Peer-reviewed articles and conference proceedings

Listed in Europe PMC, latest update: 2022-05-01.
Discover the SIB Remarkable Outputs 2021

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.

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  1. Adler A, Poirier S, Pagni M, Maillard J, Holliger C. Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environ Microbiol 2022;24(4):2136-2156
  2. Aedo-Lopez V, Gérard CL, Boughdad S, Gautron Moura B, Berthod G, Digklia A, Homicsko K, Schaefer N, Duran R, Cuendet MA, Michielin O. Safety and Efficacy of Ipilimumab plus Nivolumab and Sequential Selective Internal Radiation Therapy in Hepatic and Extrahepatic Metastatic Uveal Melanoma. Cancers (Basel) 2022;14(5)
  3. Alessandro C, Antoine D, Marta A S P, Olivier M, Vincent Z. SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface. Nucleic Acids Res 2022;50(d1):D1382-D1390
  4. Andreatta M, Berenstein AJ, Carmona SJ. scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets. Bioinformatics 2022
  5. Andreatta M, David FPA, Iseli C, Guex N, Carmona SJ. SPICA: Swiss portal for immune cell analysis. Nucleic Acids Res 2022;50(d1):D1109-D1114
  6. Antoszewski M, Fournier N, Ruiz Buendía GA, Lourenco J, Liu Y, Sugrue T, Dubey C, Nkosi M, Pritchard CEJ, Huijbers IJ, Segat GC, Alonso-Moreno S, Serracanta E, Belver L, Ferrando AA, Ciriello G, Weng AP, Koch U, Radtke F. Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL. Blood 2022;139(16):2483-2498
  7. Arizmendi Cárdenas YO, Neuenschwander S, Malaspinas AS. Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PeerJ 2022;10:e12784
  8. Arribas AJ, Napoli S, Cascione L, Sartori G, Barnabei L, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, De Moura MC, Jovic S, Bordone-Pittau R, Di Veroli A, Stathis A, Cruciani G, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. Resistance to PI3κδ inhibitors in marginal zone lymphoma can be reverted by targeting the IL-6/PDGFRA axis. Haematologica 2022
  9. Auwerx C, Lepamets M, Sadler MC, Patxot M, Stojanov M, Baud D, Mägi R, Estonian Biobank Research Team, Porcu E, Reymond A, Kutalik Z. The individual and global impact of copy-number variants on complex human traits. Am J Hum Genet 2022;109(4):647-668
  10. Auwerx C, Sadler MC, Reymond A, Kutalik Z. From pharmacogenetics to pharmaco-omics: Milestones and future directions. HGG Adv 2022;3(2):100100
  11. Babrak LM, Smakaj E, Agac T, Asprion PM, Grimberg F, der Werf DV, van Ginkel EW, Tosoni DD, Clay I, Degen M, Brodbeck D, Natali E, Schkommodau E, Miho E. RWD-Cockpit: Application for Quality Assessment of Real-World Data. JMIR Form Res 2022
  12. Bady P, Marosi C, Weller M, Grønberg BH, Schultz H, Taphoorn MJB, Gijtenbeek JMM, van den Bent MJ, von Deimling A, Stupp R, Malmström A, Hegi ME. DNA methylation-based age acceleration observed in IDH wild-type glioblastoma is associated with better outcome-including in elderly patients. Acta Neuropathol Commun 2022;10(1):39
  13. Bai Y, Caussinus E, Leo S, Bosshardt F, Myachina F, Rot G, Robinson MD, Lehner CF. Correction to: A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. BMC Genomics 2022;23(1):241
  14. Bakkeren E, Gül E, Huisman JS, Steiger Y, Rocker A, Hardt WD, Diard M. Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium. Nat Commun 2022;13(1):1939
  15. Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A. Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res 2022;50(d1):D693-D700
  16. Bauman PA, Doxey AC, Eberini I, Islamovic E, Jungo F, Kessenich C, Kough J, Krishan M, Palazzolo L, Privalle L, Rodriguez CE, Satchell KJF, Silvanovich A, Pereira Mouriès L. "From Protein Toxins to Applied Toxicological Testing" virtual workshop identifies the need for a bioinformatic framework to assess novel food protein safety. Regul Toxicol Pharmacol 2022;131:105146
  17. Beber ME, Gollub MG, Mozaffari D, Shebek KM, Flamholz AI, Milo R, Noor E. eQuilibrator 3.0: a database solution for thermodynamic constant estimation. Nucleic Acids Res 2022;50(d1):D603-D609
  18. Bianco G, Coto-Llerena M, Gallon J, Kancherla V, Taha-Mehlitz S, Marinucci M, Konantz M, Srivatsa S, Montazeri H, Panebianco F, Tirunagaru VG, De Menna M, Paradiso V, Ercan C, Dahmani A, Montaudon E, Beerenwinkel N, Kruithof-de Julio M, Terracciano LM, Lengerke C, Jeselsohn RM, Doebele RC, Bidard FC, Marangoni E, Ng CKY, Piscuoglio S. GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Commun Biol 2022;5(1):373
  19. Bick AG, Popadin K, Thorball CW, Uddin MM, Zanni MV, Yu B, Cavassini M, Rauch A, Tarr P, Schmid P, Bernasconi E, Günthard HF, Libby P, Boerwinkle E, McLaren PJ, Ballantyne CM, Grinspoon S, Natarajan P, Fellay J, Swiss HIV Cohort Study. Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV. Sci Rep 2022;12(1):577
  20. Boonen RACM, Wiegant WW, Celosse N, Vroling B, Heijl S, Kote-Jarai Z, Mijuskovic M, Cristea S, Solleveld-Westerink N, van Wezel T, Beerenwinkel N, Eeles R, Devilee P, Vreeswijk MPG, Marra G, van Attikum H. Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk. Cancer Res 2022;82(4):615-631
  21. Boyd BM, Nguyen NP, Allen JM, Waterhouse RM, Vo KB, Sweet AD, Clayton DH, Bush SE, Shapiro MD, Johnson KP. Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites. Proc Biol Sci 2022;289(1970):20220042
  22. Bragina ME, Daina A, Perez MAS, Michielin O, Zoete V. The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience. Int J Mol Sci 2022;23(2)
  23. Braunstein L, Brüningk SC, Rivens I, Civale J, Haar GT. Characterization of Acoustic, Cavitation, and Thermal Properties of Poly(vinyl alcohol) Hydrogels for Use as Therapeutic Ultrasound Tissue Mimics. Ultrasound Med Biol 2022;48(6):1095-1109
  24. Briand S, Dessimoz C, El-Mabrouk N, Nevers Y. A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem. Syst Biol 2022
  25. Brümmer A, Dreos R, Marques AC, Bergmann S. Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure. Mol Biol Evol 2022;39(2)
  26. Bues J, Biočanin M, Pezoldt J, Dainese R, Chrisnandy A, Rezakhani S, Saelens W, Gardeux V, Gupta R, Sarkis R, Russeil J, Saeys Y, Amstad E, Claassen M, Lutolf MP, Deplancke B. Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition. Nat Methods 2022;19(3):323-330
  27. Caduff L, Dreifuss D, Schindler T, Devaux AJ, Ganesanandamoorthy P, Kull A, Stachler E, Fernandez-Cassi X, Beerenwinkel N, Kohn T, Ort C, Julian TR. Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021. Euro Surveill 2022;27(10)
  28. Cano AV, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias shapes the spectrum of adaptive substitutions. Proc Natl Acad Sci U S A 2022;119(7)
  29. Chakraborty D, Guinat C, Müller NF, Briand FX, Andraud M, Scoizec A, Lebouquin S, Niqueux E, Schmitz A, Grasland B, Guerin JL, Paul MC, Vergne T. Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-2017. Transbound Emerg Dis 2022
  30. Colavin A, Atolia E, Bitbol AF, Huang KC. Extracting phylogenetic dimensions of coevolution reveals hidden functional signals. Sci Rep 2022;12(1):820
  31. Collado-Vides J, Gaudet P, de Lorenzo V. Missing Links Between Gene Function and Physiology in Genomics. Front Physiol 2022;13:815874
  32. Cortés Rodríguez F, Dal Peraro M, Abriata LA. Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web. J Mol Graph Model 2022;114:108164
  33. Coto-Llerena M, Benjak A, Gallon J, Meier MA, Boldanova T, Terracciano LM, Ng CKY, Piscuoglio S. Circulating Cell-Free DNA Captures the Intratumor Heterogeneity in Multinodular Hepatocellular Carcinoma. JCO Precis Oncol 2022;6:e2100335
  34. Cristinelli S, Angelino P, Ciuffi A. Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV. J Vis Exp 2022(181)
  35. Cumer T, Machado AP, Dumont G, Bontzorlos V, Ceccherelli R, Charter M, Dichmann K, Kassinis N, Lourenço R, Manzia F, Martens HD, Prévost L, Rakovic M, Roque I, Siverio F, Roulin A, Goudet J. Landscape and Climatic Variations Shaped Secondary Contacts amid Barn Owls of the Western Palearctic. Mol Biol Evol 2022;39(1)
  36. Cummings TFM, Gori K, Sanchez-Pulido L, Gavriilidis G, Moi D, Wilson AR, Murchison E, Dessimoz C, Ponting CP, Christophorou MA. Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria. Mol Biol Evol 2022;39(2)
  37. Dasmeh P, Doronin R, Wagner A. The length scale of multivalent interactions is evolutionarily conserved in fungal and vertebrate phase-separating proteins. Genetics 2022;220(1)
  38. Della Bella E, Koch J, Baerenfaller K. Translation and emerging functions of non-coding RNAs in inflammation and immunity. Allergy 2022
  39. Diebold M, Galli E, Kopf A, Sanderson N, Callegari I, Ingelfinger F, Núñez NG, Benkert P, Kappos L, Kuhle J, Becher B, Claassen M, Derfuss T. Immunological Predictors of Dimethyl Fumarate-Induced Lymphopenia. Ann Neurol 2022;91(5):676-681
  40. Dorn P, Pfister S, Oberhaensli S, Gioutsos K, Haenggi M, Kocher GJ. Operative versus non-operative management of rib fractures in flail chest after cardiopulmonary resuscitation manoeuvres. Interact Cardiovasc Thorac Surg 2022
  41. Du K, Pippel M, Kneitz S, Feron R, da Cruz I, Winkler S, Wilde B, Avila Luna EG, Myers G, Guiguen Y, Macias Garcia C, Schartl M. Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation. Genome Res 2022;32(3):583-594
  42. Feron R, Waterhouse RM. Exploring new genomic territories with emerging model insects. Curr Opin Insect Sci 2022;51:100902
  43. Feron R, Waterhouse RM. Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes. Gigascience 2022;11
  44. Ferreira PL, Batista R, Andermann T, Groppo M, Bacon CD, Antonelli A. Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses. Mol Phylogenet Evol 2022;169:107432
  45. Fleig S, Kapanadze T, Bernier-Latmani J, Lill JK, Wyss T, Gamrekelashvili J, Kijas D, Liu B, Hüsing AM, Bovay E, Jirmo AC, Halle S, Ricke-Hoch M, Adams RH, Engel DR, von Vietinghoff S, Förster R, Hilfiker-Kleiner D, Haller H, Petrova TV, Limbourg FP. Loss of vascular endothelial notch signaling promotes spontaneous formation of tertiary lymphoid structures. Nat Commun 2022;13(1):2022
  46. Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M, European Reference Genome Atlas (ERGA) Consortium. The era of reference genomes in conservation genomics. Trends Ecol Evol 2022;37(3):197-202
  47. Furrer L, Cornelius J, Rinaldi F. Parallel sequence tagging for concept recognition. BMC Bioinformatics 2022;22(suppl 1):623
  48. Gabella C, Duvaud S, Durinx C. Managing the life cycle of a portfolio of open data resources at the SIB Swiss Institute of Bioinformatics. Brief Bioinform 2022;23(1)
  49. García-Martín AB, Roder T, Schmitt S, Zeeh F, Bruggmann R, Perreten V. Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196. BMC Genomics 2022;23(1):131
  50. Gebhardt T, Touré V, Waltemath D, Wolkenhauer O, Scharm M. Exploring the evolution of biochemical models at the network level. PLoS One 2022;17(3):e0265735
  51. Genta S, Ghilardi G, Cascione L, Juskevicius D, Tzankov A, Schär S, Milan L, Pirosa MC, Esposito F, Ruberto T, Giovanella L, Hayoz S, Mamot C, Dirnhofer S, Zucca E, Ceriani L. Integration of Baseline Metabolic Parameters and Mutational Profiles Predicts Long-Term Response to First-Line Therapy in DLBCL Patients: A Post Hoc Analysis of the SAKK38/07 Study. Cancers (Basel) 2022;14(4)
  52. Georgiadou E, Muralidharan C, Martinez M, Chabosseau P, Akalestou E, Tomas A, Yong Su Wern F, Stylianides T, Wretlind A, Legido-Quigley C, Jones B, Lopez Noriega L, Xu Y, Gu G, Alsabeeh N, Cruciani-Guglielmacci C, Magnan C, Ibberson M, Leclerc I, Ali Y, Soleimanpour SA, Linnemann AK, Rodriguez TA, Rutter GA. Mitofusins Mfn1 and Mfn2 are Required to Preserve Glucose- But Not Incretin-Stimulated Beta Cell Connectivity and Insulin Secretion. Diabetes 2022
  53. Ghosh S, Ataman M, Bak M, Börsch A, Schmidt A, Buczak K, Martin G, Dimitriades B, Herrmann CJ, Kanitz A, Zavolan M. CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Res 2022;50(6):3096-3114
  54. Gianni' M, Goracci L, Schlaefli A, Di Veroli A, Kurosaki M, Guarrera L, Bolis M, Foglia M, Lupi M, Tschan MP, Cruciani G, Terao M, Garattini E. Role of cardiolipins, mitochondria, and autophagy in the differentiation process activated by all-trans retinoic acid in acute promyelocytic leukemia. Cell Death Dis 2022;13(1):30
  55. Gilbert KJ, Moinet A, Peischl S. Gene surfing of underdominant alleles promotes formation of hybrid zones. Philos Trans R Soc Lond B Biol Sci 2022;377(1846):20210006
  56. Glorieux L, Sapala A, Willnow D, Moulis M, Salowka A, Darrigrand JF, Edri S, Schonblum A, Sakhneny L, Schaumann L, Gómez HF, Lang C, Conrad L, Guillemot F, Levenberg S, Landsman L, Iber D, Pierreux CE, Spagnoli FM. Development of a 3D atlas of the embryonic pancreas for topological and quantitative analysis of heterologous cell interactions. Development 2022;149(3)
  57. Goetze S, Schüffler P, Athanasiou A, Koetemann A, Poyet C, Fankhauser CD, Wild PJ, Schiess R, Wollscheid B. Use of MS-GUIDE for identification of protein biomarkers for risk stratification of patients with prostate cancer. Clin Proteomics 2022;19(1):9
  58. Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Gigascience 2022;11
  59. Guilliams M, Bonnardel J, Haest B, Vanderborght B, Wagner C, Remmerie A, Bujko A, Martens L, Thoné T, Browaeys R, De Ponti FF, Vanneste B, Zwicker C, Svedberg FR, Vanhalewyn T, Gonçalves A, Lippens S, Devriendt B, Cox E, Ferrero G, Wittamer V, Willaert A, Kaptein SJF, Neyts J, Dallmeier K, Geldhof P, Casaert S, Deplancke B, Ten Dijke P, Hoorens A, Vanlander A, Berrevoet F, Van Nieuwenhove Y, Saeys Y, Saelens W, Van Vlierberghe H, Devisscher L, Scott CL. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell 2022;185(2):379-396.e38
  60. He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 2022;19(3):316-322
  61. Hersch M, Biasini A, Marques AC, Bergmann S. Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. BMC Bioinformatics 2022;23(1):147
  62. Hirt CK, Booij TH, Grob L, Simmler P, Toussaint NC, Keller D, Taube D, Ludwig V, Goryachkin A, Pauli C, Lenggenhager D, Stekhoven DJ, Stirnimann CU, Endhardt K, Ringnalda F, Villiger L, Siebenhüner A, Karkampouna S, De Menna M, Beshay J, Klett H, Kruithof-de Julio M, Schüler J, Schwank G. Drug screening and genome editing in human pancreatic cancer organoids identifies drug-gene interactions and candidates for off-label treatment. Cell Genom 2022;2(2):100095
  63. Huisman JS, Benz F, Duxbury SJN, de Visser JAGM, Hall AR, Fischer EAJ, Bonhoeffer S. Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods. Plasmid 2022;121:102627
  64. Ippolito L, Comito G, Parri M, Iozzo M, Duatti A, Virgilio F, Lorito N, Bacci M, Pardella E, Sandrini G, Bianchini F, Damiano R, Ferrone L, la Marca G, Serni S, Spatafora P, Catapano CV, Morandi A, Giannoni E, Chiarugi P. Lactate Rewires Lipid Metabolism and Sustains a Metabolic-Epigenetic Axis in Prostate Cancer. Cancer Res 2022;82(7):1267-1282
  65. Irving M, Zoete V, Bassani-Sternberg M, Coukos G. A roadmap for driving CAR T cells toward the oncogenic immunopeptidome. Cancer Cell 2022;40(1):20-22
  66. Iyengar BR, Wagner A. GroEL/S overexpression helps to purge deleterious mutations and reduce genetic diversity during adaptive protein evolution. Mol Biol Evol 2022
  67. Jablonski KP, Carron L, Mozziconacci J, Forné T, Hütt MT, Lesne A. Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study. Hum Genomics 2022;16(1):2
  68. Jaron KS, Parker DJ, Anselmetti Y, Tran Van P, Bast J, Dumas Z, Figuet E, François CM, Hayward K, Rossier V, Simion P, Robinson-Rechavi M, Galtier N, Schwander T. Convergent consequences of parthenogenesis on stick insect genomes. Sci Adv 2022;8(8):eabg3842
  69. Jeske K, Schulz J, Tekemen D, Balčiauskas L, Balčiauskienė L, Hiltbrunner M, Drewes S, Mayer-Scholl A, Heckel G, Ulrich RG. Cocirculation of Leptospira spp. and multiple orthohantaviruses in rodents, Lithuania, Northern Europe. Transbound Emerg Dis 2022
  70. Joseph CB, Mariniello M, Yoshifuji A, Schiano G, Lake J, Marten J, Richmond A, Huffman JE, Campbell A, Harris SE, Troyanov S, Cocca M, Robino A, Thériault S, Eckardt KU, Wuttke M, Cheng Y, Corre T, Kolcic I, Black C, Bruat V, Concas MP, Sala C, Aeschbacher S, Schaefer F, Bergmann S, Campbell H, Olden M, Polasek O, Porteous DJ, Deary IJ, Madore F, Awadalla P, Girotto G, Ulivi S, Conen D, Wuehl E, Olinger E, Wilson JF, Bochud M, Köttgen A, Hayward C, Devuyst O. Meta-GWAS Reveals Novel Genetic Variants Associated with Urinary Excretion of Uromodulin. J Am Soc Nephrol 2022;33(3):511-529
  71. Karaaslan C, Mayorga C, Baerenfaller K, Escribese MM. Editorial: Systems Biology Approach to the Immunology of Asthma and Allergy. Front Immunol 2022;13:857403
  72. Karve S, Wagner A. Multiple Novel Traits without Immediate Benefits Originate in Bacteria Evolving on Single Antibiotics. Mol Biol Evol 2022;39(1)
  73. Khan P, Fytianos K, Blumer S, Roux J, Gazdhar A, Savic S, Knudsen L, Jonigk D, Kuehnel MP, Mykoniati S, Tamm M, Geiser T, Hostettler KE. Basal-Like Cell-Conditioned Medium Exerts Anti-Fibrotic Effects In Vitro and In Vivo. Front Bioeng Biotechnol 2022;10:844119
  74. Kieser S, Zdobnov EM, Trajkovski M. Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart. PLoS Comput Biol 2022;18(3):e1009947
  75. Klein F, Roux J, Cvijetic G, Rodrigues PF, von Muenchow L, Lubin R, Pelczar P, Yona S, Tsapogas P, Tussiwand R. Dntt expression reveals developmental hierarchy and lineage specification of hematopoietic progenitors. Nat Immunol 2022;23(4):505-517
  76. Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods 2022;19(4):374-380
  77. Koch P, Schmitt S, Cardner M, Beerenwinkel N, Panke S, Held M. Discovery of antimicrobials by massively parallelized growth assays (Mex). Sci Rep 2022;12(1):4097
  78. Labavić D, Loverdo C, Bitbol AF. Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity. Proc Natl Acad Sci U S A 2022;119(1)
  79. Le Mercier P, Bolleman J, de Castro E, Gasteiger E, Bansal P, Auchincloss AH, Boutet E, Breuza L, Casals-Casas C, Estreicher A, Feuermann M, Lieberherr D, Rivoire C, Pedruzzi I, Redaschi N, Bridge A. SwissBioPics-an interactive library of cell images for the visualization of subcellular location data. Database (Oxford) 2022;2022
  80. Lemberg C, Martinez de San Vicente K, Fróis-Martins R, Altmeier S, Tran VDT, Mertens S, Amorim-Vaz S, Rai LS, d'Enfert C, Pagni M, Sanglard D, LeibundGut-Landmann S. Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation. PLoS Pathog 2022;18(4):e1010012
  81. Lett MJ, Mehta H, Keogh A, Jaeger T, Jacquet M, Powell K, Meier MA, Fofana I, Melhem H, Vosbeck J, Cathomas G, Heigl A, Heim MH, Burri E, Mertz KD, Niess JH, Kollmar O, Zech CJ, Ivanek R, Duthaler U, Klenerman P, Stroka D, Filipowicz Sinnreich M. Stimulatory MAIT cell antigens reach the circulation and are efficiently metabolised and presented by human liver cells. Gut 2022
  82. Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O'Brien LE, Dow JAT, FCA Consortium§, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science 2022;375(6584):eabk2432
  83. Lisacek F. Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions. J Vis Exp 2022(179)
  84. Llimos G, Gardeux V, Koch U, Kribelbauer JF, Hafner A, Alpern D, Pezoldt J, Litovchenko M, Russeil J, Dainese R, Moia R, Mahmoud AM, Rossi D, Gaidano G, Plass C, Lutsik P, Gerhauser C, Waszak SM, Boettiger A, Radtke F, Deplancke B. A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nat Commun 2022;13(1):2042
  85. Lukyanchikova V, Nuriddinov M, Belokopytova P, Taskina A, Liang J, Reijnders MJMF, Ruzzante L, Feron R, Waterhouse RM, Wu Y, Mao C, Tu Z, Sharakhov IV, Fishman V. Anopheles mosquitoes reveal new principles of 3D genome organization in insects. Nat Commun 2022;13(1):1960
  86. Machlab D, Burger L, Soneson C, Rijli FM, Schübeler D, Stadler MB. monaLisa: an R/Bioconductor package for identifying regulatory motifs. Bioinformatics 2022
  87. Marchand A, Van Hall-Beauvais AK, Correia BE. Computational design of novel protein-protein interactions - An overview on methodological approaches and applications. Curr Opin Struct Biol 2022;74:102370
  88. Mariethoz J, Alocci D, Karlsson NG, Packer NH, Lisacek F. An Interactive View of Glycosylation. Methods Mol Biol 2022;2370:41-65
  89. Maróstica AS, Nunes K, Castelli EC, Silva NSB, Weir BS, Goudet J, Meyer D. How HLA diversity is apportioned: influence of selection and relevance to transplantation. Philos Trans R Soc Lond B Biol Sci 2022;377(1852):20200420
  90. McLeod DV, Gandon S. Effects of epistasis and recombination between vaccine-escape and virulence alleles on the dynamics of pathogen adaptation. Nat Ecol Evol 2022
  91. Melhem H, Kaya B, Kaymak T, Wuggenig P, Flint E, Roux J, Oost KC, Cavelti-Weder C, Balmer ML, Walser JC, Morales RA, Riedel CU, Liberali P, Villablanca EJ, Niess JH. Epithelial GPR35 protects from Citrobacter rodentium infection by preserving goblet cells and mucosal barrier integrity. Mucosal Immunol 2022;15(3):443-458
  92. Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods 2022;19(4):429-440
  93. Miller RM, Jordan BT, Mehlferber MM, Jeffery ED, Chatzipantsiou C, Kaur S, Millikin RJ, Dai Y, Tiberi S, Castaldi PJ, Shortreed MR, Luckey CJ, Conesa A, Smith LM, Deslattes Mays A, Sheynkman GM. Enhanced protein isoform characterization through long-read proteogenomics. Genome Biol 2022;23(1):69
  94. Mohsen MO, Speiser DE, Michaux J, Pak H, Stevenson BJ, Vogel M, Inchakalody VP, de Brot S, Dermime S, Coukos G, Bassani-Sternberg M, Bachmann MF. Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma. J Immunother Cancer 2022;10(1)
  95. Moinet A, Schlichta F, Peischl S, Excoffier L. Strong neutral sweeps occurring during a population contraction. Genetics 2022;220(4)
  96. Neubauer TA, Hauffe T, Silvestro D, Scotese CR, Stelbrink B, Albrecht C, Delicado D, Harzhauser M, Wilke T. Drivers of diversification in freshwater gastropods vary over deep time. Proc Biol Sci 2022;289(1968):20212057
  97. Nicheperovich A, Altenhoff AM, Dessimoz C, Majidian S. OMAMO: orthology-based alternative model organism selection. Bioinformatics 2022
  98. Nicolae A, Bouilly J, Lara D, Fataccioli V, Lemonnier F, Drieux F, Parrens M, Robe C, Poullot E, Bisig B, Bossard C, Letourneau A, Missiaglia E, Bonnet C, Szablewski V, Traverse-Glehen A, Delfau-Larue MH, de Leval L, Gaulard P. Nodal cytotoxic peripheral T-cell lymphoma occurs frequently in the clinical setting of immunodysregulation and is associated with recurrent epigenetic alterations. Mod Pathol 2022
  99. Pasche E, Mottaz A, Caucheteur D, Gobeill J, Michel PA, Ruch P. Variomes: a high recall search engine to support the curation of genomic variants. Bioinformatics 2022
  100. Perez MAS, Cuendet MA, Röhrig UF, Michielin O, Zoete V. Structural Prediction of Peptide-MHC Binding Modes. Methods Mol Biol 2022;2405:245-282
  101. Pillet B, Méndez-Godoy A, Murat G, Favre S, Stumpe M, Falquet L, Kressler D. Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis. Elife 2022;11
  102. Pires J, Huisman JS, Bonhoeffer S, Van Boeckel TP. Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases. J Antimicrob Chemother 2022;77(3):646-655
  103. Podobas EI, Gutowska-Owsiak D, Moretti S, Poznański J, Kulińczak M, Grynberg M, Gruca A, Bonna A, Płonka D, Ogg G, Bal W. Ni2+-Assisted Hydrolysis May Affect the Human Proteome; Filaggrin Degradation Ex Vivo as an Example of Possible Consequences. Front Mol Biosci 2022;9:828674
  104. Prummel KD, Crowell HL, Nieuwenhuize S, Brombacher EC, Daetwyler S, Soneson C, Kresoja-Rakic J, Kocere A, Ronner M, Ernst A, Labbaf Z, Clouthier DE, Firulli AB, Sánchez-Iranzo H, Naganathan SR, O'Rourke R, Raz E, Mercader N, Burger A, Felley-Bosco E, Huisken J, Robinson MD, Mosimann C. Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma. Nat Commun 2022;13(1):1677
  105. Qi W, Lim YW, Patrignani A, Schläpfer P, Bratus-Neuenschwander A, Grüter S, Chanez C, Rodde N, Prat E, Vautrin S, Fustier MA, Pratas D, Schlapbach R, Gruissem W. The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. Gigascience 2022;11
  106. Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon AM, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis CA, Palopoli N, Papaleo E, Pereira PJB, Pozzati G, Promponas VJ, Pujols J, Rocha ACS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos KD, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res 2022;50(d1):D480-D487
  107. Quaglia F, Salladini E, Carraro M, Minervini G, Tosatto SCE, Le Mercier P. SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion. FEBS J 2022
  108. Rambla J, Baudis M, Ariosa R, Beck T, Fromont LA, Navarro A, Paloots R, Rueda M, Saunders G, Singh B, Spalding JD, Törnroos J, Vasallo C, Veal CD, Brookes AJ. Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond. Hum Mutat 2022
  109. Reijnders MJMF. Wei2GO: weighted sequence similarity-based protein function prediction. PeerJ 2022;10:e12931
  110. Righelli D, Weber LM, Crowell HL, Pardo B, Collado-Torres L, Ghazanfar S, Lun ATL, Hicks SC, Risso D. SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor. Bioinformatics 2022
  111. Rodriguez-Rivas J, Croce G, Muscat M, Weigt M. Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. Proc Natl Acad Sci U S A 2022;119(4)
  112. Rohm TV, Keller L, Bosch AJT, AlAsfoor S, Baumann Z, Thomas A, Wiedemann SJ, Steiger L, Dalmas E, Wehner J, Rachid L, Mooser C, Yilmaz B, Fernandez Trigo N, Jauch AJ, Wueest S, Konrad D, Henri S, Niess JH, Hruz P, Ganal-Vonarburg SC, Roux J, Meier DT, Cavelti-Weder C. Targeting colonic macrophages improves glycemic control in high-fat diet-induced obesity. Commun Biol 2022;5(1):370
  113. Rubinstein MP, Williams C, Mart C, Beall J, MacPherson L, Azar J, Swiderska-Syn M, Manca P, Gibney BC, Robinson MD, Krieg C, Hill EG, Taha SA, Rock AD, Lee JH, Soon-Shiong P, Wrangle J. Phase I Trial Characterizing the Pharmacokinetic Profile of N-803, a Chimeric IL-15 Superagonist, in Healthy Volunteers. J Immunol 2022;208(6):1362-1370
  114. Rueda-Mejia MP, Nägeli L, Lutz S, Ortiz-Merino RA, Frei D, Frey JE, Wolfe KH, Ahrens CH, Freimoser FM. Genome sequence data of the antagonistic soil-borne yeast Cyberlindnera sargentensis (SHA 17.2). Data Brief 2022;40:107799
  115. Ruzzante L, Feron R, Reijnders MJMF, Thiébaut A, Waterhouse RM. Functional Constraints on Insect Immune System Components Govern Their Evolutionary Trajectories. Mol Biol Evol 2022;39(1)
  116. Scheck A, Rosset S, Defferrard M, Loukas A, Bonet J, Vandergheynst P, Correia BE. RosettaSurf-A surface-centric computational design approach. PLoS Comput Biol 2022;18(3):e1009178
  117. Scheidmann MC, Castro-Giner F, Strittmatter K, Krol I, Paasinen-Sohns A, Scherrer R, Donato C, Gkountela S, Szczerba BM, Diamantopoulou Z, Muenst S, Vlajnic T, Kunz L, Vetter M, Rochlitz C, Taylor V, Giachino C, Schroeder T, Platt RJ, Aceto N. An In Vivo CRISPR Screen Identifies Stepwise Genetic Dependencies of Metastatic Progression. Cancer Res 2022;82(4):681-694
  118. Schmoller KM, Lanz MC, Kim J, Koivomagi M, Qu Y, Tang C, Kukhtevich IV, Schneider R, Rudolf F, Moreno DF, Aldea M, Lucena R, Skotheim JM. Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1. Mol Biol Cell 2022;33(5):lt1
  119. Seifert D, Joos B, Braun DL, Oberle CS, Schenkel CD, Kuster H, Grube C, Böni J, Yerly S, Aubert V, Klimkait T, Günthard HF, Beerenwinkel N, Metzner KJ, On Behalf Of The Swiss Hiv Cohort Study. Detecting Selection in the HIV-1 Genome during Sexual Transmission Events. Viruses 2022;14(2)
  120. Sikorski J, Baumgartner V, Birkhofer K, Boeddinghaus RS, Bunk B, Fischer M, Fösel BU, Friedrich MW, Göker M, Hölzel N, Huang S, Huber KJ, Kandeler E, Klaus VH, Kleinebecker T, Marhan S, von Mering C, Oelmann Y, Prati D, Regan KM, Richter-Heitmann T, Rodrigues JFM, Schmitt B, Schöning I, Schrumpf M, Schurig E, Solly EF, Wolters V, Overmann J. The Evolution of Ecological Diversity in Acidobacteria. Front Microbiol 2022;13:715637
  121. Sobota M, Rodilla Ramirez PN, Cambré A, Rocker A, Mortier J, Gervais T, Haas T, Cornillet D, Chauvin D, Hug I, Julou T, Aertsen A, Diard M. The expression of virulence genes increases membrane permeability and sensitivity to envelope stress in Salmonella Typhimurium. PLoS Biol 2022;20(4):e3001608
  122. Soutschek M, Gross F, Schratt G, Germain PL. scanMiR: a biochemically-based toolkit for versatile and efficient microRNA target prediction. Bioinformatics 2022
  123. Spruce T, Plass M, Gohr A, Ray D, Martínez de Lagrán M, Rot G, Nóvoa A, Burguera D, Permanyer J, Miret M, Zheng H, Swanson MS, Morris Q, Mallo M, Dierssen M, Hughes TR, Pernaute B, Irimia M. The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians. PLoS Biol 2022;20(4):e3001615
  124. Stächele L, Stekhoven DJ, Birzele JA, Risch M, Strebel RT. Impact of retrograde intrarenal surgery on biomarkers that are associated with renal parenchyma injury, a preliminary study. World J Urol 2022;40(3):841-847
  125. Stolz U, Stadler T, Müller NF, Vaughan TG. Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes. Mol Biol Evol 2022;39(1)
  126. Stravalaci M, Pagani I, Paraboschi EM, Pedotti M, Doni A, Scavello F, Mapelli SN, Sironi M, Perucchini C, Varani L, Matkovic M, Cavalli A, Cesana D, Gallina P, Pedemonte N, Capurro V, Clementi N, Mancini N, Invernizzi P, Bayarri-Olmos R, Garred P, Rappuoli R, Duga S, Bottazzi B, Uguccioni M, Asselta R, Vicenzi E, Mantovani A, Garlanda C. Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules. Nat Immunol 2022;23(2):275-286
  127. Sun Y, Züst T, Silvestro D, Erb M, Bossdorf O, Mateo P, Robert C, Müller-Schärer H. Climate warming can reduce biocontrol efficacy and promote plant invasion due to both genetic and transient metabolomic changes. Ecol Lett 2022
  128. Telenti A, Hodcroft EB, Robertson DL. The Evolution and Biology of SARS-CoV-2 Variants. Cold Spring Harb Perspect Med 2022
  129. Troiani M, Colucci M, D'Ambrosio M, Guccini I, Pasquini E, Varesi A, Valdata A, Mosole S, Revandkar A, Attanasio G, Rinaldi A, Rinaldi A, Bolis M, Cippà P, Alimonti A. Single-cell transcriptomics identifies Mcl-1 as a target for senolytic therapy in cancer. Nat Commun 2022;13(1):2177
  130. Valls-Margarit J, Galván-Femenía I, Matías-Sánchez D, Blay N, Puiggròs M, Carreras A, Salvoro C, Cortés B, Amela R, Farre X, Lerga-Jaso J, Puig M, Sánchez-Herrero JF, Moreno V, Perucho M, Sumoy L, Armengol L, Delaneau O, Cáceres M, de Cid R, Torrents D. GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing. Nucleic Acids Res 2022;50(5):2464-2479
  131. Vetter R, Iber D. Precision of morphogen gradients in neural tube development. Nat Commun 2022;13(1):1145
  132. Viacava K, Qiao J, Janowczyk A, Poudel S, Jacquemin N, Meibom KL, Shrestha HK, Reid MC, Hettich RL, Bernier-Latmani R. Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium. ISME J 2022
  133. Wagner J, Masek M, Jacobs A, Soneson C, Sivapatham S, Damond N, de Souza N, Robinson MD, Bodenmiller B. Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines. Sci Data 2022;9(1):44
  134. Walter JD, Scherer M, Hutter CAJ, Garaeva AA, Zimmermann I, Wyss M, Rheinberger J, Ruedin Y, Earp JC, Egloff P, Sorgenfrei M, Hürlimann LM, Gonda I, Meier G, Remm S, Thavarasah S, van Geest G, Bruggmann R, Zimmer G, Slotboom DJ, Paulino C, Plattet P, Seeger MA. Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. EMBO Rep 2022;23(4):e54199
  135. Wang J, Manni M, Bärenwaldt A, Wieboldt R, Kirchhammer N, Ivanek R, Stanczak M, Zippelius A, König D, Rodrigues Manutano N, Läubli H. Siglec Receptors Modulate Dendritic Cell Activation and Antigen Presentation to T Cells in Cancer. Front Cell Dev Biol 2022;10:828916
  136. Weis C, Cuénod A, Rieck B, Dubuis O, Graf S, Lang C, Oberle M, Brackmann M, Søgaard KK, Osthoff M, Borgwardt K, Egli A. Direct antimicrobial resistance prediction from clinical MALDI-TOF mass spectra using machine learning. Nat Med 2022;28(1):164-174
  137. Wen M, Pan Q, Jouanno E, Montfort J, Zahm M, Cabau C, Klopp C, Iampietro C, Roques C, Bouchez O, Castinel A, Donnadieu C, Parrinello H, Poncet C, Belmonte E, Gautier V, Avarre JC, Dugue R, Gustiano R, Hà TTT, Campet M, Sriphairoj K, Ribolli J, de Almeida FL, Desvignes T, Postlethwait JH, Floi Bucao C, Robinson-Rechavi M, Bobe J, Herpin A, Guiguen Y. An ancient truncated duplication of the anti-Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family. Mol Ecol Resour 2022
  138. Wülser J, Ernst C, Vetsch D, Emmenegger B, Michel A, Lutz S, Ahrens CH, Vorholt JA, Ledermann R, Fischer HM. Salt- and osmo-responsive sensor histidine kinases activate the Bradyrhizobium diazoefficiens general stress response to initiate functional symbiosis. Mol Plant Microbe Interact 2022
  139. Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Netherlands ATHENA HIV Observational Cohort†, BEEHIVE Collaboration†, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Pijnappel FJJ, Smalhout SY, Weijsenfeld AM, Jurriaans S, Back NKT, Zaaijer HL, Berkhout B, Cornelissen MTE, Schinkel CJ, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet N, Rey D, Cheneau C, Partisani M, Priester M, Bernard-Henry C, Batard ML, Fischer P, Berger JL, Kmiec I, Robineau O, Huleux T, Ajana F, Alcaraz I, Allienne C, Baclet V, Meybeck A, Valette M, Viget N, Aissi E, Biekre R, Cornavin P, Merrien D, Seghezzi JC, Machado M, Diab G, Raffi F, Bonnet B, Allavena C, Grossi O, Reliquet V, Billaud E, Brunet C, Bouchez S, Morineau-Le Houssine P, Sauser F, Boutoille D, Besnier M, Hue H, Hall N, Brosseau D, Souala F, Michelet C, Tattevin P, Arvieux C, Revest M, Leroy H, Chapplain JM, Dupont M, Fily F, Patra-Delo S, Lefeuvre C, Bernard L, Bastides F, Nau P, Verdon R, de la Blanchardiere A, Martin A, Feret P, Geffray L, Daniel C, Rohan J, Fialaire P, Chennebault JM, Rabier V, Abgueguen P, Rehaiem S, Luycx O, Niault M, Moreau P, Poinsignon Y, Goussef M, Mouton-Rioux V, Houlbert D, Alvarez-Huve S, Barbe F, Haret S, Perre P, Leantez-Nainville S, Esnault JL, Guimard T, Suaud I, Girard JJ, Simonet V, Debab Y, Schmit JL, Jacomet C, Weinberck P, Genet C, Pinet P, Ducroix S, Durox H, Denes É, Abraham B, Gourdon F, Antoniotti O, Molina JM, Ferret S, Lascoux-Combe C, Lafaurie M, Colin de Verdiere N, Ponscarme D, De Castro N, Aslan A, Rozenbaum W, Pintado C, Clavel F, Taulera O, Gatey C, Munier AL, Gazaigne S, Penot P, Conort G, Lerolle N, Leplatois A, Balausine S, Delgado J, Timsit J, Tabet M, Gerard L, Girard PM, Picard O, Tredup J, Bollens D, Valin N, Campa P, Bottero J, Lefebvre B, Tourneur M, Fonquernie L, Wemmert C, Lagneau JL, Yazdanpanah Y, Phung B, Pinto A, Vallois D, Cabras O, Louni F, Pialoux G, Lyavanc T, Berrebi V, Chas J, Lenagat S, Rami A, Diemer M, Parrinello M, Depond A, Salmon D, Guillevin L, Tahi T, Belarbi L, Loulergue P, Zak Dit Zbar O, Launay O, Silbermann B, Leport C, Alagna L, Pietri MP, Simon A, Bonmarchand M, Amirat N, Pichon F, Kirstetter M, Katlama C, Valantin MA, Tubiana R, Caby F, Schneider L, Ktorza N, Calin R, Merlet A, Ben Abdallah S, Weiss L, Buisson M, Batisse D, Karmochine M, Pavie J, Minozzi C, Jayle D, Castel P, Derouineau J, Kousignan P, Eliazevitch M, Pierre I, Collias L, Viard JP, Gilquin J, Sobel A, Slama L, Ghosn J, Hadacek B, Thu-Huyn N, Nait-Ighil L, Cros A, Maignan A, Duvivier C, Consigny PH, Lanternier F, Shoai-Tehrani M, Touam F, Jerbi S, Bodard L, Jung C, Goujard C, Quertainmont Y, Duracinsky M, Segeral O, Blanc A, Peretti D, Cheret A, Chantalat C, Dulucq MJ, Levy Y, Lelievre JD, Lascaux AS, Dumont C, Boue F, Chambrin V, Abgrall S, Kansau I, Raho-Moussa M, De Truchis P, Dinh A, Davido B, Marigot D, Berthe H, Devidas A, Chevojon P, Chabrol A, Agher N, Lemercier Y, Chaix F, Turpault I, Bouchaud O, Honore P, Rouveix E, Reimann E, Belan AG, Godin Collet C, Souak S, Mortier E, Bloch M, Simonpoli AM, Manceron V, Cahitte I, Hiraux E, Lafon E, Cordonnier F, Zeng AF, Zucman D, Majerholc C, Bornarel D, Uludag A, Gellen-Dautremer J, Lefort A, Bazin C, Daneluzzi V, Gerbe J, Jeantils V, Coupard M, Patey O, Bantsimba J, Delllion S, Paz PC, Cazenave B, Richier L, Garrait V, Delacroix I, Elharrar B, Vittecoq D, Bolliot C, Lepretre A, Genet P, Masse V, Perrone V, Boussard JL, Chardon P, Froguel E, Simon P, Tassi S, Avettand Fenoel V, Barin F, Bourgeois C, Cardon F, Chaix ML, Delfraissy JF, Essat A, Fischer H, Lecuroux C, Meyer L, Petrov-Sanchez V, Rouzioux C, Saez-Cirion A, Seng R, Kuldanek K, Mullaney S, Young C, Zucchetti A, Bevan MA, McKernan S, Wandolo E, Richardson C, Youssef E, Green P, Faulkner S, Faville R, Herman S, Care C, Blackman H, Bellenger K, Fairbrother K, Phillips A, Babiker A, Delpech V, Fidler S, Clarke M, Fox J, Gilson R, Goldberg D, Hawkins D, Johnson A, Johnson M, McLean K, Nastouli E, Post F, Kennedy N, Pritchard J, Andrady U, Rajda N, Donnelly C, McKernan S, Drake S, Gilleran G, White D, Ross J, Harding J, Faville R, Sweeney J, Flegg P, Toomer S, Wilding H, Woodward R, Dean G, Richardson C, Perry N, Gompels M, Jennings L, Bansaal D, Browing M, Connolly L, Stanley B, Estreich S, Magdy A, O'Mahony C, Fraser P, Jebakumar SPR, David L, Mette R, Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022;375(6580):540-545
  140. Xu ZM, Rüeger S, Zwyer M, Brites D, Hiza H, Reinhard M, Rutaihwa L, Borrell S, Isihaka F, Temba H, Maroa T, Naftari R, Hella J, Sasamalo M, Reither K, Portevin D, Gagneux S, Fellay J. Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. PLoS Comput Biol 2022;18(1):e1009628
  141. Zakany S, Smirnov S, Milinkovitch MC. Lizard Skin Patterns and the Ising Model. Phys Rev Lett 2022;128(4):048102
  142. Zancolli G, Reijnders M, Waterhouse RM, Robinson-Rechavi M. Convergent evolution of venom gland transcriptomes across Metazoa. Proc Natl Acad Sci U S A 2022;119(1)
  143. Zanoli R, Lavelli A, Löffler T, Perez Gonzalez NA, Rinaldi F. An annotated dataset for extracting gene-melanoma relations from scientific literature. J Biomed Semantics 2022;13(1):2
  144. Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Tara Oceans Coordinators‡, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB, Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, de Vargas C, Gorsky G, Guidi L, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels S, Karp-Boss L, Karsenti E, Not F, Ogata H, Poulton N, Pesant S, Sardet C, Speich S, Stemmann L, Sullivan MB, Sungawa S, Wincker P. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022;376(6589):156-162
  145. Zufferey M, Tavernari D, Ciriello G. Methods for the Analysis of Topologically Associating Domains (TADs). Methods Mol Biol 2022;2301:39-59