Peer-reviewed papers and preprints by our members

Scientific publications 2023

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: 01.11.2023

Discover the SIB Remarkable Outputs 2022

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

  1. Abler D, Courlet P, Dietz M, Gatta R, Girard P, Munafo A, Wicky A, Jreige M, Guidi M, Latifyan S, De Micheli R, Csajka C, Prior JO, Michielin O, Terranova N, Cuendet MA. Semiautomated Pipeline to Quantify Tumor Evolution From Real-World Positron Emission Tomography/Computed Tomography Imaging. JCO Clin Cancer Inform 2023;7:e2200126
  2. Adelmann JA, Vetter R, Iber D. The impact of cell size on morphogen gradient precision. Development 2023;150(10):dev201702
  3. Adelmann JA, Vetter R, Iber D. Patterning precision under non-linear morphogen decay and molecular noise. Elife 2023;12:e84757
  4. Aghagolzadeh P, Plaisance I, Bernasconi R, Treibel TA, Pulido Quetglas C, Wyss T, Wigger L, Nemir M, Sarre A, Chouvardas P, Johnson R, González A, Pedrazzini T. Assessment of the Cardiac Noncoding Transcriptome by Single-Cell RNA Sequencing Identifies FIXER, a Conserved Profibrogenic Long Noncoding RNA. Circulation 2023;148(9):778-797
  5. Agirre J, Atanasova M, Bagdonas H, Ballard CB, Baslé A, Beilsten-Edmands J, Borges RJ, Brown DG, Burgos-Mármol JJ, Berrisford JM, Bond PS, Caballero I, Catapano L, Chojnowski G, Cook AG, Cowtan KD, Croll TI, Debreczeni JÉ, Devenish NE, Dodson EJ, Drevon TR, Emsley P, Evans G, Evans PR, Fando M, Foadi J, Fuentes-Montero L, Garman EF, Gerstel M, Gildea RJ, Hatti K, Hekkelman ML, Heuser P, Hoh SW, Hough MA, Jenkins HT, Jiménez E, Joosten RP, Keegan RM, Keep N, Krissinel EB, Kolenko P, Kovalevskiy O, Lamzin VS, Lawson DM, Lebedev AA, Leslie AGW, Lohkamp B, Long F, Malý M, McCoy AJ, McNicholas SJ, Medina A, Millán C, Murray JW, Murshudov GN, Nicholls RA, Noble MEM, Oeffner R, Pannu NS, Parkhurst JM, Pearce N, Pereira J, Perrakis A, Powell HR, Read RJ, Rigden DJ, Rochira W, Sammito M, Sánchez Rodríguez F, Sheldrick GM, Shelley KL, Simkovic F, Simpkin AJ, Skubak P, Sobolev E, Steiner RA, Stevenson K, Tews I, Thomas JMH, Thorn A, Valls JT, Uski V, Usón I, Vagin A, Velankar S, Vollmar M, Walden H, Waterman D, Wilson KS, Winn MD, Winter G, Wojdyr M, Yamashita K. The CCP4 suite: integrative software for macromolecular crystallography. Acta Crystallogr D Struct Biol 2023;79(pt 6):449-461
  6. Akgül G, Pla-Díaz M, Molak M, du Plessis L, Panagiotopoulou H, Doan K, Bogdanowicz W, Dąbrowski P, Oziębłowski M, Grzelak J, Arora N, González-Candelas F, Majander K, Schuenemann VJ. Inferring patterns of recombination and divergence with ancient and modern treponemal genomes 2023
  7. Akhmetova A, Guerrero J, McAdam P, Salvador LCM, Crispell J, Lavery J, Presho E, Kao RR, Biek R, Menzies F, Trimble N, Harwood R, Pepler PT, Oravcova K, Graham J, Skuce R, du Plessis L, Thompson S, Wright L, Byrne AW, Allen AR. Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland. Microb Genom 2023;9(5)
  8. Albert JS, Carnaval AC, Flantua SGA, Lohmann LG, Ribas CC, Riff D, Carrillo JD, Fan Y, Figueiredo JJP, Guayasamin JM, Hoorn C, de Melo GH, Nascimento N, Quesada CA, Ulloa Ulloa C, Val P, Arieira J, Encalada AC, Nobre CA. Human impacts outpace natural processes in the Amazon. Science 2023;379(6630):eabo5003
  9. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023
  10. Álvarez-Prado ÁF, Maas RR, Soukup K, Klemm F, Kornete M, Krebs FS, Zoete V, Berezowska S, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors. Cell Rep Med 2023;4(1):100900
  11. Anand A, Falquet L, Abou-Mansour E, L'Haridon F, Keel C, Weisskopf L. Biological hydrogen cyanide emission globally impacts the physiology of both HCN-emitting and HCN-perceiving Pseudomonas. mBio 2023:e0085723
  12. Anchisi S, Wolfer A, Bisig B, Missiglia E, Tiab A, Kamel EM, Michielin O, Coukos G, Homicsko K. Deep and lasting response and acquired resistance to BRAFV600E targeting in a low-grade ovarian cancer patient. Cancer Biol Ther 2023;24(1):2193116
  13. Andreatta M, Gueguen P, Borcherding N, Carmona SJ. T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps. Bio Protoc 2023;13(16):e4735
  14. Andreatta M, Hérault L, Gueguen P, Gfeller D, Berenstein AJ, Carmona SJ. Semi-supervised integration of single-cell transcriptomics data 2023
  15. Angori S, Banaei-Esfahani A, Mühlbauer K, Bolck HA, Kahraman A, Karakulak T, Poyet C, Feodoroff M, Potdar S, Kallioniemi O, Pietiäinen V, Schraml P, Moch H. Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets. Eur Urol Focus 2023:S2405-4569(23)00067-6
  16. Antonello P, Pizzagalli DU, Foglierini M, Melgrati S, Radice E, Thelen S, Thelen M. ACKR3 promotes CXCL12/CXCR4-mediated cell-to-cell-induced lymphoma migration through LTB4 production. Front Immunol 2022;13:1067885
  17. Apsley AT, Domico ER, Verbiest MA, Brogan CA, Buck ER, Burich AJ, Cardone KM, Stone WJ, Anisimova M, Vandenbergh DJ. A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3). Life Sci Alliance 2023;6(4):e202201677
  18. Aros-Mualin D, Guadagno CR, Silvestro D, Kessler M. Light, rather than circadian rhythm, regulates gas exchange in ferns and lycophytes. Plant Physiol 2023;191(3):1634-1647
  19. Auf der Maur P, Trefny MP, Baumann Z, Vulin M, Correia AL, Diepenbruck M, Kramer N, Volkmann K, Preca BT, Ramos P, Leroy C, Eichlisberger T, Buczak K, Zilli F, Okamoto R, Rad R, Jensen MR, Fritsch C, Zippelius A, Stadler MB, Bentires-Alj M. N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer. Cell Rep Med 2023;4(4):101002
  20. Auwerx C, Sadler MC, Woh T, Reymond A, Kutalik Z, Porcu E. Exploiting the mediating role of the metabolome to unravel transcript-to-phenotype associations. Elife 2023;12:e81097
  21. Avalos D, Rey G, Ribeiro DM, Ramisch A, Dermitzakis ET, Delaneau O. Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity. Commun Biol 2023;6(1):335
  22. Azizoğlu A, Loureiro C, Venetz J, Brent R. Autorepression-Based Conditional Gene Expression System in Yeast for Variation-Suppressed Control of Protein Dosage. Curr Protoc 2023;3(1):e647
  23. Baby V, Ambroset C, Gaurivaud P, Falquet L, Boury C, Guichoux E, Jores J, Lartigue C, Tardy F, Sirand-Pugnet P. Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae. Microb Genom 2023;9(10)
  24. Barreiro K, Lay AC, Leparc G, Tran VDT, Rosler M, Dayalan L, Burdet F, Ibberson M, Coward RJM, Huber TB, Krämer BK, Delic D, Holthofer H. An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles. J Extracell Vesicles 2023;12(2):e12304
  25. Barrio-Hernandez I, Yeo J, Jänes J, Mirdita M, Gilchrist CLM, Wein T, Varadi M, Velankar S, Beltrao P, Steinegger M. Clustering predicted structures at the scale of the known protein universe. Nature 2023;622(7983):637-645
  26. Barut GT, Kreuzer M, Bruggmann R, Summerfield A, Talker SC. Single-cell transcriptomics reveals striking heterogeneity and functional organization of dendritic and monocytic cells in the bovine mesenteric lymph node. Front Immunol 2022;13:1099357
  27. Bassot A, Dragic H, Haddad SA, Moindrot L, Odouard S, Corlazzoli F, Marinari E, Bomane A, Brassens A, Marteyn A, Hibaoui Y, Petty TJ, Chalabi-Dchar M, Larrouquere L, Zdobnov EM, Legrand N, Tamburini J, Lincet H, Castets M, Yebra M, Migliorini D, Dutoit V, Walker PR, Preynat-Seauve O, Dietrich PY, Cosset É. Identification of a miRNA multi-targeting therapeutic strategy in glioblastoma. Cell Death Dis 2023;14(9):630
  28. Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Mol Biol Evol 2023;40(1):msac269
  29. Batavia AA, Rutishauser D, Sobottka B, Schraml P, Beerenwinkel N, Moch H. Biallelic ELOC-Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity. Mod Pathol 2023;36(8):100194
  30. Belser C, Poulain J, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S, Genoscope Technical Team, Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, Wincker P. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition. Sci Data 2023;10(1):326
  31. Bermúdez-Méndez E, Angelino P, van Keulen L, van de Water S, Rockx B, Pijlman GP, Ciuffi A, Kortekaas J, Wichgers Schreur PJ. Transcriptomic Profiling Reveals Intense Host-Pathogen Dispute Compromising Homeostasis during Acute Rift Valley Fever Virus Infection. J Virol 2023;97(6):e0041523
  32. Bertschi NL, Steck O, Luther F, Bazzini C, von Meyenn L, Schärli S, Vallone A, Felser A, Keller I, Friedli O, Freigang S, Begré N, Radonjic-Hoesli S, Lamos C, Gabutti MP, Benzaquen M, Laimer M, Simon D, Nuoffer JM, Schlapbach C. PPAR-γ regulates the effector function of human T helper 9 cells by promoting glycolysis. Nat Commun 2023;14(1):2471
  33. Beyer D, Vaccarin C, Deupi X, Mapanao AK, Cohrs S, Sozzi-Guo F, Grundler PV, van der Meulen NP, Wang J, Tanriver M, Bode JW, Schibli R, Müller C. A tool for nuclear imaging of the SARS-CoV-2 entry receptor: molecular model and preclinical development of ACE2-selective radiopeptides. EJNMMI Res 2023;13(1):32
  34. Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Cervantes Rincón T, Fava T, Podešvová L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Hönig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarström Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF. Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci Immunol 2023;8(81):eade0958
  35. Bignon Y, Wigger L, Ansermet C, Weger BD, Lagarrigue S, Centeno G, Durussel F, Götz L, Ibberson M, Pradervand S, Quadroni M, Weger M, Amati F, Gachon F, Firsov D. Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock. J Clin Invest 2023;133(8):e167133
  36. Bill R, Wirapati P, Messemaker M, Roh W, Zitti B, Duval F, Kiss M, Park JC, Saal TM, Hoelzl J, Tarussio D, Benedetti F, Tissot S, Kandalaft L, Varrone M, Ciriello G, McKee TA, Monnier Y, Mermod M, Blaum EM, Gushterova I, Gonye ALK, Hacohen N, Getz G, Mempel TR, Klein AM, Weissleder R, Faquin WC, Sadow PM, Lin D, Pai SI, Sade-Feldman M, Pittet MJ. CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers. Science 2023;381(6657):515-524
  37. Bise T, Pfefferli C, Bonvin M, Taylor L, Lischer HEL, Bruggmann R, Jaźwińska A. The regeneration-responsive element careg monitors activation of Müller glia after MNU-induced damage of photoreceptors in the zebrafish retina. Front Mol Neurosci 2023;16:1160707
  38. Blanckaert A, Sriram V, Bank C. In search of the Goldilocks zone for hybrid speciation II: hard times for hybrid speciation? Evolution 2023;77(10):2162-2172
  39. Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 Mutational Spectrum. Mol Biol Evol 2023;40(4):msad085
  40. Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins. Virus Evol 2023;9(2):vead055
  41. Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins 2023
  42. Bobisse S, Bianchi V, Tanyi JL, Sarivalasis A, Missiaglia E, Pétremand R, Benedetti F, Torigian DA, Genolet R, Barras D, Michel A, Mastroyannis SA, Zsiros E, Dangaj Laniti D, Tsourti Z, Stevenson BJ, Iseli C, Levine BL, Speiser DE, Gfeller D, Bassani-Sternberg M, Powell DJ, June CH, Dafni U, Kandalaft LE, Harari A, Coukos G. A phase 1 trial of adoptive transfer of vaccine-primed autologous circulating T cells in ovarian cancer. Nat Cancer 2023;4(10):1410-1417
  43. Borges V, Duque MP, Martins JV, Vasconcelos P, Ferreira R, Sobral D, Pelerito A, de Carvalho IL, Núncio MS, Borrego MJ, Roemer C, Neher RA, O'Driscoll M, Rocha R, Lopo S, Neves R, Palminha P, Coelho L, Nunes A, Isidro J, Pinto M, Santos JD, Mixão V, Santos D, Duarte S, Vieira L, Martins F, Machado J, Veríssimo VC, Grau B, Peralta-Santos A, Neves J, Caldeira M, Pestana M, Fernandes C, Caria J, Pinto R, Póvoas D, Maltez F, Sá AI, Salvador MB, Teófilo E, Rocha M, Moneti V, Duque LM, E Silva FF, Baptista T, Vasconcelos J, Casanova S, Mansinho K, Alves JV, Alves J, Silva A, Alpalhão M, Brazão C, Sousa D, Filipe P, Pacheco P, Peruzzu F, de Jesus RP, Ferreira L, Mendez J, Jordão S, Duarte F, Gonçalves MJ, Pena E, Silva CN, Guimarães AR, Tavares M, Freitas G, Cordeiro R, Gomes JP. Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal. Nat Med 2023;29(10):2509-2517
  44. Borgsmüller N, Valecha M, Kuipers J, Beerenwinkel N, Posada D. Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues. Cell Genom 2023;3(9):100380
  45. Bosch AJT, Keller L, Steiger L, Rohm TV, Wiedemann SJ, Low AJY, Stawiski M, Rachid L, Roux J, Konrad D, Wueest S, Tugues S, Greter M, Böni-Schnetzler M, Meier DT, Cavelti-Weder C. CSF1R inhibition with PLX5622 affects multiple immune cell compartments and induces tissue-specific metabolic effects in lean mice. Diabetologia 2023
  46. Bosch AJT, Rohm TV, AlAsfoor S, Low AJY, Baumann Z, Parayil N, Noreen F, Roux J, Meier DT, Cavelti-Weder C. Diesel Exhaust Particle (DEP)-induced glucose intolerance is driven by an intestinal innate immune response and NLRP3 activation in mice. Part Fibre Toxicol 2023;20(1):25
  47. Bossart J, Rippl A, Barton Alston AE, Flühmann B, Digigow R, Buljan M, Ayala-Nunez V, Wick P. Uncovering the dynamics of cellular responses induced by iron-carbohydrate complexes in human macrophages using quantitative proteomics and phosphoproteomics. Biomed Pharmacother 2023;166:115404
  48. Botos MA, Arora P, Chouvardas P, Mercader N. Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart. Sci Rep 2023;13(1):5418
  49. Bowler-Barnett EH, Fan J, Luo J, Magrane M, Martin MJ, Orchard S, UniProt Consortium. UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship. Mol Cell Proteomics 2023;22(8):100591
  50. Brina D, Ponzoni A, Troiani M, Calì B, Pasquini E, Attanasio G, Mosole S, Mirenda M, D'Ambrosio M, Colucci M, Guccini I, Revandkar A, Alajati A, Tebaldi T, Donzel D, Lauria F, Parhizgari N, Valdata A, Maddalena M, Calcinotto A, Bolis M, Rinaldi A, Barry S, Rüschoff JH, Sabbadin M, Sumanasuriya S, Crespo M, Sharp A, Yuan W, Grinu M, Boyle A, Miller C, Trotman L, Delaleu N, Fassan M, Moch H, Viero G, de Bono J, Alimonti A. The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. Nat Cancer 2023;4(8):1102-1121
  51. Brown AA, Fernandez-Tajes JJ, Hong MG, Brorsson CA, Koivula RW, Davtian D, Dupuis T, Sartori A, Michalettou TD, Forgie IM, Adam J, Allin KH, Caiazzo R, Cederberg H, De Masi F, Elders PJM, Giordano GN, Haid M, Hansen T, Hansen TH, Hattersley AT, Heggie AJ, Howald C, Jones AG, Kokkola T, Laakso M, Mahajan A, Mari A, McDonald TJ, McEvoy D, Mourby M, Musholt PB, Nilsson B, Pattou F, Penet D, Raverdy V, Ridderstråle M, Romano L, Rutters F, Sharma S, Teare H, 't Hart L, Tsirigos KD, Vangipurapu J, Vestergaard H, Brunak S, Franks PW, Frost G, Grallert H, Jablonka B, McCarthy MI, Pavo I, Pedersen O, Ruetten H, Walker M, DIRECT Consortium, Adamski J, Schwenk JM, Pearson ER, Dermitzakis ET, Viñuela A. Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits. Nat Commun 2023;14(1):5062
  52. Brümmer A, Bergmann S. Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs 2023
  53. Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon C, Rot G, Schärfen L, Wu P, Yoon Y, Barash Y, Zavolan M. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data 2023
  54. Buchner B, Clement TJ, de Groot DH, Zanghellini J. ecmtool: fast and memory-efficient enumeration of elementary conversion modes. Bioinformatics 2023;39(3):btad095
  55. Bugnon M, Goullieux M, Röhrig UF, Perez MAS, Daina A, Michielin O, Zoete V. SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization. J Chem Inf Model 2023
  56. Buljan M, Banaei-Esfahani A, Blattmann P, Meier-Abt F, Shao W, Vitek O, Tang H, Aebersold R. A computational framework for the inference of protein complex remodeling from whole-proteome measurements. Nat Methods 2023;20(10):1523-1529
  57. Bunne C, Stark SG, Gut G, Del Castillo JS, Levesque M, Lehmann KV, Pelkmans L, Krause A, Rätsch G. Learning single-cell perturbation responses using neural optimal transport. Nat Methods 2023
  58. Bunne C, Stark SG, Gut G, Del Castillo JS, Levesque M, Lehmann KV, Pelkmans L, Krause A, Rätsch G. Author Correction: Learning single-cell perturbation responses using neural optimal transport. Nat Methods 2023
  59. Bustamante Eduardo M, Keller I, Schuster N, Aebi S, Jaggi R. Molecular characterization of breast cancer cell pools with normal or reduced ability to respond to progesterone: a study based on RNA-seq. J Genet Eng Biotechnol 2023;21(1):81
  60. Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A. Systematic analysis of drug combinations against Gram-positive bacteria. Nat Microbiol 2023
  61. Callari M, Sola M, Magrin C, Rinaldi A, Bolis M, Paganetti P, Colnaghi L, Papin S. Cancer-specific association between Tau (MAPT) and cellular pathways, clinical outcome, and drug response. Sci Data 2023;10(1):637
  62. Camps J, Noël F, Liechti R, Massenet-Regad L, Rigade S, Götz L, Hoffmann C, Amblard E, Saichi M, Ibrahim MM, Pollard J, Medvedovic J, Roider HG, Soumelis V. Meta-Analysis of Human Cancer Single-Cell RNA-Seq Datasets Using the IMMUcan Database. Cancer Res 2023;83(3):363-373
  63. Canesi M, Douville E, Montagna P, Taviani M, Stolarski J, Bordier L, Dapoigny A, Coulibaly GEH, Simon AC, Agelou M, Fin J, Metzl N, Iwankow G, Allemand D, Planes S, Moulin C, Lombard F, Bourdin G, Troublé R, Agostini S, Banaigs B, Boissin E, Boss E, Bowler C, de Vargas C, Flores M, Forcioli D, Furla P, Gilson E, Galand PE, Pesant S, Sunagawa S, Thomas OP, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, Reynaud S. Differences in carbonate chemistry up-regulation of long-lived reef-building corals. Sci Rep 2023;13(1):11589
  64. Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023;378(1877):20220055
  65. Cao L, Ruiz Buendía GA, Fournier N, Liu Y, Armand F, Hamelin R, Pavlou M, Radtke F. Resistance mechanism to Notch inhibition and combination therapy in human T-cell acute lymphoblastic leukemia. Blood Adv 2023;7(20):6240-6252
  66. Cardner M, Marass F, Gedvilaite E, Yang JL, Tsui DWY, Beerenwinkel N. Predicting tumour content of liquid biopsies from cell-free DNA. BMC Bioinformatics 2023;24(1):368
  67. Carlisle E, Janis CM, Pisani D, Donoghue PCJ, Silvestro D. A timescale for placental mammal diversification based on Bayesian modeling of the fossil record. Curr Biol 2023;33(15):3073-3082.e3
  68. Carrillo JD, Püschel HP. Pleistocene South American native ungulates (Notoungulata and Litopterna) of the historical Roth collections in Switzerland, from the Pampean Region of Argentina. Swiss J Palaeontol 2023;142(1):28
  69. Castro LJ, Palagi PM, Beard N, Attwood TK, Brazas MD. Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources. PLoS Comput Biol 2023;19(6):e1011120
  70. Caucheteur D, May Pendlington Z, Roncaglia P, Gobeill J, Mottin L, Matentzoglu N, Agosti D, Osumi-Sutherland D, Parkinson H, Ruch P. COVoc and COVTriage: novel resources to support literature triage. Bioinformatics 2023;39(1):btac800
  71. Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SA, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff JP, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. KG-Hub -- Building and Exchanging Biological Knowledge Graphs 2023
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