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.


  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
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