RNA 27 (10) 1291 [2021-10-00; online 2021-09-18]
Marc Friedländer SciLifeLab Fellow
PubMed DOI Crossref
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.
Zeybel M, Altay O, Arif M, ..., Borén J, Mardinoglu A
Mol Syst Biol 17 (10) e10459 [2021-10-00; online 2021-10-26]
Adil Mardinoglu Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
Association of levonorgestrel intrauterine devices with stress reactivity, mental health, quality of life and sexual functioning: A systematic review.
Bürger Z, Bucher AM, Comasco E, ..., Kogler L, Derntl B
Front Neuroendocrinol 63 (-) 100943 [2021-10-00; online 2021-08-20]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
A practical guide to large-scale docking.
Bender BJ, Gahbauer S, Luttens A, ..., Irwin JJ, Shoichet BK
Nat Protoc 16 (10) 4799-4832 [2021-10-00; online 2021-09-24]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
An evaluation of a FluoroSpot assay as a diagnostic tool to determine SARS-CoV-2 specific T cell responses.
Mangsbo SM, Havervall S, Laurén I, ..., Klingström J, Thålin C
PLoS ONE 16 (9) e0258041 [2021-09-30; online 2021-09-30]
Gustaf Christoffersson SciLifeLab Fellow
PubMed DOI Crossref
Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.
Chelebian E, Avenel C, Kartasalo K, ..., Lundeberg J, Wählby C
Cancers (Basel) 13 (19) - [2021-09-28; online 2021-09-28]
Kimmo Kartasalo
PubMed DOI Crossref
Improved Radiolytic Stability of a 68Ga-labelled Collagelin Analogue for the Imaging of Fibrosis.
Velikyan I, Rosenström U, Rosestedt M, Eriksson O, Antoni G
Pharmaceuticals (Basel, Switzerland) 14 (10) - [2021-09-28; online 2021-09-28]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Discovery, optimization and biodistribution of an Affibody molecule for imaging of CD69.
Persson J, Puuvuori E, Zhang B, ..., Eriksson O, Löfblom J
Sci Rep 11 (1) 19151 [2021-09-27; online 2021-09-27]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
Lam S, Hartmann N, Benfeitas R, ..., Knight R, Mardinoglu A
Biomedicines 9 (10) - [2021-09-24; online 2021-09-24]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Optimization of an Imidazo[1,2-a]pyridine Series to Afford Highly Selective Type I1/2 Dual Mer/Axl Kinase Inhibitors with In Vivo Efficacy.
McCoull W, Boyd S, Brown MR, ..., Zhu Q, Smith PD
J Med Chem 64 (18) 13524-13539 [2021-09-23; online 2021-09-03]
SciLifeLab Fellow Yumeng Mao
DOI Crossref
A method for intuitively extracting macromolecular dynamics from structural disorder
Pearce NM, Gros P
Nat Commun 12 (1) - [2021-09-17; online 2021-09-17]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability.
Felletti M, Romilly C, Wagner EGH, Jonas K
Elife 10 (-) - [2021-09-15; online 2021-09-15]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
Selection on accessible chromatin regions in Capsella grandiflora.
Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T
Mol. Biol. Evol. - (-) - [2021-09-08; online 2021-09-08]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Dynamin inhibition causes context-dependent cell death of leukemia and lymphoma cells.
von Beek C, Alriksson L, Palle J, ..., Sellin ME, Pejler G
PLoS ONE 16 (9) e0256708 [2021-09-07; online 2021-09-07]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome.
Bacic L, Gaullier G, Sabantsev A, ..., Boulton SJ, Deindl S
Elife 10 (-) - [2021-09-06; online 2021-09-06]
SciLifeLab Fellow Sebastian Deindl
PubMed DOI Crossref
Association of Diet Quality With Prevalence of Clonal Hematopoiesis and Adverse Cardiovascular Events.
Bhattacharya R, Zekavat SM, Uddin MM, ..., Bick A, Natarajan P
JAMA Cardiol 6 (9) 1069-1077 [2021-09-01; online 2021-06-10]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing.
Beauchamp EM, Leventhal M, Bernard E, ..., Jaiswal S, Ebert BL
Blood Cancer Discov 2 (5) 500-517 [2021-09-00; online 2021-07-14]
Abhishek Niroula DDLS Fellow
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Advances in the Relationships Between Cow's Milk Protein Allergy and Gut Microbiota in Infants.
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The Uppsala APP deletion causes early onset autosomal dominant Alzheimer's disease by altering APP processing and increasing amyloid β fibril formation.
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The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.
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PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.
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DNA methylation of Vesicular Glutamate Transporters in the mesocorticolimbic brain following early-life stress and adult ethanol exposure-an explorative study.
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Anticancer effects of novel NSAIDs derivatives on cultured human glioblastoma cells.
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Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning.
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Differential regulation of oxidative stress, microbiota-derived, and energy metabolites in the mouse brain during sleep.
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Recent Progress in the Molecular Imaging of Nonalcoholic Fatty Liver Disease.
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Supplemental Association of Clonal Hematopoiesis With Incident Heart Failure.
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The Effect of the Molecular Weight of Polyvinylpyrrolidone and the Model Drug on Laser-Induced In Situ Amorphization
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Editorial: NK-Myeloid Cell Interactions in the Tumor Microenvironment: Implications for Cancer Immunotherapy.
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Simultaneous detection of SARS-CoV-2 and pandemic (H1N1) 2009 virus with real-time isothermal platform.
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Safety Assessments of Nickel Boride Nanoparticles on the Human Pulmonary Alveolar Cells by Using Cell Viability and Gene Expression Analyses.
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Biol Trace Elem Res 199 (7) 2602-2611 [2021-07-00; online 2020-09-09]
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STED and parallelized RESOLFT optical nanoscopy of the tubular endoplasmic reticulum and its mitochondrial contacts in neuronal cells.
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Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.
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Clin. Microbiol. Infect. 27 (7) 1036.e1-1036.e8 [2021-07-00; online 2021-04-02]
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On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).
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Molecular Dynamics Simulations of Ion Channels.
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Trends Biochem. Sci. 46 (7) 621-622 [2021-07-00; online 2021-04-30]
Lucie Delemotte SciLifeLab Fellow
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Effects of 6 weeks of treatment with dapagliflozin, a sodium-glucose co-transporter-2 inhibitor, on myocardial function and metabolism in patients with type 2 diabetes: A randomized, placebo-controlled, exploratory study.
Oldgren J, Laurila S, Åkerblom A, ..., Oscarsson J, Nuutila P
Diabetes Obes Metab 23 (7) 1505-1517 [2021-07-00; online 2021-03-12]
Olof Eriksson SciLifeLab Fellow
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Distinct genetic regions are associated with differential population susceptibility to chemical exposures.
Kosnik MB, Enroth S, Karlsson O
Environ Int 152 (-) 106488 [2021-07-00; online 2021-03-10]
Oskar Karlsson SciLifeLab Fellow
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DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design.
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Adv. Mater. Weinheim 33 (29) e2008457 [2021-07-00; online 2021-06-06]
Erik Benson SciLifeLab Fellow
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Brain reactivity during aggressive response in women with premenstrual dysphoric disorder treated with a selective progesterone receptor modulator.
Kaltsouni E, Fisher PM, Dubol M, ..., Comasco E, Sundström-Poromaa I
Neuropsychopharmacology 46 (8) 1460-1467 [2021-07-00; online 2021-04-29]
Erika Comasco SciLifeLab Fellow
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Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer in Biopsies-Current Status and Next Steps.
Kartasalo K, Bulten W, Delahunt B, ..., Egevad L, Eklund M
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Kimmo Kartasalo
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A single-cell type transcriptomics map of human tissues.
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Sci Adv 7 (31) - [2021-07-00; online 2021-07-28]
Adil Mardinoglu SciLifeLab Fellow
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DNA Blocks the Lethal Effect of Human Beta-Defensin 2 Against Neisseria meningitidis.
Wassing GM, Lidberg K, Sigurlásdóttir S, ..., Jonas K, Jonsson AB
Front Microbiol 12 (-) 697232 [2021-06-30; online 2021-06-30]
Kristina Jonas SciLifeLab Fellow
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Cisplatin inhibits frequency and suppressive activity of monocytic myeloid-derived suppressor cells in cancer patients.
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Oncoimmunology 10 (1) 1935557 [2021-06-27; online 2021-06-27]
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Pesticide-induced multigenerational effects on amphibian reproduction and metabolism.
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Oskar Karlsson SciLifeLab Fellow
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COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.
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Nat Commun 12 (1) 3903 [2021-06-23; online 2021-06-23]
Magda Bienko
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Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators.
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BMC Bioinformatics 22 (1) 339 [2021-06-23; online 2021-06-23]
Prashant Singh SciLifeLab Fellow
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The Influence of Drug–Polymer Solubility on Laser-Induced In Situ Drug Amorphization Using Photothermal Plasmonic Nanoparticles
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Pharmaceutics 13 (6) 917 [2021-06-21; online 2021-06-21]
Alexandra Teleki SciLifeLab Fellow
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Application of high-throughput 5'P sequencing for the study of co-translational mRNA decay.
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STAR Protoc 2 (2) 100447 [2021-06-18; online 2021-03-31]
SciLifeLab Fellow Vicent Pelechano
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Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.
Roxhed N, Bendes A, Dale M, ..., Fredolini C, Schwenk JM
Nat Commun 12 (1) 3695 [2021-06-17; online 2021-06-17]
SciLifeLab Fellow Simon Elsässer
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Means, Motive, and Opportunity: Do Non-Islet-Reactive Infiltrating T Cells Contribute to Autoimmunity in Type 1 Diabetes?
Rodriguez-Calvo T, Christoffersson G, Bender C, ..., Kent SC, James EA
Front Immunol 12 (-) 683091 [2021-06-16; online 2021-06-16]
Gustaf Christoffersson SciLifeLab Fellow
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Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology.
Shakur R, Ochoa JP, Robinson AJ, ..., Vihinen M, Monserrat L
NPJ Genom Med 6 (1) 47 [2021-06-14; online 2021-06-14]
Abhishek Niroula DDLS Fellow
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Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling.
Wendt M, Bellavita R, Gerber A, ..., Hennig S, Grossmann TN
Angew. Chem. Int. Ed. Engl. 60 (25) 13937-13944 [2021-06-14; online 2021-05-05]
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.
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Genome Biol. 22 (1) 179 [2021-06-13; online 2021-06-13]
Pascal Milesi SciLifeLab Fellow
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Utilizing Laser Activation of Photothermal Plasmonic Nanoparticles to Induce On-Demand Drug Amorphization inside a Tablet
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Mol. Pharmaceutics 18 (6) 2254-2262 [2021-06-07; online 2021-05-05]
Alexandra Teleki SciLifeLab Fellow
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The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function.
Oftedal BE, Maio S, Handel AE, ..., Maizels RM, Holländer GA
Commun Biol 4 (1) 681 [2021-06-03; online 2021-06-03]
Erdinc Sezgin SciLifeLab Fellow
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Imaging of the Glucagon Receptor in Subjects with Type 2 Diabetes.
Eriksson O, Velikyan I, Haack T, ..., Tillner J, Wagner M
Journal of nuclear medicine : official publication, Society of Nuclear Medicine 62 (6) 833-838 [2021-06-01; online 2020-10-23]
Olof Eriksson SciLifeLab Fellow
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Unboxing mutations: Connecting mutation types with evolutionary consequences.
Berdan EL, Blanckaert A, Slotte T, ..., Westram AM, Fragata I
Mol. Ecol. 30 (12) 2710-2723 [2021-06-00; online 2021-05-19]
SciLifeLab Fellow Tanja Slotte
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Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being.
Pesic M, Egamberdieva D, Kolodziejczyk B, ..., Neergheen VS, Kagansky A
Biol Futur 72 (2) 119-125 [2021-06-00; online 2020-09-07]
SciLifeLab Fellow Simon Elsässer
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More Than Just Letters and Chemistry: Genomics Goes Mechanics.
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Trends Biochem. Sci. 46 (6) 431-432 [2021-06-00; online 2021-04-12]
SciLifeLab Fellow Sebastian Deindl
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Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies.
Egevad L, Delahunt B, Samaratunga H, ..., Eklund M, Ruusuvuori P
Virchows Arch. 478 (6) 1109-1116 [2021-06-00; online 2021-02-03]
Kimmo Kartasalo
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Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells.
Erdem C, Lee AV, Taylor DL, Lezon TR
PLoS Comput Biol 17 (6) e1009125 [2021-06-00; online 2021-06-30]
Cemal Erdem DDLS Fellow
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Following spatial Aβ aggregation dynamics in evolving Alzheimer's disease pathology by imaging stable isotope labeling kinetics.
Michno W, Stringer KM, Enzlein T, ..., Edwards FA, Hanrieder J
Sci Adv 7 (25) - [2021-06-00; online 2021-06-16]
SciLifeLab Fellow Wojciech Michno
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Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides.
Muntjewerff EM, Tang K, Lutter L, ..., van den Bogaart G, Mahata SK
Acta Physiol 232 (2) e13655 [2021-06-00; online 2021-05-06]
Gustaf Christoffersson SciLifeLab Fellow
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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source.
Douangamath A, Powell A, Fearon D, ..., Gorrie-Stone T, von Delft F
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Using TIF-Seq2 to investigate association between 5´ and 3´mRNA ends.
Li B, Marques S, Wang J, Pelechano V
Meth. Enzymol. 655 (-) 85-118 [2021-05-28; online 2021-05-28]
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Perivascular Macrophages Regulate Blood Flow Following Tissue Damage.
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Editorial: Application of Systems Biology in Molecular Characterization and Diagnosis of Cancer.
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Phagocytosis and Efferocytosis by Resident Macrophages in the Mouse Pancreas.
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Front Endocrinol (Lausanne) 12 (-) 606175 [2021-05-25; online 2021-05-25]
Gustaf Christoffersson SciLifeLab Fellow
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Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.
Bohutínská M, Vlček J, Yair S, ..., Slotte T, Kolář F
Proc. Natl. Acad. Sci. U.S.A. 118 (21) - [2021-05-25; online 2021-05-19]
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A combined approach for single-cell mRNA and intracellular protein expression analysis.
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Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]
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Microbial Community Interactions Are Sensitive to Small Changes in Temperature.
Burman E, Bengtsson-Palme J
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The human exposome and health in the Anthropocene.
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Phylogenomic Insights into the Origin of Primary Plastids.
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Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.
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Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]
Sarahi Garcia SciLifeLab Fellow
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Informing Pharmacokinetic Models With Physiological Data: Oral Population Modeling of L-Serine in Humans.
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Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
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Microorganisms 9 (5) 1042 [2021-05-12; online 2021-05-12]
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Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction.
Arif M, Klevstig M, Benfeitas R, ..., Mardinoglu A, Boren J
Elife 10 (-) - [2021-05-11; online 2021-05-11]
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mSystems 6 (3) - [2021-05-11; online 2021-05-11]
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Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-20]
SciLifeLab Fellow Tanja Slotte
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Espeso-Gil S, Holik AZ, Bonnin S, ..., Hor CN, Ossowski S
Front Mol Neurosci 14 (-) 664912 [2021-05-05; online 2021-05-05]
Marc Friedländer SciLifeLab Fellow
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The Chaperonin GroESL Facilitates Caulobacter crescentus Cell Division by Supporting the Functions of the Z-Ring Regulators FtsA and FzlA.
Schroeder K, Heinrich K, Neuwirth I, Jonas K
MBio 12 (3) - [2021-05-04; online 2021-05-04]
Kristina Jonas SciLifeLab Fellow
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Andersson M, Johansson S, Bergman H, ..., Behrendt L, Tenje M
Lab Chip 21 (9) 1694-1705 [2021-05-04; online 2021-05-06]
Lars Behrendt SciLifeLab Fellow
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Carroll LM, Cheng RA, Wiedmann M, Kovac J
Crit Rev Food Sci Nutr 62 (28) 7677-7702 [2021-05-03; online 2021-05-03]
DDLS Fellow Laura Carroll
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Cannabidiol inhibits the skeletal muscle Nav1.4 by blocking its pore and by altering membrane elasticity.
Ghovanloo MR, Choudhury K, Bandaru TS, ..., Goodchild SJ, Ruben PC
J. Gen. Physiol. 153 (5) - [2021-05-03; online 2021-04-10]
Lucie Delemotte SciLifeLab Fellow
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Volumetric live cell imaging with three-dimensional parallelized RESOLFT microscopy.
Bodén A, Pennacchietti F, Coceano G, ..., Ratz M, Testa I
Nat. Biotechnol. 39 (5) 609-618 [2021-05-00; online 2021-01-11]
Ilaria Testa SciLifeLab Fellow
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Benson E, Carrascosa Marzo R, Bath J, Turberfield AJ
Small 17 (20) e2007704 [2021-05-00; online 2021-05-04]
Erik Benson SciLifeLab Fellow
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Epithelium-autonomous NAIP/NLRC4 prevents TNF-driven inflammatory destruction of the gut epithelial barrier in Salmonella-infected mice.
Fattinger SA, Geiser P, Samperio Ventayol P, ..., Hardt WD, Sellin ME
Mucosal Immunol 14 (3) 615-629 [2021-05-00; online 2021-03-17]
Mikael Sellin SciLifeLab Fellow
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Kapla J, Rodríguez-Espigares I, Ballante F, Selent J, Carlsson J
PLoS Comput Biol 17 (5) e1008936 [2021-05-00; online 2021-05-13]
Jens Carlsson SciLifeLab Fellow
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The Protein Quality Control Network in Caulobacter crescentus.
Schroeder K, Jonas K
Front Mol Biosci 8 (-) 682967 [2021-04-30; online 2021-04-30]
Kristina Jonas SciLifeLab Fellow
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Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel.
Pérez-Conesa S, Keeler EG, Zhang D, Delemotte L, McDermott AE
J Chem Phys 154 (16) 165102 [2021-04-28; online 2021-05-05]
Lucie Delemotte SciLifeLab Fellow
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How Does Liquid-Liquid Phase Separation in Model Membranes Reflect Cell Membrane Heterogeneity?
Sych T, Gurdap CO, Wedemann L, Sezgin E
Membranes (Basel) 11 (5) - [2021-04-28; online 2021-04-28]
Erdinc Sezgin SciLifeLab Fellow
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van der Kolk BW, Saari S, Lovric A, ..., Pajukanta P, Pietiläinen KH
Cell Rep Med 2 (4) 100226 [2021-04-20; online 2021-03-30]
Adil Mardinoglu SciLifeLab Fellow
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Bacterial detection by NAIP/NLRC4 elicits prompt contractions of intestinal epithelial cell layers.
Samperio Ventayol P, Geiser P, Di Martino ML, ..., Eriksson J, Sellin ME
Proc. Natl. Acad. Sci. U.S.A. 118 (16) - [2021-04-20; online 2021-04-14]
Mikael Sellin SciLifeLab Fellow
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Scalable machine learning-assisted model exploration and inference using Sciope.
Singh P, Wrede F, Hellander A
Bioinformatics 37 (2) 279-281 [2021-04-19; online 2020-07-25]
Prashant Singh SciLifeLab Fellow
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Germline variants at SOHLH2 influence multiple myeloma risk.
Duran-Lozano L, Thorleifsson G, Lopez de Lapuente Portilla A, ..., Stefansson K, Nilsson B
Blood Cancer J 11 (4) 76 [2021-04-19; online 2021-04-19]
Abhishek Niroula DDLS Fellow
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Cheung P, Zhang B, Puuvuori E, ..., Eriksson J, Eriksson O
Biomedicines 9 (4) - [2021-04-16; online 2021-04-16]
Olof Eriksson SciLifeLab Fellow
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Stress-induced transcriptional memory accelerates promoter-proximal pause release and decelerates termination over mitotic divisions.
Vihervaara A, Mahat DB, Himanen SV, ..., Lis JT, Sistonen L
Mol. Cell 81 (8) 1715-1731.e6 [2021-04-15; online 2021-03-29]
Anniina Vihervaara SciLifeLab Fellow
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A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation.
Regadas I, Dahlberg O, Vaid R, ..., Wen J, Mannervik M
Mol. Cell 81 (8) 1766-1780.e10 [2021-04-15; online 2021-02-24]
SciLifeLab Fellow Sebastian Deindl
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DNA methylation in cord blood in association with prenatal depressive symptoms.
Kallak TK, Bränn E, Fransson E, ..., Lyle R, Skalkidou A
Clin Epigenetics 13 (1) 78 [2021-04-12; online 2021-04-12]
Erika Comasco SciLifeLab Fellow
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Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling.
Altay O, Zhang C, Turkez H, ..., Uhlén M, Mardinoglu A
Metabolites 11 (4) - [2021-04-05; online 2021-04-05]
Adil Mardinoglu SciLifeLab Fellow
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Resin-acid derivatives bind to multiple sites on the voltage-sensor domain of the Shaker potassium channel.
Silverå Ejneby M, Gromova A, Ottosson NE, ..., Elinder F, Delemotte L
J. Gen. Physiol. 153 (4) - [2021-04-05; online 2021-03-09]
Lucie Delemotte SciLifeLab Fellow
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Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds.
Ottenburghs J, Geng K, Suh A, Kutter C
Genome Biol Evol 13 (4) - [2021-04-05; online 2021-02-04]
Claudia Kutter SciLifeLab Fellow
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High-throughput 5′P sequencing enables the study of degradation-associated ribosome stalls
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Cell Reports Methods 1 (1) 100001 [2021-04-02]
SciLifeLab Fellow Vicent Pelechano
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The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic.
Nowak MD, Birkeland S, Mandáková T, ..., Lysak MA, Brochmann C
Mol Ecol Resour 21 (3) 661-676 [2021-04-00; online 2020-11-12]
SciLifeLab Fellow Tanja Slotte
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Longitudinal Assessment of 11C-5-Hydroxytryptophan Uptake in Pancreas After Debut of Type 1 Diabetes.
Espes D, Carlsson PO, Selvaraju RK, ..., Korsgren O, Eriksson O
Diabetes 70 (4) 966-975 [2021-04-00; online 2021-01-21]
Olof Eriksson SciLifeLab Fellow
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Exploring the GLP-1-GLP-1R axis in porcine pancreas and gastrointestinal tract in vivo by ex vivo autoradiography.
Manell E, Puuvuori E, Svensson A, ..., Jensen Waern M, Eriksson O
BMJ Open Diabetes Res Care 9 (1) - [2021-04-00; online 2021-04-28]
Olof Eriksson SciLifeLab Fellow
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Drug Occupancy Assessment at the Glucose-Dependent Insulinotropic Polypeptide Receptor by Positron Emission Tomography.
Eriksson O, Velikyan I, Haack T, ..., Pierrou S, Wagner M
Diabetes 70 (4) 842-853 [2021-04-00; online 2021-02-05]
Olof Eriksson SciLifeLab Fellow
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A genomic catalog of Earth's microbiomes.
Nayfach S, Roux S, Seshadri R, ..., Kyrpides NC, Eloe-Fadrosh EA
Nat. Biotechnol. 39 (4) 499-509 [2021-04-00; online 2020-11-09]
Sarahi Garcia SciLifeLab Fellow
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A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids.
Strassert JFH, Irisarri I, Williams TA, Burki F
Nat Commun 12 (1) 1879 [2021-03-25; online 2021-03-25]
Fabien Burki SciLifeLab Fellow
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Addressing the heterogeneity in liver diseases using biological networks.
Lam S, Doran S, Yuksel HH, ..., Uhlen M, Mardinoglu A
Brief. Bioinformatics 22 (2) 1751-1766 [2021-03-22; online 2020-03-24]
Adil Mardinoglu SciLifeLab Fellow
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Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar.
Bostanci N, Krog MC, Hugerth LW, ..., Nielsen HS, Schuppe-Koistinen I
Front. Cell. Infect. Microbiol. 11 (-) 625229 [2021-03-19; online 2021-03-19]
DDLS Fellow Luisa Hugerth
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The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species.
Opgenoorth L, Dauphin B, Benavides R, ..., Aravanopoulos FA, Cavers S
Gigascience 10 (3) - [2021-03-18; online 2021-03-19]
Pascal Milesi SciLifeLab Fellow
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High Expression of LINC01268 is Positively Associated with Hepatocellular Carcinoma Progression via Regulating MAP3K7.
Jin X, Fu W, Li D, ..., Kutter C, Li Y
Onco Targets Ther 14 (-) 1753-1769 [2021-03-08; online 2021-03-08]
Claudia Kutter SciLifeLab Fellow
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Phosphodiesterase 4A confers resistance to PGE2-mediated suppression in CD25+ /CD54+ NK cells.
Chen Z, Yang Y, Neo SY, ..., Sarhan D, Lundqvist A
EMBO Rep. 22 (3) e51329 [2021-03-03; online 2021-01-22]
SciLifeLab Fellow Yumeng Mao
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ZFP207 <i>controls pluripotency by multiple post-transcriptional mechanisms</i>
Malla S, Bhattarai DP, Melguizo-Sanchis D, ..., Kutter C, Aguilo F
- - (-) - [2021-03-02; online 2021-03-02]
Claudia Kutter SciLifeLab Fellow
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Ulipristal Acetate for Treatment of Premenstrual Dysphoric Disorder: A Proof-of-Concept Randomized Controlled Trial.
Comasco E, Kopp Kallner H, Bixo M, ..., Epperson CN, Sundström-Poromaa I
Am J Psychiatry 178 (3) 256-265 [2021-03-01; online 2020-12-10]
Erika Comasco SciLifeLab Fellow
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The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe
Benavides R, Carvalho B, Bastias CC, ..., Fady B, Valladares F
Global Ecol. Biogeogr. 30 (3) 590-597 [2021-03-00; online 2021-01-06]
Pascal Milesi SciLifeLab Fellow
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Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease
Rosario D, Bidkhori G, Lee S, ..., Mardinoglu A, Shoaie S
Cell Reports 34 (9) 108807 [2021-03-00; online 2021-03-00]
Saeed Shoaie SciLifeLab Fellow
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No evidence for a placental microbiome in human pregnancies at term.
Sterpu I, Fransson E, Hugerth LW, ..., Wiberg-Itzel E, Schuppe-Koistinen I
Am J Obstet Gynecol 224 (3) 296.e1-296.e23 [2021-03-00; online 2020-08-29]
DDLS Fellow Luisa Hugerth
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Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes.
Bick AG, Weinstock JS, Nandakumar SK, ..., Kathiresan S, Natarajan P
Nature 591 (7851) E27 [2021-03-00; online 2021-03-13]
Abhishek Niroula DDLS Fellow
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3D-printing of solid lipid tablets from emulsion gels
Johannesson J, Khan J, Hubert M, Teleki A, Bergström CAS
Int J Pharm 597 (-) 120304 [2021-03-00; online 2021-03-00]
Alexandra Teleki SciLifeLab Fellow
DOI Crossref
The Organelle in the Ointment: cryptic mitochondria account for many unknown sequences in cross-species microbiome comparisons
Sonett D, Brown T, Bengtsson-Palme J, Padilla-Gamiño JL, Zaneveld JR
bioRxiv preprint - (-) - [2021-02-24; online 2021-02-24]
DDLS Fellow Johan Bengtsson-Palme
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Accelerating target deconvolution for therapeutic antibody candidates using highly parallelized genome editing.
Mattsson J, Ekdahl L, Junghus F, ..., Teige I, Nilsson B
Nat Commun 12 (1) 1277 [2021-02-24; online 2021-02-24]
Abhishek Niroula DDLS Fellow
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Spatial Regulation of T-Cell Signaling by Programmed Death-Ligand 1 on Wireframe DNA Origami Flat Sheets.
Fang T, Alvelid J, Spratt J, ..., Testa I, Teixeira AI
ACS Nano 15 (2) 3441-3452 [2021-02-23; online 2021-02-08]
Ilaria Testa SciLifeLab Fellow
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Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes.
Johansson H, Søndergaard JN, Jorns C, Kutter C, Ellis ECS
Front Endocrinol (Lausanne) 11 (-) 554922 [2021-02-22; online 2021-02-22]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Mechanism of membrane-tethered mitochondrial protein synthesis.
Itoh Y, Andréll J, Choi A, ..., Battersby BJ, Amunts A
Science (New York, N.Y.) 371 (6531) 846-849 [2021-02-19; online 2021-02-20]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
Defective ALC1 nucleosome remodeling confers PARPi sensitization and synthetic lethality with HRD.
Hewitt G, Borel V, Segura-Bayona S, ..., Deindl S, Boulton SJ
Mol. Cell 81 (4) 767-783.e11 [2021-02-18; online 2020-12-16]
SciLifeLab Fellow Sebastian Deindl
PubMed DOI Crossref
Premature Menopause, Clonal Hematopoiesis, and Coronary Artery Disease in Postmenopausal Women.
Honigberg MC, Zekavat SM, Niroula A, ..., NHLBI Trans-Omics for Precision Medicine Program , Natarajan P
Circulation 143 (5) 410-423 [2021-02-02; online 2020-11-09]
Abhishek Niroula DDLS Fellow
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Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence.
Carrara F, Sengupta A, Behrendt L, Vardi A, Stocker R
Proc. Natl. Acad. Sci. U.S.A. 118 (5) - [2021-02-02; online 2021-01-27]
Lars Behrendt SciLifeLab Fellow
PubMed DOI Crossref
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
Mahdessian D, Cesnik AJ, Gnann C, ..., Sullivan DP, Lundberg E
Nature 590 (7847) 649-654 [2021-02-00; online 2021-02-24]
Adil Mardinoglu SciLifeLab Fellow
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Radiolabelling and positron emission tomography imaging of a high-affinity peptide binder to collagen type 1.
Rosestedt M, Velikyan I, Rosenström U, ..., Nordeman P, Eriksson O
Nucl. Med. Biol. 93 (-) 54-62 [2021-02-00; online 2020-11-28]
Olof Eriksson SciLifeLab Fellow
DOI Crossref
Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Schneider JV, Jungcurt T, Cardoso D, ..., Berberich T, Zizka G
TAXON 70 (1) 48-71 [2021-02-00; online 2020-12-31]
DDLS Fellow Tobias Andermann
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Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.
Lee KS, Pereira FC, Palatinszky M, ..., Wagner M, Stocker R
Nat Protoc 16 (2) 634-676 [2021-02-00; online 2020-12-11]
Lars Behrendt SciLifeLab Fellow
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NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data.
Sahlin K, Lim MCW, Prost S
Ecol Evol 11 (3) 1392-1398 [2021-02-00; online 2021-01-11]
Kristoffer Sahlin SciLifeLab Fellow
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Model membrane systems to reconstitute immune cell signaling.
Céspedes PF, Beckers D, Dustin ML, Sezgin E
FEBS J. 288 (4) 1070-1090 [2021-02-00; online 2020-08-03]
Erdinc Sezgin SciLifeLab Fellow
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Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm.
Dziasek K, Simon L, Lafon-Placette C, ..., Slotte T, Köhler C
PLoS Genet 17 (2) e1009370 [2021-02-00; online 2021-02-11]
SciLifeLab Fellow Tanja Slotte
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Epithelial inflammasomes in the defense against Salmonella gut infection.
Fattinger SA, Sellin ME, Hardt WD
Curr Opin Microbiol 59 (-) 86-94 [2021-02-00; online 2020-10-28]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Comparison of two arylsulfatases for targeted mass spectrometric analysis of microbiota-derived metabolites
Jain A, Correia MSP, Meistermann H, ..., Löhr JM, Globisch D
J Pharm Biomed Anal 195 (-) 113818 [2021-02-00; online 2021-02-00]
Daniel Globisch SciLifeLab Fellow
DOI Crossref
Character and environmental lability of cyanobacteria‐derived dissolved organic matter
Patriarca C, Sedano‐Núñez VT, Garcia SL, ..., Tranvik LJ, Hawkes JA
Limnol. Oceanogr. 66 (2) 496-509 [2021-02-00; online 2020-10-09]
Sarahi Garcia SciLifeLab Fellow
DOI Crossref
Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia
Harzandi A, Lee S, Bidkhori G, ..., Shoaie S, Sharpe CC
iScience 24 (2) 102046 [2021-02-00; online 2021-02-00]
Saeed Shoaie SciLifeLab Fellow
DOI Crossref
<i>iucn_sim</i> : a new program to simulate future extinctions based on IUCN threat status
Andermann T, Faurby S, Cooke R, Silvestro D, Antonelli A
Ecography 44 (2) 162-176 [2021-02-00; online 2020-11-10]
DDLS Fellow Tobias Andermann
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Epidemiological modeling in StochSS Live!
Jiang R, Jacob B, Geiger M, ..., Hellander A, Petzold L
Bioinformatics - (-) - [2021-01-29; online 2021-01-29]
Prashant Singh SciLifeLab Fellow
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Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling.
Fleetwood O, Carlsson J, Delemotte L
Elife 10 (-) - [2021-01-28; online 2021-01-28]
Jens Carlsson Lucie Delemotte SciLifeLab Fellow
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Cellocity: A Python package for analysis of confluent cell layer dynamics
Eriksson J, Styrström D, Sellin M
JOSS 6 (57) 2818 [2021-01-28; online 2021-01-28]
Mikael Sellin SciLifeLab Fellow
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Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers.
Li X, Kim W, Arif M, ..., Zhang C, Mardinoglu A
Cancers (Basel) 13 (2) - [2021-01-19; online 2021-01-19]
Adil Mardinoglu SciLifeLab Fellow
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Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples.
Alekseenko A, Barrett D, Pareja-Sanchez Y, ..., Yin X, Pelechano V
Sci Rep 11 (1) 1820 [2021-01-19; online 2021-01-19]
SciLifeLab Fellow Simon Elsässer Vicent Pelechano
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Single-Molecule, Super-Resolution, and Functional Analysis of G Protein-Coupled Receptor Behavior Within the T Cell Immunological Synapse.
Felce JH, Parolini L, Sezgin E, ..., Frater J, Dustin ML
Front Cell Dev Biol 8 (-) 608484 [2021-01-18; online 2021-01-18]
Erdinc Sezgin SciLifeLab Fellow
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Nradd Acts as a Negative Feedback Regulator of Wnt/β-Catenin Signaling and Promotes Apoptosis.
Ozalp O, Cark O, Azbazdar Y, ..., Sezgin E, Ozhan G
Biomolecules 11 (1) - [2021-01-14; online 2021-01-14]
Erdinc Sezgin SciLifeLab Fellow
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Salmonella enterica Serovar Typhimurium Exploits Cycling through Epithelial Cells To Colonize Human and Murine Enteroids.
Geiser P, Di Martino ML, Samperio Ventayol P, ..., Hellström PM, Sellin ME
MBio 12 (1) - [2021-01-12; online 2021-01-12]
Mikael Sellin SciLifeLab Fellow
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A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae.
Rodríguez-Galán O, García-Gómez JJ, Rosado IV, ..., Kressler D, de la Cruz J
Nucleic Acids Res. 49 (1) 206-220 [2021-01-11; online 2020-12-18]
SciLifeLab Fellow Vicent Pelechano
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Obese mother offspring have hepatic lipidic modulation that contributes to sex-dependent metabolic adaptation later in life.
Savva C, Helguero LA, González-Granillo M, ..., Kutter C, Korach-André M
Commun Biol 4 (1) 14 [2021-01-04; online 2021-01-04]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis.
Sahlin K, Medvedev P
Nat Commun 12 (1) 2 [2021-01-04; online 2021-01-04]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data.
Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J
Bioinformatics - (-) - [2021-01-04; online 2021-01-04]
DDLS Fellow Johan Bengtsson-Palme
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The effect of Toll-like receptor stimulation on the motility of regulatory T cells.
Chodaczek G, Pagni PP, Christoffersson G, ..., Wegrzyn AS, von Herrath M
J. Autoimmun. 116 (-) 102563 [2021-01-00; online 2020-11-12]
Gustaf Christoffersson SciLifeLab Fellow
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Systems biology based drug repositioning for development of cancer therapy.
Turanli B, Altay O, Borén J, ..., Arga KY, Mardinoglu A
Semin. Cancer Biol. 68 (-) 47-58 [2021-01-00; online 2019-09-27]
Adil Mardinoglu SciLifeLab Fellow
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Proteomics-Informed Identification of Luminal Targets For In Situ Diagnosis of Inflammatory Bowel Disease.
Asad S, Wegler C, Ahl D, ..., Artursson P, Teleki A
J Pharm Sci 110 (1) 239-250 [2021-01-00; online 2020-11-04]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
News ways of understanding the complex biology of diabetes using PET.
Eriksson O, Långström B, Antoni G
Nucl. Med. Biol. 92 (-) 65-71 [2021-01-00; online 2020-04-27]
Olof Eriksson SciLifeLab Fellow
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Neuroimaging the menstrual cycle: A multimodal systematic review.
Dubol M, Epperson CN, Sacher J, ..., Sundström-Poromaa I, Comasco E
Front Neuroendocrinol 60 (-) 100878 [2021-01-00; online 2020-10-22]
Erika Comasco SciLifeLab Fellow
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JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality.
Stebbing J, Sánchez Nievas G, Falcone M, ..., Abizanda P, Lauschke VM
Sci Adv 7 (1) - [2021-01-00; online 2021-01-01]
Claudia Kutter SciLifeLab Fellow
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Ligand design by targeting a binding site water
Matricon P, Suresh RR, Gao ZG, ..., Jacobson KA, Carlsson J
Chem Sci 12 (3) 960-968 [2021-00-00; online 2021-00-00]
Jens Carlsson SciLifeLab Fellow
DOI Crossref
Investigation of the individual human sulfatome in plasma and urine samples reveals an age-dependency
Correia MSP, Thapa B, Vujasinovic M, Löhr JM, Globisch D
RSC Adv. 11 (55) 34788-34794 [2021-00-00; online 2021-00-00]
Daniel Globisch SciLifeLab Fellow
SciLifeLab Data Centre
Publications 9.5.1