Peer-reviewed papers and preprints by our members

Scientific publications 2026

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: 01.06.26

Discover the SIB Remarkable Outputs 2025

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. Aarts EM, Laman Trip DS, Neatu R, Martin CG, Riley B, Kraus A, Green A, Al-Hamed MH, Armstrong RE, Sayer JA, Bachmann-Gagescu R, Beltrao P. Network-based framework for studying etiology and phenotypic diversity in primary ciliopathies. Genome Biol 2026;27(1):105
  2. Abreu-Mota T, Marx AF, Winterberg D, Tintignac K, Fixemer J, Geier F, Brodmann N, Seven C, Reichmuth C, Kastner AL, Lu M, Bonilla WV, Dimitrova M, Sahin M, Zimmer G, Peipp M, Pinschewer DD. B cell immunity to the Lassa virus glycoprotein is a correlate of vaccination-induced virus control in mice. Nat Commun 2026
  3. Agabiti C, Donato E, Setti E, Dagenais P, Milinkovitch MC, Laschi C, Sabatini AM, Mazzolai B, Falotico E. Stereotypical force patterns of the elephant trunk in planar reaching movements. iScience 2026;29(4):115108
  4. Alouche N, Cannelle H, Favre S, Jokić M, Villegas JA, Maréchal S, De Nolf C, Delacrétaz M, Sifis A, Chapuis C, Burns A, Ambrosini G, Dupanloup I, Abe J, Koch U, Guex N, Stein JV, Maillard I, Cupedo T, Ludewig B, Radtke F, Janssens S, Luther SA. Homeostatic mature dendritic cells instruct fibroblast specialization via Notch2 signaling to establish T cell niches. Immunity 2026:S1074-7613(26)00134-2
  5. Anchieri L, G Amorim CE, Neuenschwander S, Malaspinas AS. Assessing Ancient DNA Sampling Strategies for Natural Selection Inference in Humans Using Allele Frequency Time Series Data. Genome Biol Evol 2026;18(2):evaf234
  6. Andreatta M, Carmona SJ. UCell and pyUCell: single-cell gene signature scoring for R and Python. Bioinformatics 2026;42(2):btag055
  7. Anglada-Girotto M, Segura-Morales C, Moakley DF, Zhang C, Miravet-Verde S, Califano A, Serrano L. Exon inclusion signatures enable accurate estimation of splicing factor activity. Nat Commun 2026;17(1):1994
  8. Aton M, McDonald D, Cañardo Alastuey J, Azom R, Batra P, Bezshapkin V, Bolyen E, Cagle A, Caporaso JG, Debelius JW, Gorlick K, Hamsanipally N, Hunger L, Keluskar A, Liao D, Lu YY, Navas-Molina JA, Pitman A, Rideout JR, Sazonov A, Sathappan B, Schwarzberg Lipson K, Sfiligoi I, Tapo C, Vázquez-Baeza Y, Wu Z, Xu ZZ, Ye MS, Zhao J, Knight R, Morton JT, Zhu Q. Scikit-bio: a fundamental Python library for biological omic data analysis. Nat Methods 2026;23(2):274-276
  9. Awada A, Thorball CW, Timonina V, Carrington M, McLaren PJ, Fellay J. Human genetics of HIV infection. Curr Opin Virol 2026;76:101535
  10. Bacon WA, Batut B, Srikakulam SK, Zierep P, Bretaudeau A, Grüning B, Le Corguillé G, Hecht H, Davis JY, Hotz HR, Serrano-Solano B. Ten common misconceptions about Galaxy (and why they are wrong!). PLoS Comput Biol 2026;22(2):e1013869
  11. Barua A, Srivastava M, Beinsteiner B, Laudet V, Robinson-Rechavi M. Estimates of molecular convergence reveal multiple genes with adaptive variation across teleost fish. Mol Biol Evol 2026;43(1):msag015
  12. Bejarano L, Hernández-Barranco A, Roh V, Méndez RS, Lamprou E, Costa CF, Ballabio M, Hegi ME, Fournier N, Joyce JA. Tumor-derived aminopeptidase N promotes early stages of brain metastatic colonization. Cell Rep 2026;45(2):116895
  13. Ben Zouari Y, Joshi O, Salvi A, Kessler S, Ducret S, Ross F, Holwerda SJB, Vilain N, Mamilla-Sanivaram S, Smallwood S, Kohler H, Stadler MB, Minoux M, Rijli FM. Polycomb chromatin topology enables long-range enhancer recruitment during craniofacial development. Nat Commun 2026
  14. Benoit RM, Wang J, Beyer D, Abbas A, Rodrigues MJ, Wieser MM, Deupi X, Müller C, Suga H, Bode JW. Development and structure-guided characterization of a novel ACE2-binding macrocyclic peptide. J Struct Biol X 2026;13:100145
  15. Bilous M, Buszta D, Bac J, Kang S, Dong Y, Tissot S, Andre S, Alexandre Gaveta M, Voize C, Peters S, Homicsko K, Gottardo R. Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics. Nat Methods 2026
  16. Blagojevic A, Rüthemann P, Widmer K, Mannes M, Caglar D, Tiric M, Sovichan ME, Pouw RB, Rabbani S, Huber-Lang M, Ricklin D. Production and characterization of gigastasin, a leech-derived inhibitor of complement and coagulation pathways. Sci Rep 2026
  17. Blöcher J, Vallini L, Velte M, Eckel R, Guyon L, Winkelbach L, Thomas MG, Gharehbaghi N, Mitchell CT, Schümann J, Köhler S, Seyr E, Krichel K, Rau S, Hirsch J, Duras J, Cloarec-Pioffet P, Füglistaler A, Klement K, Wilkenhöner M, Vetterdietz L, Gentilin F, Müller M, Mücke AL, Zedda N, Tawfik Y, Saal E, McGlynn G, Bramanti B, Orschiedt J, Molitor R, Fliß B, Spazier I, Shankland D, Vetterling C, Karpf K, Planert V, Hölzl S, Codreanu-Windauer S, Quast D, Mikić I, Fiedler S, Päffgen B, Brami M, Richter T, Chaix R, Brather-Walter S, Steffens P, Marquart M, Becker T, Haberstroh J, Meier M, Schmidt-Hofner S, Brather S, Harbeck M, Patzold S, Wegmann D, Burger J. Demography and life histories across the Roman frontier in Germany 400-700 CE. Nature 2026
  18. Bolli E, Wirapati P, Hicham M, Xie Y, Siwicki M, Duval F, Goubet AG, Kiss M, Zitti B, Zwahlen T, Mcdowell S, Bill R, Angerani S, Engblom C, Anderson S, Jiang A, Hartley O, Sykes DB, Jankovic M, Fournier N, Gunzer M, Tarussio D, Tissot S, Sadow PM, Faquin WC, Sade-Feldman M, Weissleder R, Pai S, Mercier F, Manguso R, Pittet MJ. CCL3 is produced by aged neutrophils across cancers and promotes tumor growth. Cancer Cell 2026;44(3):624-640.e12
  19. Botman D, de Groot DH, Wehrens M, van Rossum K, Yska S, van der Kieft B, Albert V, Minghetti N, Goedhart J, Teusink B. Side-by-Side Systematic Characterization of Novel FPs in Budding Yeast. ACS Synth Biol 2026;15(4):1312-1326
  20. Botos MA, Arora P, Chouvardas P, Mercader N. Correction: Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart. Sci Rep 2026;16(1):14031
  21. Bozzi D, Broomandkhoshbacht NZ, Delgado M, Buikstra JE, Amorim CEG, Kassadjikova K, Estrada MP, Greub G, Rascovan N, Šmajs D, Fehren-Schmitz L, Malaspinas AS, Nelson EA. A 5500-year-old <i>Treponema pallidum</i> genome from Sabana de Bogotá, Colombia. Science 2026;391(6783):eadw3020
  22. Brbić M. When the genome learned its own vocabulary. Nat Rev Genet 2026
  23. Bürki C, Carrara M, Fahrni L, Meyer D, Escher A, Neacsu M, Teufel S, Noppen C, Beckmann C, Kurth H, Singer F, du Plessis L, Stadler T. Characterizing co-circulating respiratory virus genomic diversity in Switzerland with hybrid-capture sequencing and phylogenetic reconstructions: Insights into the 2023/24 season.Epidemics 2026;55:100906
  24. Carrillo JD, Torres Jimenez MF, Urrea-Barreto FJ, Pino K, Cooper RB, Antonelli A, Bacon CD, Faurby S, Silvestro D. Decoupled diversity and disparity after faunistic turnover in caviomorph rodents. Proc Biol Sci 2026;293(2066):20252586
  25. Castex C, Cumer T, Goudet J, Christe P. Hitchhiking Parasites: Unstructured Populations of Bat Ectoparasites Reveal Host-Driven Dispersal. Mol Ecol 2026;35(5):e70283
  26. Charmoy M, Maier JM, Wyss T, Chennupati V, Sabatel C, Bonneaux L, Dumez A, Veber R, Guarda G, Held W. Memory-like CD8<sup>+</sup> T cells lacking PD-1 adapt to persistent stimulation by reducing TCR signal transduction rather than increasing exhaustion. Front Immunol 2026;17:1743170
  27. Ciancaglini M, Avanthay R, Marx AF, Abreu-Mota T, Finozzi D, Fixemer J, Geier F, Burri D, Wagner I, Vincenti I, Kreuzfeldt M, Merkler D, Zimmer G, Pinschewer DD. Non-cytolytic re-engineering of a viral vaccine vector enables durable effector-memory T cell immunity by reinforcing type I IFN induction. Mol Ther Nucleic Acids 2026;37(1):102852
  28. Ciernik L, Kraft A, Barkmann F, Yates J, Boeva V. Robust and efficient annotation of cell states through gene signature scoring. Genome Res 2026;36(3):630-644
  29. Cina A, Monzon M, Galbusera F, Jutzeler CR. Quantifying central canal stenosis prediction uncertainty in SpineNet with conformal prediction. Sci Rep 2026;16(1):4963
  30. Conforti S, du Plessis L, Bagutti C, Becker J, Brugger SD, Cusini A, Egli A, Gaia V, Greub G, Guler C, Huisman JS, Kocher C, Kouyos RD, Leuzinger K, Maffioli C, Neacșu M, Nolte O, Ramette A, Seiffert SN, Tschudin-Sutter S, Zumthor JP, Stadler T, Julian TR. From clinics to sewers: leveraging environmental surveillance and whole genome sequencing to inform transmission of ESBL-<i>Escherichia coli</i> in Switzerland. Appl Environ Microbiol 2026;92(5):e0184825
  31. Coumau C, Gaspar F, Zayene M, Bertrand E, Alberio L, Lovis C, Beeler PE, Rinaldi F, Lutters M, Le Pogam MA, Csajka C, SwissMADE Collaborators. Detection of Antithrombotic-Related Bleeding in Older Inpatients: Multicenter Retrospective Study Using Structured and Unstructured Electronic Health Record Data. J Med Internet Res 2026;28:e77809
  32. Crowell HL, Llaó-Cid L, Frigola G, Gunz S, Ruano I, Lorden P, Ruiz M, Kulis M, Martin-Subero JI, Heyn H, Campo E, Pascual-Reguant A. A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts. Eur J Immunol 2026;56(1):e70121
  33. Cuendet MA, Gatta R, Wicky A, Gerard CL, Dalla-Vale M, Tavazzi E, Michielin G, Delyon J, Cesbron J, Lofek S, Huber A, Pradervand S, Michielin O. Correction: A differential process mining analysis of COVID-19 management for cancer patients. Front Oncol 2026;16:1777196
  34. Darlix A, Bady P, Deverdun J, Bars EL, Coget A, Meriadec J, Carrière M, Duffau H, Hegi ME. Distinct molecular profiles characterize the spontaneous growth rate of IDHmt low-grade astrocytomas and oligodendrogliomas. Neuro Oncol 2026;28(4):911-922
  35. De Schoenmacker I, Monzon M, Sirucek L, Scheuren PS, Lütolf R, Gorrell LM, Brunner F, Curt A, Rosner J, Schweinhardt P, Hubli M, Jutzeler CR. The role of biopsychosocial factors in classifying pain intensity across various chronic pain conditions. Sci Rep 2026
  36. Deng Z, Sanchis-López C, Hernández-Plaza A, Davín AA, Huerta-Cepas J. TreeProfiler: large-scale metadata profiling along gene and species trees. Mol Biol Evol 2026;43(2):msag028
  37. Dietler N, Malbranke C, Bitbol AF. Out-of-Equilibrium Selection Pressure Enhances Inference from Protein Sequence Data. Phys Rev Lett 2026;136(10):108402
  38. Dlamini Z, Kahraman A, Chatziioannou A. Editorial: Precision oncology in checkpoint immunotherapy: leveraging predictive biomarkers for personalized treatment. Front Immunol 2025;16:1772930
  39. Domi R, Noé F, Leary P, Rehrauer H. GEO uploader: simplifying the data deposition in the GEO repository. BMC Bioinformatics 2026
  40. Dreifuss D, Czyż P, Beerenwinkel N. Learning and forecasting selection dynamics of SARS-CoV-2 variants from wastewater sequencing data using Covvfit. Water Res 2026;301:126018
  41. Dreifuss D, Topolsky I, Icer Baykal P, Beerenwinkel N. Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop. PLoS Comput Biol 2026;22(2):e1014003
  42. Driessen A, Born J, Castellanos Rueda R, Reddy ST, Rapsomaniki M. Modeling chimeric antigen receptor response at the single-cell level with conditional optimal transport. Cell Syst 2026:101591
  43. Duroux D, Melograna F, Climente-González H, Fan B, Walakira A, Gervasoni EE, Li Z, Roqueiro D, Stella F, Van Steen K. Turning heterogeneity of statistical epistasis networks to an advantage. Brief Bioinform 2026;27(1):bbaf699
  44. Duroux D, Meyer PP, Visonà G, Beerenwinkel N. Generalizable machine learning models for rapid antimicrobial resistance prediction in unseen health care settings. Gigascience 2026;15:giaf156
  45. El Makhzen N, Nater A, Rougier JS, Bokhobza A, Sanz J, Zweier C, Hämmerli AF, Bruggmann R, Bouguenouch L, Lakhdar Idrissi M, Abriel H. <i>CFTR</i> gene variant detection in moroccan individuals via nanopore long-read sequencing. Front Genet 2026;17:1769093
  46. Eldridge N, Spörri L, Kreuzer M, Haldimann G, Zinkernagel MS, Zysset-Burri DC. Uncovering the relationship between the human ocular surface microbiome and gut microbiome. BMC Microbiol 2026;26(1):335
  47. Elsner C, Hanke A, Vadas O, Gervasio FL, Bordignon E. Structural and dynamic basis of indirect apoptosis inhibition by Bcl-xL: A case study with Bid. Proc Natl Acad Sci U S A 2026;123(20):e2527963123
  48. Fadaei S, Krebs FS, Zoete V. Novel universal domain-centric method for protein classification. Sci Rep 2026;16(1):11850
  49. Falquet M, El Ahanidi H, Gomez-Cadena A, Su Z, Cornu A, Wyss T, Kizil B, Pick R, Falamaki K, Wirapati P, Fiordi B, Senoner I, Maresca DC, Kallal N, Guedj D, Kreutzfeldt M, Tille JC, Leblond MM, Michaud K, Pesce S, Candiani S, Golebski K, Dagher J, Charrier M, Pressacco Brossier C, Grobet-Jeandin E, Marone R, Hugues S, Jeker LT, Verdeil G, Merkler D, Marcenaro E, Scheiermann C, Attaleb M, Benamran D, Tsantoulis P, Ercolano G, Trabanelli S, Jandus C. Mast-cell derived nerve growth factor drives ILC2 pro-tumoral functions in bladder cancer. Nat Commun 2026;17(1):3061
  50. Farrell G, Adamidi E, Andrade Buono R, Anton M, Attafi OA, Capella Gutierrez S, Capriotti E, Castro LJ, Cirillo D, Crossman L, Dessimoz C, Dimopoulos A, Fernández-Díaz R, Fragkouli SC, Goble C, Gu W, Hancock JM, Khanteymoori A, Lenaerts T, Liberante FG, Maccallum P, Monzon AM, Palmblad M, Poveda L, Radulescu O, Shields DC, Sufi S, Vergoulis T, Psomopoulos F, Tosatto SCE. Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences. Nat Methods 2026
  51. Fayad C, Mussalo L, Afonin A, Lampinen R, Hakkarainen H, Hensel AK, Yahfoufi K, Behzadpour D, Penttilä E, Koivisto AM, Cascione L, Pennings S, Mikkonen S, Jalava P, Kanninen KM. Source-dependent temporal toxicity and transcriptomic remodeling by urban ultrafine particles: Megacity - suburban comparison in aging olfactory-brain interface. Sci Total Environ 2026;1026:181661
  52. Firtina C, Mordig M, Mustafa H, Goswami S, Mansouri Ghiasi N, Mercogliano S, Eris F, Lindegger J, Kahles A, Mutlu O. Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism. Bioinformatics 2026;42(3):btag087
  53. FitzGerald O, Smith C, Huppertz C, Brom M, Bruno D, Helliwell PS, van de Sande M, de Wit M, Werner L, Ioannidis V, Marek D, Ibberson M, Pennington SR, Koehm M, Behrens F. Definition of the terms used to describe psoriatic disease datasets: a HIPPOCRATES initiative. Ther Adv Musculoskelet Dis2026;18:1759720X261424371
  54. Fontaine G, Michie S, Beidas RS, Geng E, Fahim C, Powell BJ, Welch V, Thomas J, Chan J, Abbasgholizadeh-Rahimi S, Légaré F, Hastings J, Lambert SD, Presseau J, Straus SE, An R, Saran A, Taylor N. AI Methods for Implementation Science (AIM-IS): developing a framework, toolkit, and reporting standard for the responsible use of AI in implementation practice and research. Implement Sci 2026;21(1):37
  55. Fraga M, Kasmi S, Weber SN, Liebe R, Sempoux C, Saadat A, Fellay J, Kenngott-Kelber S, Zimmer V, Lammert F, Krawczyk M, Jüngst C. Prolonged Intrahepatic Cholestasis After Acute Hepatitis E Infection: A Case Series and Genetic Analysis. J Viral Hepat 2026;33(4):e70156
  56. Frey B, Varliero G, Rüthi J, Alekseev I, Qi W, Povazhnyi V, Zemlianskii V, Stierli B, Ermokhina K, Schaepman-Strub G, Cuartero J. Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes. Commun Biol 2026
  57. Fruet C, Alexandre A, Abbara A, Loverdo C, Bitbol AF. Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations. Nat Commun 2026
  58. Fróis-Martins R, Mertens S, Tran VDT, Maufrais C, d'Enfert C, Sanglard D, LeibundGut-Landmann S. Manipulation of regulators of morphogenesis is not sufficient to render a <i>Candida albicans</i> colonizer strain pathogenic. mBio 2026;17(5):e0041526
  59. Fuqua T, Wagner A. De novo promoters emerge more readily from random DNA than from genomic DNA. Sci Adv 2026;12(22):eaec2554
  60. Gadiya Y, Millán Acosta J, Ammar A, Adriaque Lozano A, Wetstede D, Martinát D, Sima AC, Mei H, Willighagen E, Abbassi-Daloii T. pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources. Bioinformatics 2026;42(3):btag064
  61. Gaio D, Tackmann J, Perez-Molphe-Montoya E, Näpflin N, Patsch D, Malfertheiner L, Peluso ME, von Mering C. Enhanced semantic classification of microbiome sample origins using large language models (LLMs). Gigascience 2026;15:giag015
  62. Gankin D, Beltrao P. The AlphaGenome deep learning model predicts effects of non-coding variants. Nat Struct Mol Biol 2026;33(3):373-374
  63. Gazizov A, Lian A, Goverde C, Mou J, Ovchinnikov S, Polizzi NF. AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2. Nat Methods 2026;23(3):626-635
  64. Gehre F, Oko F, Ofori-Anyinam B, Meehan CJ, Windels EM, Joof K, Faal T, Mendy F, Jobarteh T, Gitteh E, Riley AJ, Sarr-Kuyateh B, Okoi C, Demba E, Dei-Alorse W, Mlaga K, Sambou B, Kanuteh F, Lette K, Muhammad AK, Agbla S, Mulders W, Donkor S, Jeffries D, Roca A, D'Alessandro U, Antonio M, Adetifa I, De Jong B.Assessing the impact of Enhanced-Case-Finding on tuberculosis case notifications and transmission in The Gambia using epidemiological and phylodynamic approaches. Open Res Eur 2026;6:96
  65. Gerber R, Griner J, Guglietta S, Krieg C, Robinson MD. MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments. Commun Biol 2026;9(1):712
  66. Gfeller D, Racle J, Harari A, Croce G. Advances in predicting T cell epitope recognition for cancer immunotherapy. Nat Cancer 2026
  67. Giagiozis M, Curt A, Jutzeler CR, Zariffa J. Video summarization for home-based egocentric footage in spinal cord injury rehabilitation. Biomed Eng Online 2026;25(1):17
  68. Grieshop MP, Behr AA, Bowden S, Lin JD, Molari M, Reynolds GZ, Brooks EF, Doyle B, Moore AA, Rodriguez-Nava G, Salinas JL, Banaei N, Bhatt AS. Transposable elements are driving rapid adaptation of Enterococcus faecium. Nature 2026
  69. Grosicki GJ, Hippel WV, Fielding F, Chapman CJ, Presby DM, Leota J, Holmes KE. Alcohol Use Trajectories During the First 72 Weeks of WHOOP Wearable Platform Membership: Observational Cohort Study. JMIR Mhealth Uhealth 2026;14:e91288
  70. Grosicki GJ, Robinson AT, Joyner MJ, Carter JR, von Hippel W, Presby DM, Fielding F, Bigalke JA, Kim J, Chapman C, Holmes KE. Real-world effects of alcohol on heart rate, sleep, and physical activity by age and sex. PLOS Digit Health 2026;5(3):e0001284
  71. Grover A, Muser T, Kasak L, Zhang L, Krymova E, Boeva V. Early feature extraction drives model performance in high-resolution chromatin accessibility prediction. Genome Res 2026;36(3):619-629
  72. Grover A, Zhang L, Muser T, Häfliger S, Wang M, Yates J, Indilewitsch MC, Wang Y, Van Allen EM, Theis FJ, Ibarra IL, Krymova E, Boeva V. UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility. Nucleic Acids Res 2026;54(10):gkag485
  73. Guillemet M, Lehtinen S. Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure. PLoS Comput Biol 2026;22(3):e1014083
  74. Guo Y, Mallona I, Robinson MD, Li L. BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration. PLoS Comput Biol 2026;22(2):e1013932
  75. Haemmerli P, Hubert M, Gaudry A, Quiros-Guerrero LM, Mehl F, Pagni M, Marcourt L, Kirchhoffer OA, Grondin A, Constant S, Huang S, Queiroz EF, Clément S, Tapparel C, Wolfender JL. An innovative approach for anti-respiratory syncytial virus compound discovery from plant extracts, combining high-throughput screening and metabolomics. Biomed Pharmacother 2026;194:118917
  76. Harray AJ, Lucas AD, Herrmann SE, Vlaskovsky PS, Elagali A, Seewoo BJ, Chan DC, Chiarugi D, Kulkarni R, Trevenen M, Wang X, Mueller J, Thomas KV, Papendorf H, Miller C, Gaudieri S, Smith T, Salman S, Murray K, Symeonides C, Dunlop SA, Watts GF, PERTH Trial Consortium, Lucas M. Low-plastic diet and urinary levels of plastic-associated phthalates and bisphenols: the randomized controlled PERTH Trial. Nat Med 2026;32(5):1871-1883
  77. Hastings J, Wosny M, Kennett J, Homiar A, Malhi GS, Furukawa TA, Potts J, Thomas J, Cipriani A. Automatically detecting trends and open questions from mental health publications: a Wellcome-funded GALENOS project. BMJ Ment Health 2026;29(1):e302379
  78. Helmer A, Clavier A, Arnold M, Segiser A, Lischer HEL, Graf S, Masoodi M, Beer G, Ottersberg R, Egle M, Siepe M, Longnus S. Sex differences in cardiac recovery and ventricular gene expression in a rat model of donation after circulatory death. Biol Sex Differ 2026
  79. Hernández-Plaza A, Deng Z, Robledo-Yagüe F, Szklarczyk D, von Mering C, Bork P, Huerta-Cepas J. eggNOG v7: phylogeny-based orthology predictions and functional annotations. Nucleic Acids Res 2026;54(d1):D402-D408
  80. Hewett A, Lavanchy E, Topaloudis A, Cumer T, Ducrest AL, Simon C, Almasi B, Roulin A, Goudet J. Inbreeding depression in morphological and growth traits of wild barn owls (Tyto alba). Proc Biol Sci 2026;293(2070):20252708
  81. Huang Q, Szklarczyk D, Oehninger J, von Mering C. PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms. Nucleic Acids Res 2026;54(d1):D427-D439
  82. Iachizzi M, Zajac N, Ruiz JL, Güller T, Rabin R, Schalbetter S, de Cillis F, Moccia MD, Cattaneo A, Cryan JF, Richetto J. Probiotic treatment rescues behavioral deficits and gut microbial abnormalities induced by preconceptional stress in mothers and offspring. Brain Behav Immun 2026;136:106571
  83. Jauch AJ, Schmidt-Barbo P, Schultheiss C, Silling G, Hänel M, Chromik J, Stauch T, Trautmann-Grill K, Repp R, Schulte C, Fleischmann B, Welslau M, Stauch M, Quiering C, Richter F, Tesanovic T, Jahn S, Bignucolo O, Holbro A, Passweg JR, Matzdorff A, Rummel M, Meyer O, Nimmerjahn F, Binder M. Efficacy and safety of eltrombopag in combination with dexamethasone as first-line treatment in adult patients with newly diagnosed immune thrombocytopenia. Br J Haematol 2026;208(2):789-793
  84. John A, Kang S, Fuhrmann L, Topolsky I, Kent C, Quick J, Stadler T, Julian TR, Beerenwinkel N. Corrigendum to "Characterizing Influenza A Virus Lineages and Clinically Relevant Mutations Through High-Coverage Wastewater Sequencing" [Water Research (2025) Article No. 124453]. Water Res 2026;298:125781
  85. Ju W, Nair V, Vart P, Smeijer JD, Hudkins KL, Moedt E, Larkina M, Perco P, Burdet F, Shedden K, Hwang M, Lee E, O'Connor C, Hartman J, Subramanian L, Bitzer M, Ibberson M, Duffin KL, Gomez MF, Alpers CE, Kretzler M, Heerspink HJL. Urinary clusterin as a biomarker of human kidney disease progression and response to the endothelin receptor antagonist atrasentan: An exploratory analysis from the SONAR trial. Nat Commun 2026;17(1):2482
  86. Jule Z, Römer C, Hossen T, Sviridchik V, Reedoy K, Ganga Y, Silangwe S, Jackson L, Norman A, Karim F, Kekana D, Mahlangu B, Mnguni A, Nzimande A, Stock N, Bernstein M, Gosnell BI, Moosa MS, Wolter N, Khan K, Neher RA, Sigal A. Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant. Virus Evol2026;12(1):veag011
  87. Karabogdan I, Yanqui-Rivera F, Sayeeram D, Sadik A, Miller AK, Trump S, Röhrig UF, Opitz CA. Exploration of Agonist and Antagonist Binding Sites within the Cytosolic AHR Complex Using Molecular Modeling. ACS Omega 2026;11(10):16070-16087
  88. Killer HE, Pircher A, Stekhoven DJ. Reassessment of the Collaborative Normal-Tension Glaucoma Study: Statistical Evidence and Implications for Current Management. Ophthalmol Ther 2026;15(2):761-770
  89. Kondrateva O, Sonay TB, Zlobec I, Anisimova M. Tumor mutational burden predicts neoantigen profiles and immunotherapy response in microsatellite stable tumors across different cancer types. Front Immunol 2025;16:1582464
  90. Kopp OS, Morandi SC, Kreuzer M, Uldry A-C, Eldridge N, Zinkernagel MS, Zysset-Burri DC. Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease. Microbiol Spectr 2026;14(3):e0226425
  91. Koptekin D. pygenstrat: a Python package for EIGENSTRAT data processing. Bioinform Adv 2026;6(1):vbag022
  92. Kossmann D, Iizuka A, Khanna N, Rivera-Fuentes P. A Ratiometric pH Sensor for Gram-Positive and Gram-Negative Bacteria. J Am Chem Soc 2026;148(4):4754-4765
  93. Krebs FS, Michielin O, Zoete V. Swiss-PO 2025: Advancing Cancer Mutation and Structural Analysis for Precision Oncology With the Latest Release. JCO Precis Oncol 2026;10:e2501011
  94. Laslo D, Wolleb J, Monzon M, Kottke R, Sirin S, Müller T, Suhami D, Vogt F, Bhatia A, Gandhi DB, Kazerooni AF, Familiar AM, Nguyen T, Jiang Z, Parida A, Gerber NU, Stücklin AG, Nabavizadeh A, Nazarian J, Linguraru MG, Rauschecker AM, Müller S, Jutzeler C, Brüningk S. Generative AI for spatial tumor growth on MRI: a proof-of-principle study in pediatric diffuse midline glioma. BMC Med 2026
  95. Lawless D, Saadat A, Oumelloul MA, Boutry S, Stadler V, Österle S, Armida J, Haerry D, Froese DS, Schlapbach LJ, Fellay J. Application of qualifying variants for genomic analysis. Bioinformatics 2026;42(2):btaf676
  96. Lepik K, Auwerx C, Sadler MC, van der Graaf A, Ojavee SE, Kutalik Z. LiMA: Robust inference of molecular mediation from summary statistics. Am J Hum Genet 2026;113(1):202-220
  97. Li P, Hatos A, Petrovic M, Franceschini GM, Nanni L, Tavernari D, Ciriello G. TADShop: systematic benchmarking and identification of topologically associating domains. Nat Methods 2026
  98. Liu Y, Franceschini GM, Zhang Y, Oricchio E, Ciriello G. HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states. Nat Commun 2026
  99. Long F, Ghosh A, Xu T, Ding L, Wu C, Khandelwal R, Noé F, Sun W, Dong H, Wang T, Hoffmann A, Gardeux V, Deplancke B, Abu-Nawwas L, Stefanicka P, Varga L, Ruiz JR, Blüher M, Balaz M, Sharma AK, Wolfrum C. MEDAG functions as an A-kinase-anchoring protein in adipocytes. Mol Cell 2026;86(5):937-953.e9
  100. Lukas LP, Bourguignon L, Rupp R, Weidner N, Schubert M, Röhrich F, Waldmann J, Kalke YB, Abel R, Maier D, Chhabra HS, Liebscher T, Geisler F, Curt A, Brüningk SC, Jutzeler CR. Motor Score Patterns Complement the AIS Grade in the Analysis of Segmental Motor Recovery after Spinal Cord Injury. J Neurotrauma2026:8977151261434501
  101. Malbranke C, Zalaffi GP, Bitbol AF. ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa. Proc Natl Acad Sci U S A 2026;123(21):e2524201123
  102. Malfertheiner L, Tackmann J, Matias Rodrigues JF, von Mering C. Community conservatism is widespread across microbial phyla and environments. Nat Ecol Evol 2026;10(2):232-245
  103. Manakov D, Klanova M, Kolar M, Ivanek R, Geier F, Roux J, Zikmund T, Winkowska L, Kriegova E, Manakova J, Tuskova L, Spanikova S, Scasna A, Trneny M, Klener P. Single Cell RNA Transcriptomics of Mantle Cell Lymphoma Reveals the Presence of Treatment-Resistant Subclones at the Time of Diagnosis. Am J Hematol2026;101(5):1025-1035
  104. Marchi NA, Solelhac G, Imler T, Ericson I, Haba-Rubio J, Marques-Vidal P, Vollenweider P, Kutalik Z, Strippoli MF, Pistis G, Preisig M, von Gunten A, Draganski B, Heinzer R. Periodic limb movements during sleep, restless legs syndrome, and cognitive changes in older adults: a population-based longitudinal study. Sleep2026;49(2):zsaf327
  105. Marrec L, Lehtinen S. Cluster dispersal shapes microbial diversity during community assembly. PLoS Comput Biol 2026;22(2):e1013918
  106. Marrec L. Impact of genotype-dependent dispersal on mutation fixation in subdivided populations. J Evol Biol 2026;39(2):262-271
  107. Martin K, Reuther P, Geier F, Marx AF, Abreu-Mota T, Fixemer J, Kastner AL, Bonilla WV, Tintignac K, Stauffer K, Lu M, Schuler D, Wagner I, Merkler D, Pinschewer DD. Perinatal infection elicits clonally restricted T follicular helper cell responses that drive antibody-mediated viral control. Immunity 2026;59(5):1363-1380.e7
  108. Matias Rodrigues JF, Tackmann J, Malfertheiner L, Patsch D, Perez-Molphe-Montoya E, Näpflin N, Gaio D, Rot G, Danaila M, Peluso ME, Dmitrijeva M, Schmidt TSB, von Mering C. The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems. Cell 2026;189(7):2092-2107.e17
  109. Maziers N, Le Chatelier E, Plaza Oñate F, Fromentin S, Thirion F, Pons N, Borruel N, Casellas F, Torrejon A, Robles-Alonso V, Manichanh C, Varela E, Derrien M, Veiga P, Oozeer R, Sunagawa S, Lombard V, Terrapon N, Henrissat B, MetaHIT consortium, Guarner F, Ehrlich SD. Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level. Sci Rep 2026
  110. McLeod RE, Julian TR, Stadler T, Lison A. Real-time outlier detection in digital PCR data for wastewater-based pathogen surveillance. Environ Res 2026;298:124269
  111. Mehr S, Castoe T, Daly M, Jungo F, Kirchhoff KN, Koludarov I, Mackessy SP, Macrander J, Naidu P, Modica MV, Sanchez EE, Zancolli G, Holford M. A Proposed Unified, Scalable Platform for Integrative Research on Venomous Species. Gigascience 2026:giaf153
  112. Miho E, Marquez S, Stervbo U, Mertz KD, Kruta J, Schkommodau E, Pieter M. Medical software for precision diagnostics of infection with immunoprofiling and artificial intelligence. J Transl Med 2026;24(1):561
  113. Miravet-Verde S, Cacace E, Mores CR, Rutschmann C, Lin CW, Ruscheweyh HJ, Cuénod A, Barazzone EC, Marrec E, Vershynina K, Schumann R, Bower DJ, Schubert M, Egli A, Fiebig T, Slack E, Sunagawa S, Keys TG. In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules. Nat Microbiol2026;11(5):1217-1232
  114. Mishra N, Kimmig F, Vandeputte D, Talevi V, De Commer L, Verspecht C, Vich Vila A, El-Sayed Moustafa JS, Kreft L, Botzki A, El Darzi Y, Proost S, Devolder L, Wang D, Bernardes JP, Aziz NA, SYSCID consortium, Franke A, Schreiber S, Dermitzakis ET, Vieira-Silva S, Falony G, Small KS, Breteler MMB, Schultze JL, Raes J, Rosenstiel P. Large-scale analysis of temporal gene expression variation in peripheral blood. Nat Commun 2026
  115. Mlakar V, Jurković Mlakar S, Gloor Y, Dupanloup I, Sarmiento Y, Boudal-Khosbheen M, Marino D, Uppugunduri CRS, Ansari M. Busulfan resistance in AML is associated with changes in mitochondrial copy number and lipid metabolism. Sci Rep 2026;16(1):10213
  116. Morales-Tirado A, Blitz-Castro E, Tabares-González A, Gascón-Galindo C, Vicente-Santamaría S, Luna-Paredes C, Salcedo-Lobato E, Boutry S, Lamas-Ferreiro A. Long-term Outcomes of Pediatric CFSPID: A 15-Year Clinical and Genomic Study Across Newborn Screening Cystic Fibrosis Units. Arch Bronconeumol2026;62(4):236-243
  117. Moreno JM, Grossmann J, Kunz L, Dittmann A, Sousa VC, Santos R. Molecular Responses to Climate Change: How Warming and Acidification Reshape the Proteome and Phosphoproteome of the Endangered Mira Chub. Ecol Evol 2026;16(3):e72933
  118. Moretti S, Niknejad A, Pagni M, Mehl F. MetaNetX: a bridge between metabolic resources for enhanced curation and multi-omics data harmonization. Nucleic Acids Res 2026;54(d1):D617-D622
  119. Moxon SAT, Solbrig H, Harris NL, Kalita P, Miller MA, Patil S, Schaper K, Bizon C, Caufield JH, Cuesta SC, Cox C, Dekervel F, Dooley DM, Duncan WD, Fliss T, Gehrke S, Graefe ASL, Hegde H, Ireland AJ, Jacobsen JOB, Krishnamurthy M, Kroll C, Linke D, Ly R, Matentzoglu N, Overton JA, Saunders JL, Unni DR, Vaidya G, Vierdag WAM, LinkML Community Contributors, Ruebel O, Chute CG, Brush MH, Haendel MA, Mungall CJ. LinkML: an open data modeling framework. Gigascience 2026;15:giaf152
  120. Mulberry N, Pilarski J, Dinger J, Stadler T. Age-dependent Phylodynamics with Application to Single-cell Lineage Trees. Mol Biol Evol 2026;43(4):msag080
  121. Mulberry N, Stadler T. Strategies for resolving cellular phylogenies from sequential lineage tracing data. Theor Popul Biol 2026;168:32-43
  122. Munteanu V, Saldana MA, Dreifuss D, Ouyang WO, Ferdous J, Mohebbi F, Roseberry JS, Ciorba D, Bostan V, Gordeev V, Drabcinski N, Su JM, Kasianchuk N, Sharma NK, Knyazev S, Aßmann E, Lobiuc A, Covasa M, Crandall KA, Wu NC, Mason CE, Tierney BT, Lucaci AG, Ophoff RA, Gibas C, Rzymski P, Skums P, Solo-Gabriele H, Niko B, Zelikovsky A, Hölzer M, Smith A, Mangul S. SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities. Genome Biol 2026;27(1):1
  123. Muralidharan A, Costa AR, Fierlier D, van den Berg DF, van den Bossche H, Zoumaro-Djayoon AD, Rodríguez-Molina A, Pabst M, Pacesa M, Correia BE, Brouns SJJ. Molecular basis for anti-jumbo phage immunity by AVAST type 5. Mol Cell 2026;86(4):740-756.e9
  124. Neher RA, Huddleston J, Bedford T, Lewis NS, Harvey R, Galiano M, Byrne AMP, James S, Smith D, Łuksza M, Ruchnewitz D, Laessig M, Fujisaki S, Watanabe S, Hasegawa H, Hassell N, Wentworth DE, Kondor R, Deng YM, Dapat C, Subbarao K, Barr I. Nomenclature for Tracking of Genetic Variation of Seasonal Influenza Viruses. Influenza Other Respir Viruses 2026;20(2):e70230
  125. Nikolakopoulou K, Ybañez W, Klaeylé L, Frugoli L, Cindrova-Davies T, Hotz HR, Soneson C, Turco MY. An in vitro menstrual cycle using organoids captures epithelial cell transitions during menstruation and regeneration of the human endometrium. Cell Stem Cell 2026;33(5):747-762.e8
  126. Nivina A, Thiel Pizarro P. Evolutionary strategies of late-stage diversification in bacterial biosynthetic gene clusters. Essays Biochem 2026:EBC20250026
  127. Nonchev K, Andani S, Ficek-Pascual J, Nowak M, Sobottka B, Consortium TP, Koelzer VH, Rätsch G. Representation learning for multi-modal spatially resolved transcriptomics data. Bioinformatics 2026:btag316
  128. Ortín Vela S, Bergmann S. Cross-organ analysis reveals associations between vascular properties of the retina, the carotid and aortic arteries, and the brain. Commun Med (Lond) 2026;6(1):102
  129. Pecnik J, Ventresca Miller AR, Panse C, Kunz L, Dittmann A, Johnson JA, Makhortykh S, Litvinova L, Andrukh S, Toschev G, Krützen M, Schuenemann VJ, Wilkin S. Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy. PLoS One 2026;21(1):e0339464
  130. Perez MAS, Zoete V. Universal paratope-epitope interaction patterns in antibody-antigen structures. Protein Sci 2026;35(1):e70401
  131. Postma A, Klynsmith L, Duong TA, Allison JD, Smidt W, Waterhouse RM, Lesny P, Oeyen JP, Petersen M, Petersen M, Martin S, Liu S, Zhou X, Ziesmann T, Donath A, Mayer C, Misof B, Niehuis O, Peters RS, Podsiadlowski L, Coetzee MPA, Joubert F, Slippers B. Genome and transcriptome-based identification and expression profiling of chemosensory gene families across developmental stages and tissues in Sirex noctilio (Hymenoptera: Siricidae). Insect Mol Biol 2026;35(3):270-283
  132. Poveda L, Farrell G, Tosatto SCE, Zahn-Zabal M, Ruch P, Gobeill J, Waterhouse RM, Dessimoz C. The missing link in FAIR data policy: biodata resources in life sciences. Sci Data 2026;13(1):373
  133. Proietti L, Beltrao P, Bruna A, Cortés-Ciriano I, Garnett MJ, Gonçalves E, Herranz-Ors C, Kaulich M, Lord CJ, Petsalaki E, Rad R, Ryan CJ, Savino A, Sesia D, Wessels L, Iorio F. Genetic interactions, synthetic lethality and complexity in cancer vulnerability mapping-Insights and perspectives from the 2nd EuroDepMap symposium. FEBS Lett 2026;600(7):997-1005
  134. Prélot L, Chen J, Hüser M, Kahles A, Rätsch G. ImmunoPepper: extracting personalized peptides from complex splicing graphs. Bioinformatics 2026;42(1):btaf492
  135. Pu T, Peddle AM, Wirapati P, Tsantoulis P, Wu Q, Hong Y, Samuel L, Desai J, Riener M, Saridaki Z, Cunningham D, Tejpar S. Exploratory biomarker analysis of RAS/BRAF somatic mutations and gene expression signatures for predicting treatment effects of aflibercept in the velour trial. NPJ Precis Oncol 2026;10(1):50
  136. Reichel K, Pohjoismäki J, Astrin JJ, Böhne A, Bortoluzzi C, Bužan E, Del Campo J, Ciofi C, Di-Nizo CB, Divakar PK, Greve C, Hampl V, Hilgers L, Laine VN, Leonard JA, Lozano-Fernandez J, Lukić Bilela L, Mazzoni CJ, McCartney AM, Melo-Ferreira J, Monteiro R, Oomen RA, Pavlek M, Pimenta J, Rindos M, Seehausen O, Tarieiev A, Tomasello S, Vinnere Pettersson O, Waterhouse RM, Weber AA, Zinenko O, de Guttry C. From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe. Mol Ecol Resour 2026;26(2):e70100
  137. Rigutto A, Núñez NG, Kienzler JC, Opitz I, Meerang M, Haberecker M, Fournier N, Lourenço J, Gottardo R, Silina K, Gupta A, Becher B, Curioni-Fontecedro A. Multiplexed single-cell and spatial profiling reveal B cells and tertiary lymphoid structures as prognostic indicators in pleural mesothelioma. Br J Cancer 2026
  138. Rodler JP, Yushchuk O, Gavriilidou A, Siegert AK, Kulik A, Wohlleben W, Ziemert N, Stegmann E. Exploring shikimate pathway enzyme diversity for engineering of glycopeptide antibiotic biosynthesis. Metab Eng 2026;96:277-289
  139. Roese Mores C, Field CM, Ruscheweyh H-J, Slack E, Keys TG, Sunagawa S. Complete genomes of <i>E. coli</i> with diverse K antigens. Microbiol Resour Announc 2026:e0001326
  140. Rotzetter J, Spörri L, Herzog EL, Kreuzer M, Zinkernagel MS, Zysset-Burri DC. A preliminary investigation on the influence of sample storage on the low-abundant ocular surface microbiome. J Microbiol Methods 2026;243:107437
  141. Ruiz-López MJ, Cebrián-Camisón S, Irisarri I, Magallanes S, Martínez-de la Puente J, Figuerola J, Waterhouse RM, Wellcome Sanger Institute Tree Of Life Management Samples And Laboratory Team, Wellcome Sanger Institute Scientific Operations Sequencing Operations, Wellcome Sanger Institute Tree Of Life Core Informatics Team, Haggerty L, Martin F, Brown T. ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin. Genome Biol Evol 2026;18(2):evaf245
  142. Rutz A, Probst D, Aguilar C, Akiyama DY, Alberti F, Augustijn HE, Avalon NE, Beemelmanns C, Barbieri HB, Biermann F, Bridge AJ, Girón EC, Cox R, Crüsemann M, D'Agostino PM, Feuermann M, Gerke J, García KG, Holme JE, Hwang JY, Iacovelli R, Jeronimo Barbosa JC, Kaur N, Klapper M, Köhler AM, Korenskaia A, Kubach N, Lee BT, Loureiro C, Mantri S, Narula S, Meijer D, Navarro-Muñoz JC, Nguyen GS, Paliyal S, Panghal M, Rao L, Sieber S, Sokolova N, Sowa ST, Szenei J, Terlouw BR, Weddeling HG, Yu J, Ziemert N, Weber T, Blin K, van der Hooft JJJ, Medema MH, Zdouc MM. MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis. Nucleic Acids Res 2026;54(d1):D635-D642
  143. Ryan B, Fellay J, Thorball CW. Genetic determinants of HIV-1 elite control. Curr Opin HIV AIDS 2026;21(3):218-223
  144. Saadat A, Fellay J. From mutation to degradation: predicting nonsense-mediated mRNA decay with NMDap. Biochem Biophys Res Commun 2026;819:153833
  145. Santini F, Monzon M, Poncioni S, Bonaretti S, Hirvasniemi J, Froeling M, Cameron D. ORMIR-MIDS: an open standard for curating and sharing musculoskeletal imaging data. JBMR Plus 2026;10(3):ziag013
  146. Sarton-Lohéac G, Romashchenko N, Train CM, Majidian S, Glover N. Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups. J Mol Evol 2026;94(1):275-278
  147. Schedel J, Lin S, Bock T, Burri D, Rüegg MA. Laminin-α2 is required for the maintenance of the myotendinous junction in vivo. Matrix Biol 2026;145:39-51
  148. Scheuren PS, Schubert M, Hubli M, Jutzeler CR, Rupp R, Abel R, Maier D, Röhl K, Baumberger M, Hund-Georgiadis M, Saur M, Benito-Penalva J, Rehahn K, Aach M, Badke A, Kriz J, Freund P, Weidner N, Schwab ME, Kramer JLK, Curt A. Enhanced clinical trial stratification in spinal cord injury: the value of electrophysiology.Brain 2026;149(3):908-917
  149. Schmid RM, Studer E, Kapopoulou A, Yilmaz B, Becker J. Long-term persistence of clonal resistant and multidrug resistant E. coli despite absence of antimicrobial use in weaned dairy heifer rearing systems in Switzerland. Vet Microbiol 2026;315:110884
  150. Schneider-Lunitz V, Kensche PR, Kraatz L, Strubel P, Borufka S, Parala G, Kanitz A, Eils R, Buchhalter I, Twardziok SO. Managing workflow executions with WESkit. Bioinformatics 2026;42(3):btag091
  151. Seppey M, Benavides A, Berkeley MR, Manni M, Zdobnov EM. LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools. Genome Biol 2026
  152. Seth-Smith HMB, Greutmann M, Findlay J, Beckmann C, Berlinger L, Brugger SD, Capaul R, Greub G, Gruner E, Keller PM, Nolte O, Roloff T, Tschudin-Sutter S, Zingg W, Nordmann P, Poirel L, Egli A, NARA Network. Investigation of VIM-1-producing <i>Enterobacter</i> spp. across Switzerland: clonal dissemination and plasmid transmission. Antimicrob Agents Chemother 2026:e0182725
  153. Shapiro I, Kräuchi C, Luca E, Dettwiler S, Peitzsch M, Qi W, Reul A, Beuschlein F, Maccio U, Nölting S, Debaix H, Hantel C. A novel 2D and 3D model for primary adrenocortical carcinoma of advanced and metastasized stage co-secreting cortisol, aldosterone, testosterone, 18-oxocortisol and 18-hydroxycortisol. Endocr Relat Cancer 2026;33(1):e250385
  154. Sigrist CJA, Cuche BA, de Castro E, Coudert E, Redaschi N, Bridge A. The PROSITE database for protein families, domains, and sites. Nucleic Acids Res 2026;54(d1):D451-D458
  155. Spriano F, Cascione L, Tarantelli C, Sartori G, Arribas AJ, Velasova A, Napoli S, Havranek O, Toretsky JA, Bertoni F. Exploring Resistance to ETS Targeting Agents in Diffuse Large B-Cell Lymphoma. Cancer Med 2026;15(5):e71935
  156. Spörri L, Studer JM, Kreuzer M, Rotzetter J, Schärer D, Largiadèr CR, Jaggi D, Zinkernagel MS, Zysset-Burri DC. Linking the microbiome to the complement system in geographic atrophy. NPJ Genom Med 2026;11(1):14
  157. Srivastava M, Louis AA, Martin NS. Predicting the topography of fitness landscapes from the structure of genotype-phenotype maps. Genetics 2026;232(4):iyag026
  158. Stein JV, Lischer HEL, Palou CVI, Seth A, Bruggmann R. Integration of biochemical and physical cues by patrolling CD8<sup>+</sup> T cells. Trends Immunol 2026:S1471-4906(26)00035-9
  159. Steuer J, Kahraman A. Unlocking the undruggable spliceosome: generative AI and structural dynamics in cancer therapy. Front Cell Dev Biol 2026;14:1774239
  160. Struck TH, Marcussen T, Böhne A, Fernández R, Melo-Ferreira J, Florent I, Gissi C, de Guttry C, Leonard JA, McTaggart S, Mazzoni CJ, Monteiro R, Vinnere Pettersson O, Pimenta J, Pohjoismäki J, Reichel K, Tarieiev A, Oomen RA. An automated decision-making procedure for ranking and selecting species in biodiversity projects. NPJ Biodivers 2026
  161. Taboada S, Gracia-Sancha C, Galià-Camps C, Böhne A, Monteiro R, Marcussen T, Oomen RA, Struck TH, Gut M, Aguilera L, Câmara Ferreira F, Cruz F, Gómez-Garrido J, Alioto TS, Martin F, Lazar A, Haggerty L, Bortoluzzi C. ERGA-BGE reference genome of <i>Xylophaga dorsalis -</i> a common deep-sea wood-boring bivalve with Atlantic-Mediterranean distribution. Open Res Eur 2026;6:33
  162. Tandon D, De Farias TM, Allard PM, Defossez E. METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions. Gigascience 2026:giag051
  163. Tauriello G, Lill Y, Sgrignani J, Zoete V, Singer B, Vallat B, Webb BM, Garello T, Bienert S, Feig M, Papaleo E, Burley SK, Sali A, Lill MA, Cavalli A, Dal Peraro M, Schwede T. ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models. J Mol Biol 2026:169658
  164. Ter Voert E, Witte H, Touré V, Menze B, Österle S. Seeing Is Believing - FAIR Metadata for Medical Imaging Data in the SPHN Semantic Interoperability Framework. Stud Health Technol Inform 2026;336:7-11
  165. Thienger P, Paassen I, Yao X, Rubin PD, Lehner M, Lillis N, Benjak A, Shah SR, Leung AK, de Brot S, Naveed A, Daniel B, Shi M, Tremblay J, Triscott J, Cassanmagnago GA, Bolis M, Mela L, Beltran H, Chen Y, Piscuoglio S, Yu H, Ng CKY, Quigley DA, Yauch RL, Rubin MA. A Double-Negative Prostate Cancer Subtype Is Vulnerable to SWI/SNF-Targeting Degrader Molecules. Cancer Res 2026;86(7):1570-1585
  166. Tobias-Hünefeldt SP, Woodhouse JN, Ruscheweyh H-J, Sunagawa S, Russnak V, Streit WR, Grossart H-P. Osmotolerance is a driver of microbial carbon processes in the Elbe estuary. mSystems 2026;11(4):e0179025
  167. Topaloudis A, Cumer T, Lavanchy E, Hewett A, Bachmann Salvy M, Ducrest AL, Simon C, Almasi B, Roulin A, Delaneau O, Goudet J. Benchmarking imputation accuracy in the presence or absence of a reference panel. Mol Biol Evol 2026;43(4):msag094
  168. Touré V, Unni D, Krauss P, Marto AB, Kalt K, Stoira N, Pickl M, Österle S. SPHN Connector - a scalable pipeline for generating validated knowledge graphs from federated and semantically enriched health data. BMC Med Inform Decis Mak 2026;26(1):72
  169. Touré V, Unni D, Witte H, Armida J, Österle S. Five Years of the SPHN RDF Journey: FAIR Enough? Stud Health Technol Inform 2026;336:1192-1196
  170. Tranchellini F, Farag Y, Jutzeler C, Meegahapola L. Evaluating deep learning sepsis prediction models in ICUs under distribution shift: a multi-centre retrospective cohort study. NPJ Digit Med 2026;9(1):306
  171. Trofimova O, Iuliani I, Bergmann S. Bidirectional genetic and phenotypic links between smoking and striatal iron content involving dopaminergic and inflammatory pathways. Addiction 2026;121(6):1580-1593
  172. Tsui JL, Sambaturu P, Pena RE, Too L, Gutierrez B, Inward R, Kraemer MUG, du Plessis L, Pybus OG. Transmission lineage dynamics and the detection of viral importation in emerging epidemics. Epidemics 2026;54:100893
  173. Tuci M, Steck L, Lukas LP, Taran O, Rupp R, Weidner N, Schubert M, Röhrich F, Waldmann J, Kalke YB, Abel R, Maier D, Liebscher T, Zörner B, Curt A, Bolliger M, Brüningk SC, Jutzeler CR. Linking neurological status to functional outcomes in spinal cord injury: a multi-class, task-specific approach. BMC Biomed Eng2026;8(1):9
  174. Unni D, Klopfenstein SAI, Witte H, Debertshäuser T, Hölter TA, Österle S. Interoperability of Swiss Personalized Health Network RDF Schema with FHIR. Stud Health Technol Inform 2026;336:1282-1286
  175. Vallois D, Missiaglia E, Veloza L, Fischer A, Cavalieri D, Rattina V, Bisig B, Roh V, Wiehle L, Sarkis R, Bachy E, Bonnet C, Bruneau J, Cairoli A, De Wind R, Drieux F, Dubois R, Emile JF, Fataccioli V, Laribi K, Ledoux-Pilon A, Lemonnier F, Llamas-Gutierrez F, Morel P, Parrens M, Poullot E, Quintanilla-Martinez L, Sandrini J, Somja J, Xerri L, Tournilhac O, Gaulard P, Siebert R, de Leval L. Correction: Divergent molecular pathways drive monomorphic epitheliotropic and enteropathy-associated intestinal T-cell lymphoma. Leukemia 2026;40(1):252-259
  176. Varliero G, Bauder A, Stierli B, Qi W, Frey B. Erratum: Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier. Microb Genom 2026;12(1)
  177. Vasilevsky NA, Toro S, Matentzoglu N, Flack JE, Mullen KR, Hegde H, Gehrke S, Whetzel PL, Shwetar Y, Harris NL, Ngu MS, Alyea GL, Kane MS, Roncaglia P, Sid E, Thaxton CL, Wood V, Abraham RS, Achatz MI, Ajuyah P, Amberger JS, Babb L, Baker J, Balhoff JP, Berg JS, Bhalla A, Bofill-De Ros X, Braun IR, Broeren EC, Byer BK, Byrne AB, Callahan TJ, Carmody LC, Chan LE, Clause AR, Cohen JS, DeLuca M, Deuitch NT, Flowers M, Fraser J, Fujiwara T, Gitau V, Goldstein JL, Gration D, Groza T, Gyori BM, Hankey W, Hilton JA, Himmelstein DS, Hong SS, Hoyt CT, Huether R, Hurwitz E, Jacobsen JOB, Kikuchi A, Köhler S, Korn DR, Lagorce D, Laraway BJ, Li JY, Malheiro AJ, McLaughlin J, Meldal BHM, Mohan S, Moxon SAT, Munoz-Torres MC, Nelson TH, Nicholas FW, Ochoa D, Olson D, Oprea TI, Oskotsky TT, Osumi-Sutherland D, Paris K, Parkinson HE, Pendlington ZM, Peng XP, Pizzino A, Plon SE, Powell BC, Ratliff JC, Rehm HL, Remennik L, Riggs ER, Roberts S, Robinson PN, Ross JE, Schaper K, Schilder BM, Schmidt JL, Sharp EW, Similuk MN, Smedley D, Sneddon TP, Sparks R, Stefancsik R, Stupp GS, Sundar S, Takatsuki T, Tammen I, Tshering KC, Unni DR, Valasek E, Vanderver A, Wagner AH, Webb RF, Welter D, Yaya-Stupp D, Zankl A, Zhang XA, McMurry JA, Chute CG, Hamosh A, Mungall CJ, Haendel MA. Mondo: integrating disease terminology across communities. Genetics 2026;232(4):iyaf215
  178. Vessman B, Guridi-Fernández P, Arias-Sánchez FI, Mitri S. Novel artificial selection method improves function of simulated microbial communities. PLoS Comput Biol 2026;22(1):e1013863
  179. Villani A, Wittmann J, Wyss T, Mallona I, Santisteban Ortiz I, Tichy N, Biermeier CM, Pena M, Pal AA, Gilmour D, Schafer ST, Peri F. A scalable human-zebrafish xenotransplantation model reveals gastrosome-mediated processing of dying neurons by human microglia. Commun Biol 2026
  180. Wang Y, Huang C, Cai G, Andreatta M, Kurum A, Zhao Y, Feng B, Gao M, Carmona SJ, Zhou Z, Sun C, Guo Y, Tang L. Metabolic reinvigoration of NK cells by IL-21 enhances immunotherapy against MHC class I-deficient solid tumors. Cell Rep 2026;45(3):117035
  181. Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR, Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser S, Grand RS, Stadler MB, Deindl S, Thomä NH. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4-SOX2. Mol Cell 2026;86(4):625-639.e8
  182. Wetterwald L, Köck A, Wyss T, Arroz-Madeira S, Prat-Luri B, Jaquet M, Petit B, Vozenin MC, Ylä-Herttuala S, Dutoit V, Migliorini D, Schaeuble K, Brisken C, Delorenzi M, Sabine A, Petrova TV. MYCT1-IFITM2/3 interaction links endothelial endolysosomal trafficking to white adipose tissue expansion. J Exp Med2026;223(5):e20251497
  183. Wiederkehr F, Paoli L, Richter D, Racunica D, Ruscheweyh HJ, Sperfeld M, O'Brien J, Miravet-Verde S, Streiff AB, Ransome J, Chepkirui C, Priest T, Sintsova A, Salazar G, Bistolas KSI, Sawyer T, Labadie K, Mayer KI, Perdereau A, Reddy MM, Moulin C, Boissin E, Bourdin G, Cailliau J, Iwankow G, Poulain J, Romac S, Tara Pacific Consortium Coordinators, Planes S, Allemand D, Agostini S, Bowler C, Douville E, Forcioli D, Galand PE, Lombard F, Oliveira PH, Thomas OP, Vega Thurber R, Troublé R, Voolstra CR, Wincker P, Ziegler M, Piel J, Sunagawa S. Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity. Nature2026;652(8110):686-693
  184. Wissel D, Mehlferber MM, Nguyen KM, Pavelko V, Tseng E, Robinson MD, Sheynkman GM. A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification. Genome Biol 2026;27(1):110
  185. Wright YJK, Whiston R, Brewer A, Adnane M, Nanni P, Grossmann J, Kunz L, de Almeida AM, Chapwanya A. Unravelling proteomic changes of primary bovine endometrial epithelial cells to lipopolysaccharide and lipoteichoic acid bacterial ligand stimulation. Res Vet Sci 2026;205:106162
  186. Xu Y, Shangguan Y, Chuang YM, Chang TH, Liu W, Peng JJ, Garnica J, Xie L, Hsueh PC, Lin MC, Wang YH, Hajdu KL, Wu Y, Akrami M, Wang C, Kohl A, Zippelius A, Qi W, Wang M, Budiarto BR, Chen SY, Xiao Z, Vardaka P, Roychoudhuri R, Bai Z, Fan R, Carmona S, Yu YR, Scheiermann C, Wang J, Ho PC. Proteasome-guided haem signalling axis contributes to T cell exhaustion. Nature 2026;653(8114):548-557
  187. Xu Y, Shangguan Y, Chuang YM, Chang TH, Liu W, Peng JJ, Garnica J, Xie L, Hsueh PC, Lin MC, Wang YH, Hajdu KL, Wu Y, Akrami M, Wang C, Kohl A, Zippelius A, Qi W, Wang M, Budiarto BR, Chen SY, Xiao Z, Vardaka P, Roychoudhuri R, Bai Z, Fan R, Carmona S, Yu YR, Scheiermann C, Wang J, Ho PC. Author Correction: Proteasome-guided haem signalling axis contributes to T cell exhaustion. Nature 2026;653(8115):E11
  188. Yang Z, Baudis M. CNAttention: an attention-based deep multiple-instance method for uncovering copy number aberration signatures across cancers. Brief Bioinform 2026;27(1):bbaf696
  189. Yepes-García J, Falquet L. 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction. mSystems 2026;11(2):e0084425
  190. Zavolan M, Yeo GW. System-level measurement, modeling, and manipulation of RNA. RNA 2026;32(4):409-411
  191. Zwyer M, Xu ZM, Ross A, Hella J, Sasamalo M, Rotival M, Hiza HC, Rutaihwa LK, Borrell S, Reither K, Fellay J, Portevin D, Quintana-Murci L, Gagneux S, Brites D. Human genetic ancestry, <i>Mycobacterium tuberculosis</i> diversity, and tuberculosis disease severity in Dar es Salaam, Tanzania. Elife 2026;14:RP103533
  192. van Oosterhout C, Speak SA, Birley T, Hitchings LWG, Bortoluzzi C, Percival-Alwyn L, Urban L, Groombridge JJ, Segelbacher G, Morales HE. Genomic Erosion in the Assessment of Species' Extinction Risk and Recovery Potential. J Hered 2026:esag011
  193. van der Elst A, Herrero-Saboya D, Michon L, Morfouace M, Liechti R, Devanand P, Schulz D, Persoons M, Rusakiewicz S, Eling N, Nicolas PA, Robert MS, Tissot S, Déglise S, Palau Fernandez B, Bodenmiller B, Hong HS, Galot R, Bossi P, Oliveira J, Pracht M, Even C, Saintigny P, Lefebvre C, Martignetti L, Machiels JP.Molecular and immune landscape of recurrent and/or distant metastatic squamous cell carcinoma of the head and neck: an EORTC/IMMUCAN project. Clin Cancer Res 2026
  194. van der Elst A, Herrero-Saboya D, Michon L, Morfouace M, Liechti R, Devanand P, Schulz D, Persoons M, Rusakiewicz S, Eling N, Nicolas PA, Robert MS, Tissot SR, Daniel M, Bodenmiller B, Hong HS, Galot R, Bossi P, Oliveira J, Estrade F, Even C, Lucas S, Saintigny P, Martignetti L, Lefebvre C, Machiels JH. Genomic and Immune Landscape of Recurrent and/or Metastatic Squamous Cell Carcinoma of the Head and Neck Progressing on Anti-PD-1 Treatment. Cancer Immunol Res 2026;14(4):608-624
  195. van der Graaf A, Rizi S, Auwerx C, Kutalik Z. Mendelian randomization linking metabolites with enzymes reveals pathway regulation and therapeutic avenues. Am J Hum Genet 2026;113(2):309-323
  196. Škrinjar P, Eberhardt J, Studer G, Tauriello G, Schwede T, Durairaj J. Evaluating generalization in protein-ligand cofolding methods. Nat Struct Mol Biol 2026;33(5):782-794

Browse other years