Publications 2021

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Title Authors Journal Published Online
Accurate spliced alignment of long RNA sequencing reads Sahlin K, Mäkinen V Bioinformatics 37 (24) 4643-4651 2021-12-11 2021-07-24
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 2021-12-08
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 2021-12-08
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 2021-12-08
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 2021-11-18
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 2021-12-07
Proactive autoscaling for edge computing systems with kubernetes Ju L, Singh P, Toor S - - (-) - 2021-12-06 2022-02-07
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 2021-09-06
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 2021-10-31
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 2021-11-30
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 2021-05-10
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 2021-11-27
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 2021-11-26
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 2021-11-19
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 2021-11-17
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 2021-11-18
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 2021-09-13
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 2021-11-15
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 2021-11-11
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 2021-11-09
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 2021-09-16
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 2021-10-20
Effective sequence similarity detection with strobemers Sahlin K Genome Res. 31 (11) 2080-2094 2021-11-00 2021-10-19
Event-triggered STED imaging Alvelid J, Damenti M, Testa I - - (-) - 2021-10-28 2021-10-28
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 2021-10-28
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 2021-10-26
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 2021-10-25
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 2021-09-17
Diversity and ecology of protists revealed by metabarcoding. Burki F, Sandin MM, Jamy M Curr. Biol. 31 (19) R1267-R1280 2021-10-11 2021-10-13
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 2021-08-12
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 2021-10-04
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 2021-06-11
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 2021-12-16
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-10-26
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 2021-09-18
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 2021-10-25
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 2021-08-20
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 2021-09-24
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 2021-09-30
A method for intuitively extracting macromolecular dynamics from structural disorder Pearce NM, Gros P Nat Commun 12 (1) - 2021-09-17 2021-09-17
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 2021-09-15
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 2021-09-09
Selection on accessible chromatin regions in Capsella grandiflora. Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T Mol. Biol. Evol. - (-) - 2021-09-08 2021-09-08
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 2021-09-07
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 2021-09-06
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 2021-09-04
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 2021-07-12
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 2021-09-01
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 2021-09-08
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 2021-08-05
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 2021-08-31
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 2021-09-02
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 2021-08-30
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 2021-08-26
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 2021-06-06
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 2021-08-11
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 2021-08-16
ImSwitch: Generalizing microscope control in Python Moreno X, Al-Kadhimi S, Alvelid J, Bodén A, Testa I JOSS 6 (64) 3394 2021-08-14 2021-08-14
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 2021-08-12
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 2021-07-16
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 2021-06-11
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 2021-12-02
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 2021-07-22
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 2021-08-04
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 2020-11-01
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 2021-08-06
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 2020-04-19
Getting a grip with kirigami Teleki A, Artursson P Nat. Mater. 20 (8) 1043-1044 2021-08-00 2021-07-28
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 2021-07-07
ADP-ribosyltransferases, an update on function and nomenclature. Lüscher B, Ahel I, Altmeyer M, ..., Zaja R, Ziegler M FEBS J. - (-) - 2021-07-29 2021-07-29
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 2021-07-28
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 2020-09-05
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 2021-07-22
Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis. Kundu S, Ali MA, Handin N, ..., Globisch D, Sjöblom T J. Exp. Clin. Cancer Res. 40 (1) 225 2021-07-07 2021-07-07
iNetModels 2.0: an interactive visualization and database of multi-omics data. Arif M, Zhang C, Li X, ..., Uhlen M, Mardinoglu A Nucleic Acids Res. 49 (W1) W271-W276 2021-07-02 2021-04-14
The Effect of the Molecular Weight of Polyvinylpyrrolidone and the Model Drug on Laser-Induced In Situ Amorphization Hempel NJ, Merkl P, Knopp MM, ..., Sotiriou GA, Löbmann K Molecules 26 (13) 4035 2021-07-01 2021-07-01
CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells Geng K, Merino LG, Wedemann L, ..., White RJ, Kutter C - - (-) - 2021-07-01 2021-07-01
Simultaneous detection of SARS-CoV-2 and pandemic (H1N1) 2009 virus with real-time isothermal platform. Yu L, Wang J, Li X, ..., Guo X, Yin X Heliyon 7 (7) e07584 2021-07-00 2021-07-15
Safety Assessments of Nickel Boride Nanoparticles on the Human Pulmonary Alveolar Cells by Using Cell Viability and Gene Expression Analyses. Türkez H, Arslan ME, Sönmez E, ..., Açikyildiz M, Mardinoğlu A Biol Trace Elem Res 199 (7) 2602-2611 2021-07-00 2020-09-09
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 2021-04-12
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 2021-04-02
On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae). Bachmann JA, Tedder A, Fracassetti M, ..., Köhler C, Slotte T Heredity (Edinb) 127 (1) 124-134 2021-07-00 2021-04-19
Molecular Dynamics Simulations of Ion Channels. Carnevale V, Delemotte L, Howard RJ Trends Biochem. Sci. 46 (7) 621-622 2021-07-00 2021-04-30
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 2021-03-10
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 2021-04-29
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 2021-06-30
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 2021-02-11
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 2021-06-23
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 2021-06-21
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 2021-03-31
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 2021-06-17
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 2021-06-16
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 2021-05-05
Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis. Chen ZQ, Zan Y, Milesi P, ..., Lascoux M, Wu HX Genome Biol. 22 (1) 179 2021-06-13 2021-06-13
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 2021-05-05
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 2021-06-03
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 2020-10-23
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 2021-05-19
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 2020-09-07
More Than Just Letters and Chemistry: Genomics Goes Mechanics. Deindl S, Elf J Trends Biochem. Sci. 46 (6) 431-432 2021-06-00 2021-04-12
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 2021-05-06
Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source. Douangamath A, Powell A, Fearon D, ..., Gorrie-Stone T, von Delft F J Vis Exp - (171) - 2021-05-29 2021-05-29
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 2021-05-28
Perivascular Macrophages Regulate Blood Flow Following Tissue Damage. Vågesjö E, Parv K, Ahl D, ..., Christoffersson G, Phillipson M Circ. Res. 128 (11) 1694-1707 2021-05-28 2021-04-21
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 2021-05-25
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 2021-05-19
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 2021-05-25
Microbial Community Interactions Are Sensitive to Small Changes in Temperature. Burman E, Bengtsson-Palme J Front Microbiol 12 (-) 672910 2021-05-21 2021-05-21
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 2020-12-23
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 - - (-) - 2021-05-17 2021-05-17
Phylogenomic Insights into the Origin of Primary Plastids. Irisarri I, Strassert JFH, Burki F Syst. Biol. - (-) - 2021-05-14 2021-05-14
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 2021-05-14
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 2021-05-13
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 2021-05-12
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 2021-05-11
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 2021-03-20
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 2021-05-05
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 2021-05-04
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 2021-04-10
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 2021-01-11
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 2021-03-17
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 2021-05-13
The Protein Quality Control Network in Caulobacter crescentus. Schroeder K, Jonas K Front Mol Biosci 8 (-) 682967 2021-04-30 2021-04-30
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 2021-05-05
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 2021-04-28
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 2021-04-14
Scalable machine learning-assisted model exploration and inference using Sciope. Singh P, Wrede F, Hellander A Bioinformatics 37 (2) 279-281 2021-04-19 2020-07-25
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 2021-03-29
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 2021-02-24
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 2021-04-12
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 2021-03-09
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 2021-02-04
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 -
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 2020-11-12
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 2020-11-09
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 2021-03-25
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 2020-03-24
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 2021-03-19
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 2021-03-19
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 2021-03-08
ZFP207 <i>controls pluripotency by multiple post-transcriptional mechanisms</i> Malla S, Bhattarai DP, Melguizo-Sanchis D, ..., Kutter C, Aguilo F - - (-) - 2021-03-02 2021-03-02
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 2021-03-01
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 2021-01-06
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 2021-03-00
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 2020-08-29
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 2021-03-00
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 2021-02-24
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 2021-02-08
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 2021-02-22
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 2020-12-16
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 2021-02-24
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 2020-12-31
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 2021-01-11
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 2020-08-03
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 2021-02-11
Epithelial inflammasomes in the defense against Salmonella gut infection. Fattinger SA, Sellin ME, Hardt WD Curr Opin Microbiol 59 (-) 86-94 2021-02-00 2020-10-28
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 2021-02-00
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 2020-10-09
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 2021-02-00
<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 2020-11-10
Epidemiological modeling in StochSS Live! Jiang R, Jacob B, Geiger M, ..., Hellander A, Petzold L Bioinformatics - (-) - 2021-01-29 2021-01-29
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 2021-01-28
Cellocity: A Python package for analysis of confluent cell layer dynamics Eriksson J, Styrström D, Sellin M JOSS 6 (57) 2818 2021-01-28 2021-01-28
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 2021-01-19
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 2021-01-19
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 2021-01-18
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 2021-01-14
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 2021-01-12
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 2020-12-18
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 2021-01-04
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 2021-01-04
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 2021-01-04
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 2020-11-12
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 2019-09-27
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 2020-11-04
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 2020-04-27
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 2020-10-22
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 2021-01-01
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 2021-00-00
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 2021-00-00
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