Peer-reviewed articles and conference proceedings

Listed in Europe PMC, latest update: 01.05.2023.
Discover the SIB Remarkable Outputs 2022

The Remarkable Outputs are selected by the Award Committee to provide the community with the yearly achievements by SIB Scientists that are particularly deserving attention. From new algorithms to detect disease-related genes to exploring the origins of sexual reproduction, discover this shortlist of publications, software tools, databases and outreach projects.

Search

  1. Adelmann JA, Vetter R, Iber D. Patterning precision under non-linear morphogen decay and molecular noise. Elife 2023;12:e84757
  2. Akgül G, Pla-Díaz M, Molak M, du Plessis L, Panagiotopoulou H, Doan K, Bogdanowicz W, Dąbrowski P, Oziębłowski M, Grzelak J, Arora N, González-Candelas F, Majander K, Schuenemann VJ. Inferring patterns of recombination and divergence with ancient and modern treponemal genomes 2023
  3. Albert JS, Carnaval AC, Flantua SGA, Lohmann LG, Ribas CC, Riff D, Carrillo JD, Fan Y, Figueiredo JJP, Guayasamin JM, Hoorn C, de Melo GH, Nascimento N, Quesada CA, Ulloa Ulloa C, Val P, Arieira J, Encalada AC, Nobre CA. Human impacts outpace natural processes in the Amazon. Science 2023;379(6630):eabo5003
  4. Álvarez-Prado ÁF, Maas RR, Soukup K, Klemm F, Kornete M, Krebs FS, Zoete V, Berezowska S, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors. Cell Rep Med 2023;4(1):100900
  5. Anchisi S, Wolfer A, Bisig B, Missiglia E, Tiab A, Kamel EM, Michielin O, Coukos G, Homicsko K. Deep and lasting response and acquired resistance to BRAFV600E targeting in a low-grade ovarian cancer patient. Cancer Biol Ther 2023;24(1):2193116
  6. Angori S, Banaei-Esfahani A, Mühlbauer K, Bolck HA, Kahraman A, Karakulak T, Poyet C, Feodoroff M, Potdar S, Kallioniemi O, Pietiäinen V, Schraml P, Moch H. Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets. Eur Urol Focus 2023:S2405-4569(23)00067-6
  7. Antonello P, Pizzagalli DU, Foglierini M, Melgrati S, Radice E, Thelen S, Thelen M. ACKR3 promotes CXCL12/CXCR4-mediated cell-to-cell-induced lymphoma migration through LTB4 production. Front Immunol 2022;13:1067885
  8. Apsley AT, Domico ER, Verbiest MA, Brogan CA, Buck ER, Burich AJ, Cardone KM, Stone WJ, Anisimova M, Vandenbergh DJ. A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3). Life Sci Alliance 2023;6(4):e202201677
  9. Aros-Mualin D, Guadagno CR, Silvestro D, Kessler M. Light, rather than circadian rhythm, regulates gas exchange in ferns and lycophytes. Plant Physiol 2023;191(3):1634-1647
  10. Auf der Maur P, Trefny MP, Baumann Z, Vulin M, Correia AL, Diepenbruck M, Kramer N, Volkmann K, Preca BT, Ramos P, Leroy C, Eichlisberger T, Buczak K, Zilli F, Okamoto R, Rad R, Jensen MR, Fritsch C, Zippelius A, Stadler MB, Bentires-Alj M. N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer. Cell Rep Med 2023;4(4):101002
  11. Auwerx C, Sadler MC, Woh T, Reymond A, Kutalik Z, Porcu E. Exploiting the mediating role of the metabolome to unravel transcript-to-phenotype associations. Elife 2023;12:e81097
  12. Avalos D, Rey G, Ribeiro DM, Ramisch A, Dermitzakis ET, Delaneau O. Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity. Commun Biol 2023;6(1):335
  13. Azizoğlu A, Loureiro C, Venetz J, Brent R. Autorepression-Based Conditional Gene Expression System in Yeast for Variation-Suppressed Control of Protein Dosage. Curr Protoc 2023;3(1):e647
  14. Barreiro K, Lay AC, Leparc G, Tran VDT, Rosler M, Dayalan L, Burdet F, Ibberson M, Coward RJM, Huber TB, Krämer BK, Delic D, Holthofer H. An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles. J Extracell Vesicles 2023;12(2):e12304
  15. Barut GT, Kreuzer M, Bruggmann R, Summerfield A, Talker SC. Single-cell transcriptomics reveals striking heterogeneity and functional organization of dendritic and monocytic cells in the bovine mesenteric lymph node. Front Immunol 2022;13:1099357
  16. Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Mol Biol Evol 2023;40(1):msac269
  17. Batavia AA, Rutishauser D, Sobottka B, Schraml P, Beerenwinkel N, Moch H. Biallelic ELOC Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity. Mod Pathol 2023:100194
  18. Bertschi NL, Steck O, Luther F, Bazzini C, von Meyenn L, Schärli S, Vallone A, Felser A, Keller I, Friedli O, Freigang S, Begré N, Radonjic-Hoesli S, Lamos C, Gabutti MP, Benzaquen M, Laimer M, Simon D, Nuoffer JM, Schlapbach C. PPAR-γ regulates the effector function of human T helper 9 cells by promoting glycolysis. Nat Commun 2023;14(1):2471
  19. Beyer D, Vaccarin C, Deupi X, Mapanao AK, Cohrs S, Sozzi-Guo F, Grundler PV, van der Meulen NP, Wang J, Tanriver M, Bode JW, Schibli R, Müller C. A tool for nuclear imaging of the SARS-CoV-2 entry receptor: molecular model and preclinical development of ACE2-selective radiopeptides. EJNMMI Res 2023;13(1):32
  20. Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Cervantes Rincón T, Fava T, Podešvová L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Hönig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarström Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF. Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci Immunol 2023;8(81):eade0958
  21. Bignon Y, Wigger L, Ansermet C, Weger BD, Lagarrigue S, Centeno G, Durussel F, Götz L, Ibberson M, Pradervand S, Quadroni M, Weger M, Amati F, Gachon F, Firsov D. Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock. J Clin Invest 2023;133(8):e167133
  22. Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 Mutational Spectrum. Mol Biol Evol 2023;40(4):msad085
  23. Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins 2023
  24. Botos MA, Arora P, Chouvardas P, Mercader N. Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart. Sci Rep 2023;13(1):5418
  25. Buchner B, Clement TJ, de Groot DH, Zanghellini J. ecmtool: fast and memory-efficient enumeration of elementary conversion modes. Bioinformatics 2023;39(3):btad095
  26. Camps J, Noël F, Liechti R, Massenet-Regad L, Rigade S, Götz L, Hoffmann C, Amblard E, Saichi M, Ibrahim MM, Pollard J, Medvedovic J, Roider HG, Soumelis V. Meta-Analysis of Human Cancer Single-Cell RNA-Seq Datasets Using the IMMUcan Database. Cancer Res 2023;83(3):363-373
  27. Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023;378(1877):20220055
  28. Caucheteur D, May Pendlington Z, Roncaglia P, Gobeill J, Mottin L, Matentzoglu N, Agosti D, Osumi-Sutherland D, Parkinson H, Ruch P. COVoc and COVTriage: novel resources to support literature triage. Bioinformatics 2023;39(1):btac800
  29. Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SA, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff JP, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. KG-Hub -- Building and Exchanging Biological Knowledge Graphs 2023
  30. Chen C, Taepper A, Engelniederhammer F, Kellerer J, Roemer C, Stadler T. LAPIS is a fast web API for massive open virus sequencing databases 2023
  31. Chen X, Portran D, Widmer LA, Stangier MM, Czub MP, Liakopoulos D, Stelling J, Steinmetz MO, Barral Y. The motor domain of the kinesin Kip2 promotes microtubule polymerization at microtubule tips. J Cell Biol 2023;222(7):e202110126
  32. Cheval B, Darrous L, Choi KW, Klimentidis YC, Raichlen DA, Alexander GE, Cullati S, Kutalik Z, Boisgontier MP. Genetic insights into the causal relationship between physical activity and cognitive functioning. Sci Rep 2023;13(1):5310
  33. Corona Ramirez A, Bregnard D, Junier T, Cailleau G, Dorador C, Bindschedler S, Junier P. Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis. BMC Microbiol 2023;23(1):68
  34. Corval H, Cumer T, Topaloudis A, Roulin A, Goudet J. Where and when local adaptation happens: lessons from the European barn owl (Tyto alba) 2023
  35. Coudert E, Gehant S, de Castro E, Pozzato M, Baratin D, Neto T, Sigrist CJA, Redaschi N, Bridge A, UniProt Consortium. Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinformatics 2023;39(1):btac793
  36. Crocker J, Payne JL, Walczak AM, Wittkopp PJ. Interdisciplinary approaches to predicting evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2023;378(1877):20220042
  37. Crowell HL, Morillo Leonardo SX, Soneson C, Robinson MD. The shaky foundations of simulating single-cell RNA sequencing data. Genome Biol 2023;24(1):62
  38. Cumer T, Machado AP, San-Jose LM, Ducrest A, Simon C, Roulin A, Goudet J. The genomic architecture of a continuous color polymorphism in the European barn owl (Tyto alba) 2023
  39. Dadonaite B, Crawford KHD, Radford CE, Farrell AG, Yu TC, Hannon WW, Zhou P, Andrabi R, Burton DR, Liu L, Ho DD, Chu HY, Neher RA, Bloom JD. A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike. Cell 2023;186(6):1263-1278.e20
  40. Darrous L, Hemani G, Smith GD, Kutalik Z. PheWAS-based clustering of Mendelian Randomisation instruments reveals distinct mechanism-specific causal effects between obesity and educational attainment 2023
  41. de Groot DH, Tjalma AJ, Bruggeman FJ, van Nimwegen E. Effective bet-hedging through growth rate dependent stability. Proc Natl Acad Sci U S A 2023;120(8):e2211091120
  42. de Souza VBC, Jordan BT, Tseng E, Nelson EA, Hirschi KK, Sheynkman G, Robinson MD. Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. Genome Biol 2023;24(1):91
  43. Deichmann J, Bachmann S, Burckhardt MA, Pfister M, Szinnai G, Kaltenbach HM. New model of glucose-insulin regulation characterizes effects of physical activity and facilitates personalized treatment evaluation in children and adults with type 1 diabetes. PLoS Comput Biol 2023;19(2):e1010289
  44. Dietler N, Lupo U, Bitbol AF. Impact of phylogeny on structural contact inference from protein sequence data. J R Soc Interface 2023;20(199):20220707
  45. Dijokaite-Guraliuc A, Das R, Zhou D, Ginn HM, Liu C, Duyvesteyn HME, Huo J, Nutalai R, Supasa P, Selvaraj M, de Silva TI, Plowright M, Newman TAH, Hornsby H, Mentzer AJ, Skelly D, Ritter TG, Temperton N, Klenerman P, Barnes E, Dunachie SJ, OPTIC consortium, Roemer C, Peacock TP, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Cell Rep 2023;42(4):112271
  46. Durairaj J, Waterhouse AM, Mets T, Brodiazhenko T, Abdullah M, Studer G, Akdel M, Andreeva A, Bateman A, Tenson T, Tenson T, Hauryliuk V, Schwede T, Pereira J. What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds 2023
  47. Duruz J, Sprecher M, Kaldun JC, Al-Soudy AS, Lischer HEL, van Geest G, Nicholson P, Bruggmann R, Sprecher SG. Molecular characterization of cell types in the squid Loligo vulgaris. Elife 2023;12:e80670
  48. Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol 2023
  49. Edelson JL, Schneider LD, Amar D, Brink-Kjaer A, Cederberg KL, Kutalik Z, Hagen EW, Peppard PE, Tempaku PF, Tufik S, Evans DS, Stone K, Tranah G, Cade B, Redline S, Haba-Rubio J, Heinzer R, Marques-Vidal P, Vollenweider P, Winkelmann J, Zou J, Mignot E. The genetic etiology of periodic limb movement in sleep. Sleep 2023;46(4):zsac121
  50. Fava M, Stahl SM, De Martin S, Mattarei A, Bettini E, Comai S, Alimonti A, Bifari F, Pani L, Folli F, Guidetti C, Furlan A, Sgrignani J, Locatelli P, Cavalli A, O'Gorman C, Traversa S, Inturrisi CE, Pappagallo M, Manfredi PL. Esmethadone-HCl (REL-1017): a promising rapid antidepressant. Eur Arch Psychiatry Clin Neurosci 2023
  51. Ferdowsi S, Knafou J, Borissov N, Vicente Alvarez D, Mishra R, Amini P, Teodoro D. Deep learning-based risk prediction for interventional clinical trials based on protocol design: A retrospective study. Patterns (N Y) 2023;4(3):100689
  52. Forny P, Bonilla X, Lamparter D, Shao W, Plessl T, Frei C, Bingisser A, Goetze S, van Drogen A, Harshman K, Pedrioli PGA, Howald C, Poms M, Traversi F, Bürer C, Cherkaoui S, Morscher RJ, Simmons L, Forny M, Xenarios I, Aebersold R, Zamboni N, Rätsch G, Dermitzakis ET, Wollscheid B, Baumgartner MR, Froese DS. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency. Nat Metab 2023;5(1):80-95
  53. Foster WJ, Allen BJ, Kitzmann NH, Münchmeyer J, Rettelbach T, Witts JD, Whittle RJ, Larina E, Clapham ME, Dunhill AM. How predictable are mass extinction events? R Soc Open Sci 2023;10(3):221507
  54. Frachon L, Arrigo L, Rusman Q, Poveda L, Qi W, Scopece G, Schiestl FP. Putative Signals of Generalist Plant Species Adaptation to Local Pollinator Communities and Abiotic Factors. Mol Biol Evol 2023;40(3):msad036
  55. Frey K, Rohrer L, Potapenko A, Goetze S, von Eckardstein A, Wollscheid B. Mapping the dynamic cell surface interactome of high-density lipoprotein reveals Aminopeptidase N as modulator of its endothelial uptake 2023
  56. Fritah H, Graciotti M, Lai-Lai Chiang C, Huguenin-Bergenat AL, Petremand R, Ahmed R, Guillaume P, Schmidt J, Stevenson BJ, Gfeller D, Harari A, Kandalaft LE. Cancer vaccines based on whole-tumor lysate or neoepitopes with validated HLA binding outperform those with predicted HLA-binding affinity. iScience 2023;26(4):106288
  57. Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res 2023;51(d1):D760-D766
  58. Gainza P, Wehrle S, Van Hall-Beauvais A, Marchand A, Scheck A, Harteveld Z, Buckley S, Ni D, Tan S, Sverrisson F, Goverde C, Turelli P, Raclot C, Teslenko A, Pacesa M, Rosset S, Georgeon S, Marsden J, Petruzzella A, Liu K, Xu Z, Chai Y, Han P, Gao GF, Oricchio E, Fierz B, Trono D, Stahlberg H, Bronstein M, Correia BE. De novo design of protein interactions with learned surface fingerprints. Nature 2023
  59. Gallon J, Rodriguez-Calero A, Benjak A, Akhoundova D, Maletti S, Amstutz U, Hewer E, Genitsch V, Fleischmann A, Rushing EJ, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya AO, Bubendorf L, Moch H, Thalmann G, Feng FY, Gillessen S, Ng CKY, Rubin MA, Piscuoglio S. DNA Methylation Landscapes of Prostate Cancer Brain Metastasis Are Shaped by Early Driver Genetic Alterations. Cancer Res 2023;83(8):1203-1213
  60. Gandarilla-Pérez CA, Pinilla S, Bitbol AF, Weigt M. Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins. PLoS Comput Biol 2023;19(3):e1011010
  61. Gendre M, Hauffe T, Pimiento C, Silvestro D. Benchmarking imputation methods for discrete biological data 2023
  62. Gfeller D, Liu Y, Racle J. Contemplating immunopeptidomes to better predict them. Semin Immunol 2023;66:101708
  63. Gfeller D, Schmidt J, Croce G, Guillaume P, Bobisse S, Genolet R, Queiroz L, Cesbron J, Racle J, Harari A. Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes. Cell Syst 2023;14(1):72-83.e5
  64. Ghenu AH, Amado A, Gordo I, Bank C. Epistasis decreases with increasing antibiotic pressure but not temperature. Philos Trans R Soc Lond B Biol Sci 2023;378(1877):20220058
  65. Gitschlag BL, Cano AV, Payne JL, McCandlish DM, Stoltzfus A. Mutation and selection induce correlations between selection coefficients and mutation rates 2023
  66. Gollub MG, Backes T, Kaltenbach H, Stelling J. ENKIE: A package for predicting enzyme kinetic parameter values and their uncertainties 2023
  67. Gómez HF, Doumpas N, Iber D. Time-lapse and cleared imaging of mouse embryonic lung explants to study three-dimensional cell morphology and topology dynamics. STAR Protoc 2023;4(2):102187
  68. Gruhl T, Weinert T, Rodrigues MJ, Milne CJ, Ortolani G, Nass K, Nango E, Sen S, Johnson PJM, Cirelli C, Furrer A, Mous S, Skopintsev P, James D, Dworkowski F, Båth P, Kekilli D, Ozerov D, Tanaka R, Glover H, Bacellar C, Brünle S, Casadei CM, Diethelm AD, Gashi D, Gotthard G, Guixà-González R, Joti Y, Kabanova V, Knopp G, Lesca E, Ma P, Martiel I, Mühle J, Owada S, Pamula F, Sarabi D, Tejero O, Tsai CJ, Varma N, Wach A, Boutet S, Tono K, Nogly P, Deupi X, Iwata S, Neutze R, Standfuss J, Schertler G, Panneels V. Ultrafast structural changes direct the first molecular events of vision. Nature 2023;615(7954):939-944
  69. Guidetti F, Arribas AJ, Sartori G, Spriano F, Barnabei L, Tarantelli C, Von Roemeling R, Martinez E, Zucca E, Bertoni F. Targeting IRAK4 with Emavusertib in Lymphoma Models with Secondary Resistance to PI3K and BTK Inhibitors. J Clin Med 2023;12(2):399
  70. Guinat C, Tang H, Yang Q, Valenzuela Agüí C, Vaughan TG, Scire J, Yu H, Wang W, Chen Z, Ducatez MF, Stadler T. Bayesian phylodynamics reveals the transmission dynamics of avian influenza A(H7N9) virus at the human-live bird market interface in China. Proc Natl Acad Sci U S A 2023;120(17):e2215610120
  71. Hansen SB, Bozzi D, Mak SST, Clausen CG, Nielsen TK, Kodama M, Hansen LH, Gilbert MTP, Limborg MT. Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Genomics 2023:110629
  72. Hatos A, Teixeira JM, Barrera-Vilarmau S, Horvath A, Tosatto SCE, Vendruscolo M, Fuxreiter M. FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins. Nucleic Acids Res 2023:gkad214
  73. Hausmann D, Todorski I, Pindur A, Weiland E, Benkert T, Bosshard L, Prummer M, Kubik-Huch RA. Advanced Diffusion-Weighted Imaging Sequences for Breast MRI: Comprehensive Comparison of Improved Sequences and Ultra-High B-Values to Identify the Optimal Combination. Diagnostics (Basel) 2023;13(4):607
  74. Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res 2023;51(d1):D389-D394
  75. Herzig A, Rubinacci S, Marenne G, Perdry H, Dina C, Redon R, Delaneau O, Génin E, FrEx Consortium, FranceGenRef Consortium. SURFBAT: a surrogate family-based association test building on large imputation reference panels 2023
  76. Hiltemann S, Rasche H, Gladman S, Hotz HR, Larivière D, Blankenberg D, Jagtap PD, Wollmann T, Bretaudeau A, Goué N, Griffin TJ, Royaux C, Le Bras Y, Mehta S, Syme A, Coppens F, Droesbeke B, Soranzo N, Bacon W, Psomopoulos F, Gallardo-Alba C, Davis J, Föll MC, Fahrner M, Doyle MA, Serrano-Solano B, Fouilloux AC, van Heusden P, Maier W, Clements D, Heyl F, Galaxy Training Network, Grüning B, Batut B. Galaxy Training: A powerful framework for teaching! PLoS Comput Biol 2023;19(1):e1010752
  77. Hodel F, Xu ZM, Thorball CW, de La Harpe R, Letang-Mathieu P, Brenner N, Butt J, Bender N, Waterboer T, Marques-Vidal PM, Vollenweider P, Vaucher J, Fellay J. Associations of genetic and infectious risk factors with coronary heart disease. Elife 2023;12:e79742
  78. Huang Q, Baudis M. Candidate targets of copy number deletion events across 17 cancer types. Front Genet 2022;13:1017657
  79. Humbert M, Olofsson A, Wullimann D, Niessl J, Hodcroft EB, Cai C, Gao Y, Sohlberg E, Dyrdak R, Mikaeloff F, Neogi U, Albert J, Malmberg KJ, Lund-Johansen F, Aleman S, Björkhem-Bergman L, Jenmalm MC, Ljunggren HG, Buggert M, Karlsson AC. Functional SARS-CoV-2 cross-reactive CD4+ T cells established in early childhood decline with age. Proc Natl Acad Sci U S A 2023;120(12):e2220320120
  80. Jauch AJ, Bignucolo O, Seki S, Ghraichy M, Delmonte OM, von Niederhäusern V, Higgins R, Ghosh A, Nishizawa M, Tanaka M, Baldrich A, Köppen J, Hirsiger JR, Hupfer R, Ehl S, Rensing-Ehl A, Hopfer H, Prince SS, Daley SR, Marquardsen FA, Meyer BJ, Tamm M, Daikeler TD, Diesch T, Kühne T, Helbling A, Berkemeier C, Heijnen I, Navarini AA, Trück J, de Villartay JP, Oxenius A, Berger CT, Hess C, Notarangelo LD, Yamamoto H, Recher M. Autoimmunity and immunodeficiency associated with monoallelic LIG4 mutations via haploinsufficiency. J Allergy Clin Immunol 2023:S0091-6749(23)00422-0
  81. Jaume-Santero F, Bornet A, Valery A, Naderi N, Vicente Alvarez D, Proios D, Yazdani A, Bournez C, Fessard T, Teodoro D. Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios. J Chem Inf Model 2023;63(7):1914-1924
  82. Johnson Z, Tarantelli C, Civanelli E, Cascione L, Spriano F, Fraser A, Shah P, Nomanbhoy T, Napoli S, Rinaldi A, Niewola-Staszkowska K, Lahn M, Perrin D, Wenes M, Migliorini D, Bertoni F, van der Veen L, Di Conza G. IOA-244 is a Non-ATP-competitive, Highly Selective, Tolerable PI3K Delta Inhibitor That Targets Solid Tumors and Breaks Immune Tolerance. Cancer Res Commun 2023;3(4):576-591
  83. Kashani E, Schnidrig D, Gheinani AH, Ninck MS, Zens P, Maragkou T, Baumgartner U, Schucht P, Rätsch G, Rubin MA, SOCIBP consortium, Berezowska S, Ng CKY, Vassella E. Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors. Neuro Oncol 2023;25(4):662-673
  84. Katsantoni M, van Nimwegen E, Zavolan M. Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs. Genome Biol 2023;24(1):77
  85. Kentistou KA, Luan J, Wittemans LBL, Hambly C, Klaric L, Kutalik Z, Speakman JR, Wareham NJ, Kendall TJ, Langenberg C, Wilson JF, Joshi PK, Morton NM. Large scale phenotype imputation and in vivo functional validation implicate ADAMTS14 as an adiposity gene. Nat Commun 2023;14(1):307
  86. Khameneh HJ, Fonta N, Zenobi A, Niogret C, Ventura P, Guerra C, Kwee I, Rinaldi A, Pecoraro M, Geiger R, Cavalli A, Bertoni F, Vivier E, Trumpp A, Guarda G. Myc controls NK cell development, IL-15-driven expansion, and translational machinery. Life Sci Alliance 2023;6(7):e202302069
  87. Kim T, Chen D, Hornauer P, Emmenegger V, Bartram J, Ronchi S, Hierlemann A, Schröter M, Roqueiro D. Predicting in vitro single-neuron firing rates upon pharmacological perturbation using Graph Neural Networks. Front Neuroinform 2022;16:1032538
  88. Krapp LF, Abriata LA, Cortés Rodriguez F, Dal Peraro M. PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces. Nat Commun 2023;14(1):2175
  89. Krebs FS, Moura B, Missiaglia E, Aedo-Lopez V, Michielin O, Tsantoulis P, Bisig B, Trimech M, Zoete V, Homicsko K. Response and Resistance to Trametinib in MAP2K1-Mutant Triple-Negative Melanoma. Int J Mol Sci 2023;24(5):4520
  90. Kropivsek K, Kachel P, Goetze S, Wegmann R, Festl Y, Severin Y, Hale BD, Mena J, van Drogen A, Dietliker N, Tchinda J, Wollscheid B, Manz MG, Snijder B. Ex vivo drug response heterogeneity reveals personalized therapeutic strategies for patients with multiple myeloma. Nat Cancer 2023
  91. Kuhlmeier E, Chan T, Agüí CV, Willi B, Wolfensberger A, Beisel C, Topolsky I, Beerenwinkel N, Stadler T, Swiss Sars-CoV-Sequencing Consortium, Jones S, Tyson G, Hosie MJ, Reitt K, Hüttl J, Meli ML, Hofmann-Lehmann R. Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 2023;15(1):245
  92. Kuznetsov D, Tegenfeldt F, Manni M, Seppey M, Berkeley M, Kriventseva EV, Zdobnov EM. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res 2023;51(d1):D445-D451
  93. Labbé F, Abdeladhim M, Abrudan J, Araki AS, Araujo RN, Arensburger P, Benoit JB, Brazil RP, Bruno RV, Bueno da Silva Rivas G, Carvalho de Abreu V, Charamis J, Coutinho-Abreu IV, da Costa-Latgé SG, Darby A, Dillon VM, Emrich SJ, Fernandez-Medina D, Figueiredo Gontijo N, Flanley CM, Gatherer D, Genta FA, Gesing S, Giraldo-Calderón GI, Gomes B, Aguiar ERGR, Hamilton JGC, Hamarsheh O, Hawksworth M, Hendershot JM, Hickner PV, Imler JL, Ioannidis P, Jennings EC, Kamhawi S, Karageorgiou C, Kennedy RC, Krueger A, Latorre-Estivalis JM, Ligoxygakis P, Meireles-Filho ACA, Minx P, Miranda JC, Montague MJ, Nowling RJ, Oliveira F, Ortigão-Farias J, Pavan MG, Horacio Pereira M, Nobrega Pitaluga A, Proveti Olmo R, Ramalho-Ortigao M, Ribeiro JMC, Rosendale AJ, Sant'Anna MRV, Scherer SE, Secundino NFC, Shoue DA, da Silva Moraes C, Gesto JSM, Souza NA, Syed Z, Tadros S, Teles-de-Freitas R, Telleria EL, Tomlinson C, Traub-Csekö YM, Marques JT, Tu Z, Unger MF, Valenzuela J, Ferreira FV, de Oliveira KPV, Vigoder FM, Vontas J, Wang L, Weedall GD, Zhioua E, Richards S, Warren WC, Waterhouse RM, Dillon RJ, McDowell MA. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World. PLoS Negl Trop Dis 2023;17(4):e0010862
  94. Laganenka L, Lee JW, Malfertheiner L, Dieterich CL, Fuchs L, Piel J, von Mering C, Sourjik V, Hardt WD. Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nat Microbiol 2023;8(2):204-217
  95. Lambuta RA, Nanni L, Liu Y, Diaz-Miyar J, Iyer A, Tavernari D, Katanayeva N, Ciriello G, Oricchio E. Whole-genome doubling drives oncogenic loss of chromatin segregation. Nature 2023;615(7954):925-933
  96. Lavanchy E, Goudet J. Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization. Mol Ecol Resour 2023;23(4):787-802
  97. Lee J, Hadfield J, Black A, Sibley TR, Neher RA, Bedford T, Huddleston J. Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. Front Bioinform 2023;3:1069487
  98. Loiseau C, Windels EM, Gygli SM, Jugheli L, Maghradze N, Brites D, Ross A, Goig G, Reinhard M, Borrell S, Trauner A, Dötsch A, Aspindzelashvili R, Denes R, Reither K, Beisel C, Tukvadze N, Avaliani Z, Stadler T, Gagneux S. The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot. Nat Commun 2023;14(1):1988
  99. Long Y, Vetter R, Iber D. 2D Effects Enhance Precision of Gradient-Based Tissue Patterning 2023
  100. Lopez Vazquez A, Allenbach Petrolati L, Legris M, Dessimoz C, Lampugnani ER, Glover N, Fankhauser C. Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE. Plant Cell 2023:koad096
  101. Luqman H, Wegmann D, Fior S, Widmer A. Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles. Nat Commun 2023;14(1):1080
  102. Lussi YC, Magrane M, Martin MJ, Orchard S, UniProt Consortium. Searching and Navigating UniProt Databases. Curr Protoc 2023;3(3):e700
  103. Macnair W, Robinson M. SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data. Genome Biol 2023;24(1):23
  104. Mao K, Borel C, Ansar M, Jolly A, Makrythanasis P, Froehlich C, Iwaszkiewicz J, Wang B, Xu X, Li Q, Blanc X, Zhu H, Chen Q, Jin F, Ankamreddy H, Singh S, Zhang H, Wang X, Chen P, Ranza E, Paracha SA, Shah SF, Guida V, Piceci-Sparascio F, Melis D, Dallapiccola B, Digilio MC, Novelli A, Magliozzi M, Fadda MT, Streff H, Machol K, Lewis RA, Zoete V, Squeo GM, Prontera P, Mancano G, Gori G, Mariani M, Selicorni A, Psoni S, Fryssira H, Douzgou S, Marlin S, Biskup S, De Luca A, Merla G, Zhao S, Cox TC, Groves AK, Lupski JR, Zhang Q, Zhang YB, Antonarakis SE. FOXI3 pathogenic variants cause one form of craniofacial microsomia. Nat Commun 2023;14(1):2026
  105. Martani A, Geneviève LD, Wangmo T, Maurer J, Crameri K, Erard F, Spoendlin J, Pauli-Magnus C, Pittet V, Sengstag T, Soldini E, Hirschel B, Borisch B, Kruschel Weber C, Zwahlen M, Elger BS. Sensing the (digital) pulse. Future steps for improving the secondary use of data for research in Switzerland. Digit Health 2023;9:20552076231169826
  106. Marx AF, Kallert SM, Brunner TM, Villegas JA, Geier F, Fixemer J, Abreu-Mota T, Reuther P, Bonilla WV, Fadejeva J, Kreutzfeldt M, Wagner I, Aparicio-Domingo P, Scarpellino L, Charmoy M, Utzschneider DT, Hagedorn C, Lu M, Cornille K, Stauffer K, Kreppel F, Merkler D, Zehn D, Held W, Luther SA, Löhning M, Pinschewer DD. The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8+ T cells in chronic viral infection. Immunity 2023;56(4):813-828.e10
  107. Mastelic-Gavillet B, Sarivalasis A, Lozano LE, Lofek S, Wyss T, Melero I, de Vries IJM, Harari A, Romero P, Kandalaft LE, Viganó S. Longitudinal analysis of DC subsets in patients with ovarian cancer: Implications for immunotherapy. Front Immunol 2023;14:1119371
  108. Mathieson I, Day FR, Barban N, Tropf FC, Brazel DM, eQTLGen Consortium, BIOS Consortium, Vaez A, van Zuydam N, Bitarello BD, Gardner EJ, Akimova ET, Azad A, Bergmann S, Bielak LF, Boomsma DI, Bosak K, Brumat M, Buring JE, Cesarini D, Chasman DI, Chavarro JE, Cocca M, Concas MP, Davey Smith G, Davies G, Deary IJ, Esko T, Faul JD, FinnGen Study, Franco O, Ganna A, Gaskins AJ, Gelemanovic A, de Geus EJC, Gieger C, Girotto G, Gopinath B, Grabe HJ, Gunderson EP, Hayward C, He C, van Heemst D, Hill WD, Hoffmann ER, Homuth G, Hottenga JJ, Huang H, Hyppӧnen E, Ikram MA, Jansen R, Johannesson M, Kamali Z, Kardia SLR, Kavousi M, Kifley A, Kiiskinen T, Kraft P, Kühnel B, Langenberg C, Liew G, Lifelines Cohort Study, Lind PA, Luan J, Mägi R, Magnusson PKE, Mahajan A, Martin NG, Mbarek H, McCarthy MI, McMahon G, Medland SE, Meitinger T, Metspalu A, Mihailov E, Milani L, Missmer SA, Mitchell P, Møllegaard S, Mook-Kanamori DO, Morgan A, van der Most PJ, de Mutsert R, Nauck M, Nolte IM, Noordam R, Penninx BWJH, Peters A, Peyser PA, Polašek O, Power C, Pribisalic A, Redmond P, Rich-Edwards JW, Ridker PM, Rietveld CA, Ring SM, Rose LM, Rueedi R, Shukla V, Smith JA, Stankovic S, Stefánsson K, Stöckl D, Strauch K, Swertz MA, Teumer A, Thorleifsson G, Thorsteinsdottir U, Thurik AR, Timpson NJ, Turman C, Uitterlinden AG, Waldenberger M, Wareham NJ, Weir DR, Willemsen G, Zhao JH, Zhao W, Zhao Y, Snieder H, den Hoed M, Ong KK, Mills MC, Perry JRB. Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus. Nat Hum Behav 2023
  109. Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Abou Tayoun A, Aiuti A, Alavi Darazam I, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Metin Akcan O, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, COVID Human Genetic Effort, COVIDeF Study Group, French COVID Cohort Study Group, CoV-Contact Cohort, COVID-STORM Clinicians, COVID Clinicians, Orchestra Working Group, Amsterdam UMC Covid-19 Biobank, NIAID-USUHS COVID Study Group, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. Genome Med 2023;15(1):22
  110. McBroome J, de Bernardi Schneider A, Roemer C, Wolfinger MT, Hinrichs AS, O’Toole AN, Ruis C, Turakhia Y, Rambaut A, Corbett-Detig R. Automated Agnostic Designation of Pathogen Lineages 2023
  111. Mounier N, Kutalik Z. Bias correction for inverse variance weighting Mendelian randomization. Genet Epidemiol 2023
  112. Mounier N, Robertson DS, Kutalik Z, Dudbridge F, Bowden J. Incorporating discovery and replication GWAS into summary data Mendelian randomization studies: A review of current methods and a simple, general and powerful alternative 2023
  113. Muri J, Cecchinato V, Cavalli A, Shanbhag AA, Matkovic M, Biggiogero M, Maida PA, Moritz J, Toscano C, Ghovehoud E, Furlan R, Barbic F, Voza A, De Nadai G, Cervia C, Zurbuchen Y, Taeschler P, Murray LA, Danelon-Sargenti G, Moro S, Gong T, Piffaretti P, Bianchini F, Crivelli V, Podešvová L, Pedotti M, Jarrossay D, Sgrignani J, Thelen S, Uhr M, Bernasconi E, Rauch A, Manzo A, Ciurea A, Rocchi MBL, Varani L, Moser B, Bottazzi B, Thelen M, Fallon BA, Boyman O, Mantovani A, Garzoni C, Franzetti-Pellanda A, Uguccioni M, Robbiani DF. Autoantibodies against chemokines post-SARS-CoV-2 infection correlate with disease course. Nat Immunol 2023;24(4):604-611
  114. Nadeau S, Devaux A, Bagutti C, Alt M, Hampe EI, Kraus M, Würfel E, Koch KN, Fuchs S, Tschudin-Sutter S, Holschneider A, Ort C, Chen C, Huisman JS, Julian TR, Stadler T. Influenza transmission dynamics quantified from wastewater 2023
  115. Nadeau SA, Vaughan TG, Beckmann C, Topolsky I, Chen C, Hodcroft E, Schär T, Nissen I, Santacroce N, Burcklen E, Ferreira P, Jablonski KP, Posada-Céspedes S, Capece V, Seidel S, Santamaria de Souza N, Martinez-Gomez JM, Cheng P, Bosshard PP, Levesque MP, Kufner V, Schmutz S, Zaheri M, Huber M, Trkola A, Cordey S, Laubscher F, Gonçalves AR, Aeby S, Pillonel T, Jacot D, Bertelli C, Greub G, Leuzinger K, Stange M, Mari A, Roloff T, Seth-Smith H, Hirsch HH, Egli A, Redondo M, Kobel O, Noppen C, du Plessis L, Beerenwinkel N, Neher RA, Beisel C, Stadler T. Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Sci Transl Med 2023;15(680):eabn7979
  116. Neuenschwander S, Cruz Dávalos DI, Anchieri L, Sousa da Mota B, Bozzi D, Rubinacci S, Delaneau O, Rasmussen S, Malaspinas AS. Mapache: a flexible pipeline to map ancient DNA. Bioinformatics 2023;39(2):btad028
  117. O’Toole Á, Neher RA, Ndodo N, Borges V, Gannon B, Gomes JP, Groves N, King DJ, Maloney D, Lemey P, Lewandowski K, Loman N, Myers R, Suchard MA, Worobey M, Chand M, Ihekweazu C, Ulaeto D, Adetifa I, Rambaut A. Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016 2023
  118. Papkou A, Garcia-Pastor L, Escudero JA, Wagner A. A rugged yet easily navigable fitness landscape of antibiotic resistance 2023
  119. Parey E, Louis A, Montfort J, Bouchez O, Roques C, Iampietro C, Lluch J, Castinel A, Donnadieu C, Desvignes T, Floi Bucao C, Jouanno E, Wen M, Mejri S, Dirks R, Jansen H, Henkel C, Chen WJ, Zahm M, Cabau C, Klopp C, Thompson AW, Robinson-Rechavi M, Braasch I, Lecointre G, Bobe J, Postlethwait JH, Berthelot C, Roest Crollius H, Guiguen Y. Genome structures resolve the early diversification of teleost fishes. Science 2023;379(6632):572-575
  120. Pasche E, Mottaz A, Gobeill J, Michel PA, Caucheteur D, Naderi N, Ruch P. Assessing the use of supplementary materials to improve genomic variant discovery. Database (Oxford) 2023;2023:baad017
  121. Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunić I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A. InterPro in 2022. Nucleic Acids Res 2023;51(d1):D418-D427
  122. PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Consortium. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023;614(7948):E37
  123. Pfaendler R, Hanimann J, Lee S, Snijder B. Self-supervised vision transformers accurately decode cellular state heterogeneity 2023
  124. Planas-Paz L, Pliego-Mendieta A, Hagedorn C, Aguilera-Garcia D, Haberecker M, Arnold F, Herzog M, Bankel L, Guggenberger R, Steiner S, Chen Y, Kahraman A, Zoche M, Rubin MA, Moch H, Britschgi C, Pauli C. Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma. EMBO Mol Med 2023;15(4):e16863
  125. Racle J, Guillaume P, Schmidt J, Michaux J, Larabi A, Lau K, Perez MAS, Croce G, Genolet R, Coukos G, Zoete V, Pojer F, Bassani-Sternberg M, Harari A, Gfeller D. Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes. Immunity 2023:S1074-7613(23)00129-2
  126. Radoux-Mergault A, Oberhauser L, Aureli S, Gervasio FL, Stoeber M. Subcellular location defines GPCR signal transduction. Sci Adv 2023;9(16):eadf6059
  127. Ramon C, Stelling J. Functional comparison of metabolic networks across species. Nat Commun 2023;14(1):1699
  128. Reichmuth ML, Hodcroft EB, Althaus CL. Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: phylogenetic analysis and intervention scenarios 2023
  129. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G, PCAWG Consortium. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2023;614(7948):E40
  130. Rieder J, Kapopoulou A, Bank C, Adrian-Kalchhauser I. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. Environ Microbiome 2023;18(1):8
  131. Rizzi V, Aureli S, Ansari N, Gervasio FL. OneOPES, a combined enhanced sampling method to rule them all 2023
  132. Rodrigues PF, Kouklas A, Cvijetic G, Bouladoux N, Mitrovic M, Desai JV, Lima-Junior DS, Lionakis MS, Belkaid Y, Ivanek R, Tussiwand R. pDC-like cells are pre-DC2 and require KLF4 to control homeostatic CD4 T cells. Sci Immunol 2023;8(80):eadd4132
  133. Rozzi R, Lomolino MV, van der Geer AAE, Silvestro D, Lyons SK, Bover P, Alcover JA, Benítez-López A, Tsai CH, Fujita M, Kubo MO, Ochoa J, Scarborough ME, Turvey ST, Zizka A, Chase JM. Dwarfism and gigantism drive human-mediated extinctions on islands. Science 2023;379(6636):1054-1059
  134. Ruiz F, Peter B, Rebeaud J, Vigne S, Bressoud V, Roumain M, Wyss T, Yersin Y, Wagner I, Kreutzfeldt M, Pimentel Mendes M, Kowalski C, Boivin G, Roth L, Schwaninger M, Merkler D, Muccioli GG, Hugues S, Petrova TV, Pot C. Endothelial cell-derived oxysterol ablation attenuates experimental autoimmune encephalomyelitis. EMBO Rep 2023;24(3):e55328
  135. Sabatier M, Birsen R, Lauture L, Mouche S, Angelino P, Dehairs J, Goupille L, Boussaid I, Heiblig M, Boet E, Sahal A, Saland E, Santos JC, Armengol M, Fernandez-Serrano M, Farge T, Cognet G, Simonetta F, Pignon C, Graffeuil A, Mazzotti C, Avet-Loiseau H, Delos O, Bertrand-Michel J, Chedru A, Dembitz V, Gallipoli P, Anstee NS, Loo S, Wei AH, Carroll M, Goubard A, Castellano R, Collette Y, Vergez F, Mansat-De Mas V, Bertoli S, Tavitian S, Picard M, Recher C, Bourges-Abella N, Granat F, Kosmider O, Sujobert P, Colsch B, Joffre C, Stuani L, Swinnen JV, Guillou H, Roue G, Hakim N, Dejean AS, Tsantoulis P, Larrue C, Bouscary D, Tamburini J, Sarry JE. C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia. Cancer Discov 2023:CD-22-0411
  136. Sadler MC, Auwerx C, Deelen P, Kutalik Z. Multi-layered genetic approaches to identify approved drug targets 2023
  137. Saini JS, Manni M, Hassler C, Cable RN, Duhaime MB, Zdobnov EM. Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno. ISME J 2023
  138. Sandoz PA, Denhardt-Eriksson RA, Abrami L, Abriata LA, Spreemann G, Maclachlan C, Ho S, Kunz B, Hess K, Knott G, S Mesquita F, Hatzimanikatis V, van der Goot FG. Dynamics of CLIMP-63 S-acylation control ER morphology. Nat Commun 2023;14(1):264
  139. Santos-Moreno J, Tasiudi E, Kusumawardhani H, Stelling J, Schaerli Y. Robustness and innovation in synthetic genotype networks. Nat Commun 2023;14(1):2454
  140. Sarkis R, Burri O, Royer-Chardon C, Schyrr F, Blum S, Costanza M, Cherix S, Piazzon N, Barcena C, Bisig B, Nardi V, Sarro R, Ambrosini G, Weigert M, Spertini O, Blum S, Deplancke B, Seitz A, de Leval L, Naveiras O. MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology. Mod Pathol 2023;36(4):100088
  141. Sarton-Lohéac G, Nunes da Silva CG, Mazel F, Baud G, de Bakker V, Das S, El Chazli Y, Ellegaard K, Garcia-Garcera M, Glover N, Liberti J, Nacif Marçal L, Prasad A, Somerville V, SAGE class 2019-2020 and 2020-2021, Bonilla-Rosso G, Engel P. Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees. mBio 2023;14(2):e0353822
  142. Schnider B, Escudero FL, Imberty A, Lisacek F. BiotechLec: an interactive guide of commercial lectins for glycobiology and biomedical research applications. Glycobiology 2023:cwad034
  143. Schnidrig D, Garofoli A, Benjak A, Rätsch G, Rubin MA, SOCIBP consortium, Piscuoglio S, Ng CKY. PipeIT2: A tumor-only somatic variant calling workflow for molecular diagnostic Ion Torrent sequencing data. Genomics 2023;115(2):110587
  144. Schoeler T, Speed D, Porcu E, Pirastu N, Pingault JB, Kutalik Z. Participation bias in the UK Biobank distorts genetic associations and downstream analyses. Nat Hum Behav 2023
  145. Schütz S, Liechti N, Altpeter E, Labutin A, Wütrich T, Schmidt K, Buettcher M, Moser M, Bruggmann R, Wittwer M. Phylogeography of Francisella tularensis subspecies holarctica and epidemiology of tularemia in Switzerland Front Microbiol 2023;14
  146. Schütz SD, Liechti N, Altpeter E, Labutin A, Wütrich T, Schmidt KM, Buettcher M, Moser M, Bruggmann R, Wittwer M. Phylogeography of Francisella tularensis subspecies holarctica and epidemiology of tularemia in Switzerland. Front Microbiol 2023;14:1151049
  147. Serey-Gaut M, Cortes M, Makrythanasis P, Suri M, Taylor AMR, Sullivan JA, Asleh AN, Mitra J, Dar MA, McNamara A, Shashi V, Dugan S, Song X, Rosenfeld JA, Cabrol C, Iwaszkiewicz J, Zoete V, Pehlivan D, Akdemir ZC, Roeder ER, Littlejohn RO, Dibra HK, Byrd PJ, Stewart GS, Geckinli BB, Posey J, Westman R, Jungbluth C, Eason J, Sachdev R, Evans CA, Lemire G, VanNoy GE, O'Donnell-Luria A, Mau-Them FT, Juven A, Piard J, Nixon CY, Zhu Y, Ha T, Buckley MF, Thauvin C, Essien Umanah GK, Van Maldergem L, Lupski JR, Roscioli T, Dawson VL, Dawson TM, Antonarakis SE. Bi-allelic TTI1 variants cause an autosomal-recessive neurodevelopmental disorder with microcephaly. Am J Hum Genet 2023;110(3):499-515
  148. Servajean R, Bitbol AF. Impact of population size on early adaptation in rugged fitness landscapes. Philos Trans R Soc Lond B Biol Sci 2023;378(1877):20220045
  149. Sgarbossa D, Lupo U, Bitbol AF. Generative power of a protein language model trained on multiple sequence alignments. Elife 2023;12:e79854
  150. Sianta SA, Peischl S, Moeller DA, Brandvain Y. The efficacy of selection may increase or decrease with selfing depending upon the recombination environment. Evolution 2023;77(2):394-408
  151. Sjaarda J, Kutalik Z. Partner choice, confounding and trait convergence all contribute to phenotypic partner similarity. Nat Hum Behav 2023
  152. Steiner M, Pingel M, Falquet L, Giffard B, Griesser M, Leyer I, Preda C, Uzman D, Bacher S, Reineke A. Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards. PLoS One 2023;18(1):e0280516
  153. Stetka J, Usart M, Kubovcakova L, Rai S, Rao TN, Sutter J, Hao-Shen H, Dirnhofer S, Geier F, Bader MS, Passweg JR, Manolova V, Dürrenberger F, Ahmed N, Schroeder T, Ganz T, Nemeth E, Silvestri L, Nai A, Camaschella C, Skoda RC. Iron is a modifier of the phenotypes of JAK2-mutant myeloproliferative neoplasms. Blood 2023;141(17):2127-2140
  154. Strässle M, Grossmann J, Eppenberger P, Faas A, Jerkovic I, Floris J, Öhrström L, Akgül G, Aldakak L, Rühli F, Bender N, Staub K. Short-termed changes in quantitative ultrasound estimated bone density among young men in an 18-weeks follow-up during their basic training for the Swiss Armed Forces. PeerJ 2023;11:e15205
  155. Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res 2023;51(d1):D638-D646
  156. Tadros DM, Eggenschwiler S, Racle J, Gfeller D. The MHC Motif Atlas: a database of MHC binding specificities and ligands. Nucleic Acids Res 2023;51(d1):D428-D437
  157. Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J, European Reference Genome Atlas Consortium. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3
  158. Tichet M, Wullschleger S, Chryplewicz A, Fournier N, Marcone R, Kauzlaric A, Homicsko K, Deak LC, Umaña P, Klein C, Hanahan D. Bispecific PD1-IL2v and anti-PD-L1 break tumor immunity resistance by enhancing stem-like tumor-reactive CD8+ T cells and reprogramming macrophages. Immunity 2023;56(1):162-179.e6
  159. Timasheva Y, Lepik K, Liska O, Papp B, Kutalik Z. Widespread natural selection on metabolite levels in humans 2023
  160. Timin G, Milinkovitch MC. High-resolution confocal and light-sheet imaging of collagen 3D network architecture in very large samples. iScience 2023;26(4):106452
  161. Tofilo M, Voronova N, Nigmatullina L, Kuznetsova E, Timonina V, Efimenko B, Turgunkhujaev O, Avdeichik S, Ansar M, Popadin K, Kirillova A, Mazunin I. Live Birth of a Healthy Child in a Couple with Identical mtDNA Carrying a Pathogenic c.471_477delTTTAAAAinsG Variant in the MOCS2 Gene. Genes (Basel) 2023;14(3):720
  162. Touré H, Galindo LA, Lagune M, Glatigny S, Waterhouse RM, Guénal I, Herrmann JL, Girard-Misguich F, Szuplewski S. Mycobacterium abscessus resists the innate cellular response by surviving cell lysis of infected phagocytes. PLoS Pathog 2023;19(3):e1011257
  163. Touré V, Krauss P, Gnodtke K, Buchhorn J, Unni D, Horki P, Raisaro JL, Kalt K, Teixeira D, Crameri K, Österle S. FAIRification of health-related data using semantic web technologies in the Swiss Personalized Health Network. Sci Data 2023;10(1):127
  164. Trefny MP, Kirchhammer N, Auf der Maur P, Natoli M, Schmid D, Germann M, Fernandez Rodriguez L, Herzig P, Lötscher J, Akrami M, Stinchcombe JC, Stanczak MA, Zingg A, Buchi M, Roux J, Marone R, Don L, Lardinois D, Wiese M, Jeker LT, Bentires-Alj M, Rossy J, Thommen DS, Griffiths GM, Läubli H, Hess C, Zippelius A. Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy. Nat Commun 2023;14(1):86
  165. Trofimova O, Latypova A, DiDomenicantonio G, Lutti A, de Lange AG, Kliegel M, Stringhini S, Marques-Vidal P, Vaucher J, Vollenweider P, Strippoli MF, Preisig M, Kherif F, Draganski B. Topography of associations between cardiovascular risk factors and myelin loss in the ageing human brain. Commun Biol 2023;6(1):392
  166. Valentin JDP, Altenried S, Varadarajan AR, Ahrens CH, Schreiber F, Webb JS, van der Mei HC, Ren Q. Identification of Potential Antimicrobial Targets of Pseudomonas aeruginosa Biofilms through a Novel Screening Approach. Microbiol Spectr 2023:e0309922
  167. Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models. J Mol Biol 2023:168021
  168. Vora J, Navelkar R, Vijay-Shanker K, Edwards N, Martinez K, Ding X, Wang T, Su P, Ross K, Lisacek F, Hayes C, Kahsay R, Ranzinger R, Tiemeyer M, Mazumder R. The glycan structure dictionary-a dictionary describing commonly used glycan structure terms. Glycobiology 2023:cwad014
  169. Waespe N, Mlakar SJ, Dupanloup I, Rezgui MA, Bittencourt H, Krajinovic M, Kuehni CE, Nava T, Ansari M. A novel integrative multi-omics approach to unravel the genetic determinants of rare diseases with application in sinusoidal obstruction syndrome. PLoS One 2023;18(4):e0281892
  170. Wegmann D, Eckel R. Human evolution: When admixture met selection. Curr Biol 2023;33(7):R259-R261
  171. Weiler P, Van den Berge K, Street K, Tiberi S. A Guide to Trajectory Inference and RNA Velocity. Methods Mol Biol 2023;2584:269-292
  172. Wicky A, Gatta R, Latifyan S, Micheli R, Gerard C, Pradervand S, Michielin O, Cuendet MA. Interactive process mining of cancer treatment sequences with melanoma real-world data. Front Oncol 2023;13:1043683
  173. Winstanley-Zarach P, Rot G, Kuba S, Smagul A, Peffers MJ, Tew SR. Analysis of RNA Polyadenylation in Healthy and Osteoarthritic Human Articular Cartilage. Int J Mol Sci 2023;24(7):6611
  174. Wolfe AJ, Rademacher DJ, Mores CR, Evans RJ, Overholt T, Halverson T, Limeira R, Matthews C, Badlani G, Brubaker L, Walker SJ. Detection of Bacteria in Bladder Mucosa of Adult Females. J Urol 2023;209(5):937-949
  175. Wolski WE, Nanni P, Grossmann J, d'Errico M, Schlapbach R, Panse C. prolfqua: A Comprehensive R-Package for Proteomics Differential Expression Analysis. J Proteome Res 2023;22(4):1092-1104
  176. Xu ZM, Naret O, Fellay J. G2GSnake: A Snakemake workflow for host-pathogen genomic association studies 2023
  177. Yang L, Sadler MC, Altman RB. Genetic association studies using disease liabilities from deep neural networks 2023
  178. Zamariolli M, Auwerx C, Sadler MC, van der Graaf A, Lepik K, Schoeler T, Moysés-Oliveira M, Dantas AG, Melaragno MI, Kutalik Z. The impact of 22q11.2 copy-number variants on human traits in the general population. Am J Hum Genet 2023;110(2):300-313
  179. Zaru R, Orchard S, UniProt Consortium. UniProt Tools: BLAST, Align, Peptide Search, and ID Mapping. Curr Protoc 2023;3(3):e697
  180. Zwyer M, Rutaihwa LK, Windels E, Hella J, Menardo F, Sasamalo M, Sommer G, Schmülling L, Borrell S, Reinhard M, Dötsch A, Hiza H, Stritt C, Sikalengo G, Fenner L, De Jong BC, Kato-Maeda M, Jugheli L, Ernst JD, Niemann S, Jeljeli L, Ballif M, Egger M, Rakotosamimanana N, Yeboah-Manu D, Asare P, Malla B, Dou HY, Zetola N, Wilkinson RJ, Cox H, Carter EJ, Gnokoro J, Yotebieng M, Gotuzzo E, Abimiku A, Avihingsanon A, Xu ZM, Fellay J, Portevin D, Reither K, Stadler T, Gagneux S, Brites D. Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania. PLoS Pathog 2023;19(4):e1010893

 

Previous publications

Publications 2022

Publications 2021

Publications 2020

Publications 2019

Publications 2018

Publications 2017

Publications 2016

Publications 2015