Scientific publications 2025

Abdelrahman O, Coxon Q, Abou-Mansour E, L'Haridon F, Falquet L, Allard PM, Weisskopf L. Mining Actinomycetes' Metabolomes and Genomes for Anti-Phytophthora infestans Compounds. Microb Biotechnol 2025;18(12):e70269
Abriata LA, Dal Peraro M. Practical Outcomes From CASP16 for Users in Need of Biomolecular Structure Prediction. Proteins 2025
Alencar GF, Mohamed AO, Burnett MG, Jean SS, Nelson AR, Su Y, Voillet V, Bates BM, Rodgers Suarez M, Ruskin SL, Trieu L, Lam JL, Bekiranov S, Gottardo R, Greenberg PD, Anderson KG. Triple checkpoint blockade of PD-1, Tim-3, and Lag-3 enhances adoptive T cell immunotherapy in a mouse model of ovarian cancer.Proc Natl Acad Sci U S A 2025;122(39):e2419888122
Alexander LT, Follonier OM, Kryshtafovych A, Abesamis K, Bibi-Triki S, Box HG, Breyton C, Bringel F, Carrique L, d'Acapito A, Dong G, DuBois R, Fass D, Fiesco JM, Fox DR, Grimes JM, Grinter R, Jenkins M, Kamyshinsky R, Keown JR, Lackner G, Lammers M, Liu S, Lovering AL, Malinauskas T, Masquida B, Palm GJ, Siebold C, Su T, Zhang P, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein Target Highlights in CASP16: Insights From the Structure Providers. Proteins 2025
Alexandre A, Guérin T, Dean DS. Effective description of Taylor dispersion in strongly corrugated channels. Phys Rev E 2025;111(6-1):064124
Andani S, Chen B, Ficek-Pascual J, Heinke S, Casanova R, Hild BF, Sobottka B, Bodenmiller B, Tumor Profiler Consortium, Koelzer VH, Rätsch G. Histopathology-based protein multiplex generation using deep learning. Nat Mach Intell 2025;7(8):1292-1307
Andreatta M, Garnica J, Carmona SJ. Identification of malignant cells in single-cell transcriptomics data. Commun Biol 2025;8(1):1264
Anglada-Girotto M, Miravet-Verde S, Serrano L. Using single-cell perturbation screens to decode the regulatory architecture of splicing factor programs. Nucleic Acids Res 2025;53(19):gkaf855
Aoki-Kinoshita KF, Lisacek F, Mazumder R, Ranzinger R, Tiemeyer M, Yamada I, Packer NH. Meeting report of the GlySpace Alliance and GaLSIC symposium. Glycobiology 2025;35(5):cwaf019
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
Arnold P, Döppes D, Alberti F, Füglistaler A, Lindauer S, Hoselmann C, Friedrich R, Hajdas I, Dickinson M, Menger F, Paijmans JLA, Dalén L, Wegmann D, Penkman KEH, Barlow A, Rosendahl W, Hofreiter M. Ancient DNA and dating evidence for the dispersal of hippos into central Europe during the last glacial. Curr Biol2025;35(21):5363-5371.e6
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 2025
Auberson M, Wang D, Ehret E, Corre T, Anand D, Mechakra A, Staub O, Bochud M, Hummler E. Combination of genetic studies and animal modeling proposes TMPRSS9 as a candidate gene for serum K+ variations. Sci Rep 2025;15(1):25211
Baciu-Drăgan MA, Beerenwinkel N. OncotreeVIS-an interactive graphical user interface for visualizing mutation tree cohorts. Bioinform Adv 2025;5(1):vbaf247
Balajti M, Kandhari R, Jurič B, Zavolan M, Kanitz A. HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries. Bioinformatics 2025;41(3):btaf076
Banholzer N, Munday JD, Jent P, Bittel P, Dall'Amico L, Furrer L, Bürki C, Stadler T, Egger M, Hascher T, Cattuto C, Fenner L. The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools. Nat Commun 2025
Bao K, Afacan B, Grossmann J, Silbereisen A, Öztürk VÖ, Emingil G, Belibasakis GN, Bostanci N. Saliva Versus All-Site Microbiome and Proteome Mapping in Periodontitis. J Clin Periodontol 2025;52(11):1540-1549
Bao K, Oscarsson J, Gehring P, Grossmann J, Belibasakis GN, Bostanci N. Aggregatibacteraphrophilus T6SS Effectors in Host-Bacterial Interactions. J Dent Res 2025;104(13):1487-1494
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
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
Bauer A, Zambounis L, Kritikos I, Lütge A, Sabine A, Heron C, Petkova M, Giampietro C, Blatter K, Bianco SD, Gschwend D, Restivo G, Proulx ST, Levesque MP, Lindenblatt N, Mazza E, Detmar M, Gousopoulos E, Robinson MD, Petrova TV, Halin C. Transcriptomics- and 3D imaging-based characterization of the lymphatic vasculature in human skin. J Exp Med 2026;223(1):e20242353
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
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
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
Bernard C, Nevers Y, Karampudi NBR, Gilbert KJ, Train C, Warwick Vesztrocy A, Glover N, Altenhoff A, Dessimoz C. EdgeHOG: a method for fine-grained ancestral gene order inference at large scale. Nat Ecol Evol 2025;9(10):1951-1961
Bersier L, Lorenzo-Martin LF, Chiang YH, Durot S, Czauderna A, Yarahmadov T, Wyss Lozano T, Roci I, Kim J, Zamboni N, Vannini N, Pot C, Collet TH, Stroka D, Bernier-Latmani J, Lutolf MP, Becattini S, Koessler T, Petrova TV. Chemotherapy-driven intestinal dysbiosis and indole-3-propionic acid rewire myelopoiesis to promote a metastasis-refractory state. Nat Commun 2025
Berthod G, Cisarovsky C, Petrova T, Decosterd LA, Choong E, Celestini D, Cuendet MA, Boughdad S, Prior JO, Meuwly JY, Figg WD, Michielin O, Leyvraz S. Sorafenib plus selective internal radiotherapy with 90Y resin microspheres for the treatment of uveal melanoma with liver metastasis: a phase I trial. Br J Cancer 2025
Besse A, Kraus M, Totu T, Buljan M, Janssen APA, Van der Stelt M, Matisikova K, Veprkova J, Sedlarikova L, Jurinakova T, Truger M, Haferlach C, Lopez MM, Kortum MK, Rasche L, Driessen C, Besse L. Ceritinib overcomes proteasome inhibitor resistance in multiple myeloma by suppressing the protein folding response.Haematologica 2025
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
Bignucolo O, Molton O, Gautschi I, Kellenberger S. Molecular mechanisms and hotspots of pH sensing in ASIC1a revealed by computational and functional analysis. Commun Biol 2025;8(1):1692
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
Blumer S, Khan P, Roux J, Artysh N, Plappert L, Savic S, Prasse A, Hostettler KE. Characteristics of ectopic alveolar basal cells relative to airway basal cells in fibrosis. ERJ Open Res 2025;11(6):1259-2024
Bocker MT, Fanourgakis G, Wetzel K, Komarov PA, Royo H, Rohmer A, Chun S, Liang CY, Kohler H, Chen T, Mao X, Labow MA, Valdez RA, Stadler MB, de Rooij DG, Capodieci P, Tallarico J, Peters AHFM, Nicholson TB. The histone H3 lysine 36 demethylase KDM2A/FBXL11 controls Polycomb-mediated gene repression and germ cell development in male mice. Nat Commun 2025;16(1):6803
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
Bouchez V, Lefrancq N, Toubiana J, Rodrigues C, Brisse S. Microbes know no borders: importation of macrolide-resistant Bordetella pertussis into France in 2024. Clin Microbiol Infect 2025;31(10):1737-1739
Bouchez V, Lefrancq N, Toubiana J, Rodrigues C, Brisse S. Microbes know no borders: importation of macrolide-resistant Bordetella pertussis into France in 2024: author's reply. Clin Microbiol Infect 2025;31(12):2090-2091
Bramon Mora B, Lindsay H, Thiébaut A, Stuart KD, Gottardo R. tagtango: an application to compare single-cell annotations. Bioinformatics 2025;41(2):btaf012
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
Brasó-Vives M, Hartasánchez DA, Ayroles JF, Bucao CF, Furlan-Magaril M, Majic P, Pallares LF, Phipps-Tan J, Rogers TF, Ruiz-Herrera A, Santos-Rodriguez G, Vellnow N, Wilcox JJS, Rodríguez JA. The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity. Genome Biol Evol2025;17(11):evaf204
Bugajska J, Lukas LP, Rupp R, Weidner N, Schubert M, Röhrich F, Waldmann J, Kalke YB, Abel R, Maier D, Chhabra HS, Liebscher T, Curt A, Brüningk S, Jutzeler CR. Reassessing the Role of Machine Learning in Clinical Prediction: A Benchmark of Predicting Walking Function after Spinal Cord Injury. J Neurotrauma 2025
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
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;34(23):e70001
Castoe TA, Daly M, Jungo F, Kirchhoff KN, Koludarov I, Mackessy S, Macrander J, Mehr S, Modica MV, Sanchez EE, Zancolli G, Holford M. A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications. Integr Org Biol 2025;7(1):obaf026
Causevic S, Tackmann J, Sentchilo V, Malfertheiner L, von Mering C, van der Meer JR. Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil. ISME J 2025;19(1):wraf162
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 Rep2025;45(4):BSR20241663
Chaparro-Pedraza PC, Bank C. Evolving life-history traits promote biodiversity via eco-evolutionary feedback mechanisms. PLoS Biol 2025;23(11):e3003492
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
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 Microbe2025;33(3):358-372.e4
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
Châtel-Soulet HÉ, Juge S, Pereira AL, Seguin J, El Taher A, Valigi F, Jevtic Z, Sivalingam R, Bagger FO, Büschl P, Almosailleakh M, Tzankov A, Tong W, Kurokawa M, Nombela Arrieta C, Schwaller J. Thrombopoietin increases susceptibility for EVI1 + KMT2A-MLLT3-driven AML expressing stem cell genes linked to poor outcome. Nat Commun 2025
Cina A, Tuci M, Pellisé F, Yilgor C, Alanay A, Pizones J, Kleinstück F, Obeid I, Charles YP, Richner-Wunderlin S, Galbusera F, Jutzeler CR, European Spine Study Group. Simulating Federated Learning to Enable Multi-Hospital Collaboration for Lumbopelvic Alignment Estimation. JOR Spine 2025;8(4):e70120
Civenni G, Sandrini G, Merulla J, Musumeci C, Federici E, Vallegra A, Kokanovic A, Mosole S, Shinde D, Sorrenti E, Paganoni AJJ, Marchetti M, Valzelli R, Albino D, Pecoraro M, Rinaldi A, Bolis M, Geiger R, Winge T, Holtschulte C, Laurini E, Pricl S, Carbone GM, Wünsch B, Catapano CV. Integrated control of cancer stemness by σ1 receptor in advanced prostate cancer. Oncogene 2025;44(42):4032-4046
Cogne T, Ait Oumelloul M, Saadat A, Hastings J, Fellay J. Structure-based metabolite function prediction using graph neural networks. Bioinform Adv 2025;5(1):vbaf174
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;43(7):1204-1226
Conconi A, Janikova A, Vannata B, Ramírez-Ibarguen AF, Lobetti-Bodoni C, Belada D, Pirosa MC, Mian M, Ferreri AJM, Ryan G, Pangalis G, Cabrera ME, Luminari S, Montoto S, Tsang R, Aurer I, Visco C, Casaluci GM, Prochazka V, Hricko S, Stathis A, Mazzucchelli L, Ponzoni M, Federico M, Gaidano G, Lopez-Guillermo A, Pro B, Rossi D, Cascione L, Nowakowsky G, Trneny M, Zucca E. Primary Extranodal Follicular Lymphoma: A Retrospective Survey of the International Extranodal Lymphoma Study Group (IELSG). Hematol Oncol 2025;43(4):e70111
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
Cooper R, Jahanbakhsh E, Milinkovitch M. Chemical and mechanical patterning of tortoise skin scales occur in different regions of the head iScience 2025;28(6)
Cooper RL, Jahanbakhsh E, Milinkovitch MC. Chemical and mechanical patterning of tortoise skin scales occur in different regions of the head. iScience 2025;28(6):112684
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
Cornelius J, Detering H, Lithgow-Serrano O, Agosti D, Rinaldi F, Waterhouse R. From literature to biodiversity data: mining arthropod organismal traits with machine learning Biodiversity Data Journal 2025;13
Cornelius J, Detering H, Lithgow-Serrano O, Agosti D, Rinaldi F, Waterhouse RM. From literature to biodiversity data: mining arthropod organismal traits with machine learning. Biodivers Data J 2025;13:e153070
Correa Marrero M, Mello VH, Sartori P, Beltrao P. Global comparative structural analysis of responses to protein phosphorylation. Nat Commun 2025;16(1):9407
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 Adv2025;11(24):eads5589
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. Nature 2025;640(8059):623-633
DaSilva LF, Senan S, Kribelbauer-Swietek JF, Patel ZM, Louis LK, Reddy AJ, Gabbita S, Rosen JD, Nussbaum Z, Córdova CMV, Wenteler A, Weber N, Tunjic TM, Mansoldo M, Khan TA, Hwang GH, Gardeux V, Humphreys DT, Smith C, Bejan M, Bromley P, Connell W, Deplancke B, Love MI, Wong ES, Meuleman W, Pinello L.Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion. Nat Genet 2025
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
Dennstädt F, Fauser S, Cihoric N, Schmerder M, Lombardo P, Cereghetti GM, von Däniken S, Minder T, Meyer J, Chiang L, Gaio R, Lerch L, Filchenko I, Reichenpfader D, Denecke K, Vojvodic C, Tatalovic I, Sander A, Hastings J, Aebersold DM, von Tengg-Kobligk H, Nairz K. Implementing a Resource-Light and Low-Code Large Language Model System for Information Extraction from Mammography Reports: A Pilot Study. J Imaging Inform Med 2025
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 Med 2025;8(1):143
Dennstädt F, Hastings J, Putora PM, Vu E, Fischer G, Süveg K, Glatzer M, Riggenbach E, Hà HL, Cihoric N. In Reply to Sengul I and Sengul D. Adv Radiat Oncol 2025;10(7):101800
Dennstädt F, Lerch L, Schmerder M, Cihoric N, Cereghetti GM, Gaio R, Bonel H, Filchenko I, Hastings J, Dammann F, Aebersold DM, von Tengg-Kobligk H, Nairz K. A comparative performance analysis of regular expressions and a large language model-based approach to extract the BI-RADS score from radiological reports.JAMIA Open 2025;8(6):ooaf128
Dennstädt F, Schmalfuss M, Zink J, Hastings J, Gaio R, Schmerder M, Cihoric N, Putora PM. A CDE-based data structure for radiotherapeutic decision-making in breast cancer. BMC Med Inform Decis Mak 2025;25(1):220
Dennstädt F, Schmerder M, Riggenbach E, Mose L, Bryjova K, Bachmann N, Mackeprang PH, Ahmadsei M, Sinovcic D, Windisch P, Zwahlen D, Rogers S, Riesterer O, Maffei M, Gkika E, Haddad H, Peeken J, Putora PM, Glatzer M, Putz F, Hoefler D, Christ SM, Filchenko I, Hastings J, Gaio R, Chiang L, Aebersold DM, Cihoric N. Comparative Evaluation of a Medical Large Language Model in Answering Real-World Radiation Oncology Questions: Multicenter Observational Study. J Med Internet Res 2025;27:e69752
Dennstädt F, Windisch P, Filchenko I, Zink J, Putora PM, Shaheen A, Gaio R, Cihoric N, Wosny M, Aeppli S, Schmerder M, Shelan M, Hastings J. Application of a General Large Language Model-Based Classification System to Retrieve Information about Oncological Trials. Oncology 2025:1-11
Dennstädt F, Windisch P, Filchenko I, Zink J, Putora PM, Shaheen A, Gaio R, Cihoric N, Wosny M, Aeppli S, Schmerder M, Shelan M, Hastings J. Consensus Finding Among LLMs to Retrieve Information About Oncological Trials. Stud Health Technol Inform 2025;329:239-243
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
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;100(5):2131-2149
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
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
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
Dreifuss D, Huisman JS, Rusch JC, Caduff L, Ganesanandamoorthy P, Devaux AJ, Gan C, Stadler T, Kohn T, Ort C, Beerenwinkel N, Julian TR. Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding. Nat Commun 2025;16(1):7456
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
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
Duarte Ritter C, Muñoz J, Fabrício Machado A, Albert JS, Ribas CC, Carnaval AC, Ulloa Ulloa C, Carrillo JD, Tuomisto H, Armenteras D, Guayasamin JM. Indigenous territories and protected areas are crucial for ecosystem connectivity in the Amazon basin. Proc Natl Acad Sci U S A 2025;122(31):e2418189122
Durdu S, Iskar M, Isbel L, Hoerner L, Wirbelauer C, Burger L, Hess D, Iesmantavicius V, Schübeler D. Chromatin-dependent motif syntax defines differentiation trajectories. Mol Cell 2025;85(15):2900-2918.e16
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. iScience 2025;28(5):112498
Eling N, Dorier J, Rusakiewicz S, Liechti R, Devanand P, Daniel M, Windhager J, Fernandez BP, Déglise S, Despland L, Benyagoub A, Możejko M, Uchal D, Szczurek E, Loboda A, Sandkuijl D, Parsotam N, Hong HS, Morfouace M, Guex N, Coukos G, Bodenmiller B, Tissot S, Schulz D. Multi-modal image analysis for large-scale cancer tissue studies within IMMUcan. Cell Rep Methods 2025;5(9):101170
Elsworth JD, Neutzner A, Roux J, Gordevicius J, Milciute M, Dzikiti L, Wakeman DR, Danielsson B, Agca C, Lawrence MS. Proteomic Signatures of Epigenetic Age in African Green Monkey Cerebrospinal Fluid and Plasma. Aging Cell 2025;24(10):e70168
Emons M, Blanquart F, Lehtinen S. The evolution of antibiotic resistance in Europe, 1998-2019. PLoS Pathog 2025;21(4):e1012945
Emons M, Gunz S, Crowell HL, Mallona I, Kuehl M, Furrer R, Robinson MD. Harnessing the potential of spatial statistics for spatial omics data with pasta. Nucleic Acids Res 2025;53(17):gkaf870
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