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: 01.07.2023

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. 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
  5. 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
  6. 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)
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 Mutational Spectrum. Mol Biol Evol 2023;40(4):msad085
  30. Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins 2023
  31. 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
  32. Brümmer A, Bergmann S. Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs 2023
  33. Buchner B, Clement TJ, de Groot DH, Zanghellini J. ecmtool: fast and memory-efficient enumeration of elementary conversion modes. Bioinformatics 2023;39(3):btad095
  34. 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
  35. 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
  36. 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:bloodadvances.2023010380
  37. 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:S0960-9822(23)00767-4
  38. 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
  39. 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
  40. 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
  41. Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, 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. Bioinformatics 2023:btad418
  42. Chen C, Stadler T. GenSpectrum Chat: Data Exploration in Public Health Using Large Language Models 2023
  43. Chen C, Taepper A, Engelniederhammer F, Kellerer J, Roemer C, Stadler T. LAPIS is a fast web API for massive open virus sequencing data. BMC Bioinformatics 2023;24(1):232
  44. Chen C, Taepper A, Engelniederhammer F, Kellerer J, Roemer C, Stadler T. LAPIS is a fast web API for massive open virus sequencing databases 2023
  45. Chen X, Portran D, Widmer LA, Stangier MM, Czub MP, Liakopoulos D, Stelling J, Steinmetz MO, Barral Y. The motor domain of the kinesin Kip2 promotes microtubule polymerization at microtubule tips. J Cell Biol 2023;222(7):e202110126
  46. Cheval B, Darrous L, Choi KW, Klimentidis YC, Raichlen DA, Alexander GE, Cullati S, Kutalik Z, Boisgontier MP. Genetic insights into the causal relationship between physical activity and cognitive functioning. Sci Rep 2023;13(1):5310
  47. Claudel C, Loiseau O, Silvestro D, Lev-Yadun S, Antonelli A. Patterns and drivers of heat production in the plant genus Amorphophallus. Plant J 2023
  48. Cobat A, Zhang Q, Covid Human Genetic Effort, Abel L, Casanova JL, Fellay J. Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants. Annu Rev Biomed Data Sci 2023
  49. Cooper RL, Milinkovitch MC. Transient agonism of the sonic hedgehog pathway triggers a permanent transition of skin appendage fate in the chicken embryo. Sci Adv 2023;9(20):eadg9619
  50. Cooper RL, Santos-Durán G, Milinkovitch MC. Protocol for the rapid intravenous in ovo injection of developing amniote embryos. STAR Protoc 2023;4(2):102324
  51. Corona Ramirez A, Bregnard D, Junier T, Cailleau G, Dorador C, Bindschedler S, Junier P. Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis. BMC Microbiol 2023;23(1):68
  52. Corval H, Cumer T, Topaloudis A, Roulin A, Goudet J. Where and when local adaptation happens: lessons from the European barn owl (Tyto alba) 2023
  53. Costa J, Hayes C, Lisacek F. Protein glycosylation and glycoinformatics for novel biomarker discovery in neurodegenerative diseases. Ageing Res Rev 2023;89:101991
  54. Coudert E, Gehant S, de Castro E, Pozzato M, Baratin D, Neto T, Sigrist CJA, Redaschi N, Bridge A, UniProt Consortium. Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinformatics 2023;39(1):btac793
  55. Courlet P, Abler D, Guidi M, Girard P, Amato F, Vietti Violi N, Dietz M, Guignard N, Wicky A, Latifyan S, De Micheli R, Jreige M, Dromain C, Csajka C, Prior JO, Venkatakrishnan K, Michielin O, Cuendet MA, Terranova N. Modeling tumor size dynamics based on real-world electronic health records and image data in advanced melanoma patients receiving immunotherapy. CPT Pharmacometrics Syst Pharmacol 2023
  56. Couto JP, Vulin M, Jehanno C, Coissieux MM, Hamelin B, Schmidt A, Ivanek R, Sethi A, Bräutigam K, Frei AL, Hager C, Manivannan M, Gómez-Miragaya J, Obradović MM, Varga Z, Koelzer VH, Mertz KD, Bentires-Alj M. Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancer. EMBO J 2023;42(13):e112559
  57. Crocker J, Payne JL, Walczak AM, Wittkopp PJ. Interdisciplinary approaches to predicting evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2023;378(1877):20220042
  58. Crowell HL, Morillo Leonardo SX, Soneson C, Robinson MD. The shaky foundations of simulating single-cell RNA sequencing data. Genome Biol 2023;24(1):62
  59. Cumer T, Machado AP, San-Jose LM, Ducrest A, Simon C, Roulin A, Goudet J. The genomic architecture of a continuous color polymorphism in the European barn owl (Tyto alba) 2023
  60. Dadonaite B, Crawford KHD, Radford CE, Farrell AG, Yu TC, Hannon WW, Zhou P, Andrabi R, Burton DR, Liu L, Ho DD, Chu HY, Neher RA, Bloom JD. A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike. Cell 2023;186(6):1263-1278.e20
  61. Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One 2023;18(5):e0285433
  62. Darrous L, Hemani G, Smith GD, Kutalik Z. PheWAS-based clustering of Mendelian Randomisation instruments reveals distinct mechanism-specific causal effects between obesity and educational attainment 2023
  63. de Groot DH, Tjalma AJ, Bruggeman FJ, van Nimwegen E. Effective bet-hedging through growth rate dependent stability. Proc Natl Acad Sci U S A 2023;120(8):e2211091120
  64. de Souza VBC, Jordan BT, Tseng E, Nelson EA, Hirschi KK, Sheynkman G, Robinson MD. Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. Genome Biol 2023;24(1):91
  65. Deichmann J, Bachmann S, Burckhardt MA, Pfister M, Szinnai G, Kaltenbach HM. New model of glucose-insulin regulation characterizes effects of physical activity and facilitates personalized treatment evaluation in children and adults with type 1 diabetes. PLoS Comput Biol 2023;19(2):e1010289
  66. Dhrangadhariya A, Hilfiker R, Sattelmayer M, Giacomino K, Caliesch R, Elsig S, Naderi N, Müller H. First Steps Towards a Risk of Bias Corpus of Randomized Controlled Trials. Stud Health Technol Inform 2023;302:586-590
  67. Dietler N, Lupo U, Bitbol AF. Impact of phylogeny on structural contact inference from protein sequence data. J R Soc Interface 2023;20(199):20220707
  68. Dijokaite-Guraliuc A, Das R, Zhou D, Ginn HM, Liu C, Duyvesteyn HME, Huo J, Nutalai R, Supasa P, Selvaraj M, de Silva TI, Plowright M, Newman TAH, Hornsby H, Mentzer AJ, Skelly D, Ritter TG, Temperton N, Klenerman P, Barnes E, Dunachie SJ, OPTIC consortium, Roemer C, Peacock TP, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Cell Rep 2023;42(4):112271
  69. Durairaj J, Waterhouse AM, Mets T, Brodiazhenko T, Abdullah M, Studer G, Akdel M, Andreeva A, Bateman A, Tenson T, Tenson T, Hauryliuk V, Schwede T, Pereira J. What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds 2023
  70. Duruz J, Sprecher M, Kaldun JC, Al-Soudy AS, Lischer HEL, van Geest G, Nicholson P, Bruggmann R, Sprecher SG. Molecular characterization of cell types in the squid Loligo vulgaris. Elife 2023;12:e80670
  71. Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol 2023
  72. Edelson JL, Schneider LD, Amar D, Brink-Kjaer A, Cederberg KL, Kutalik Z, Hagen EW, Peppard PE, Tempaku PF, Tufik S, Evans DS, Stone K, Tranah G, Cade B, Redline S, Haba-Rubio J, Heinzer R, Marques-Vidal P, Vollenweider P, Winkelmann J, Zou J, Mignot E. The genetic etiology of periodic limb movement in sleep. Sleep 2023;46(4):zsac121
  73. Farina B, Godoy P, Benson R, Langer M, Ferreira G. Turtle body size evolution is determined by lineage‐specific specializations rather than global trends Ecol Evol 2023;13(6)
  74. Farina BM, Godoy PL, Benson RBJ, Langer MC, Ferreira GS. Turtle body size evolution is determined by lineage-specific specializations rather than global trends. Ecol Evol 2023;13(6):e10201
  75. Fava M, Stahl SM, De Martin S, Mattarei A, Bettini E, Comai S, Alimonti A, Bifari F, Pani L, Folli F, Guidetti C, Furlan A, Sgrignani J, Locatelli P, Cavalli A, O'Gorman C, Traversa S, Inturrisi CE, Pappagallo M, Manfredi PL. Esmethadone-HCl (REL-1017): a promising rapid antidepressant. Eur Arch Psychiatry Clin Neurosci 2023
  76. Featherstone LA, Duchene S, Vaughan TG. Decoding the Fundamental Drivers of Phylodynamic Inference. Mol Biol Evol 2023;40(6):msad132
  77. Ferdowsi S, Knafou J, Borissov N, Vicente Alvarez D, Mishra R, Amini P, Teodoro D. Deep learning-based risk prediction for interventional clinical trials based on protocol design: A retrospective study. Patterns (N Y) 2023;4(3):100689
  78. Forny P, Bonilla X, Lamparter D, Shao W, Plessl T, Frei C, Bingisser A, Goetze S, van Drogen A, Harshman K, Pedrioli PGA, Howald C, Poms M, Traversi F, Bürer C, Cherkaoui S, Morscher RJ, Simmons L, Forny M, Xenarios I, Aebersold R, Zamboni N, Rätsch G, Dermitzakis ET, Wollscheid B, Baumgartner MR, Froese DS. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency. Nat Metab 2023;5(1):80-95
  79. Foster WJ, Allen BJ, Kitzmann NH, Münchmeyer J, Rettelbach T, Witts JD, Whittle RJ, Larina E, Clapham ME, Dunhill AM. How predictable are mass extinction events? R Soc Open Sci 2023;10(3):221507
  80. Frachon L, Arrigo L, Rusman Q, Poveda L, Qi W, Scopece G, Schiestl FP. Putative Signals of Generalist Plant Species Adaptation to Local Pollinator Communities and Abiotic Factors. Mol Biol Evol 2023;40(3):msad036
  81. Frey K, Rohrer L, Potapenko A, Goetze S, von Eckardstein A, Wollscheid B. Mapping the dynamic cell surface interactome of high-density lipoprotein reveals Aminopeptidase N as modulator of its endothelial uptake 2023
  82. Fritah H, Graciotti M, Lai-Lai Chiang C, Huguenin-Bergenat AL, Petremand R, Ahmed R, Guillaume P, Schmidt J, Stevenson BJ, Gfeller D, Harari A, Kandalaft LE. Cancer vaccines based on whole-tumor lysate or neoepitopes with validated HLA binding outperform those with predicted HLA-binding affinity. iScience 2023;26(4):106288
  83. Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res 2023;51(d1):D760-D766
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