Peer-reviewed articles and conference proceedings

Listed in Europe PMC, latest update: 2021-04-27.
Discover the SIB Remarkable Outputs 2020

In 2020, the SIB Remarkable Outputs were launched to provide the global bioinformatics community with the 'must-reads' of the year by SIB Scientists. See here the last selection. The next edition of the SIB remarkable Output will be announced early next year.

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  1. Ahluwalia TS, Prins BP, Abdollahi M, Armstrong NJ, Aslibekyan S, Bain L, Jefferis B, Baumert J, Beekman M, Ben-Shlomo Y, Bis JC, Mitchell BD, de Geus E, Delgado GE, Marek D, Eriksson J, Kajantie E, Kanoni S, Kemp JP, Lu C, Marioni RE, McLachlan S, Milaneschi Y, Nolte IM, Petrelis AM, Porcu E, Sabater-Lleal M, Naderi E, Seppälä I, Shah T, Singhal G, Standl M, Teumer A, Thalamuthu A, Thiering E, Trompet S, Ballantyne CM, Benjamin EJ, Casas JP, Toben C, Dedoussis G, Deelen J, Durda P, Engmann J, Feitosa MF, Grallert H, Hammarstedt A, Harris SE, Homuth G, Hottenga JJ, Jalkanen S, Jamshidi Y, Jawahar MC, Jess T, Kivimaki M, Kleber ME, Lahti J, Liu Y, Marques-Vidal P, Mellström D, Mooijaart SP, Müller-Nurasyid M, Penninx B, Revez JA, Rossing P, Räikkönen K, Sattar N, Scharnagl H, Sennblad B, Silveira A, Pourcain BS, Timpson NJ, Trollor J, CHARGE Inflammation Working Group, van Dongen J, Van Heemst D, Visvikis-Siest S, Vollenweider P, Völker U, Waldenberger M, Willemsen G, Zabaneh D, Morris RW, Arnett DK, Baune BT, Boomsma DI, Chang YC, Deary IJ, Deloukas P, Eriksson JG, Evans DM, Ferreira MA, Gaunt T, Gudnason V, Hamsten A, Heinrich J, Hingorani A, Humphries SE, Jukema JW, Koeing W, Kumari M, Kutalik Z, Lawlor DA, Lehtimäki T, März W, Mather K, Naitza S, Nauck M, Ohlsson C, Price JF, Raitakari O, Rice K, Sachdev PS, Slagboom E, Sørensen TIA, Spector T, Stacey D, Stathopoulou MG, Tanaka T, Wannamethee SG, Whincup P, Rotter JI, Dehghan A, Boerwinkle E, Psaty BM, Snieder H, Alizadeh BZ. Genome-Wide Association Study of Circulating Interleukin 6 Levels Identifies Novel Loci. Hum Mol Genet 2021
  2. Altenhoff AM, Train CM, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova HS, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C. OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. Nucleic Acids Res 2021;49(d1):D373-D379
  3. Ancey PB, Contat C, Boivin G, Sabatino S, Pascual J, Zangger N, Perentes JY, Peters S, Abel ED, Kirsch DG, Rathmell JC, Vozenin MC, Meylan E. Glut1 expression in tumor-associated neutrophils promotes lung cancer growth and resistance to radiotherapy. Cancer Res 2021
  4. Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett KS, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik MF, Henaff E, Huch M, Iliev ID, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez MA, Miura K, Molloy J, Cruz AO, Platt RJ, Posey AD, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe LH, Varshney RK, Wang J. Voices of biotech research. Nat Biotechnol 2021;39(3):281-286
  5. Antonarakis SE, Holoubek A, Rapti M, Rademaker J, Meylan J, Iwaszkiewicz J, Zoete V, Wilson C, Taylor J, Ansar M, Borel C, Menzel O, Kuželová K, Santoni FA. Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2. Hum Mol Genet 2021
  6. Arguello JR, Abuin L, Armida J, Mika K, Chai PC, Benton R. Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. Elife 2021;10
  7. Armstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, Kang JTL, Redondo SA, Prost S, Barsh G, Kaelin C, Phalke S, Chugani A, Gilbert M, Miquelle D, Zachariah A, Borthakur U, Reddy A, Louis E, Ryder OA, Jhala YV, Petrov D, Excoffier L, Hadly E, Ramakrishnan U. Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. Mol Biol Evol 2021
  8. Bakker MK, van der Spek RAA, van Rheenen W, Morel S, Bourcier R, Hostettler IC, Alg VS, van Eijk KR, Koido M, Akiyama M, Terao C, Matsuda K, Walters RG, Lin K, Li L, Millwood IY, Chen Z, Rouleau GA, Zhou S, Rannikmäe K, Sudlow CLM, Houlden H, van den Berg LH, Dina C, Naggara O, Gentric JC, Shotar E, Eugène F, Desal H, Winsvold BS, Børte S, Johnsen MB, Brumpton BM, Sandvei MS, Willer CJ, Hveem K, Zwart JA, Verschuren WMM, Friedrich CM, Hirsch S, Schilling S, Dauvillier J, Martin O, HUNT All-In Stroke, China Kadoorie Biobank Collaborative Group, BioBank Japan Project Consortium, ICAN Study Group, CADISP Group, Genetics and Observational Subarachnoid Haemorrhage (GOSH) Study investigators, International Stroke Genetics Consortium (ISGC), Jones GT, Bown MJ, Ko NU, Kim H, Coleman JRI, Breen G, Zaroff JG, Klijn CJM, Malik R, Dichgans M, Sargurupremraj M, Tatlisumak T, Amouyel P, Debette S, Rinkel GJE, Worrall BB, Pera J, Slowik A, Gaál-Paavola EI, Niemelä M, Jääskeläinen JE, von Und Zu Fraunberg M, Lindgren A, Broderick JP, Werring DJ, Woo D, Redon R, Bijlenga P, Kamatani Y, Veldink JH, Ruigrok YM. Author Correction: Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors. Nat Genet 2021;53(2):254
  9. Barrat-Charlaix P, Huddleston J, Bedford T, Neher RA. Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses. Mol Biol Evol 2021
  10. Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, de Farias TM, Moretti S, Parmentier G, de Laval VR, Rosikiewicz M, Wollbrett J, Echchiki A, Escoriza A, Gharib WH, Gonzales-Porta M, Jarosz Y, Laurenczy B, Moret P, Person E, Roelli P, Sanjeev K, Seppey M, Robinson-Rechavi M. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Res 2021;49(d1):D831-D847
  11. Begum T, Robinson-Rechavi M. Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes. Mol Biol Evol 2021;38(4):1614-1626
  12. Benet S, Gálvez C, Drobniewski F, Kontsevaya I, Arias L, Monguió-Tortajada M, Erkizia I, Urrea V, Ong RY, Luquin M, Dupont M, Chojnacki J, Dalmau J, Cardona P, Neyrolles O, Lugo-Villarino G, Vérollet C, Julián E, Furrer H, Günthard HF, Crocker PR, Tapia G, Borràs FE, Fellay J, McLaren PJ, Telenti A, Cardona PJ, Clotet B, Vilaplana C, Martinez-Picado J, Izquierdo-Useros N. Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles. J Extracell Vesicles 2021;10(3):e12046
  13. Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 2021;49(d1):D344-D354
  14. Bock C, Moor M, Jutzeler CR, Borgwardt K. Machine Learning for Biomedical Time Series Classification: From Shapelets to Deep Learning. Methods Mol Biol 2021;2190:33-71
  15. Bonnardel F, Mariethoz J, Pérez S, Imberty A, Lisacek F. LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. Nucleic Acids Res 2021;49(d1):D1548-D1554
  16. Börsch A, Ham DJ, Mittal N, Tintignac LA, Migliavacca E, Feige JN, Rüegg MA, Zavolan M. Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Commun Biol 2021;4(1):194
  17. Bourguignon L, Vo AK, Tong B, Geisler F, Mach O, Maier D, Kramer J, Grassner L, Jutzeler CR. Natural Progression of Routine Laboratory Markers following Spinal Trauma: A longitudinal, multi-cohort study. J Neurotrauma 2021
  18. Buetti-Dinh A, Ruinelli M, Czerski D, Scapozza C, Martignier A, Roman S, Caminada A, Tonolla M. Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps. PLoS One 2021;16(3):e0248877
  19. Burton-Pimentel KJ, Pimentel G, Hughes M, Michielsen CC, Fatima A, Vionnet N, Afman LA, Roche HM, Brennan L, Ibberson M, Vergères G. Discriminating Dietary Responses by Combining Transcriptomics and Metabolomics Data in Nutrition Intervention Studies. Mol Nutr Food Res 2021;65(4):e2000647
  20. Cachot A, Bilous M, Liu YC, Li X, Saillard M, Cenerenti M, Rockinger GA, Wyss T, Guillaume P, Schmidt J, Genolet R, Ercolano G, Protti MP, Reith W, Ioannidou K, de Leval L, Trapani JA, Coukos G, Harari A, Speiser DE, Mathis A, Gfeller D, Altug H, Romero P, Jandus C. Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer. Sci Adv 2021;7(9)
  21. Carmeli C, Kutalik Z, Mishra PP, Porcu E, Delpierre C, Delaneau O, Kelly-Irving M, Bochud M, Dhayat NA, Ponte B, Pruijm M, Ehret G, Kähönen M, Lehtimäki T, Raitakari OT, Vineis P, Kivimäki M, Chadeau-Hyam M, Dermitzakis E, Vuilleumier N, Stringhini S. Gene regulation contributes to explain the impact of early life socioeconomic disadvantage on adult inflammatory levels in two cohort studies. Sci Rep 2021;11(1):3100
  22. Cavallaro M, Walsh MD, Jones M, Teahan J, Tiberi S, Finkenstädt B, Hebenstreit D. 3 '-5 ' crosstalk contributes to transcriptional bursting. Genome Biol 2021;22(1):56
  23. Chen Y, Xu K, Piccoli L, Foglierini M, Tan J, Jin W, Gorman J, Tsybovsky Y, Zhang B, Traore B, Silacci-Fregni C, Daubenberger C, Crompton PD, Geiger R, Sallusto F, Kwong PD, Lanzavecchia A. Structural basis of malaria RIFIN binding by LILRB1-containing antibodies. Nature 2021;592(7855):639-643
  24. Choin J, Mendoza-Revilla J, Arauna LR, Cuadros-Espinoza S, Cassar O, Larena M, Ko AM, Harmant C, Laurent R, Verdu P, Laval G, Boland A, Olaso R, Deleuze JF, Valentin F, Ko YC, Jakobsson M, Gessain A, Excoffier L, Stoneking M, Patin E, Quintana-Murci L. Genomic insights into population history and biological adaptation in Oceania. Nature 2021;592(7855):583-589
  25. Dasmeh P, Wagner A. Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution. Mol Biol Evol 2021;38(3):940-951
  26. de Jonge K, Tillé L, Lourenco J, Maby-El Hajjami H, Nassiri S, Racle J, Gfeller D, Delorenzi M, Verdeil G, Baumgaertner P, Speiser DE. Inflammatory B cells correlate with failure to checkpoint blockade in melanoma patients. Oncoimmunology 2021;10(1):1873585
  27. de Vries JJC, Brown JR, Couto N, Beer M, Le Mercier P, Sidorov I, Papa A, Fischer N, Oude Munnink BB, Rodriquez C, Zaheri M, Sayiner A, Hönemann M, Cataluna AP, Carbo EC, Bachofen C, Kubacki J, Schmitz D, Tsioka K, Matamoros S, Höper D, Hernandez M, Puchhammer-Stöckl E, Lebrand A, Huber M, Simmonds P, Claas ECJ, López-Labrador FX, ESCV Network on Next-Generation Sequencing. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. J Clin Virol 2021;138:104812
  28. Defosset A, Kress A, Nevers Y, Ripp R, Thompson JD, Poch O, Lecompte O. Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR. Genome Biol Evol 2021;13(1)
  29. Deibel A, Deng L, Cheng CY, Schlander M, Ran T, Lang B, Krupka N, Beerenwinkel N, Rogler G, Wiest R, Sonnenberg A, Poleszczuk J, Misselwitz B. Evaluating key characteristics of ideal colorectal cancer screening modalities: the microsimulation approach. Gastrointest Endosc 2021
  30. Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021;9:e10911
  31. Dmitrijeva M, Kahlert CR, Feigelman R, Kleiner RL, Nolte O, Albrich WC, Baty F, von Mering C. Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis. mBio 2021;12(2)
  32. Duvaud S, Gabella C, Lisacek F, Stockinger H, Ioannidis V, Durinx C. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. Nucleic Acids Res 2021
  33. Dyrdak R, Hodcroft EB, Wahlund M, Neher RA, Albert J. Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020. J Clin Virol 2021;136:104754
  34. Fall A, Elawar F, Hodcroft EB, Jallow MM, Toure CT, Barry MA, Kiori DE, Sy S, Diaw Y, Goudiaby D, Niang MN, Dia N. Genetic diversity and evolutionary dynamics of respiratory syncytial virus over eleven consecutive years of surveillance in Senegal. Infect Genet Evol 2021:104864
  35. Feron R, Pan Q, Wen M, Imarazene B, Jouanno E, Anderson J, Herpin A, Journot L, Parrinello H, Klopp C, Kottler VA, Roco AS, Du K, Kneitz S, Adolfi M, Wilson CA, McCluskey B, Amores A, Desvignes T, Goetz FW, Takanashi A, Kawaguchi M, Detrich HW, Oliveira MA, Nóbrega RH, Sakamoto T, Nakamoto M, Wargelius A, Karlsen Ø, Wang Z, Stöck M, Waterhouse RM, Braasch I, Postlethwait JH, Schartl M, Guiguen Y. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data. Mol Ecol Resour 2021
  36. Feuermann M, Boutet E, Morgat A, Axelsen KB, Bansal P, Bolleman J, de Castro E, Coudert E, Gasteiger E, Géhant S, Lieberherr D, Lombardot T, Neto TB, Pedruzzi I, Poux S, Pozzato M, Redaschi N, Bridge A, On Behalf Of The UniProt Consortium. Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. Metabolites 2021;11(1)
  37. Fofonjka A, Milinkovitch MC. Reaction-diffusion in a growing 3D domain of skin scales generates a discrete cellular automaton. Nat Commun 2021;12(1):2433
  38. Forlani G, Michaux J, Pak H, Huber F, Marie Joseph EL, Ramia E, Stevenson BJ, Linnebacher M, Accolla RS, Bassani-Sternberg M. CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens. Mol Cell Proteomics 2021;20:100032
  39. Fossati A, Li C, Uliana F, Wendt F, Frommelt F, Sykacek P, Heusel M, Hallal M, Bludau I, Capraz T, Xue P, Song J, Wollscheid B, Purcell AW, Gstaiger M, Aebersold R. PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nat Methods 2021
  40. Gerber S, Schratt G, Germain PL. Streamlining differential exon and 3' UTR usage with diffUTR. BMC Bioinformatics 2021;22(1):189
  41. Ghisoni E, Wicky A, Bouchaab H, Imbimbo M, Delyon J, Gautron Moura B, Gérard CL, Latifyan S, Özdemir BC, Caikovski M, Pradervand S, Tavazzi E, Gatta R, Marandino L, Valabrega G, Aglietta M, Obeid M, Homicsko K, Mederos Alfonso NN, Zimmermann S, Coukos G, Peters S, Cuendet MA, Di Maio M, Michielin O. Late-onset and long-lasting immune-related adverse events from immune checkpoint-inhibitors: An overlooked aspect in immunotherapy. Eur J Cancer 2021;149:153-164
  42. Ghosh S, Börsch A, Ghosh S, Zavolan M. The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. BMC Genomics 2021;22(1):238
  43. Glover N, Sheppard S, Dessimoz C. Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs. Genome Biol Evol 2021
  44. Gollub MG, Kaltenbach HM, Stelling J. Probabilistic Thermodynamic Analysis of Metabolic Networks. Bioinformatics 2021
  45. Gómez HF, Hodel L, Michos O, Iber D. Morphological study of embryonic Chd8+/- mouse brains using light-sheet microscopy. BMC Res Notes 2021;14(1):23
  46. Gumbsch T, Borgwardt K. Ethnicity-based bias in clinical severity scores. Lancet Digit Health 2021;3(4):e209-e210
  47. Gumpinger AC, Rieck B, Grimm DG, International Headache Genetics Consortium, Borgwardt K. Network-guided search for genetic heterogeneity between gene pairs. Bioinformatics 2021;37(1):57-65
  48. Hadziselimovic F, Verkauskas G, Stadler MB. Molecular clues in the regulation of mini-puberty involve neuronal DNA binding transcription factor NHLH2. Basic Clin Androl 2021;31(1):6
  49. Harrington L, Alexander LT, Knapp S, Bayley H. Nanopore Enzymology to Study Protein Kinases and Their Inhibition by Small Molecules. Methods Mol Biol 2021;2186:95-114
  50. Hartmann JE, Albrich WC, Dmitrijeva M, Kahlert CR. The Effects of Corticosteroids on the Respiratory Microbiome: A Systematic Review. Front Med (Lausanne) 2021;8:588584
  51. Hoffmann MD, Mathony J, Upmeier Zu Belzen J, Harteveld Z, Aschenbrenner S, Stengl C, Grimm D, Correia BE, Eils R, Niopek D. Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein. Nucleic Acids Res 2021;49(5):e29
  52. Hu M, Cebola I, Carrat G, Jiang S, Nawaz S, Khamis A, Canouil M, Froguel P, Schulte A, Solimena M, Ibberson M, Marchetti P, Cardenas-Diaz FL, Gadue PJ, Hastoy B, Almeida-Souza L, McMahon H, Rutter GA. Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a regulator of insulin secretion. Cell Rep 2021;34(5):108703
  53. Iber D. The control of lung branching morphogenesis. Curr Top Dev Biol 2021;143:205-237
  54. Irmisch A, Bonilla X, Chevrier S, Lehmann KV, Singer F, Toussaint NC, Esposito C, Mena J, Milani ES, Casanova R, Stekhoven DJ, Wegmann R, Jacob F, Sobottka B, Goetze S, Kuipers J, Sarabia Del Castillo J, Prummer M, Tuncel MA, Menzel U, Jacobs A, Engler S, Sivapatham S, Frei AL, Gut G, Ficek J, Miglino N, Tumor Profiler Consortium, Aebersold R, Bacac M, Beerenwinkel N, Beisel C, Bodenmiller B, Dummer R, Heinzelmann-Schwarz V, Koelzer VH, Manz MG, Moch H, Pelkmans L, Snijder B, Theocharides APA, Tolnay M, Wicki A, Wollscheid B, Rätsch G, Levesque MP. The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell 2021;39(3):288-293
  55. Iurlaro M, Stadler MB, Masoni F, Jagani Z, Galli GG, Schübeler D. Mammalian SWI/SNF continuously restores local accessibility to chromatin. Nat Genet 2021;53(3):279-287
  56. Jaron KS, Bast J, Nowell RW, Ranallo-Benavidez TR, Robinson-Rechavi M, Schwander T. Genomic Features of Parthenogenetic Animals. J Hered 2021;112(1):19-33
  57. Jeske K, Herzig-Straschil B, Răileanu C, Kunec D, Tauchmann O, Emirhar D, Schmidt S, Trimpert J, Silaghi C, Heckel G, Ulrich RG, Drewes S. Zoonotic pathogen screening of striped field mice (Apodemus agrarius) from Austria. Transbound Emerg Dis 2021
  58. Joerger-Messerli MS, Thomi G, Haesler V, Keller I, Renz P, Surbek DV, Schoeberlein A. Human Wharton's Jelly Mesenchymal Stromal Cell-Derived Small Extracellular Vesicles Drive Oligodendroglial Maturation by Restraining MAPK/ERK and Notch Signaling Pathways. Front Cell Dev Biol 2021;9:622539
  59. Johansson D, Rauld C, Roux J, Regairaz C, Galli E, Callegari I, Raad L, Waldt A, Cuttat R, Roma G, Diebold M, Becher B, Kuhle J, Derfuss T, Carballido JM, Sanderson NSR. Mass Cytometry of CSF Identifies an MS-Associated B-cell Population. Neurol Neuroimmunol Neuroinflamm 2021;8(2)
  60. Johri P, Riall K, Becher H, Excoffier L, Charlesworth B, Jensen JD. The impact of purifying and background selection on the inference of population history: problems and prospects. Mol Biol Evol 2021
  61. Juanola O, Hassan M, Kumar P, Yilmaz B, Keller I, Simillion C, Engelmann C, Tacke F, Dufour JF, De Gottardi A, Moghadamrad S. Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns. Gut Microbes 2021;13(1):1-20
  62. Junier P, Cailleau G, Palmieri I, Vallotton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, House GL, Morales D, Gallegos-Graves V, Dichosa AEK, Lupini S, Nguyen HN, Young JD, Rodrigues DF, Parra-Vasquez ANG, Bindschedler S, Chain PSG. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiol Ecol 2021;97(2)
  63. Kanev K, Roelli P, Wu M, Wurmser C, Delorenzi M, Pfaffl MW, Zehn D. Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells. Nat Commun 2021;12(1):569
  64. Karkampouna S, La Manna F, Benjak A, Kiener M, De Menna M, Zoni E, Grosjean J, Klima I, Garofoli A, Bolis M, Vallerga A, Theurillat JP, De Filippo MR, Genitsch V, Keller D, Booij TH, Stirnimann CU, Eng K, Sboner A, Ng CKY, Piscuoglio S, Gray PC, Spahn M, Rubin MA, Thalmann GN, Kruithof-de Julio M. Patient-derived xenografts and organoids model therapy response in prostate cancer. Nat Commun 2021;12(1):1117
  65. Kaushal A, Mohana G, Dorier J, Özdemir I, Omer A, Cousin P, Semenova A, Taschner M, Dergai O, Marzetta F, Iseli C, Eliaz Y, Weisz D, Shamim MS, Guex N, Lieberman Aiden E, Gambetta MC. CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions. Nat Commun 2021;12(1):1011
  66. Kerdivel G, Boeva V. Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma. Methods Mol Biol 2021;2226:265-284
  67. Kern U, Fröhlich K, Bedacht J, Schmidt N, Biniossek ML, Gensch N, Baerenfaller K, Schilling O. Impact of DJ-1 and Helix 8 on the Proteome and Degradome of Neuron-Like Cells. Cells 2021;10(2)
  68. Kitazawa T, Machlab D, Joshi O, Maiorano N, Kohler H, Ducret S, Kessler S, Gezelius H, Soneson C, Papasaikas P, López-Bendito G, Stadler MB, Rijli FM. A unique bipartite Polycomb signature regulates stimulus-response transcription during development. Nat Genet 2021;53(3):379-391
  69. Kläsener K, Jellusova J, Andrieux G, Salzer U, Böhler C, Steiner SN, Albinus JB, Cavallari M, Süß B, Voll RE, Boerries M, Wollscheid B, Reth M. CD20 as a gatekeeper of the resting state of human B cells. Proc Natl Acad Sci U S A 2021;118(7)
  70. Klaus J, Meli ML, Willi B, Nadeau S, Beisel C, Stadler T, Eth Sars-CoV-Sequencing Team, Egberink H, Zhao S, Lutz H, Riond B, Rösinger N, Stalder H, Renzullo S, Hofmann-Lehmann R. Detection and Genome Sequencing of SARS-CoV-2 in a Domestic Cat with Respiratory Signs in Switzerland. Viruses 2021;13(3)
  71. Kockmann T, Panse C. The rawrr R Package: Direct Access to Orbitrap Data and Beyond. J Proteome Res 2021;20(4):2028-2034
  72. Koivula RW, Atabaki-Pasdar N, Giordano GN, White T, Adamski J, Bell JD, Beulens J, Brage S, Brunak S, De Masi F, Dermitzakis ET, Forgie IM, Frost G, Hansen T, Hansen TH, Hattersley A, Kokkola T, Kurbasic A, Laakso M, Mari A, McDonald TJ, Pedersen O, Rutters F, Schwenk JM, Teare HJA, Thomas EL, Vinuela A, Mahajan A, McCarthy MI, Ruetten H, Walker M, Pearson E, Pavo I, Franks PW, IMI DIRECT Consortium. Correction to: The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes: an IMI DIRECT study. Diabetologia 2021;64(1):260-261
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