Publications 2021

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192 publications

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
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]
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
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
Biophysical Journal 121 (1) 11-22 [2021-12-07; online 2021-12-07]
Lucie Delemotte SciLifeLab Fellow
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
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
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
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. - (-) 112431 [2021-11-27; online 2021-11-27]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Tumorigenic activity of alternative per- and polyfluoroalkyl substances (PFAS): Mechanistic in vitro studies.
Pierozan P, Cattani D, Karlsson O
Sci. Total Environ. - (-) 151945 [2021-11-26; online 2021-11-26]
Oskar Karlsson SciLifeLab Fellow
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
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
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
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
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
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
DOI Crossref
Event-triggered STED imaging
Alvelid J, Damenti M, Testa I
- - (-) - [2021-10-28; online 2021-10-28]
Ilaria Testa 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
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]
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
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
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
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
DOI Crossref
Nanoengineered DNA origami with repurposed TOP1 inhibitors targeting myeloid cells for the mitigation of neuroinflammation
Zhu K, Wang Y, Sarlus H, ..., Högberg B, Harris RA
- - (-) - [2021-10-04; online 2021-10-04]
Claudia Kutter SciLifeLab Fellow
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
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
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) - [2021-10-00; online 2021-10-25]
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
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
DOI Crossref
Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain
Chi G, Liang Q, Srid A, ..., Covarrubias M, Duerr K
- - (-) - [2021-09-09; online 2021-09-09]
Lucie Delemotte 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
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. - (-) - [2021-09-04; online 2021-09-04]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
The long-time orphan protist Meringosphaera mediterranea Lohmann, 1902 [1903] is a centrohelid heliozoan.
Zlatogursky VV, Shɨshkin Y, Drachko D, Burki F
J. Eukaryot. Microbiol. 68 (5) e12860 [2021-09-00; online 2021-07-12]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
RecA finds homologous DNA by reduced dimensionality search.
Wiktor J, Gynnå AH, Leroy P, ..., Testa I, Elf J
Nature 597 (7876) 426-429 [2021-09-00; online 2021-09-01]
Ilaria Testa SciLifeLab Fellow
PubMed DOI Crossref
Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia.
Draper-Joyce CJ, Bhola R, Wang J, ..., Imlach WL, Christopoulos A
Nature 597 (7877) 571-576 [2021-09-00; online 2021-09-08]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
Killing two enemies with one stone? Genomics of resistance to two sympatric pathogens in Norway spruce.
Capador-Barreto HD, Bernhardsson C, Milesi P, ..., Stenlid J, Elfstrand M
Mol. Ecol. 30 (18) 4433-4447 [2021-09-00; online 2021-08-05]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies.
Ezzamouri B, Shoaie S, Ledesma-Amaro R
Front Microbiol 12 (-) 681982 [2021-08-31; online 2021-08-31]
Saeed Shoaie SciLifeLab Fellow
PubMed DOI Crossref
Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A.
Allen GE, Panasenko OO, Villanyi Z, ..., Ignatova Z, Collart MA
Cell Reports 36 (9) 109633 [2021-08-31; online 2021-09-02]
SciLifeLab Fellow Vicent Pelechano
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 PP (-) - [2021-08-30; online 2021-08-30]
Prashant Singh SciLifeLab Fellow
DOI Crossref
Enterotoxigenic Escherichia coli display a distinct growth phase before entry into stationary phase with shifts in tryptophan- fucose- and putrescine metabolism and degradation of neurotransmitter precursors
Joffré E, Xiao X, Correia MSP, ..., Zhu B, Sjöling Å
- - (-) - [2021-08-26; online 2021-08-26]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Structure and Sequence-based Computational Approaches to Allosteric Signal Transduction: Application to Electromechanical Coupling in Voltage-gated Ion Channels.
Elbahnsi A, Delemotte L
J. Mol. Biol. 433 (17) 167095 [2021-08-20; online 2021-06-06]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Functional cross-talk between phosphorylation and disease-causing mutations in the cardiac sodium channel Nav1.5.
Galleano I, Harms H, Choudhury K, ..., Delemotte L, Pless SA
Proc. Natl. Acad. Sci. U.S.A. 118 (33) - [2021-08-17; online 2021-08-11]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Advances in the Relationships Between Cow's Milk Protein Allergy and Gut Microbiota in Infants.
Yang Y, Li X, Yang Y, ..., Ji B, Wei Y
Front Microbiol 12 (-) 716667 [2021-08-16; online 2021-08-16]
Saeed Shoaie SciLifeLab Fellow
DOI Crossref
ImSwitch: Generalizing microscope control in Python
Moreno X, Al-Kadhimi S, Alvelid J, Bodén A, Testa I
JOSS 6 (64) 3394 [2021-08-14; online 2021-08-14]
Ilaria Testa SciLifeLab Fellow
PubMed DOI Crossref
Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.
Martin G, Rissanen AJ, Garcia SL, ..., Buck M, Peura S
Front Microbiol 12 (-) 669937 [2021-08-12; online 2021-08-12]
Sarahi Garcia SciLifeLab Fellow
PubMed DOI Crossref
Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology.
Kampen S, Duy Vo D, Zhang X, ..., Kihlberg J, Carlsson J
Angew. Chem. Int. Ed. Engl. 60 (33) 18022-18030 [2021-08-09; online 2021-07-16]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
Sample-to-answer COVID-19 nucleic acid testing using a low-cost centrifugal microfluidic platform with bead-based signal enhancement and smartphone read-out.
Soares RRG, Akhtar AS, Pinto IF, ..., Pelechano V, Russom A
Lab Chip 21 (15) 2932-2944 [2021-08-07; online 2021-06-11]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Genome assemblies of three closely related leaf beetle species (Galerucella spp.).
Yang X, Slotte T, Dainat J, Hambäck PA
G3 11 (8) - [2021-08-07; online 2021-12-02]
SciLifeLab Fellow Tanja Slotte
DOI Crossref
Microbial retention and resistances in stormwater quality improvement devices treating road runoff
Liguori R, Rommel SH, Bengtsson-Palme J, Helmreich B, Wurzbacher C
FEMS Microbes 2 (-) - [2021-08-03; online 2021-07-22]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.
Kanellis DC, Espinoza JA, Zisi A, ..., Lindström MS, Bartek J
Sci Adv 7 (32) - [2021-08-00; online 2021-08-04]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.
Garrido-Godino AI, Gupta I, Gutiérrez-Santiago F, ..., Pelechano V, Navarro F
RNA Biol 18 (8) 1206-1220 [2021-08-00; online 2020-11-01]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.
Tice AK, Žihala D, Pánek T, ..., Kolísko M, Brown MW
PLoS Biol. 19 (8) e3001365 [2021-08-00; online 2021-08-06]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
In vitro neuroprotective effects of farnesene sesquiterpene on alzheimer's disease model of differentiated neuroblastoma cell line.
Arslan ME, Türkez H, Mardinoğlu A
Int J Neurosci 131 (8) 745-754 [2021-08-00; online 2020-04-19]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Getting a grip with kirigami
Teleki A, Artursson P
Nat. Mater. 20 (8) 1043-1044 [2021-08-00; online 2021-07-28]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Aggregation and mobility of membrane proteins interplay with local lipid order in the plasma membrane of T cells.
Urbančič I, Schiffelers L, Jenkins E, ..., Sezgin E, Eggeling C
FEBS Lett. 595 (16) 2127-2146 [2021-08-00; online 2021-07-07]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
ADP-ribosyltransferases, an update on function and nomenclature.
Lüscher B, Ahel I, Altmeyer M, ..., Zaja R, Ziegler M
FEBS J. - (-) - [2021-07-29; online 2021-07-29]
SciLifeLab Fellow Sebastian Deindl
PubMed DOI Crossref
DNA methylation of Vesicular Glutamate Transporters in the mesocorticolimbic brain following early-life stress and adult ethanol exposure-an explorative study.
Vrettou M, Yan L, Nilsson KW, ..., Nylander I, Comasco E
Sci Rep 11 (1) 15322 [2021-07-28; online 2021-07-28]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Anticancer effects of novel NSAIDs derivatives on cultured human glioblastoma cells.
Özdemir Ö, Marinelli L, Cacciatore I, ..., Mardinoglu A, Turkez H
Z Naturforsch C J Biosci 76 (7-8) 329-335 [2021-07-27; online 2020-09-05]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Differential regulation of oxidative stress, microbiota-derived, and energy metabolites in the mouse brain during sleep.
Vallianatou T, Lin W, Bèchet NB, ..., Lundgaard I, Globisch D
J. Cereb. Blood Flow Metab. - (-) 271678X211033358 [2021-07-22; online 2021-07-22]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.
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J. Exp. Clin. Cancer Res. 40 (1) 225 [2021-07-07; online 2021-07-07]
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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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Geng K, Merino LG, Wedemann L, ..., White RJ, Kutter C
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Yu L, Wang J, Li X, ..., Guo X, Yin X
Heliyon 7 (7) e07584 [2021-07-00; online 2021-07-15]
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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.
Damenti M, Coceano G, Pennacchietti F, Bodén A, Testa I
Neurobiol. Dis. 155 (-) 105361 [2021-07-00; online 2021-04-12]
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Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.
Kubik S, Marques AC, Xing X, ..., Willig A, Xu Z
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).
Bachmann JA, Tedder A, Fracassetti M, ..., Köhler C, Slotte T
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Molecular Dynamics Simulations of Ion Channels.
Carnevale V, Delemotte L, Howard RJ
Trends Biochem. Sci. 46 (7) 621-622 [2021-07-00; online 2021-04-30]
Lucie Delemotte 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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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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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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Pesticide-induced multigenerational effects on amphibian reproduction and metabolism.
Karlsson O, Svanholm S, Eriksson A, ..., Jernerén F, Berg C
Sci. Total Environ. 775 (-) 145771 [2021-06-25; online 2021-02-11]
Oskar Karlsson SciLifeLab Fellow
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Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators.
Jiang RM, Wrede F, Singh P, Hellander A, Petzold LR
BMC Bioinformatics 22 (1) 339 [2021-06-23; online 2021-06-23]
Prashant Singh SciLifeLab Fellow
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The Influence of Drug–Polymer Solubility on Laser-Induced In Situ Drug Amorphization Using Photothermal Plasmonic Nanoparticles
Hempel NJ, Merkl P, Knopp MM, ..., Sotiriou GA, Löbmann K
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.
Zhang Y, Pelechano V
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?
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Front Immunol 12 (-) 683091 [2021-06-16; online 2021-06-16]
Gustaf Christoffersson SciLifeLab 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
Hempel NJ, Merkl P, Asad S, ..., Sotiriou GA, Löbmann K
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]
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More Than Just Letters and Chemistry: Genomics Goes Mechanics.
Deindl S, Elf J
Trends Biochem. Sci. 46 (6) 431-432 [2021-06-00; online 2021-04-12]
SciLifeLab Fellow Sebastian Deindl
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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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DDLS Fellow Nicholas Pearce
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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]
SciLifeLab Fellow Vicent Pelechano
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Perivascular Macrophages Regulate Blood Flow Following Tissue Damage.
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Circ. Res. 128 (11) 1694-1707 [2021-05-28; online 2021-04-21]
Gustaf Christoffersson SciLifeLab Fellow
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Phagocytosis and Efferocytosis by Resident Macrophages in the Mouse Pancreas.
Parv K, Westerlund N, Merchant K, ..., Lindsay RS, Christoffersson G
Front Endocrinol (Lausanne) 12 (-) 606175 [2021-05-25; online 2021-05-25]
Gustaf Christoffersson SciLifeLab Fellow
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Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.
Bohutínská M, Vlček J, Yair S, ..., Slotte T, Kolář F
Proc. Natl. Acad. Sci. U.S.A. 118 (21) - [2021-05-25; online 2021-05-19]
SciLifeLab Fellow Tanja Slotte
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A combined approach for single-cell mRNA and intracellular protein expression analysis.
Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ
Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]
Marc Friedländer SciLifeLab Fellow
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Microbial Community Interactions Are Sensitive to Small Changes in Temperature.
Burman E, Bengtsson-Palme J
Front Microbiol 12 (-) 672910 [2021-05-21; online 2021-05-21]
DDLS Fellow Johan Bengtsson-Palme
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The human exposome and health in the Anthropocene.
Karlsson O, Rocklöv J, Lehoux AP, ..., Blunt MJ, Birnbaum LS
Int J Epidemiol 50 (2) 378-389 [2021-05-17; online 2020-12-23]
Oskar Karlsson SciLifeLab Fellow
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A pipeline for systematic comparison of model levels and parameter inference settings applied to negative feedback gene regulation
Coulier A, Singh P, Sturrock M, Hellander A
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Prashant Singh SciLifeLab Fellow
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Phylogenomic Insights into the Origin of Primary Plastids.
Irisarri I, Strassert JFH, Burki F
Syst. Biol. - (-) - [2021-05-14; online 2021-05-14]
Fabien Burki SciLifeLab Fellow
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Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.
Buck M, Garcia SL, Fernandez L, ..., Bertilsson S, Peura S
Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]
Sarahi Garcia SciLifeLab Fellow
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Informing Pharmacokinetic Models With Physiological Data: Oral Population Modeling of L-Serine in Humans.
Bosley JR, Björnson E, Zhang C, ..., Borén J, Mardinoglu A
Front. Pharmacol. 12 (-) 643179 [2021-05-13; online 2021-05-13]
Adil Mardinoglu SciLifeLab Fellow
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Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
Kang D, Shoaie S, Jacquiod S, Sørensen SJ, Ledesma-Amaro R
Microorganisms 9 (5) 1042 [2021-05-12; online 2021-05-12]
Saeed Shoaie SciLifeLab Fellow
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Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.
Garcia SL, Mehrshad M, Buck M, ..., Greening C, Peura S
mSystems 6 (3) - [2021-05-11; online 2021-05-11]
Sarahi Garcia SciLifeLab Fellow
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The Genomic Architecture and Evolutionary Fates of Supergenes.
Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-20]
SciLifeLab Fellow Tanja Slotte
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Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition.
Espeso-Gil S, Holik AZ, Bonnin S, ..., Hor CN, Ossowski S
Front Mol Neurosci 14 (-) 664912 [2021-05-05; online 2021-05-05]
Marc Friedländer SciLifeLab Fellow
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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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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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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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Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
Kapla J, Rodríguez-Espigares I, Ballante F, Selent J, Carlsson J
PLoS Comput Biol 17 (5) e1008936 [2021-05-00; online 2021-05-13]
Jens Carlsson SciLifeLab Fellow
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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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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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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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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
Zhang Y, Pelechano V
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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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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ZFP207 <i>controls pluripotency by multiple post-transcriptional mechanisms</i>
Malla S, Bhattarai DP, Melguizo-Sanchis D, ..., Kutter C, Aguilo F
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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
AJP 178 (3) 256-265 [2021-03-01; online 2021-03-01]
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
DOI Crossref
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
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The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis
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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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
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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
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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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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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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
PubMed DOI Crossref
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
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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
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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
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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
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<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
PubMed DOI Crossref
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
DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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
PubMed DOI Crossref
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

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