Peer-reviewed papers and preprints by our members

Scientific publications 2025

Bioinformatics has become essential to convert biological questions into answers. Discover the breadth of our scientists' work and contributions through their publications. 

 

Source: Europe PMC, latest update: 01.07.25

Discover the SIB Remarkable Outputs 2024

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.

Peer-reviewed articles and preprints

  1. Aoki-Kinoshita KF, Lisacek F, Mazumder R, Ranzinger R, Tiemeyer M, Yamada I, Packer NH. Meeting report of the GlySpace Alliance and GaLSIC symposium. Glycobiology2025;35(5):cwaf019
  2. Aparo A, Avesani S, Parmigiani L, Napoli S, Bertoni F, Bonnici V, Cascione L, Giugno R. EasyCircR: Detection and reconstruction of circular RNAs post-transcriptional regulatory interaction networks. Comput Biol Med 2025;188:109846
  3. Balajti M, Kandhari R, Jurič B, Zavolan M, Kanitz A. HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries. Bioinformatics 2025;41(3):btaf076
  4. Bao K, Oscarsson J, Gehring P, Grossmann J, Belibasakis GN, Bostanci N. <i>Aggregatibacter</i><i>aphrophilus</i> T6SS Effectors in Host-Bacterial Interactions. J Dent Res2025:220345251337745
  5. Barbera MC, Guarrera L, Re Cecconi AD, Cassanmagnago GA, Vallerga A, Lunardi M, Checchi F, Di Rito L, Romeo M, Mapelli SN, Schoser B, Generozov EV, Molecular Genetics Group, Jansen R, de Geus EJC, Penninx B, van Dongen J, Craparotta I, Piccirillo R, Ahmetov II, Bolis M. Increased ectodysplasin-A2-receptor EDA2R is a ubiquitous hallmark of aging and mediates parainflammatory responses. Nat Commun 2025;16(1):1898
  6. Bastian FB, Cammarata AB, Carsanaro S, Detering H, Huang WT, Joye S, Niknejad A, Nyamari M, Mendes de Farias T, Moretti S, Tzivanopoulou M, Wollbrett J, Robinson-Rechavi M. Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools. Nucleic Acids Res 2025;53(d1):D878-D885
  7. Bayer F, Roncador M, Moffa G, Morita K, Takahashi K, Beerenwinkel N, Kuipers J. Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies. Nat Commun 2025;16(1):4043
  8. Bağcı C, Nuhamunada M, Goyat H, Ladanyi C, Sehnal L, Blin K, Kautsar SA, Tagirdzhanov A, Gurevich A, Mantri S, von Mering C, Udwary D, Medema MH, Weber T, Ziemert N. BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes. Nucleic Acids Res 2025;53(d1):D618-D624
  9. Bejarano L, Lourenco J, Kauzlaric A, Lamprou E, Costa CF, Galland S, Maas RR, Guerrero Aruffo P, Fournier N, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Single-cell atlas of endothelial and mural cells across primary and metastatic brain tumors. Immunity 2025;58(4):1015-1032.e6
  10. Beyer D, Vaccarin C, Schmid JV, Deberle LM, Deupi X, Schibli R, Müller C. Design and Preclinical Evaluation of Novel uPAR-Targeting Radiopeptides Modified with an Albumin-Binding Entity.Mol Pharm 2025;22(6):3242-3254
  11. Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, Pinto BL, Orr A, Paysan-Lafosse T, Ponamareva I, Salazar GA, Bordin N, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Llinares-López F, Marchler-Bauer A, Meng-Papaxanthos L, Mi H, Natale DA, Orengo CA, Pandurangan AP, Piovesan D, Rivoire C, Sigrist CJA, Thanki N, Thibaud-Nissen F, Thomas PD, Tosatto SCE, Wu CH, Bateman A. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res 2025;53(d1):D444-D456
  12. Bolleman J, Emonet V, Altenhoff A, Bairoch A, Blatter MC, Bridge A, Duvaud S, Gasteiger E, Kuznetsov D, Moretti S, Michel PA, Morgat A, Pagni M, Redaschi N, Zahn-Zabal M, de Farias TM, Sima AC. A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications. Gigascience 2025;14:giaf045
  13. Bramon Mora B, Lindsay H, Thiébaut A, Stuart KD, Gottardo R. tagtango: an application to compare single-cell annotations. Bioinformatics 2025;41(2):btaf012
  14. Brasier N, Niederberger C, Zanella M, Othman A, Schlapbach R, Kunz L, Dittmann A, Reeve K, Prummer M, Goldhahn J. The molecular signature of heat stress in sweat reveals non-invasive biomarker candidates for health monitoring. Commun Biol 2025;8(1):650
  15. Bulliard M, Pinjusic K, Iacobucci L, Schmuziger C, Fournier N, Constam DB. Kallikrein-8 mediates furin-independent Activin-A precursor processing to stimulate tumor growth in melanoma.Nat Commun 2025;16(1):2354
  16. Buzan E, de Guttry C, Bortoluzzi C, Street NR, Lucek K, Rosling A, Ometto L, Mouton A, Marins LS, Ruiz-López MJ, Melo-Ferreira J, Ottosson E, Mazzoni CJ, Waterhouse RM. Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation. Mol Ecol 2025:e70001
  17. Chamberlain JD, Ackermann D, Bochud M, Booth T, Chapatte L, Corley J, Cox SR, Harris SE, Kinnaer C, Juster RP, Locatelli I, Nanchen D, Ponte B, Pruijm M, Pradervand S, Shiels PG, Stringhini S, Nusslé S, Gonseth-Nusslé S. Development and validation of an epigenetic signature of allostatic load. Biosci Rep 2025;45(4):BSR20241663
  18. Chen Z, Tsui JL, Cai J, Su S, Viboud C, du Plessis L, Lemey P, Kraemer MUG, Yu H. Disruption of seasonal influenza circulation and evolution during the 2009 H1N1 and COVID-19 pandemics in Southeastern Asia. Nat Commun 2025;16(1):475
  19. Cherrak Y, Younes AA, Perez-Molphe-Montoya E, Maurer L, Yilmaz K, Enz U, Zeder C, Kiefer P, Christen P, Gül E, Vorholt JA, von Mering C, Hardt WD. Neutrophil recruitment during intestinal inflammation primes Salmonella elimination by commensal E. coli in a context-dependent manner. Cell Host Microbe 2025;33(3):358-372.e4
  20. Chiva C, Olivella R, Staes A, Mendes Maia T, Panse C, Stejskal K, Douché T, Lombard B, Schuhmann A, Loew D, Mechtler K, Matondo M, Rettel M, Helm D, Impens F, Devos S, Shevchenko A, Nanni P, Sabidó E. A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities. J Proteome Res 2025;24(2):397-409
  21. Colucci M, Sarill M, Maddalena M, Valdata A, Troiani M, Massarotti M, Bolis M, Bressan S, Kohl A, Robesti D, Saponaro M, Shi Q, Song P, Brina D, Calì B, Alimonti A. Senescence in cancer.Cancer Cell 2025:S1535-6108(25)00224-7
  22. Conforti S, Rossi Orts P, Tamminen M, Julian TR. High-Throughput Multiplex Detection of Antibiotic-Resistant Genes and Virulence Factors in Escherichia coli Using Digital Multiplex Ligation Assay. J Mol Diagn 2025;27(6):511-524
  23. Cooper RL, Milinkovitch MC. In vivo sonic hedgehog pathway antagonism temporarily results in ancestral proto-feather-like structures in the chicken. PLoS Biol 2025;23(3):e3003061
  24. Croce G, Lani R, Tardivon D, Bobisse S, de Tiani M, Bragina M, Perez MAS, Michaux J, Pak HS, Michel A, Gehret T, Schmidt J, Guillame P, Bassani-Sternberg M, Zoete V, Harari A, Rufer N, Hebeisen M, Dunn SM, Gfeller D. Phage display enables machine learning discovery of cancer antigen-specific TCRs. Sci Adv 2025;11(24):eads5589
  25. Cui H, Tejada-Lapuerta A, Brbić M, Saez-Rodriguez J, Cristea S, Goodarzi H, Lotfollahi M, Theis FJ, Wang B. Towards multimodal foundation models in molecular cell biology. Nature2025;640(8059):623-633
  26. Das SG, Mungan M, Krug J. Epistasis-mediated compensatory evolution in a fitness landscape with adaptational tradeoffs. Proc Natl Acad Sci U S A 2025;122(15):e2422520122
  27. Dennstädt F, Hastings J, Putora PM, Schmerder M, Cihoric N. Implementing large language models in healthcare while balancing control, collaboration, costs and security. NPJ Digit Med2025;8(1):143
  28. Di Giacomo AM, Subudhi S, Vos W, Andreatta M, Carmona S, McTavish W, Seliger B, Ibrahim R, Lahn M, Smith M, Eggermont A, Fox BA, Maio M. Perspectives on the role of "-Omics" in predicting response to immunotherapy. Eur J Cancer 2025;220:115393
  29. Ding W, Silvestro D, Onstein RE, Wu M, Zhou Z, Xing Y. The stepwise rise of angiosperm-dominated terrestrial ecosystems. Biol Rev Camb Philos Soc 2025
  30. Dmitrijeva M, Ruscheweyh HJ, Feer L, Li K, Miravet-Verde S, Sintsova A, Mende DR, Zeller G, Sunagawa S. The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities. Nucleic Acids Res 2025;53(d1):D797-D805
  31. Dondi A, Borgsmüller N, Ferreira PF, Haas BJ, Jacob F, Heinzelmann-Schwarz V, Tumor Profiler Consortium, Beerenwinkel N. De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data. Genome Res 2025;35(4):900-913
  32. Dong Y, Saglietti C, Bayard Q, Espin Perez A, Carpentier S, Buszta D, Tissot S, Dubois R, Kamburov A, Kang S, Haignere C, Sarkis R, Andre S, Alexandre Gaveta M, Lopez Lastra S, Piazzon N, Santos R, von Loga K, Hoffmann C, Coukos G, Peters S, Soumelis V, Durand EY, de Leval L, Gottardo R, Homicsko K, Madissoon E. Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity. Nat Commun 2025;16(1):4400
  33. Drnevich J, Tan FJ, Almeida-Silva F, Castelo R, Culhane AC, Davis S, Doyle MA, Geistlinger L, Ghazi AR, Holmes S, Lahti L, Mahmoud A, Nishida K, Ramos M, Rue-Albrecht K, Shih DJH, Gatto L, Soneson C. Learning and teaching biological data science in the Bioconductor community. PLoS Comput Biol 2025;21(4):e1012925
  34. Droghetti R, Fuchs P, Iuliani I, Firmano V, Tallarico G, Calabrese L, Grilli J, Sclavi B, Ciandrini L, Cosentino Lagomarsino M. Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing E. coli. Nat Commun 2025;16(1):3063
  35. Duval F, Lourenco J, Hicham M, Boivin G, Guichard A, Wyser-Rmili C, Fournier N, Mansouri N, De Palma M. Trajectories of macrophage ontogeny and reprogramming in cancer. iScience2025;28(5):112498
  36. Duval F, Lourenco J, Hicham M, Boivin G, Guichard A, Wyser-Rmili C, Fournier N, Mansouri N, De Palma M. Trajectories of macrophage ontogeny and reprogramming in cancer iScience2025;28(5)
  37. Emons M, Blanquart F, Lehtinen S. The evolution of antibiotic resistance in Europe, 1998-2019. PLoS Pathog 2025;21(4):e1012945
  38. Feuermann M, Mi H, Gaudet P, Muruganujan A, Lewis SE, Ebert D, Mushayahama T, Gene Ontology Consortium, Thomas PD. A compendium of human gene functions derived from evolutionary modelling. Nature 2025;640(8057):146-154
  39. Fu J, Zanotelli VRT, Howald C, Chammartin N, Kolpakov I, Xenarios I, Froese DS, Wollscheid B, Pedrioli PGA, Goetze S. A Multi-Omics Framework for Decoding Disease Mechanisms: Insights From Methylmalonic Aciduria. Mol Cell Proteomics 2025;24(7):100998
  40. Fuqua T, Wagner A. The latent cis-regulatory potential of mobile DNA in Escherichia coli. Nat Commun 2025;16(1):4740
  41. Gaboriau T, Tobias JA, Silvestro D, Salamin N. Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation. Syst Biol 2025;74(2):267-281
  42. Gaio D, Tackmann J, Perez-Molphe-Montoya E, Näpflin N, Patsch D, Malfertheiner L, von Mering C. Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs) 2025
  43. Gayet-Ageron A, Ben Messaoud K, Richards M, Jaksic C, Gobeill J, Liyanapathirana J, Mottin L, Naderi N, Ruch P, Mariot Z, Calmy A, Friedman J, Leibovici L, Schroter S. Gender and geographical bias in the editorial decision-making process of biomedical journals: a case-control study. BMJ Evid Based Med 2025;30(3):149-162
  44. Geng A, Brenig RG, Roux J, Lütge M, Cheng HW, Flint EE, Lussier POG, Meier MA, Pop OT, Künzler-Heule P, Matter MS, Wendon J, McPhail MJW, Soysal S, Semela D, Heim M, Weston CJ, Ludewig B, Bernsmeier C. Circulating monocytes upregulate CD52 and sustain innate immune function in cirrhosis unless acute decompensation emerges. J Hepatol 2025;83(1):146-160
  45. German J, Cordioli M, Tozzo V, Urbut S, Arumäe K, Smit RAJ, Lee J, Li JH, Janucik A, Ding Y, Akinkuolie A, Heyne HO, Eoli A, Saad C, Al-Sarraj Y, Abdel-Latif R, Mohammed S, Hail MA, Barry A, Wang Z, Cajuso T, Corbetta A, Natarajan P, Ripatti S, Philippakis A, Szczerbinski L, Pasaniuc B, Kutalik Z, Mbarek H, Loos RJF, Vainik U, Ganna A. Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery. Nat Med 2025
  46. German J, Yang Z, Urbut S, Vartiainen P, FinnGen, Natarajan P, Patorno E, Kutalik Z, Philippakis A, Ganna A. Incorporating genetic data improves target trial emulations and informs the use of polygenic scores in randomized controlled trial design. Nat Genet 2025
  47. German J, Yang Z, Urbut S, Vartiainen P, FinnGen, Natarajan P, Patorno E, Kutalik Z, Philippakis A, Ganna A. Author Correction: Incorporating genetic data improves target trial emulations and informs the use of polygenic scores in randomized controlled trial design. Nat Genet 2025
  48. Glaus AN, Brechet M, Swinnen G, Lebeigle L, Iwaszkiewicz J, Ambrosini G, Julca I, Zhang J, Roberts R, Iseli C, Guex N, Jiménez-Gómez J, Glover N, Martin GB, Strickler S, Soyk S. Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing. Nat Genet 2025;57(1):231-241
  49. Godbold G, Proescher J, Gaudet P. New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern. J Biomed Semantics 2025;16(1):4
  50. Gremmelspacher D, Gawron J, Szczerba BM, Jahn K, Castro-Giner F, Kuipers J, Singer J, Marass F, Gvozdenovic A, Budinjas S, Pueschel H, Rentsch CA, Zippelius A, Heinzelmann-Schwarz V, Kurzeder C, Weber WP, Rochlitz C, Vetter M, Beerenwinkel N, Aceto N. Phylogenetic inference reveals clonal heterogeneity in circulating tumor cell clusters. Nat Genet 2025;57(6):1357-1361
  51. Hablützel L, Mullon C, Schmid M. The evolution of local adaptation in long-lived species. Evolution 2025:qpaf031
  52. Haddox HK, Angehrn G, Sesta L, Jennings-Shaffer C, Temple SD, Galloway JG, Hinrichs AS, DeWitt WS, Bloom JD, Iv FAM, Neher RA. The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure. Nucleic Acids Res 2025;53(11):gkaf503
  53. Hamilton FW, Hughes DA, Lu T, Kutalik Z, Gkatzionis A, Tilling K, Hartwig FP, Davey Smith G. Non-linear Mendelian randomization: evaluation of effect modification in the residual and doubly-ranked methods with simulated and empirical examples. Eur J Epidemiol 2025
  54. Hinz FB, Masters MR, Nguyen JT, Mahmoud AH, Lill MA. Accelerated Hydration Site Localization and Thermodynamic Profiling. J Chem Inf Model 2025;65(6):2794-2805
  55. Hodcroft EB, Wohlfender MS, Neher RA, Riou J, Althaus CL. Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2. PLoS Comput Biol 2025;21(4):e1012960
  56. Huang YH, Escalona HE, Sun YF, Zhang PF, Du XY, Gong SR, Tang XF, Liang YS, Yang D, Chen PT, Yang HY, Chen ML, Hüttel B, Hlinka O, Wang X, Meusemann K, Ślipiński A, Zwick A, Waterhouse RM, Misof B, Niehuis O, Li HS, Pang H. Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory. BMC Biol2025;23(1):67
  57. Huang YN, Munteanu V, Love MI, Ronkowski CF, Deshpande D, Wong-Beringer A, Corbett-Detig R, Dimian M, Moore JH, Garmire LX, Reddy TBK, Butte AJ, Robinson MD, Eskin E, Abedalthagafi MS, Mangul S. Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies. Cell Genom 2025;5(5):100845
  58. Höcketstaller K, Marti IA, Bank C, Yilmaz B, Becker J. Antimicrobial resistance in wildlife: Associations with environmental factors and taxonomic variation. Environ Res 2025;281:121968
  59. Iber D, Mederacke M, Vetter R. Coordination of nephrogenesis with branching of the urinary collecting system, the vasculature and the nervous system. Curr Top Dev Biol 2025;163:45-82
  60. Ito J, Strange A, Liu W, Joas G, Lytras S, Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato K. A protein language model for exploring viral fitness landscapes. Nat Commun2025;16(1):4236
  61. Jamy M, Huber T, Antoine T, Ruscheweyh H, Paoli L, Pelletier E, Delmont TO, Burki F. New deep-branching environmental plastid genomes on the algal tree of life 2025
  62. Jelcic I, Naghavian R, Fanaswala I, Macnair W, Esposito C, Calini D, Han Y, Marti Z, Raposo C, Sarabia Del Castillo J, Oldrati P, Erny D, Kana V, Zheleznyakova G, Al Nimer F, Tackenberg B, Reichen I, Khademi M, Piehl F, Robinson MD, Jelcic I, Sospedra M, Pelkmans L, Malhotra D, Reynolds R, Jagodic M, Martin R. T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis. Cell Rep Med 2025;6(3):102027
  63. Julou T, Gervais T, de Groot D, van Nimwegen E. Growth rate controls the sensitivity of gene regulatory circuits. Sci Adv 2025;11(17):eadu9279
  64. Jung V, Vincent-Cuaz C, Tumescheit C, Fournier L, Darsinou M, Xu ZM, Saadat A, Wang Y, Tsantoulis P, Michielin O, Fellay J, Patani R, Ramos A, Frossard P, Hastings J, Riccio A, van der Plas L, Luisier R. Decoding the interactions and functions of non-coding RNA with artificial intelligence. Nat Rev Mol Cell Biol 2025
  65. Karakulak T, Zajac N, Bolck HA, Bratus-Neuenschwander A, Zhang Q, Qi W, Basu D, Oltra TC, Rehrauer H, von Mering C, Moch H, Kahraman A. Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids. Genome Res 2025;35(4):698-711
  66. Kim KM, Lizano AMD, Toonen RJ, Ravago-Gotanco R. Genomic Divergence of Sympatric Lineages Within <i>Stichopus</i> cf. <i>horrens</i> (Echinodermata: Stichopodidae): Insights on Reproductive Isolation Inferred From SNP Markers. Ecol Evol 2025;15(4):e71283
  67. Kirchhoffer OA, Quirós-Guerrero L, Nitschke J, Nothias LF, Burdet F, Marcourt L, Hanna N, Mehl F, David B, Grondin A, Queiroz EF, Pagni M, Soldati T, Wolfender JL. Prioritization of novel anti-infective stilbene derivatives by combining metabolomic data organization and a stringent 3R-infection model in a knowledge graph. RSC Adv 2025;15(17):13010-13030
  68. Komarov N, Fritsch C, Maier GL, Bues J, Biočanin M, Avalos CB, Dodero A, Kwon JY, Deplancke B, Sprecher SG. Food hardness preference reveals multisensory contributions of fly larval gustatory organs in behaviour and physiology. PLoS Biol 2025;23(1):e3002730
  69. Koptekin D, Aydoğan A, Karamurat C, Altınışık NE, Vural KB, Kazancı DD, Doğu AK, Kaptan D, Gemici HC, Yüncü E, Moots HM, Umurtak G, Duru R, Fidan E, Çevik Ö, Erdoğu B, Korkut T, Knüsel CJ, Haddow S, Larsen CS, Özbal R, Gerritsen F, Özdoğan E, Akbaba A, Usanmaz UO, Derici YC, Uçmazoğlu M, Jay F, Özdoğan M, Götherström A, Erdal YS, Malaspinas AS, Atakuman Ç, Özer F, Somel M. Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean. Science 2025;388(6754):eadr3326
  70. Koptekin D, Yapar E, Vural KB, Sağlıcan E, Altınışık NE, Malaspinas AS, Alkan C, Somel M. Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data. Genome Biol 2025;26(1):6
  71. Koutsovoulos GD, Poullet M, Elashry A, Kozlowski DKL, Sallet E, Da Rocha M, Perfus-Barbeoch L, Martin-Jimenez C, Frey JE, Ahrens CH, Kiewnick S, Danchin EGJ. Retraction Note: Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. Sci Data 2025;12(1):183
  72. Kraemer MUG, Tsui JL, Chang SY, Lytras S, Khurana MP, Vanderslott S, Bajaj S, Scheidwasser N, Curran-Sebastian JL, Semenova E, Zhang M, Unwin HJT, Watson OJ, Mills C, Dasgupta A, Ferretti L, Scarpino SV, Koua E, Morgan O, Tegally H, Paquet U, Moutsianas L, Fraser C, Ferguson NM, Topol EJ, Duchêne DA, Stadler T, Kingori P, Parker MJ, Dominici F, Shadbolt N, Suchard MA, Ratmann O, Flaxman S, Holmes EC, Gomez-Rodriguez M, Schölkopf B, Donnelly CA, Pybus OG, Cauchemez S, Bhatt S. Artificial intelligence for modelling infectious disease epidemics.Nature 2025;638(8051):623-635
  73. Kraft A, Kirschner MB, Orlowski V, Ronner M, Bodmer C, Boeva V, Opitz I, Meerang M. Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection. BMC Cancer2025;25(1):212
  74. Kuipers J, Tuncel MA, Ferreira PF, Jahn K, Beerenwinkel N. Single-cell copy number calling and event history reconstruction. Bioinformatics 2025;41(3):btaf072
  75. Kushida T, de Farias TM, Sima AC, Dessimoz C, Chiba H, Bastian FB, Masuya H. Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs. BMC Med Inform Decis Mak 2025;25(suppl 1):189
  76. Kweon H, Burik CAP, Ning Y, Ahlskog R, Xia C, Abner E, Bao Y, Bhatta L, Faquih TO, de Feijter M, Fisher P, Gelemanović A, Giannelis A, Hottenga JJ, Khalili B, Lee Y, Li-Gao R, Masso J, Myhre R, Palviainen T, Rietveld CA, Teumer A, Verweij RM, Willoughby EA, Agerbo E, Bergmann S, Boomsma DI, Børglum AD, Brumpton BM, Davies NM, Esko T, Gordon SD, Homuth G, Ikram MA, Johannesson M, Kaprio J, Kidd MP, Kutalik Z, Kwong ASF, Lee JJ, Luik AI, Magnus P, Marques-Vidal P, Martin NG, Mook-Kanamori DO, Mortensen PB, Oskarsson S, Pedersen EM, Polašek O, Rosendaal FR, Smart MC, Snieder H, van der Most PJ, Vollenweider P, Völzke H, Willemsen G, Beauchamp JP, DiPrete TA, Linnér RK, Lu Q, Morris TT, Okbay A, Harden KP, Abdellaoui A, Hill WD, de Vlaming R, Benjamin DJ, Koellinger PD. Associations between common genetic variants and income provide insights about the socio-economic health gradient. Nat Hum Behav2025;9(4):794-805
  77. Labarile M, Thorball CW, Hodel F, Fellay J, Tepekule B, Calmy A, Stöckle M, Damonti L, Surial B, Cavassini M, Bernasconi E, Notter J, Günthard HF, Nemeth J, Tarr PE, Pasin C, Kouyos RD, and the Swiss HIV Cohort Study. Polygenic Risk Scores for Type 2 Diabetes in the Swiss HIV Cohort Study. J Acquir Immune Defic Syndr 2025
  78. Laman Trip DS, van Oostrum M, Memon D, Frommelt F, Baptista D, Panneerselvam K, Bradley G, Licata L, Hermjakob H, Orchard S, Trynka G, McDonagh EM, Fossati A, Aebersold R, Gstaiger M, Wollscheid B, Beltrao P. A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes. Nat Biotechnol 2025
  79. Landi M, Carluccio AV, Shah T, Niazi A, Stavolone L, Falquet L, Gisel A, Bongcam-Rudloff E. Genome-wide comparison reveals large structural variants in cassava landraces. BMC Genomics2025;26(1):362
  80. Lecointre M, Guillot J, Marcone R, Ozdoganlar D, Cayatte M, Jaensson Gyllenbäck E, Liberg D, Fournier N, Homicsko K, Hanahan D. HPV16-Expressing Tumors Release Multiple IL-1 Ligands to Orchestrate Systemic Immunosuppression Whose Disruption Enables Efficacy of a Therapeutic Vaccine. Cancer Discov 2025:OF1-OF26
  81. Leota J, Presby DM, Le F, Czeisler MÉ, Mascaro L, Capodilupo ER, Wiley JF, Drummond SPA, Rajaratnam SMW, Facer-Childs ER. Dose-response relationship between evening exercise and sleep. Nat Commun 2025;16(1):3297
  82. Li J, Farrow M, Ibrahim K, McTigue DM, Kramer J, Tong B, Jutzeler C, Jones L, Yarar-Fisher C. Racial differences in serological markers across the first year of injury in spinal cord injury: responses to the letter to editor. Spinal Cord 2025
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