Peer-reviewed articles and conference proceedings

Listed in Europe PMC, latest update: 01.09.2022.
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. Ademi H, Djari C, Mayère C, Neirijnck Y, Sararols P, Rands CM, Stévant I, Conne B, Nef S. Deciphering the origins and fates of steroidogenic lineages in the mouse testis. Cell Rep 2022;39(11):110935
  2. 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
  3. 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):1162
  4. Agostinetto G, Bozzi D, Porro D, Casiraghi M, Labra M, Bruno A. SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata. Database (Oxford) 2022;2022:baac033
  5. 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
  6. Alharbi E, Gadiya Y, Henderson D, Zaliani A, Delfin-Rossaro A, Cambon-Thomsen A, Kohler M, Witt G, Welter D, Juty N, Jay C, Engkvist O, Goble C, Reilly DS, Satagopam V, Ioannidis V, Gu W, Gribbon P. Selection of data sets for FAIRification in drug discovery and development: Which, why, and how? Drug Discov Today 2022;27(8):2080-2085
  7. Andermann T, Antonelli A, Barrett RL, Silvestro D. Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning. Front Plant Sci 2022;13:839407
  8. Andermann T, Strömberg CAE, Antonelli A, Silvestro D. The origin and evolution of open habitats in North America inferred by Bayesian deep learning models. Nat Commun 2022;13(1):4833
  9. Andreatta M, Berenstein AJ, Carmona SJ. scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets. Bioinformatics 2022:btac141
  10. 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
  11. Andreatta M, Tjitropranoto A, Sherman Z, Kelly MC, Ciucci T, Carmona SJ. A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections. Elife 2022;11:e76339
  12. 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
  13. Arizmendi Cárdenas YO, Neuenschwander S, Malaspinas AS. Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PeerJ 2022;10:e12784
  14. 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
  15. Asplund O, Storm P, Chandra V, Hatem G, Ottosson-Laakso E, Mansour-Aly D, Krus U, Ibrahim H, Ahlqvist E, Tuomi T, Renström E, Korsgren O, Wierup N, Ibberson M, Solimena M, Marchetti P, Wollheim C, Artner I, Mulder H, Hansson O, Otonkoski T, Groop L, Prasad RB. Islet Gene View-a tool to facilitate islet research. Life Sci Alliance 2022;5(12):e202201376
  16. Asselta R, Paraboschi EM, Stravalaci M, Invernizzi P, Bonfanti P, Biondi A, Pagani I, 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, Bayarri-Olmos R, Garred P, Rappuoli R, Duga S, Bottazzi B, Uguccioni M, Vicenzi E, Mantovani A, Garlanda C. Reply to: Hultström et al., Genetic determinants of mannose-binding lectin activity predispose to thromboembolic complications in critical COVID-19. Mannose-binding lectin genetics in COVID-19. Nat Immunol 2022;23(6):865-867
  17. Auer TO, Álvarez-Ocaña R, Cruchet S, Benton R, Arguello JR. Copy number changes in co-expressed odorant receptor genes enable selection for sensory differences in drosophilid species. Nat Ecol Evol 2022
  18. 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
  19. Auwerx C, Sadler MC, Reymond A, Kutalik Z. From pharmacogenetics to pharmaco-omics: Milestones and future directions. HGG Adv 2022;3(2):100100
  20. Babrak L, Marquez S, Busse CE, Lees WD, Miho E, Ohlin M, Rosenfeld AM, Stervbo U, Watson CT, Schramm CA, AIRR Community. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. Methods Mol Biol 2022;2453:279-296
  21. 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
  22. 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
  23. Bagutti C, Alt Hug M, Heim P, Maurer Pekerman L, Ilg Hampe E, Hübner P, Fuchs S, Savic M, Stadler T, Topolsky I, Icer Baykal P, Dreifuss D, Beerenwinkel N, Tschudin Sutter S. Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study. Swiss Med Wkly 2022;152:w30202
  24. 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
  25. 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
  26. 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
  27. Bao K, Claesson R, Gehrig P, Grossmann J, Oscarsson J, Belibasakis GN. Proteomic Characterization of the Oral Pathogen Filifactor alocis Reveals Key Inter-Protein Interactions of Its RTX Toxin: FtxA. Pathogens 2022;11(5):590
  28. Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 2022;54(7):1037-1050
  29. Barrat-Charlaix P, Vaughan TG, Neher RA. TreeKnit: Inferring ancestral reassortment graphs of influenza viruses. PLoS Comput Biol 2022;18(8):e1010394
  30. Barreto de Albuquerque J, Altenburger LM, Abe J, von Werdt D, Wissmann S, Martínez Magdaleno J, Francisco D, van Geest G, Ficht X, Iannacone M, Bruggmann R, Mueller C, Stein JV. Microbial uptake in oral mucosa-draining lymph nodes leads to rapid release of cytotoxic CD8+ T cells lacking a gut-homing phenotype. Sci Immunol 2022;7(72):eabf1861
  31. 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
  32. 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
  33. Bernier-Latmani J, Cisarovsky C, Mahfoud S, Ragusa S, Dupanloup I, Barras D, Renevey F, Nassiri S, Anderle P, Squadrito M, Siegert S, Davanture S, González-Loyola A, Fournier N, Luther S, Benedito R, Valet P, Zhou B, De Palma M, Delorenzi M, Sempoux C, Petrova T. Apelin-driven endothelial cell migration sustains intestinal progenitor cells and tumor growth Nat Cardiovasc Res 2022;1(5):476-490
  34. Bernier-Latmani J, Cisarovsky C, Mahfoud S, Ragusa S, Dupanloup I, Barras D, Renevey F, Nassiri S, Anderle P, Squadrito ML, Siegert S, Davanture S, González-Loyola A, Fournier N, Luther SA, Benedito R, Valet P, Zhou B, De Palma M, Delorenzi M, Sempoux C, Petrova TV. Apelin-driven endothelial cell migration sustains intestinal progenitor cells and tumor growth. Nat Cardiovasc Res 2022;1(5):476-490
  35. Bernier-Latmani J, Mauri C, Marcone R, Renevey F, Durot S, He L, Vanlandewijck M, Maclachlan C, Davanture S, Zamboni N, Knott GW, Luther SA, Betsholtz C, Delorenzi M, Brisken C, Petrova TV. ADAMTS18+ villus tip telocytes maintain a polarized VEGFA signaling domain and fenestrations in nutrient-absorbing intestinal blood vessels. Nat Commun 2022;13(1):3983
  36. Bertolini A, Prummer M, Tuncel MA, Menzel U, Rosano-González ML, Kuipers J, Stekhoven DJ, Tumor Profiler consortium, Beerenwinkel N, Singer F. scAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS Comput Biol 2022;18(6):e1010097
  37. Bettini E, Stahl SM, De Martin S, Mattarei A, Sgrignani J, Carignani C, Nola S, Locatelli P, Pappagallo M, Inturrisi CE, Bifari F, Cavalli A, Alimonti A, Pani L, Fava M, Traversa S, Folli F, Manfredi PL. Pharmacological Comparative Characterization of REL-1017 (Esmethadone-HCl) and Other NMDAR Channel Blockers in Human Heterodimeric N-Methyl-D-Aspartate Receptors. Pharmaceuticals (Basel) 2022;15(8):997
  38. 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
  39. 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. Author Correction: GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Commun Biol 2022;5(1):658
  40. 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
  41. 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. Author Correction: Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV. Sci Rep 2022;12(1):11638
  42. Bidgood SR, Samolej J, Novy K, Collopy A, Albrecht D, Krause M, Burden JJ, Wollscheid B, Mercer J. Poxviruses package viral redox proteins in lateral bodies and modulate the host oxidative response. PLoS Pathog 2022;18(7):e1010614
  43. Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TTT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell 2022;185(14):2591-2608.e30
  44. Billault-Chaumartin I, Michon L, Anderson CA, Yde SE, Suarez C, Iwaszkiewicz J, Zoete V, Kovar DR, Martin SG. Actin assembly requirements of the formin Fus1 to build the fusion focus. J Cell Sci 2022;135(13):jcs260289
  45. Bilous M, Tran L, Cianciaruso C, Gabriel A, Michel H, Carmona SJ, Pittet MJ, Gfeller D. Metacells untangle large and complex single-cell transcriptome networks. BMC Bioinformatics 2022;23(1):336
  46. Bojar D, Lisacek F. Glycoinformatics in the Artificial Intelligence Era. Chem Rev 2022
  47. 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
  48. Bourguignon L, Tong B, Geisler F, Schubert M, Röhrich F, Saur M, Weidner N, Rupp R, Kalke YB, Abel R, Maier D, Grassner L, Chhabra HS, Liebscher T, Cragg JJ, EMSCI study group, Kramer J, Curt A, Jutzeler CR. International surveillance study in acute spinal cord injury confirms viability of multinational clinical trials. BMC Med 2022;20(1):225
  49. 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
  50. 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):811
  51. 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
  52. Breda J, Banerjee A, Jayachandran R, Pieters J, Zavolan M. A novel approach to single-cell analysis reveals intrinsic differences in immune marker expression in unstimulated BALB/c and C57BL/6 macrophages. FEBS Lett 2022
  53. Briand S, Dessimoz C, El-Mabrouk N, Nevers Y. A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem. Syst Biol 2022:syac028
  54. 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):msab356
  55. Bruschi M, Cavalli A, Moll S, Candiano G, Scapozza L, Patel JJ, Tan JC, Lo KC, Angeletti A, Ghiggeri GM, Prunotto M. Discovery of anti-Formin-like 1 protein (FMNL1) antibodies in membranous nephropathy and other glomerular diseases. Sci Rep 2022;12(1):13659
  56. 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
  57. Buhre C, Born J, Wiedemann N, Cossio M, Brändle G, Leidermann K, Aujayeb A, Rieck B, Bogwardt K. ACCELERATING COVID-19 DIFFERENTIAL DIAGNOSISWITH EXPLAINABLE ULTRASOUND IMAGE ANALYSIS: AN AI TOOL Ultrasound Med Biol 2022;48(1):S1-S1
  58. Burja B, Paul D, Tastanova A, Edalat SG, Gerber R, Houtman M, Elhai M, Bürki K, Staeger R, Restivo G, Lang R, Sodin-Semrl S, Lakota K, Tomšič M, Levesque MP, Distler O, Rotar Ž, Robinson MD, Frank-Bertoncelj M. An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies. Front Cell Dev Biol 2022;10:872688
  59. Burzan N, Murad Lima R, Frutschi M, Janowczyk A, Reddy B, Rance A, Diomidis N, Bernier-Latmani R. Growth and Persistence of an Aerobic Microbial Community in Wyoming Bentonite MX-80 Despite Anoxic in situ Conditions. Front Microbiol 2022;13:858324
  60. 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)
  61. 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):e2119720119
  62. Casadei L, Sarchet P, de Faria FCC, Calore F, Nigita G, Tahara S, Cascione L, Wabitsch M, Hornicek FJ, Grignol V, Croce CM, Pollock RE. In situ hybridization to detect DNA amplification in extracellular vesicles. J Extracell Vesicles 2022;11(9):e12251
  63. Cascino P, Nevone A, Piscitelli M, Scopelliti C, Girelli M, Mazzini G, Caminito S, Russo G, Milani P, Basset M, Foli A, Fazio F, Casarini S, Massa M, Bozzola M, Ripepi J, Sesta MA, Acquafredda G, De Cicco M, Moretta A, Rognoni P, Milan E, Ricagno S, Lavatelli F, Petrucci MT, Miho E, Klersy C, Merlini G, Palladini G, Nuvolone M. Single-molecule real-time sequencing of the M protein: Toward personalized medicine in monoclonal gammopathies. Am J Hematol 2022
  64. 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
  65. Chen C, Nadeau S, Topolsky I, Beerenwinkel N, Stadler T. Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example. Epidemics 2022;39:100576
  66. Chen W, Guillaume-Gentil O, Rainer PY, Gäbelein CG, Saelens W, Gardeux V, Klaeger A, Dainese R, Zachara M, Zambelli T, Vorholt JA, Deplancke B. Live-seq enables temporal transcriptomic recording of single cells. Nature 2022;608(7924):733-740
  67. Chilà R, Chiappa M, Guffanti F, Panini N, Conconi D, Rinaldi A, Cascione L, Bertoni F, Fratelli M, Damia G. Stable CDK12 Knock-Out Ovarian Cancer Cells Do Not Show Increased Sensitivity to Cisplatin and PARP Inhibitor Treatment. Front Oncol 2022;12:903536
  68. Colavin A, Atolia E, Bitbol AF, Huang KC. Extracting phylogenetic dimensions of coevolution reveals hidden functional signals. Sci Rep 2022;12(1):820
  69. Collado-Vides J, Gaudet P, de Lorenzo V. Missing Links Between Gene Function and Physiology in Genomics. Front Physiol 2022;13:815874
  70. Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM, Ulirsch J, Everett S, Howrigan DP, Boone PM, Fu J, Karczewski KJ, Kellaris G, Lowther C, Lucente D, Mohajeri K, Nõukas M, Nuttle X, Samocha KE, Trinh M, Ullah F, Võsa U, Epi25 Consortium, Estonian Biobank Research Team, Hurles ME, Aradhya S, Davis EE, Finucane H, Gusella JF, Janze A, Katsanis N, Matyakhina L, Neale BM, Sanders D, Warren S, Hodge JC, Lal D, Ruderfer DM, Meck J, Mägi R, Esko T, Reymond A, Kutalik Z, Hakonarson H, Sunyaev S, Brand H, Talkowski ME. A cross-disorder dosage sensitivity map of the human genome. Cell 2022;185(16):3041-3055.e25
  71. 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
  72. 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
  73. Cristinelli S, Angelino P, Ciuffi A. Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV. J Vis Exp 2022(181)
  74. 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):msab343
  75. 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):msab317
  76. Cuny AP, Tanuj Sapra K, Martinez-Martin D, Fläschner G, Adams JD, Martin S, Gerber C, Rudolf F, Müller DJ. High-resolution mass measurements of single budding yeast reveal linear growth segments. Nat Commun 2022;13(1):3483
  77. Cvitas I, Oberhaensli S, Leeb T, Marti E. Equine keratinocytes in the pathogenesis of insect bite hypersensitivity: Just another brick in the wall? PLoS One 2022;17(8):e0266263
  78. 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):iyab184
  79. de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford) 2022;2022:baac062
  80. de Goederen V, Vetter R, McDole K, Iber D. Hinge point emergence in mammalian spinal neurulation. Proc Natl Acad Sci U S A 2022;119(20):e2117075119
  81. Della Bella E, Koch J, Baerenfaller K. Translation and emerging functions of non-coding RNAs in inflammation and immunity. Allergy 2022;77(7):2025-2037
  82. Deng H, Gao Y, Trappetti V, Hertig D, Karatkevich D, Losmanova T, Urzi C, Ge H, Geest GA, Bruggmann R, Djonov V, Nuoffer JM, Vermathen P, Zamboni N, Riether C, Ochsenbein A, Peng RW, Kocher GJ, Schmid RA, Dorn P, Marti TM. Targeting lactate dehydrogenase B-dependent mitochondrial metabolism affects tumor initiating cells and inhibits tumorigenesis of non-small cell lung cancer by inducing mtDNA damage. Cell Mol Life Sci 2022;79(8):445
  83. Dessimoz C, Roy S. ISMB 2022 proceedings. Bioinformatics 2022;38(supplement_1):i8-i9
  84. 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
  85. Diebold M, Galli E, Kopf A, Sanderson NSR, Callegari I, Benkert P, Gonzalo Núñez N, Ingelfinger F, Herms S, Cichon S, Kappos L, Kuhle J, Becher B, Claassen M, Derfuss T. High-dimensional immune profiling identifies a biomarker to monitor dimethyl fumarate response in multiple sclerosis. Proc Natl Acad Sci U S A 2022;119(31):e2205042119
  86. Djordjevic J, Dumas Z, Robinson-Rechavi M, Schwander T, Parker DJ. Dynamics of sex-biased gene expression during development in the stick insect Timema californicum. Heredity (Edinb) 2022;129(2):113-122
  87. 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;34(5):768-774
  88. 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
  89. 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 Leg Movement in Sleep. Sleep 2022:zsac121
  90. Ercan C, Coto-Llerena M, Gallon J, Fourie L, Marinucci M, Hess GF, Vosbeck J, Taha-Mehlitz S, Boldanova T, Meier MA, Tzankov A, Matter MS, Hoffmann MHK, Di Tommaso L, von Flüe M, Ng CKY, Heim MH, Soysal SD, Terracciano LM, Kollmar O, Piscuoglio S. Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma unveils its malignant potential: a case report. Commun Med (Lond) 2022;2:11
  91. Fan B, Klatt J, Moor MM, Daniels LA, Swiss Pediatric Sepsis Study, Sanchez-Pinto LN, Agyeman PKA, Schlapbach LJ, Borgwardt KM. Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients. Bioinformatics 2022;38(suppl 1):i101-i108
  92. Feron R, Waterhouse RM. Exploring new genomic territories with emerging model insects. Curr Opin Insect Sci 2022;51:100902
  93. Feron R, Waterhouse RM. Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes. Gigascience 2022;11:giac006
  94. 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
  95. Fiorucci AS, Michaud O, Schmid-Siegert E, Trevisan M, Allenbach Petrolati L, Çaka Ince Y, Fankhauser C. Shade suppresses wound-induced leaf repositioning through a mechanism involving PHYTOCHROME KINASE SUBSTRATE (PKS) genes. PLoS Genet 2022;18(5):e1010213
  96. 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
  97. 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
  98. Franco M, Pickett SJ, Fleischmann Z, Khrapko M, Cote-L'Heureux A, Aidlen D, Stein D, Markuzon N, Popadin K, Braverman M, Woods DC, Tilly JL, Turnbull DM, Khrapko K. Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline. Hum Mol Genet 2022:ddac149
  99. Frey K, Goetze S, Rohrer L, von Eckardstein A, Wollscheid B. Decoding Functional High-Density Lipoprotein Particle Surfaceome Interactions. Int J Mol Sci 2022;23(16):9506
  100. Fröhlich K, Brombacher E, Fahrner M, Vogele D, Kook L, Pinter N, Bronsert P, Timme-Bronsert S, Schmidt A, Bärenfaller K, Kreutz C, Schilling O. Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. Nat Commun 2022;13(1):2622
  101. Furrer L, Cornelius J, Rinaldi F. Parallel sequence tagging for concept recognition. BMC Bioinformatics 2022;22(suppl 1):623
  102. 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):bbab478
  103. 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
  104. Garofoli A, Schnidrig D, Ng CKY. PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data. Methods Mol Biol 2022;2493:195-204
  105. Gatti L, Koenen MH, Zhang JD, Anisimova M, Verhagen LM, Schutten M, Osterhaus A, van der Vries E. Cross-reactive immunity potentially drives global oscillation and opposed alternation patterns of seasonal influenza A viruses. Sci Rep 2022;12(1):8883
  106. 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
  107. 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):1018
  108. Georgiadou E, Muralidharan C, Martinez M, Chabosseau P, Akalestou E, Tomas A, Wern FYS, 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 β-Cell Connectivity and Insulin Secretion. Diabetes 2022;71(7):1472-1489
  109. Gerardos A, Dietler N, Bitbol AF. Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences. PLoS Comput Biol 2022;18(5):e1010147
  110. 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
  111. 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
  112. Giannuzzi G, Chatron N, Mannik K, Auwerx C, Pradervand S, Willemin G, Hoekzema K, Nuttle X, Chrast J, Sadler MC, Porcu E, 16p11.2 Consortium, Herault Y, Isidor B, Gilbert-Dussardier B, Eichler EE, Kutalik Z, Reymond A. Possible association of 16p11.2 copy number variation with altered lymphocyte and neutrophil counts. NPJ Genom Med 2022;7(1):38
  113. 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
  114. 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):dev199655
  115. Gloyn AL, Ibberson M, Marchetti P, Powers AC, Rorsman P, Sander M, Solimena M. Every islet matters: improving the impact of human islet research. Nat Metab 2022;4(8):970-977
  116. 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
  117. Goldman JP, Mottin L, Zaghir J, Keszthelyi D, Lokaj B, Turbé H, Gobeil J, Ruch P, Ehrsam J, Lovis C. Classification of Oncology Treatment Responses from French Radiology Reports with Supervised Machine Learning. Stud Health Technol Inform 2022;294:849-853
  118. 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:giac003
  119. Guggisberg D, Burton-Pimentel KJ, Walther B, Badertscher R, Blaser C, Portmann R, Schmid A, Radtke T, Saner H, Fournier N, Bütikofer U, Vergères G. Molecular effects of the consumption of margarine and butter varying in trans fat composition: a parallel human intervention study. Lipids Health Dis 2022;21(1):74
  120. 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
  121. Guse K, Hagemann N, Thiele L, Remlinger J, Salmen A, Hoepner R, Keller I, Meyer P, Grandgirard D, Leib SL, Vassella E, Locatelli G, Hermann DM, Chan A. CNS Antigen-Specific Neuroinflammation Attenuates Ischemic Stroke With Involvement of Polarized Myeloid Cells. Neurol Neuroimmunol Neuroinflamm 2022;9(4):e1168
  122. Hadziselimovic F, Verkauskas G, Stadler M. A novel role for CFTR interaction with LH and FGF in azoospermia and epididymal maldevelopment caused by cryptorchidism. Basic Clin Androl 2022;32(1):10
  123. Haellman V, Pirkl M, Akmammedov A, Saxena P, Beerenwinkel N, Paro R, Teixeira AP, Fussenegger M. dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation. Metab Eng 2022;73:70-81
  124. Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O'Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Freitas L, Resende PC, Lee RTC, Maurer-Stroh S, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biol 2022;20(8):e3001769
  125. Hassan M, Juanola O, Keller I, Nanni P, Wolski W, Martínez-López S, Caparrós E, Francés R, Moghadamrad S. Paneth Cells Regulate Lymphangiogenesis under Control of Microbial Signals during Experimental Portal Hypertension. Biomedicines 2022;10(7):1503
  126. 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
  127. 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
  128. 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
  129. Hiza H, Hella J, Arbués A, Sasamalo M, Misana V, Fellay J, Gagneux S, Reither K, Portevin D. CD38 Expression by Antigen-Specific CD4 T Cells Is Significantly Restored 5 Months After Treatment Initiation Independently of Sputum Bacterial Load at the Time of Tuberculosis Diagnosis. Front Med (Lausanne) 2022;9:821776
  130. Hodcroft EB, Dyrdak R, Andrés C, Egli A, Reist J, García Martínez de Artola D, Alcoba-Flórez J, Niesters HGM, Antón A, Poelman R, Reynders M, Wollants E, Neher RA, Albert J. Evolution, geographic spreading, and demographic distribution of Enterovirus D68. PLoS Pathog 2022;18(5):e1010515
  131. Hufsky F, Beslic D, Boeckaerts D, Duchene S, González-Tortuero E, Gruber AJ, Guo J, Jansen D, Juma J, Kongkitimanon K, Luque A, Ritsch M, Lencioni Lovate G, Nishimura L, Pas C, Domingo E, Hodcroft E, Lemey P, Sullivan MB, Weber F, González-Candelas F, Krautwurst S, Pérez-Cataluña A, Randazzo W, Sánchez G, Marz M. The International Virus Bioinformatics Meeting 2022. Viruses 2022;14(5):973
  132. 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
  133. Huisman JS, Scire J, Caduff L, Fernandez-Cassi X, Ganesanandamoorthy P, Kull A, Scheidegger A, Stachler E, Boehm AB, Hughes B, Knudson A, Topol A, Wigginton KR, Wolfe MK, Kohn T, Ort C, Stadler T, Julian TR. Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2. Environ Health Perspect 2022;130(5):57011
  134. Huisman JS, Vaughan TG, Egli A, Tschudin-Sutter S, Stadler T, Bonhoeffer S. The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies. Philos Trans R Soc Lond B Biol Sci 2022;377(1861):20210245
  135. Iber D, Mederacke M. Tracheal Ring Formation. Front Cell Dev Biol 2022;10:900447
  136. Iber D, Vetter R. Relationship between epithelial organization and morphogen interpretation. Curr Opin Genet Dev 2022;75:101916
  137. 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
  138. 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
  139. Iyengar BR, Wagner A. GroEL/S Overexpression Helps to Purge Deleterious Mutations and Reduce Genetic Diversity during Adaptive Protein Evolution. Mol Biol Evol 2022;39(6):msac047
  140. 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
  141. Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, GAGH Phenopacket Modeling Consortium, Haendel MA, Robinson PN. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol 2022;40(6):817-820
  142. Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, Bänziger C, Devaux AJ, Stachler E, Caduff L, Cariti F, Corzón AT, Fuhrmann L, Chen C, Jablonski KP, Nadeau S, Feldkamp M, Beisel C, Aquino C, Stadler T, Ort C, Kohn T, Julian TR, Beerenwinkel N. Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nat Microbiol 2022;7(8):1151-1160
  143. Janowczyk A, Baumhoer D, Dirnhofer S, Grobholz R, Kipar A, de Leval L, Merkler D, Michielin O, Moch H, Perren A, Rottenberg S, Rubbia-Brandt L, Rubin MA, Sempoux C, Tolnay M, Zlobec I, Koelzer VH, Swiss Digital Pathology Consortium (SDiPath). Towards a national strategy for digital pathology in Switzerland. Virchows Arch 2022
  144. 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
  145. 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
  146. Joanito I, Wirapati P, Zhao N, Nawaz Z, Yeo G, Lee F, Eng CLP, Macalinao DC, Kahraman M, Srinivasan H, Lakshmanan V, Verbandt S, Tsantoulis P, Gunn N, Venkatesh PN, Poh ZW, Nahar R, Oh HLJ, Loo JM, Chia S, Cheow LF, Cheruba E, Wong MT, Kua L, Chua C, Nguyen A, Golovan J, Gan A, Lim WJ, Guo YA, Yap CK, Tay B, Hong Y, Chong DQ, Chok AY, Park WY, Han S, Chang MH, Seow-En I, Fu C, Mathew R, Toh EL, Hong LZ, Skanderup AJ, DasGupta R, Ong CJ, Lim KH, Tan EKW, Koo SL, Leow WQ, Tejpar S, Prabhakar S, Tan IB. Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer. Nat Genet 2022;54(7):963-975
  147. 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
  148. Jowkar G, Pečerska J, Maiolo M, Gil M, Anisimova M. ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process. Syst Biol 2022:syac050
  149. Kahraman A, Arnold FM, Hanimann J, Nowak M, Pauli C, Britschgi C, Moch H, Zoche M. MTPpilot: An Interactive Software for Visualization of Next-Generation Sequencing Results in Molecular Tumor Boards. JCO Clin Cancer Inform 2022;6:e2200032
  150. Kannan A, Suomalainen M, Volle R, Bauer M, Amsler M, Trinh HV, Vavassori S, Schmid JP, Vilhena G, Marín-González A, Perez R, Franceschini A, Mering CV, Hemmi S, Greber UF. Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects. Viruses 2022;14(7):1407
  151. Karaaslan C, Mayorga C, Baerenfaller K, Escribese MM. Editorial: Systems Biology Approach to the Immunology of Asthma and Allergy. Front Immunol 2022;13:857403
  152. Karve S, Dasmeh P, Zheng J, Wagner A. Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability. Nat Ecol Evol 2022;6(8):1155-1164
  153. Karve S, Wagner A. Multiple Novel Traits without Immediate Benefits Originate in Bacteria Evolving on Single Antibiotics. Mol Biol Evol 2022;39(1):msab341
  154. Kaymak T, Kaya B, Wuggenig P, Nuciforo S, Göldi A, Swiss EoE Cohort Study Group (SEECS), Oswald F, Roux J, Noti M, Melhem H, Hruz P, Niess JH. IL-20 subfamily cytokines impair the oesophageal epithelial barrier by diminishing filaggrin in eosinophilic oesophagitis. Gut 2022:gutjnl-2022-327166
  155. Kazmierski J, Elsner C, Döhner K, Xu S, Ducroux A, Pott F, Jansen J, Thorball CW, Zeymer O, Zhou X, Fedorov R, Fellay J, Löffler MW, Weber ANR, Sodeik B, Goffinet C. A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913. J Immunol 2022:ji2100685
  156. 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
  157. Khan P, Roux J, Blumer S, Knudsen L, Jonigk D, Kuehnel MP, Tamm M, Hostettler KE. Alveolar Basal Cells Differentiate towards Secretory Epithelial- and Aberrant Basaloid-like Cells In Vitro. Cells 2022;11(11):1820
  158. 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
  159. 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
  160. 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
  161. 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
  162. Kolter R, Balaban N, Julou T. Bacteria grow swiftly and live thriftily. Curr Biol 2022;32(12):R599-R605
  163. Krebs FS, Britschgi C, Pradervand S, Achermann R, Tsantoulis P, Haefliger S, Wicki A, Michielin O, Zoete V. Structure-based prediction of BRAF mutation classes using machine-learning approaches. Sci Rep 2022;12(1):12528
  164. Kuipers J, Singer J, Beerenwinkel N. Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinformatics 2022:btac577
  165. 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):e2108671119
  166. Lansch-Justen L, Cusseddu D, Schmitz MA, Bank C. The extinction time under mutational meltdown driven by high mutation rates. Ecol Evol 2022;12(7):e9046
  167. 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:baac026
  168. Lee RJ, Wysocki O, Zhou C, Shotton R, Tivey A, Lever L, Woodcock J, Albiges L, Angelakas A, Arnold D, Aung T, Banfill K, Baxter M, Barlesi F, Bayle A, Besse B, Bhogal T, Boyce H, Britton F, Calles A, Castelo-Branco L, Copson E, Croitoru AE, Dani SS, Dickens E, Eastlake L, Fitzpatrick P, Foulon S, Frederiksen H, Frost H, Ganatra S, Gennatas S, Glenthøj A, Gomes F, Graham DM, Hague C, Harrington K, Harrison M, Horsley L, Hoskins R, Huddar P, Hudson Z, Jakobsen LH, Joharatnam-Hogan N, Khan S, Khan UT, Khan K, Massard C, Maynard A, McKenzie H, Michielin O, Mosenthal AC, Obispo B, Patel R, Pentheroudakis G, Peters S, Rieger-Christ K, Robinson T, Rogado J, Romano E, Rowe M, Sekacheva M, Sheehan R, Stevenson J, Stockdale A, Thomas A, Turtle L, Viñal D, Weaver J, Williams S, Wilson C, Palmieri C, Landers D, Cooksley T, ESMO Co-Care, Dive C, Freitas A, Armstrong AC. Establishment of CORONET, COVID-19 Risk in Oncology Evaluation Tool, to Identify Patients With Cancer at Low Versus High Risk of Severe Complications of COVID-19 Disease On Presentation to Hospital. JCO Clin Cancer Inform 2022;6:e2100177
  169. Lefteri DA, Bryden SR, Pingen M, Terry S, McCafferty A, Beswick EF, Georgiev G, Van der Laan M, Mastrullo V, Campagnolo P, Waterhouse RM, Varjak M, Merits A, Fragkoudis R, Griffin S, Shams K, Pondeville E, McKimmie CS. Mosquito  saliva enhances virus infection through sialokinin-dependent vascular leakage. Proc Natl Acad Sci U S A 2022;119(24):e2114309119
  170. Lehmann KV, Kahles A, Murr M, Rätsch G. RNA Instant Quality Check: Alignment-Free RNA-Degradation Detection. J Comput Biol 2022;29(8):857-866
  171. 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
  172. Lepamets M, Auwerx C, Nõukas M, Claringbould A, Porcu E, Kals M, Jürgenson T, Estonian Biobank Research Team, Morris AP, Võsa U, Bochud M, Stringhini S, Wijmenga C, Franke L, Peterson H, Vilo J, Lepik K, Mägi R, Kutalik Z. Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations. HGG Adv 2022;3(4):100133
  173. 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:gutjnl-2021-324478
  174. 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
  175. Liao Y, Wang J, Zhu Z, Liu Y, Chen J, Zhou Y, Liu F, Lei J, Gaut BS, Cao B, Emerson JJ, Chen C. The 3D architecture of the pepper genome and its relationship to function and evolution. Nat Commun 2022;13(1):3479
  176. Lisacek F. Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions. J Vis Exp 2022(179)
  177. 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
  178. 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
  179. M Ribeiro D, Ziyani C, Delaneau O. Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis. Commun Biol 2022;5(1):876
  180. Machlab D, Burger L, Soneson C, Rijli FM, Schübeler D, Stadler MB. monaLisa: an R/Bioconductor package for identifying regulatory motifs. Bioinformatics 2022:btac102
  181. Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. The long and winding road to understanding organismal construction: Reply to comments on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics". Phys Life Rev 2022;42:19-24
  182. Manry J, Bastard P, Gervais A, Le Voyer T, Rosain J, Philippot Q, Michailidis E, Hoffmann HH, Eto S, Garcia-Prat M, Bizien L, Parra-Martínez A, Yang R, Haljasmägi L, Migaud M, Särekannu K, Maslovskaja J, de Prost N, Tandjaoui-Lambiotte Y, Luyt CE, Amador-Borrero B, Gaudet A, Poissy J, Morel P, Richard P, Cognasse F, Troya J, Trouillet-Assant S, Belot A, Saker K, Garçon P, Rivière JG, Lagier JC, Gentile S, Rosen LB, Shaw E, Morio T, Tanaka J, Dalmau D, Tharaux PL, Sene D, Stepanian A, Mégarbane B, Triantafyllia V, Fekkar A, Heath JR, Franco JL, Anaya JM, Solé-Violán J, Imberti L, Biondi A, Bonfanti P, Castagnoli R, Delmonte OM, Zhang Y, Snow AL, Holland SM, Biggs CM, Moncada-Vélez M, Arias AA, Lorenzo L, Boucherit S, Anglicheau D, Planas AM, Haerynck F, Duvlis S, Ozcelik T, Keles S, Bousfiha AA, El Bakkouri J, Ramirez-Santana C, Paul S, Pan-Hammarström Q, Hammarström L, Dupont A, Kurolap A, Metz CN, Aiuti A, Casari G, Lampasona V, Ciceri F, Barreiros LA, Dominguez-Garrido E, Vidigal M, Zatz M, van de Beek D, Sahanic S, Tancevski I, Stepanovskyy Y, Boyarchuk O, Nukui Y, Tsumura M, Vidaur L, Tangye SG, Burrel S, Duffy D, Quintana-Murci L, Klocperk A, Kann NY, Shcherbina A, Lau YL, Leung D, Coulongeat M, Marlet J, Koning R, Reyes LF, Chauvineau-Grenier A, Venet F, Monneret G, Nussenzweig MC, Arrestier R, Boudhabhay I, Baris-Feldman H, Hagin D, Wauters J, Meyts I, Dyer AH, Kennelly SP, Bourke NM, Halwani R, Sharif-Askari FS, Dorgham K, Sallette J, Sedkaoui SM, AlKhater S, Rigo-Bonnin R, Morandeira F, Roussel L, Vinh DC, Erikstrup C, Condino-Neto A, Prando C, Bondarenko A, Spaan AN, Gilardin L, Fellay J, Lyonnet S, Bilguvar K, Lifton RP, Mane S, HGID Lab, COVID Clinicians, COVID-STORM Clinicians, NIAID Immune Response to COVID Group, NH-COVAIR Study Group, Danish CHGE, Danish Blood Donor Study, St. James's Hospital, SARS CoV2 Interest Group, French COVID Cohort Study Group, Imagine COVID-Group, Milieu Intérieur Consortium, CoV-Contact Cohort, Amsterdam UMC Covid-19 Biobank Investigators, COVID Human Genetic Effort, CP-COVID-19 Group, CONSTANCES cohort, 3C-Dijon Study, Cerba Health-Care, Etablissement Français du Sang Study group, Anderson MS, Boisson B, Béziat V, Zhang SY, Andreakos E, Hermine O, Pujol A, Peterson P, Mogensen TH, Rowen L, Mond J, Debette S, de Lamballerie X, Burdet C, Bouadma L, Zins M, Soler-Palacin P, Colobran R, Gorochov G, Solanich X, Susen S, Martinez-Picado J, Raoult D, Vasse M, Gregersen PK, Piemonti L, Rodríguez-Gallego C, Notarangelo LD, Su HC, Kisand K, Okada S, Puel A, Jouanguy E, Rice CM, Tiberghien P, Zhang Q, Casanova JL, Abel L, Cobat A. The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies. Proc Natl Acad Sci U S A 2022;119(21):e2200413119
  183. Mansour M, Giudice E, Xu X, Akarsu H, Bordes P, Guillet V, Bigot DJ, Slama N, D'urso G, Chat S, Redder P, Falquet L, Mourey L, Gillet R, Genevaux P. Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis. Nat Commun 2022;13(1):2641
  184. 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
  185. Marchi N, Winkelbach L, Schulz I, Brami M, Hofmanová Z, Blöcher J, Reyna-Blanco CS, Diekmann Y, Thiéry A, Kapopoulou A, Link V, Piuz V, Kreutzer S, Figarska SM, Ganiatsou E, Pukaj A, Struck TJ, Gutenkunst RN, Karul N, Gerritsen F, Pechtl J, Peters J, Zeeb-Lanz A, Lenneis E, Teschler-Nicola M, Triantaphyllou S, Stefanović S, Papageorgopoulou C, Wegmann D, Burger J, Excoffier L. The genomic origins of the world's first farmers. Cell 2022;185(11):1842-1859.e18
  186. Mariethoz J, Alocci D, Karlsson NG, Packer NH, Lisacek F. An Interactive View of Glycosylation. Methods Mol Biol 2022;2370:41-65
  187. Markolin P, Rätsch G, Kahles A. Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq Data Using SplAdder. Methods Mol Biol 2022;2493:167-193
  188. 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
  189. Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U, AIRR Community. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022;2453:297-316
  190. Mashinchian O, De Franceschi F, Nassiri S, Michaud J, Migliavacca E, Aouad P, Metairon S, Pruvost S, Karaz S, Fabre P, Molina T, Stuelsatz P, Hegde N, Le Moal E, Dammone G, Dumont NA, Lutolf MP, Feige JN, Bentzinger CF. An engineered multicellular stem cell niche for the 3D derivation of human myogenic progenitors from iPSCs. EMBO J 2022;41(14):e110655
  191. Maurer DJ, Barletta E, Heider A, Stocker N, Wallimann A, Villiger M, Villiger B, Bärenfaller K, Akdis CA, Kistler W. Immune-inflammatory proteome of elite ice hockey players before and after SARS-CoV-2 infection. Allergy 2022
  192. McDonald AG, Mariethoz J, Davey GP, Lisacek F. In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis. Sci Rep 2022;12(1):10846
  193. 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;6(6):786-793
  194. 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
  195. Meuwissen M, Verstraeten A, Ranza E, Iwaszkiewicz J, Bastiaansen M, Mateiu L, Nemegeer M, Meester JAN, Afenjar A, Amaral M, Ballhausen D, Barnett S, Barth M, Asselbergh B, Spaas K, Heeman B, Bassetti J, Blackburn P, Schaer M, Blanc X, Zoete V, Casas K, Courtin T, Doummar D, Guerry F, Keren B, Pappas J, Rabin R, Begtrup A, Shinawi M, Vulto-van Silfhout AT, Kleefstra T, Wagner M, Ziegler A, Schaefer E, Gerard B, De Bie CI, Holwerda SJB, Abbot MA, Antonarakis SE, Loeys B. Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder. Genet Med 2022;24(7):1583-1591
  196. 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
  197. 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
  198. 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):e002927
  199. Moi D, Nishio S, Li X, Valansi C, Langleib M, Brukman NG, Flyak K, Dessimoz C, de Sanctis D, Tunyasuvunakool K, Jumper J, Graña M, Romero H, Aguilar PS, Jovine L, Podbilewicz B. Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins. Nat Commun 2022;13(1):3880
  200. Moinet A, Schlichta F, Peischl S, Excoffier L. Strong neutral sweeps occurring during a population contraction. Genetics 2022;220(4):iyac021
  201. Mottaz A, Pasche E, Michel PA, Mottin L, Teodoro D, Ruch P. Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service. Stud Health Technol Inform 2022;294:839-843
  202. Moulis M, Runser SVM, Glorieux L, Dauguet N, Vanderaa C, Gatto L, Tyteca D, Henriet P, Spagnoli FM, Iber D, Pierreux CE. Identification and implication of tissue-enriched ligands in epithelial-endothelial crosstalk during pancreas development. Sci Rep 2022;12(1):12498
  203. Nadeau S, Thorball CW, Kouyos R, Günthard HF, Böni J, Yerly S, Perreau M, Klimkait T, Rauch A, Hirsch HH, Cavassini M, Vernazza P, Bernasconi E, Fellay J, Mitov V, Stadler T, Swiss HIV Cohort Study (SHCS) . A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits. Mol Biol Evol 2022;39(8):msac163
  204. Naderi N, Mottaz A, Teodoro D, Ruch P. Analyzing the Information Content of Text-Based Files in Supplementary Materials of Biomedical Literature. Stud Health Technol Inform 2022;294:876-877
  205. Napoli S, Cascione L, Rinaldi A, Spriano F, Guidetti F, Zhang F, Cacciapuoti MT, Mensah AA, Sartori G, Munz N, Forcato M, Bicciato S, Chiappella A, Ghione P, Elemento O, Cerchietti L, Inghirami G, Bertoni F. Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma. Haematologica 2022;107(5):1131-1143
  206. Naret O, Kutalik Z, Hodel F, Xu ZM, Marques-Vidal P, Fellay J. Improving polygenic prediction with genetically inferred ancestry. HGG Adv 2022;3(3):100109
  207. 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
  208. Ng CKY, Dazert E, Boldanova T, Coto-Llerena M, Nuciforo S, Ercan C, Suslov A, Meier MA, Bock T, Schmidt A, Ketterer S, Wang X, Wieland S, Matter MS, Colombi M, Piscuoglio S, Terracciano LM, Hall MN, Heim MH. Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages. Nat Commun 2022;13(1):2436
  209. Nicheperovich A, Altenhoff AM, Dessimoz C, Majidian S. OMAMO: orthology-based alternative model organism selection. Bioinformatics 2022;38(10):2965-2966
  210. 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;35(8):1126-1136
  211. Pantano F, Zalfa F, Iuliani M, Simonetti S, Manca P, Napolitano A, Tiberi S, Russano M, Citarella F, Foderaro S, Vulpis E, Zingoni A, Masuelli L, Bei R, Ribelli G, Del Re M, Danesi R, Vincenzi B, Perrone G, Tonini G, Santini D. Large-Scale Profiling of Extracellular Vesicles Identified miR-625-5p as a Novel Biomarker of Immunotherapy Response in Advanced Non-Small-Cell Lung Cancer Patients. Cancers (Basel) 2022;14(10):2435
  212. Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlström CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sánchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL, Piel J, Sunagawa S. Biosynthetic potential of the global ocean microbiome. Nature 2022;607(7917):111-118
  213. Parikh VN, Ioannidis AG, Jimenez-Morales D, Gorzynski JE, De Jong HN, Liu X, Roque J, Cepeda-Espinoza VP, Osoegawa K, Hughes C, Sutton SC, Youlton N, Joshi R, Amar D, Tanigawa Y, Russo D, Wong J, Lauzon JT, Edelson J, Mas Montserrat D, Kwon Y, Rubinacci S, Delaneau O, Cappello L, Kim J, Shoura MJ, Raja AN, Watson N, Hammond N, Spiteri E, Mallempati KC, Montero-Martín G, Christle J, Kim J, Kirillova A, Seo K, Huang Y, Zhao C, Moreno-Grau S, Hershman SG, Dalton KP, Zhen J, Kamm J, Bhatt KD, Isakova A, Morri M, Ranganath T, Blish CA, Rogers AJ, Nadeau K, Yang S, Blomkalns A, O'Hara R, Neff NF, DeBoever C, Szalma S, Wheeler MT, Gates CM, Farh K, Schroth GP, Febbo P, deSouza F, Cornejo OE, Fernandez-Vina M, Kistler A, Palacios JA, Pinsky BA, Bustamante CD, Rivas MA, Ashley EA. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy. Nat Commun 2022;13(1):5107
  214. Parker DJ, Jaron KS, Dumas Z, Robinson-Rechavi M, Schwander T. X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species. J Evol Biol 2022
  215. Parmigiani E, Ivanek R, Rolando C, Hafen K, Turchinovich G, Lehmann FM, Gerber A, Brkic S, Frank S, Meyer SC, Wakimoto H, Günel M, Louvi A, Mariani L, Finke D, Holländer G, Hutter G, Tussiwand R, Taylor V, Giachino C. Interferon-γ resistance and immune evasion in glioma develop via Notch-regulated co-evolution of malignant and immune cells. Dev Cell 2022;57(15):1847-1865.e9
  216. 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:btac146
  217. Perdiguero B, Asbach B, Gómez CE, Köstler J, Barnett SW, Koutsoukos M, Weiss DE, Cristillo AD, Foulds KE, Roederer M, Montefiori DC, Yates NL, Ferrari G, Shen X, Sawant S, Tomaras GD, Sato A, Fulp WJ, Gottardo R, Ding S, Heeney JL, Pantaleo G, Esteban M, Wagner R. Early and Long-Term HIV-1 Immunogenicity Induced in Macaques by the Combined Administration of DNA, NYVAC and Env Protein-Based Vaccine Candidates: The AUP512 Study. Front Immunol 2022;13:939627
  218. Perez MAS, Cuendet MA, Röhrig UF, Michielin O, Zoete V. Structural Prediction of Peptide-MHC Binding Modes. Methods Mol Biol 2022;2405:245-282
  219. Peter JK, Wegner F, Gsponer S, Helfenstein F, Roloff T, Tarnutzer R, Grosheintz K, Back M, Schaubhut C, Wagner S, Seth-Smith HMB, Scotton P, Redondo M, Beckmann C, Stadler T, Salzmann A, Kurth H, Leuzinger K, Bassetti S, Bingisser R, Siegemund M, Weisser M, Battegay M, Sutter ST, Lebrand A, Hirsch HH, Fuchs S, Egli A. SARS-CoV-2 Vaccine Alpha and Delta Variant Breakthrough Infections Are Rare and Mild but Can Happen Relatively Early after Vaccination. Microorganisms 2022;10(5):857
  220. 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:e74255
  221. Pinjusic K, Dubey OA, Egorova O, Nassiri S, Meylan E, Faget J, Constam DB. Activin-A impairs CD8 T cell-mediated immunity and immune checkpoint therapy response in melanoma. J Immunother Cancer 2022;10(5):e004533
  222. Pirastu N, McDonnell C, Grzeszkowiak EJ, Mounier N, Imamura F, Merino J, Day FR, Zheng J, Taba N, Concas MP, Repetto L, Kentistou KA, Robino A, Esko T, Joshi PK, Fischer K, Ong KK, Gaunt TR, Kutalik Z, Perry JRB, Wilson JF. Using genetic variation to disentangle the complex relationship between food intake and health outcomes. PLoS Genet 2022;18(6):e1010162
  223. 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
  224. Pitton M, Oberhaensli S, Appiah F, Pagani JL, Fournier A, Jakob SM, Que YA, Cameron DR. Mutation to ispA Produces Stable Small-Colony Variants of Pseudomonas aeruginosa That Have Enhanced Aminoglycoside Resistance. Antimicrob Agents Chemother 2022;66(7):e0062122
  225. 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
  226. Popadin K, Gunbin K, Peshkin L, Annis S, Fleischmann Z, Franco M, Kraytsberg Y, Markuzon N, Ackermann RR, Khrapko K. Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors. Genes (Basel) 2022;13(5):810
  227. Porcu E, Claringbould A, Weihs A, Lepik K, BIOS Consortium, Richardson TG, Völker U, Santoni FA, Teumer A, Franke L, Reymond A, Kutalik Z. Limited evidence for blood eQTLs in human sexual dimorphism. Genome Med 2022;14(1):89
  228. 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
  229. 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:giac028
  230. 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
  231. 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;289(14):4240-4250
  232. Radzikowska U, Baerenfaller K, Cornejo-Garcia JA, Karaaslan C, Barletta E, Sarac BE, Zhakparov D, Villaseñor A, Eguiluz-Gracia I, Mayorga C, Sokolowska M, Barbas C, Barber D, Ollert M, Chivato T, Agache I, Escribese MM. Omics technologies in allergy and asthma research: An EAACI position paper. Allergy 2022
  233. 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;43(6):791-799
  234. Ramdas S, Judd J, Graham SE, Kanoni S, Wang Y, Surakka I, Wenz B, Clarke SL, Chesi A, Wells A, Bhatti KF, Vedantam S, Winkler TW, Locke AE, Marouli E, Zajac GJM, Wu KH, Ntalla I, Hui Q, Klarin D, Hilliard AT, Wang Z, Xue C, Thorleifsson G, Helgadottir A, Gudbjartsson DF, Holm H, Olafsson I, Hwang MY, Han S, Akiyama M, Sakaue S, Terao C, Kanai M, Zhou W, Brumpton BM, Rasheed H, Havulinna AS, Veturi Y, Pacheco JA, Rosenthal EA, Lingren T, Feng Q, Kullo IJ, Narita A, Takayama J, Martin HC, Hunt KA, Trivedi B, Haessler J, Giulianini F, Bradford Y, Miller JE, Campbell A, Lin K, Millwood IY, Rasheed A, Hindy G, Faul JD, Zhao W, Weir DR, Turman C, Huang H, Graff M, Choudhury A, Sengupta D, Mahajan A, Brown MR, Zhang W, Yu K, Schmidt EM, Pandit A, Gustafsson S, Yin X, Luan J, Zhao JH, Matsuda F, Jang HM, Yoon K, Medina-Gomez C, Pitsillides A, Hottenga JJ, Wood AR, Ji Y, Gao Z, Haworth S, Mitchell RE, Chai JF, Aadahl M, Bjerregaard AA, Yao J, Manichaikul A, Lee WJ, Hsiung CA, Warren HR, Ramirez J, Bork-Jensen J, Kårhus LL, Goel A, Sabater-Lleal M, Noordam R, Mauro P, Matteo F, McDaid AF, Marques-Vidal P, Wielscher M, Trompet S, Sattar N, Møllehave LT, Munz M, Zeng L, Huang J, Yang B, Poveda A, Kurbasic A, Schönherr S, Forer L, Scholz M, Galesloot TE, Bradfield JP, Ruotsalainen SE, Daw EW, Zmuda JM, Mitchell JS, Fuchsberger C, Christensen H, Brody JA, Le P, Feitosa MF, Wojczynski MK, Hemerich D, Preuss M, Mangino M, Christofidou P, Verweij N, Benjamins JW, Engmann J, Noah TL, Verma A, Slieker RC, Lo KS, Zilhao NR, Kleber ME, Delgado GE, Huo S, Ikeda DD, Iha H, Yang J, Liu J, Demirkan A, Leonard HL, Marten J, Emmel C, Schmidt B, Smyth LJ, Cañadas-Garre M, Wang C, Nakatochi M, Wong A, Hutri-Kähönen N, Sim X, Xia R, Huerta-Chagoya A, Fernandez-Lopez JC, Lyssenko V, Nongmaithem SS, Sankareswaran A, Irvin MR, Oldmeadow C, Kim HN, Ryu S, Timmers PRHJ, Arbeeva L, Dorajoo R, Lange LA, Prasad G, Lorés-Motta L, Pauper M, Long J, Li X, Theusch E, Takeuchi F, Spracklen CN, Loukola A, Bollepalli S, Warner SC, Wang YX, Wei WB, Nutile T, Ruggiero D, Sung YJ, Chen S, Liu F, Yang J, Kentistou KA, Banas B, Morgan A, Meidtner K, Bielak LF, Smith JA, Hebbar P, Farmaki AE, Hofer E, Lin M, Concas MP, Vaccargiu S, van der Most PJ, Pitkänen N, Cade BE, van der Laan SW, Chitrala KN, Weiss S, Bentley AR, Doumatey AP, Adeyemo AA, Lee JY, Petersen ERB, Nielsen AA, Choi HS, Nethander M, Freitag-Wolf S, Southam L, Rayner NW, Wang CA, Lin SY, Wang JS, Couture C, Lyytikäinen LP, Nikus K, Cuellar-Partida G, Vestergaard H, Hidalgo B, Giannakopoulou O, Cai Q, Obura MO, van Setten J, He KY, Tang H, Terzikhan N, Shin JH, Jackson RD, Reiner AP, Martin LW, Chen Z, Li L, Kawaguchi T, Thiery J, Bis JC, Launer LJ, Li H, Nalls MA, Raitakari OT, Ichihara S, Wild SH, Nelson CP, Campbell H, Jäger S, Nabika T, Al-Mulla F, Niinikoski H, Braund PS, Kolcic I, Kovacs P, Giardoglou T, Katsuya T, de Kleijn D, de Borst GJ, Kim EK, Adams HHH, Ikram MA, Zhu X, Asselbergs FW, Kraaijeveld AO, Beulens JWJ, Shu XO, Rallidis LS, Pedersen O, Hansen T, Mitchell P, Hewitt AW, Kähönen M, Pérusse L, Bouchard C, Tönjes A, Ida Chen YD, Pennell CE, Mori TA, Lieb W, Franke A, Ohlsson C, Mellström D, Cho YS, Lee H, Yuan JM, Koh WP, Rhee SY, Woo JT, Heid IM, Stark KJ, Zimmermann ME, Völzke H, Homuth G, Evans MK, Zonderman AB, Polasek O, Pasterkamp G, Hoefer IE, Redline S, Pahkala K, Oldehinkel AJ, Snieder H, Biino G, Schmidt R, Schmidt H, Bandinelli S, Dedoussis G, Thanaraj TA, Peyser PA, Kato N, Schulze MB, Girotto G, Böger CA, Jung B, Joshi PK, Bennett DA, De Jager PL, Lu X, Mamakou V, Brown M, Caulfield MJ, Munroe PB, Guo X, Ciullo M, Jonas JB, Samani NJ, Kaprio J, Pajukanta P, Tusié-Luna T, Aguilar-Salinas CA, Adair LS, Bechayda SA, de Silva HJ, Wickremasinghe AR, Krauss RM, Wu JY, Zheng W, den Hollander AI, Bharadwaj D, Correa A, Wilson JG, Lind L, Heng CK, Nelson AE, Golightly YM, Wilson JF, Penninx B, Kim HL, Attia J, Scott RJ, Rao DC, Arnett DK, Walker M, Scott LJ, Koistinen HA, Chandak GR, Mercader JM, Villalpando CG, Orozco L, Fornage M, Tai ES, van Dam RM, Lehtimäki T, Chaturvedi N, Yokota M, Liu J, Reilly DF, McKnight AJ, Kee F, Jöckel KH, McCarthy MI, Palmer CNA, Vitart V, Hayward C, Simonsick E, van Duijn CM, Jin ZB, Lu F, Hishigaki H, Lin X, März W, Gudnason V, Tardif JC, Lettre G, T Hart LM, Elders PJM, Rader DJ, Damrauer SM, Kumari M, Kivimaki M, van der Harst P, Spector TD, Loos RJF, Province MA, Parra EJ, Cruz M, Psaty BM, Brandslund I, Pramstaller PP, Rotimi CN, Christensen K, Ripatti S, Widén E, Hakonarson H, Grant SFA, Kiemeney L, de Graaf J, Loeffler M, Kronenberg F, Gu D, Erdmann J, Schunkert H, Franks PW, Linneberg A, Jukema JW, Khera AV, Männikkö M, Jarvelin MR, Kutalik Z, Francesco C, Mook-Kanamori DO, Willems van Dijk K, Watkins H, Strachan DP, Grarup N, Sever P, Poulter N, Huey-Herng Sheu W, Rotter JI, Dantoft TM, Karpe F, Neville MJ, Timpson NJ, Cheng CY, Wong TY, Khor CC, Li H, Sabanayagam C, Peters A, Gieger C, Hattersley AT, Pedersen NL, Magnusson PKE, Boomsma DI, de Geus EJC, Cupples LA, van Meurs JBJ, Ikram A, Ghanbari M, Gordon-Larsen P, Huang W, Kim YJ, Tabara Y, Wareham NJ, Langenberg C, Zeggini E, Tuomilehto J, Kuusisto J, Laakso M, Ingelsson E, Abecasis G, Chambers JC, Kooner JS, de Vries PS, Morrison AC, Hazelhurst S, Ramsay M, North KE, Daviglus M, Kraft P, Martin NG, Whitfield JB, Abbas S, Saleheen D, Walters RG, Holmes MV, Black C, Smith BH, Baras A, Justice AE, Buring JE, Ridker PM, Chasman DI, Kooperberg C, Tamiya G, Yamamoto M, van Heel DA, Trembath RC, Wei WQ, Jarvik GP, Namjou B, Hayes MG, Ritchie MD, Jousilahti P, Salomaa V, Hveem K, Åsvold BO, Kubo M, Kamatani Y, Okada Y, Murakami Y, Kim BJ, Thorsteinsdottir U, Stefansson K, Zhang J, Chen YE, Ho YL, Lynch JA, Tsao PS, Chang KM, Cho K, O'Donnell CJ, Gaziano JM, Wilson P, Mohlke KL, Frayling TM, Hirschhorn JN, Kathiresan S, Boehnke M, Million Veterans Program, Global Lipids Genetics Consortium, Struan Grant, Natarajan P, Sun YV, Morris AP, Deloukas P, Peloso G, Assimes TL, Willer CJ, Zhu X, Brown CD. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids. Am J Hum Genet 2022;109(8):1366-1387
  235. Redin C, Thorball CW, Fellay J. Host genomics of SARS-CoV-2 infection. Eur J Hum Genet 2022;30(8):908-914
  236. Reijnders MJMF, Waterhouse RM. CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation. PLoS Comput Biol 2022;18(5):e1010075
  237. Reijnders MJMF. Wei2GO: weighted sequence similarity-based protein function prediction. PeerJ 2022;10:e12931
  238. Riesbeck S, Petruschke H, Rolle-Kampczyk U, Schori C, Ahrens CH, Eberlein C, Heipieper HJ, von Bergen M, Jehmlich N. Adaptation and Resistance: How Bacteroides thetaiotaomicron Copes with the Bisphenol A Substitute Bisphenol F. Microorganisms 2022;10(8):1610
  239. 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:btac299
  240. 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):e2113118119
  241. 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
  242. Röhrig UF, Majjigapu SR, Vogel P, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascenção K, Irving M, Coukos G, Michielin O, Zoete V. Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. J Enzyme Inhib Med Chem 2022;37(1):1773-1811
  243. Rozhoňová H, Danciu D, Stark S, Rätsch G, Kahles A, Lehmann KV. SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing. Bioinformatics 2022:btac510
  244. 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
  245. 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
  246. 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):msab352
  247. Saini JS, Hassler C, Cable R, Fourquez M, Danza F, Roman S, Tonolla M, Storelli N, Jacquet S, Zdobnov EM, Duhaime MB. Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop. mBio 2022:e0005222
  248. 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
  249. 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
  250. Scheuring I, Rasmussen JA, Bozzi D, Limborg MT. A strategic model of a host-microbe-microbe system reveals the importance of a joint host-microbe immune response to combat stress-induced gut dysbiosis. Front Microbiol 2022;13:912806
  251. 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
  252. Schneider TD, Roschitzki B, Grossmann J, Kraemer T, Steuer AE. Determination of the Time since Deposition of Blood Traces Utilizing a Liquid Chromatography-Mass Spectrometry-Based Proteomics Approach. Anal Chem 2022;94(30):10695-10704
  253. Schrevens S, Durandau E, Tran VDT, Sanglard D. Using in vivo transcriptomics and RNA enrichment to identify genes involved in virulence of Candida glabrata. Virulence 2022;13(1):1285-1303
  254. Schwab S, Janiaud P, Dayan M, Amrhein V, Panczak R, Palagi PM, Hemkens LG, Ramon M, Rothen N, Senn S, Furrer E, Held L. Ten simple rules for good research practice. PLoS Comput Biol 2022;18(6):e1010139
  255. Scire J, Barido-Sottani J, Kühnert D, Vaughan TG, Stadler T. Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations. Viruses 2022;14(8):1648
  256. 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):406
  257. Sharma VS, Fossati A, Ciuffa R, Buljan M, Williams EG, Chen Z, Shao W, Pedrioli PGA, Purcell AW, Martínez MR, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Brief Bioinform 2022;23(4):bbac239
  258. 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
  259. Silva NM, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, Adaktylou F, Chondroyianni-Metoki A, Pappa M, Ziota C, Sampson A, Papathanasiou A, Vitelli K, Cullen T, Kyparissi-Apostolika N, Lanz AZ, Peters J, Rio J, Wegmann D, Burger J, Currat M, Papageorgopoulou C. Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis. Sci Rep 2022;12(1):13474
  260. Silva SV, Andermann T, Zizka A, Kozlowski G, Silvestro D. Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence. Front Plant Sci 2022;13:839792
  261. Silvestro D, Goria S, Sterner T, Antonelli A. Improving biodiversity protection through artificial intelligence. Nat Sustain 2022;5(5):415-424
  262. Simmons JD, Dill-McFarland KA, Stein CM, Van PT, Chihota V, Ntshiqa T, Maenetje P, Peterson GJ, Benchek P, Nsereko M, Velen K, Fielding KL, Grant AD, Gottardo R, Mayanja-Kizza H, Wallis RS, Churchyard G, Boom WH, Hawn TR. Monocyte Transcriptional Responses to Mycobacterium tuberculosis Associate with Resistance to Tuberculin Skin Test and Interferon Gamma Release Assay Conversion. mSphere 2022;7(3):e0015922
  263. 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
  264. Solleder M, Racle J, Guillaume P, Coukos G, Bassani-Sternberg M, Gfeller D. Deciphering the landscape of phosphorylated HLA-II ligands. iScience 2022;25(5):104215
  265. Somerville V, Schowing T, Chabas H, Schmidt RS, von Ah U, Bruggmann R, Engel P. Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. Microbiome 2022;10(1):137
  266. Soutschek M, Germade T, Germain PL, Schratt G. enrichMiR predicts functionally relevant microRNAs based on target collections. Nucleic Acids Res 2022:gkac395
  267. Soutschek M, Gross F, Schratt G, Germain PL. scanMiR: a biochemically-based toolkit for versatile and efficient microRNA target prediction. Bioinformatics 2022:btac110
  268. Spataro S, Guerra C, Cavalli A, Sgrignani J, Sleeman J, Poulain L, Boland A, Scapozza L, Moll S, Prunotto M. CEMIP (HYBID, KIAA1199): Structure, function and expression in health and disease. FEBS J 2022
  269. Spataro V, Buetti-Dinh A. POH1/Rpn11/PSMD14: a journey from basic research in fission yeast to a prognostic marker and a druggable target in cancer cells. Br J Cancer 2022
  270. 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
  271. Staaf J, Häkkinen J, Hegardt C, Saal LH, Kimbung S, Hedenfalk I, Lien T, Sørlie T, Naume B, Russnes H, Marcone R, Ayyanan A, Brisken C, Malterling RR, Asking B, Olofsson H, Lindman H, Bendahl PO, Ehinger A, Larsson C, Loman N, Rydén L, Malmberg M, Borg Å, Vallon-Christersson J. RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer. NPJ Breast Cancer 2022;8(1):94
  272. 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
  273. Stajic D, Bank C, Gordo I. Adaptive Potential of Epigenetic Switching During Adaptation to Fluctuating Environments. Genome Biol Evol 2022;14(5):evac065
  274. 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):msab342
  275. 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
  276. Sulc J, Sjaarda J, Kutalik Z. Polynomial Mendelian randomization reveals non-linear causal effects for obesity-related traits. HGG Adv 2022;3(3):100124
  277. 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;25(6):1387-1400
  278. Suter P, Kuipers J, Beerenwinkel N. Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. Brief Bioinform 2022;23(4):bbac219
  279. Talker SC, Barut GT, Lischer HEL, Rufener R, von Münchow L, Bruggmann R, Summerfield A. Monocyte biology conserved across species: Functional insights from cattle. Front Immunol 2022;13:889175
  280. Tan G, Wolski WE, Kummer S, Hofstetter M, Theocharides APA, Manz MG, Aebersold R, Meier-Abt F. Proteomic identification of proliferation and progression markers in human polycythemia vera stem and progenitor cells. Blood Adv 2022;6(11):3480-3493
  281. Telenti A, Hodcroft EB, Robertson DL. The Evolution and Biology of SARS-CoV-2 Variants. Cold Spring Harb Perspect Med 2022;12(5):a041390
  282. Toll-Riera M, Olombrada M, Castro-Giner F, Wagner A. A limit on the evolutionary rescue of an Antarctic bacterium from rising temperatures. Sci Adv 2022;8(28):eabk3511
  283. 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
  284. Turgay M, Falentin H, Irmler S, Fröhlich-Wyder MT, Meola M, Oberhaensli S, Berthoud-Dit-Gallon Marchand H. Genomic rearrangements in the aspA-dcuA locus of Propionibacterium freudenreichii are associated with aspartase activity. Food Microbiol 2022;106:104030
  285. 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
  286. Varone E, Decio A, Barbera MC, Bolis M, Di Rito L, Pisati F, Giavazzi R, Zito E. Endoplasmic reticulum oxidoreductin 1-alpha deficiency and activation of protein translation synergistically impair breast tumour resilience. Br J Pharmacol 2022
  287. Vernette C, Lecubin J, Sánchez P, Tara Oceans Coordinators , Sunagawa S, Delmont TO, Acinas SG, Pelletier E, Hingamp P, Lescot M. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic Acids Res 2022:gkac420
  288. Vetter R, Iber D. Precision of morphogen gradients in neural tube development. Nat Commun 2022;13(1):1145
  289. 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;16(7):1740-1749
  290. Vigué L, Croce G, Petitjean M, Ruppé E, Tenaillon O, Weigt M. Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes. Nat Commun 2022;13(1):4030
  291. VijayKrishna N, Joshi J, Coraor N, Hillman-Jackson J, Bouvier D, van den Beek M, Eguinoa I, Coppens F, Davis J, Stolarczyk M, Sheffield NC, Gladman S, Cuccuru G, Grüning B, Soranzo N, Rasche H, Langhorst BW, Bernt M, Fornika D, de Lima Morais DA, Barrette M, van Heusden P, Petrillo M, Puertas-Gallardo A, Patak A, Hotz HR, Blankenberg D. Expanding the Galaxy's reference data. Bioinform Adv 2022;2(1):vbac030
  292. von Reumont BM, Anderluh G, Antunes A, Ayvazyan N, Beis D, Caliskan F, Crnković A, Damm M, Dutertre S, Ellgaard L, Gajski G, German H, Halassy B, Hempel BF, Hucho T, Igci N, Ikonomopoulou MP, Karbat I, Klapa MI, Koludarov I, Kool J, Lüddecke T, Ben Mansour R, Vittoria Modica M, Moran Y, Nalbantsoy A, Ibáñez MEP, Panagiotopoulos A, Reuveny E, Céspedes JS, Sombke A, Surm JM, Undheim EAB, Verdes A, Zancolli G. Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research. Gigascience 2022;11:giac048
  293. Vulin M, Jehanno C, Sethi A, Correia AL, Obradović MMS, Couto JP, Coissieux MM, Diepenbruck M, Preca BT, Volkmann K, der Maur PA, Schmidt A, Münst S, Sauteur L, Kloc M, Palafox M, Britschgi A, Unterreiner V, Galuba O, Claerr I, Lopez-Romero S, Galli GG, Baeschlin D, Okamoto R, Soysal SD, Mechera R, Weber WP, Radimerski T, Bentires-Alj M. A high-throughput drug screen reveals means to differentiate triple-negative breast cancer. Oncogene 2022
  294. Wagner A. Competition for nutrients increases invasion resistance during assembly of microbial communities. Mol Ecol 2022;31(15):4188-4203
  295. 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
  296. 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
  297. 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
  298. Weber M, Zanolari P, Ardüser F, Stucki D, Akarsu H, Overesch G. Prevalence and antimicrobial resistance of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) in Swiss sheep flocks. Prev Vet Med 2022;206:105697
  299. 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
  300. 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, Bucao CF, 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;22(6):2411-2428
  301. Winkler TW, Rasheed H, Teumer A, Gorski M, Rowan BX, Stanzick KJ, Thomas LF, Tin A, Hoppmann A, Chu AY, Tayo B, Thio CHL, Cusi D, Chai JF, Sieber KB, Horn K, Li M, Scholz M, Cocca M, Wuttke M, van der Most PJ, Yang Q, Ghasemi S, Nutile T, Li Y, Pontali G, Günther F, Dehghan A, Correa A, Parsa A, Feresin A, de Vries APJ, Zonderman AB, Smith AV, Oldehinkel AJ, De Grandi A, Rosenkranz AR, Franke A, Teren A, Metspalu A, Hicks AA, Morris AP, Tönjes A, Morgan A, Podgornaia AI, Peters A, Körner A, Mahajan A, Campbell A, Freedman BI, Spedicati B, Ponte B, Schöttker B, Brumpton B, Banas B, Krämer BK, Jung B, Åsvold BO, Smith BH, Ning B, Penninx BWJH, Vanderwerff BR, Psaty BM, Kammerer CM, Langefeld CD, Hayward C, Spracklen CN, Robinson-Cohen C, Hartman CA, Lindgren CM, Wang C, Sabanayagam C, Heng CK, Lanzani C, Khor CC, Cheng CY, Fuchsberger C, Gieger C, Shaffer CM, Schulz CA, Willer CJ, Chasman DI, Gudbjartsson DF, Ruggiero D, Toniolo D, Czamara D, Porteous DJ, Waterworth DM, Mascalzoni D, Mook-Kanamori DO, Reilly DF, Daw EW, Hofer E, Boerwinkle E, Salvi E, Bottinger EP, Tai ES, Catamo E, Rizzi F, Guo F, Rivadeneira F, Guilianini F, Sveinbjornsson G, Ehret G, Waeber G, Biino G, Girotto G, Pistis G, Nadkarni GN, Delgado GE, Montgomery GW, Snieder H, Campbell H, White HD, Gao H, Stringham HM, Schmidt H, Li H, Brenner H, Holm H, Kirsten H, Kramer H, Rudan I, Nolte IM, Tzoulaki I, Olafsson I, Martins J, Cook JP, Wilson JF, Halbritter J, Felix JF, Divers J, Kooner JS, Lee JJ, O'Connell J, Rotter JI, Liu J, Xu J, Thiery J, Ärnlöv J, Kuusisto J, Jakobsdottir J, Tremblay J, Chambers JC, Whitfield JB, Gaziano JM, Marten J, Coresh J, Jonas JB, Mychaleckyj JC, Christensen K, Eckardt KU, Mohlke KL, Endlich K, Dittrich K, Ryan KA, Rice KM, Taylor KD, Ho K, Nikus K, Matsuda K, Strauch K, Miliku K, Hveem K, Lind L, Wallentin L, Yerges-Armstrong LM, Raffield LM, Phillips LS, Launer LJ, Lyytikäinen LP, Lange LA, Citterio L, Klaric L, Ikram MA, Ising M, Kleber ME, Francescatto M, Concas MP, Ciullo M, Piratsu M, Orho-Melander M, Laakso M, Loeffler M, Perola M, de Borst MH, Gögele M, Bianca M, Lukas MA, Feitosa MF, Biggs ML, Wojczynski MK, Kavousi M, Kanai M, Akiyama M, Yasuda M, Nauck M, Waldenberger M, Chee ML, Chee ML, Boehnke M, Preuss MH, Stumvoll M, Province MA, Evans MK, O'Donoghue ML, Kubo M, Kähönen M, Kastarinen M, Nalls MA, Kuokkanen M, Ghanbari M, Bochud M, Josyula NS, Martin NG, Tan NYQ, Palmer ND, Pirastu N, Schupf N, Verweij N, Hutri-Kähönen N, Mononen N, Bansal N, Devuyst O, Melander O, Raitakari OT, Polasek O, Manunta P, Gasparini P, Mishra PP, Sulem P, Magnusson PKE, Elliott P, Ridker PM, Hamet P, Svensson PO, Joshi PK, Kovacs P, Pramstaller PP, Rossing P, Vollenweider P, van der Harst P, Dorajoo R, Sim RZH, Burkhardt R, Tao R, Noordam R, Mägi R, Schmidt R, de Mutsert R, Rueedi R, van Dam RM, Carroll RJ, Gansevoort RT, Loos RJF, Felicita SC, Sedaghat S, Padmanabhan S, Freitag-Wolf S, Pendergrass SA, Graham SE, Gordon SD, Hwang SJ, Kerr SM, Vaccargiu S, Patil SB, Hallan S, Bakker SJL, Lim SC, Lucae S, Vogelezang S, Bergmann S, Corre T, Ahluwalia TS, Lehtimäki T, Boutin TS, Meitinger T, Wong TY, Bergler T, Rabelink TJ, Esko T, Haller T, Thorsteinsdottir U, Völker U, Foo VHX, Salomaa V, Vitart V, Giedraitis V, Gudnason V, Jaddoe VWV, Huang W, Zhang W, Wei WB, Kiess W, März W, Koenig W, Lieb W, Gao X, Sim X, Wang YX, Friedlander Y, Tham YC, Kamatani Y, Okada Y, Milaneschi Y, Yu Z, Lifelines cohort study, DiscovEHR/MyCode study, VA Million Veteran Program, Stark KJ, Stefansson K, Böger CA, Hung AM, Kronenberg F, Köttgen A, Pattaro C, Heid IM. Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals. Commun Biol 2022;5(1):580
  302. 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;35(7):604-615
  303. 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
  304. Wysocki O, Zhou C, Rogado J, Huddar P, Shotton R, Tivey A, Albiges L, Angelakas A, Arnold D, Aung T, Banfill K, Baxter M, Barlesi F, Bayle A, Besse B, Bhogal T, Boyce H, Britton F, Calles A, Castelo-Branco L, Copson E, Croitoru A, Dani S, Dickens E, Eastlake L, Fitzpatrick P, Foulon S, Frederiksen H, Ganatra S, Gennatas S, Glenthøj A, Gomes F, Graham D, Hague C, Harrington K, Harrison M, Horsley L, Hoskins R, Hudson Z, Jakobsen L, Joharatnam-Hogan N, Khan S, Khan U, Khan K, Lewis A, Massard C, Maynard A, McKenzie H, Michielin O, Mosenthal A, Obispo B, Palmieri C, Patel R, Pentheroudakis G, Peters S, Rieger-Christ K, Robinson T, Romano E, Rowe M, Sekacheva M, Sheehan R, Stockdale A, Thomas A, Turtle L, Viñal D, Weaver J, Williams S, Wilson C, Dive C, Landers D, Cooksley T, Freitas A, Armstrong A, Lee R, on behalf of the ESMO Co-Care. An International Comparison of Presentation, Outcomes and CORONET Predictive Score Performance in Patients with Cancer Presenting with COVID-19 across Different Pandemic Waves Cancers (Basel) 2022;14(16)
  305. Wysocki O, Zhou C, Rogado J, Huddar P, Shotton R, Tivey A, Albiges L, Angelakas A, Arnold D, Aung T, Banfill K, Baxter M, Barlesi F, Bayle A, Besse B, Bhogal T, Boyce H, Britton F, Calles A, Castelo-Branco L, Copson E, Croitoru A, Dani SS, Dickens E, Eastlake L, Fitzpatrick P, Foulon S, Frederiksen H, Ganatra S, Gennatas S, Glenthøj A, Gomes F, Graham DM, Hague C, Harrington K, Harrison M, Horsley L, Hoskins R, Hudson Z, Jakobsen LH, Joharatnam-Hogan N, Khan S, Khan UT, Khan K, Lewis A, Massard C, Maynard A, McKenzie H, Michielin O, Mosenthal AC, Obispo B, Palmieri C, Patel R, Pentheroudakis G, Peters S, Rieger-Christ K, Robinson T, Romano E, Rowe M, Sekacheva M, Sheehan R, Stockdale A, Thomas A, Turtle L, Viñal D, Weaver J, Williams S, Wilson C, Dive C, Landers D, Cooksley T, Freitas A, Armstrong AC, Lee RJ, On Behalf Of The Esmo Co-Care. An International Comparison of Presentation, Outcomes and CORONET Predictive Score Performance in Patients with Cancer Presenting with COVID-19 across Different Pandemic Waves. Cancers (Basel) 2022;14(16):3931
  306. 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
  307. Yamada T, Yaguchi T, Maeda M, Alshahni MM, Salamin K, Guenova E, Feuermann M, Monod M. Gene Amplification of CYP51B: a New Mechanism of Resistance to Azole Compounds in Trichophyton indotineae. Antimicrob Agents Chemother 2022;66(6):e0005922
  308. Yerly L, Pich-Bavastro C, Di Domizio J, Wyss T, Tissot-Renaud S, Cangkrama M, Gilliet M, Werner S, Kuonen F. Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma. Nat Commun 2022;13(1):4897
  309. Zachara M, Rainer PY, Hashimi H, Russeil JM, Alpern D, Ferrero R, Litovchenko M, Deplancke B. Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner. EMBO J 2022:e108206
  310. Zakany S, Smirnov S, Milinkovitch MC. Lizard Skin Patterns and the Ising Model. Phys Rev Lett 2022;128(4):048102
  311. 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):e2111392119
  312. 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
  313. Zanotti S, Boot GF, Coto-Llerena M, Gallon J, Hess GF, Soysal SD, Kollmar O, Ng CKY, Piscuoglio S. The Role of Chronic Liver Diseases in the Emergence and Recurrence of Hepatocellular Carcinoma: An Omics Perspective. Front Med (Lausanne) 2022;9:888850
  314. 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
  315. Zufferey M, Tavernari D, Ciriello G. Methods for the Analysis of Topologically Associating Domains (TADs). Methods Mol Biol 2022;2301:39-59