Peer-reviewed articles and conference proceedings

Listed in Europe PMC, latest update: 01.03.2023.
Discover the SIB Remarkable Outputs 2022

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

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  1. Albert JS, Carnaval AC, Flantua SGA, Lohmann LG, Ribas CC, Riff D, Carrillo JD, Fan Y, Figueiredo JJP, Guayasamin JM, Hoorn C, de Melo GH, Nascimento N, Quesada CA, Ulloa Ulloa C, Val P, Arieira J, Encalada AC, Nobre CA. Human impacts outpace natural processes in the Amazon. Science 2023;379(6630):eabo5003
  2. Álvarez-Prado ÁF, Maas RR, Soukup K, Klemm F, Kornete M, Krebs FS, Zoete V, Berezowska S, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors. Cell Rep Med 2023;4(1):100900
  3. Antonello P, Pizzagalli DU, Foglierini M, Melgrati S, Radice E, Thelen S, Thelen M. ACKR3 promotes CXCL12/CXCR4-mediated cell-to-cell-induced lymphoma migration through LTB4 production. Front Immunol 2022;13:1067885
  4. Apsley AT, Domico ER, Verbiest MA, Brogan CA, Buck ER, Burich AJ, Cardone KM, Stone WJ, Anisimova M, Vandenbergh DJ. A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3). Life Sci Alliance 2023;6(4):e202201677
  5. Aros-Mualin D, Guadagno CR, Silvestro D, Kessler M. Light, rather than circadian rhythm, regulates gas exchange in ferns and lycophytes. Plant Physiol 2023:kiad036
  6. Azizoğlu A, Loureiro C, Venetz J, Brent R. Autorepression-Based Conditional Gene Expression System in Yeast for Variation-Suppressed Control of Protein Dosage. Curr Protoc 2023;3(1):e647
  7. Barreiro K, Lay AC, Leparc G, Tran VDT, Rosler M, Dayalan L, Burdet F, Ibberson M, Coward RJM, Huber TB, Krämer BK, Delic D, Holthofer H. An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles. J Extracell Vesicles 2023;12(2):e12304
  8. Barut GT, Kreuzer M, Bruggmann R, Summerfield A, Talker SC. Single-cell transcriptomics reveals striking heterogeneity and functional organization of dendritic and monocytic cells in the bovine mesenteric lymph node. Front Immunol 2022;13:1099357
  9. Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Mol Biol Evol 2023;40(1):msac269
  10. Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Cervantes Rincón T, Fava T, Podešvová L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Hönig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarström Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF. Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci Immunol 2023:eade0958
  11. Buchner B, Clement T, de Groot D, Zanghellini J. ecmtool: fast and memory efficient enumeration of elementary conversion modes. Bioinformatics 2023:btad095
  12. Camps J, Noël F, Liechti R, Massenet-Regad L, Rigade S, Götz L, Hoffmann C, Amblard E, Saichi M, Ibrahim MM, Pollard J, Medvedovic J, Roider HG, Soumelis V. Meta-Analysis of Human Cancer Single-Cell RNA-Seq Datasets Using the IMMUcan Database. Cancer Res 2023;83(3):363-373
  13. Caucheteur D, May Pendlington Z, Roncaglia P, Gobeill J, Mottin L, Matentzoglu N, Agosti D, Osumi-Sutherland D, Parkinson H, Ruch P. COVoc and COVTriage: novel resources to support literature triage. Bioinformatics 2023;39(1):btac800
  14. Coudert E, Gehant S, de Castro E, Pozzato M, Baratin D, Neto T, Sigrist CJA, Redaschi N, Bridge A, UniProt Consortium. Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinformatics 2023;39(1):btac793
  15. Dadonaite B, Crawford K, Radford C, Farrell A, Yu T, Hannon W, Zhou P, Andrabi R, Burton D, Liu L, Ho D, Chu H, Neher R, Bloom J. A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike Cell 2023
  16. de Groot DH, Tjalma AJ, Bruggeman FJ, van Nimwegen E. Effective bet-hedging through growth rate dependent stability. Proc Natl Acad Sci U S A 2023;120(8):e2211091120
  17. Deichmann J, Bachmann S, Burckhardt MA, Pfister M, Szinnai G, Kaltenbach HM. New model of glucose-insulin regulation characterizes effects of physical activity and facilitates personalized treatment evaluation in children and adults with type 1 diabetes. PLoS Comput Biol 2023;19(2):e1010289
  18. Dietler N, Lupo U, Bitbol AF. Impact of phylogeny on structural contact inference from protein sequence data. J R Soc Interface 2023;20(199):20220707
  19. Duruz J, Sprecher M, Kaldun JC, Al-Soudy AS, Lischer HEL, van Geest G, Nicholson P, Bruggmann R, Sprecher SG. Molecular characterization of cell types in the squid Loligo vulgaris. Elife 2023;12:e80670
  20. Forny P, Bonilla X, Lamparter D, Shao W, Plessl T, Frei C, Bingisser A, Goetze S, van Drogen A, Harshman K, Pedrioli PGA, Howald C, Poms M, Traversi F, Bürer C, Cherkaoui S, Morscher RJ, Simmons L, Forny M, Xenarios I, Aebersold R, Zamboni N, Rätsch G, Dermitzakis ET, Wollscheid B, Baumgartner MR, Froese DS. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency. Nat Metab 2023;5(1):80-95
  21. Frachon L, Arrigo L, Rusman Q, Poveda L, Qi W, Scopece G, Schiestl FP. Putative signals of generalist plant species adaptation to local pollinator communities and abiotic factors. Mol Biol Evol 2023:msad036
  22. Frey K, Rohrer L, Potapenko A, Goetze S, von Eckardstein A, Wollscheid B. Mapping the dynamic cell surface interactome of high-density lipoprotein reveals Aminopeptidase N as modulator of its endothelial uptake 2023
  23. Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res 2023;51(d1):D760-D766
  24. Gfeller D, Liu Y, Racle J. Contemplating immunopeptidomes to better predict them. Semin Immunol 2023;66:101708
  25. Gfeller D, Schmidt J, Croce G, Guillaume P, Bobisse S, Genolet R, Queiroz L, Cesbron J, Racle J, Harari A. Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes. Cell Syst 2023;14(1):72-83.e5
  26. Guidetti F, Arribas AJ, Sartori G, Spriano F, Barnabei L, Tarantelli C, Von Roemeling R, Martinez E, Zucca E, Bertoni F. Targeting IRAK4 with Emavusertib in Lymphoma Models with Secondary Resistance to PI3K and BTK Inhibitors. J Clin Med 2023;12(2):399
  27. Hausmann D, Todorski I, Pindur A, Weiland E, Benkert T, Bosshard L, Prummer M, Kubik-Huch RA. Advanced Diffusion-Weighted Imaging Sequences for Breast MRI: Comprehensive Comparison of Improved Sequences and Ultra-High B-Values to Identify the Optimal Combination. Diagnostics (Basel) 2023;13(4):607
  28. Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res 2023;51(d1):D389-D394
  29. Herzig A, Rubinacci S, Marenne G, Perdry H, Dina C, Redon R, Delaneau O, Génin E, FrEx Consortium, FranceGenRef Consortium. SURFBAT: a surrogate family-based association test building on large imputation reference panels 2023
  30. Hiltemann S, Rasche H, Gladman S, Hotz HR, Larivière D, Blankenberg D, Jagtap PD, Wollmann T, Bretaudeau A, Goué N, Griffin TJ, Royaux C, Le Bras Y, Mehta S, Syme A, Coppens F, Droesbeke B, Soranzo N, Bacon W, Psomopoulos F, Gallardo-Alba C, Davis J, Föll MC, Fahrner M, Doyle MA, Serrano-Solano B, Fouilloux AC, van Heusden P, Maier W, Clements D, Heyl F, Galaxy Training Network, Grüning B, Batut B. Galaxy Training: A powerful framework for teaching! PLoS Comput Biol 2023;19(1):e1010752
  31. Hodel F, Xu ZM, Thorball CW, de La Harpe R, Letang-Mathieu P, Brenner N, Butt J, Bender N, Waterboer T, Marques-Vidal PM, Vollenweider P, Vaucher J, Fellay J. Associations of genetic and infectious risk factors with coronary heart disease. Elife 2023;12:e79742
  32. Kentistou KA, Luan J, Wittemans LBL, Hambly C, Klaric L, Kutalik Z, Speakman JR, Wareham NJ, Kendall TJ, Langenberg C, Wilson JF, Joshi PK, Morton NM. Large scale phenotype imputation and in vivo functional validation implicate ADAMTS14 as an adiposity gene. Nat Commun 2023;14(1):307
  33. Kuhlmeier E, Chan T, Agüí CV, Willi B, Wolfensberger A, Beisel C, Topolsky I, Beerenwinkel N, Stadler T, Swiss Sars-CoV-Sequencing Consortium, Jones S, Tyson G, Hosie MJ, Reitt K, Hüttl J, Meli ML, Hofmann-Lehmann R. Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 2023;15(1):245
  34. Kuznetsov D, Tegenfeldt F, Manni M, Seppey M, Berkeley M, Kriventseva EV, Zdobnov EM. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res 2023;51(d1):D445-D451
  35. Laganenka L, Lee JW, Malfertheiner L, Dieterich CL, Fuchs L, Piel J, von Mering C, Sourjik V, Hardt WD. Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nat Microbiol 2023;8(2):204-217
  36. Lavanchy E, Goudet J. Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization. Mol Ecol Resour 2023
  37. Luqman H, Wegmann D, Fior S, Widmer A. Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles. Nat Commun 2023;14(1):1080
  38. Macnair W, Robinson M. SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data. Genome Biol 2023;24(1):23
  39. Marx AF, Kallert SM, Brunner TM, Villegas JA, Geier F, Fixemer J, Abreu-Mota T, Reuther P, Bonilla WV, Fadejeva J, Kreutzfeldt M, Wagner I, Aparicio-Domingo P, Scarpellino L, Charmoy M, Utzschneider DT, Hagedorn C, Lu M, Cornille K, Stauffer K, Kreppel F, Merkler D, Zehn D, Held W, Luther SA, Löhning M, Pinschewer DD. The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8+ T cells in chronic viral infection. Immunity 2023:S1074-7613(23)00041-9
  40. Mastelic-Gavillet B, Sarivalasis A, Lozano LE, Lofek S, Wyss T, Melero I, de Vries IJM, Harari A, Romero P, Kandalaft LE, Viganó S. Longitudinal analysis of DC subsets in patients with ovarian cancer: Implications for immunotherapy. Front Immunol 2023;14:1119371
  41. Mounier N, Robertson DS, Kutalik Z, Dudbridge F, Bowden J. Incorporating discovery and replication GWAS into summary data Mendelian randomization studies: A review of current methods and a simple, general and powerful alternative 2023
  42. Nadeau SA, Vaughan TG, Beckmann C, Topolsky I, Chen C, Hodcroft E, Schär T, Nissen I, Santacroce N, Burcklen E, Ferreira P, Jablonski KP, Posada-Céspedes S, Capece V, Seidel S, Santamaria de Souza N, Martinez-Gomez JM, Cheng P, Bosshard PP, Levesque MP, Kufner V, Schmutz S, Zaheri M, Huber M, Trkola A, Cordey S, Laubscher F, Gonçalves AR, Aeby S, Pillonel T, Jacot D, Bertelli C, Greub G, Leuzinger K, Stange M, Mari A, Roloff T, Seth-Smith H, Hirsch HH, Egli A, Redondo M, Kobel O, Noppen C, du Plessis L, Beerenwinkel N, Neher RA, Beisel C, Stadler T. Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Sci Transl Med 2023;15(680):eabn7979
  43. Neuenschwander S, Cruz Dávalos DI, Anchieri L, Sousa da Mota B, Bozzi D, Rubinacci S, Delaneau O, Rasmussen S, Malaspinas AS. Mapache: a flexible pipeline to map ancient DNA. Bioinformatics 2023;39(2):btad028
  44. O’Toole Á, Neher RA, Ndodo N, Borges V, Gannon B, Gomes JP, Groves N, King DJ, Maloney D, Lemey P, Lewandowski K, Loman N, Myers R, Suchard MA, Worobey M, Chand M, Ihekweazu C, Ulaeto D, Adetifa I, Rambaut A. Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016 2023
  45. Parey E, Louis A, Montfort J, Bouchez O, Roques C, Iampietro C, Lluch J, Castinel A, Donnadieu C, Desvignes T, Floi Bucao C, Jouanno E, Wen M, Mejri S, Dirks R, Jansen H, Henkel C, Chen WJ, Zahm M, Cabau C, Klopp C, Thompson AW, Robinson-Rechavi M, Braasch I, Lecointre G, Bobe J, Postlethwait JH, Berthelot C, Crollius HR, Guiguen Y. Genome structures resolve the early diversification of teleost fishes. Science 2023;379(6632):572-575
  46. Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunić I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A. InterPro in 2022. Nucleic Acids Res 2023;51(d1):D418-D427
  47. PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Consortium. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023;614(7948):E37
  48. Pfaendler R, Hanimann J, Lee S, Snijder B. Self-supervised vision transformers accurately decode cellular state heterogeneity 2023
  49. Planas-Paz L, Pliego-Mendieta A, Hagedorn C, Aguilera-Garcia D, Haberecker M, Arnold F, Herzog M, Bankel L, Guggenberger R, Steiner S, Chen Y, Kahraman A, Zoche M, Rubin MA, Moch H, Britschgi C, Pauli C. Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma. EMBO Mol Med 2023:e16863
  50. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G, PCAWG Consortium. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2023;614(7948):E40
  51. Rieder J, Kapopoulou A, Bank C, Adrian-Kalchhauser I. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. Environ Microbiome 2023;18(1):8
  52. Rodrigues PF, Kouklas A, Cvijetic G, Bouladoux N, Mitrovic M, Desai JV, Lima-Junior DS, Lionakis MS, Belkaid Y, Ivanek R, Tussiwand R. pDC-like cells are pre-DC2 and require KLF4 to control homeostatic CD4 T cells. Sci Immunol 2023;8(80):eadd4132
  53. Ruiz F, Peter B, Rebeaud J, Vigne S, Bressoud V, Roumain M, Wyss T, Yersin Y, Wagner I, Kreutzfeldt M, Pimentel Mendes M, Kowalski C, Boivin G, Roth L, Schwaninger M, Merkler D, Muccioli GG, Hugues S, Petrova TV, Pot C. Endothelial cell-derived oxysterol ablation attenuates experimental autoimmune encephalomyelitis. EMBO Rep 2023:e55328
  54. Sandoz PA, Denhardt-Eriksson RA, Abrami L, Abriata LA, Spreemann G, Maclachlan C, Ho S, Kunz B, Hess K, Knott G, S Mesquita F, Hatzimanikatis V, van der Goot FG. Dynamics of CLIMP-63 S-acylation control ER morphology. Nat Commun 2023;14(1):264
  55. Sarkis R, Burri O, Royer-Chardon C, Schyrr F, Blum S, Costanza M, Cherix S, Piazzon N, Barcena C, Bisig B, Nardi V, Sarro R, Ambrosini G, Weigert M, Spertini O, Blum S, Deplancke B, Seitz A, de Leval L, Naveiras O. MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology. Mod Pathol 2023;36(4):100088
  56. Schnidrig D, Garofoli A, Benjak A, Rätsch G, Rubin MA, SOCIBP consortium, Piscuoglio S, Ng CKY. PipeIT2: A tumor-only somatic variant calling workflow for molecular diagnostic Ion Torrent sequencing data. Genomics 2023;115(2):110587
  57. Serey-Gaut M, Cortes M, Makrythanasis P, Suri M, Taylor AMR, Sullivan JA, Asleh AN, Mitra J, Dar MA, McNamara A, Shashi V, Dugan S, Song X, Rosenfeld JA, Cabrol C, Iwaszkiewicz J, Zoete V, Pehlivan D, Akdemir ZC, Roeder ER, Littlejohn RO, Dibra HK, Byrd PJ, Stewart GS, Geckinli BB, Posey J, Westman R, Jungbluth C, Eason J, Sachdev R, Evans CA, Lemire G, VanNoy GE, O'Donnell-Luria A, Mau-Them FT, Juven A, Piard J, Nixon CY, Zhu Y, Ha T, Buckley MF, Thauvin C, Essien Umanah GK, Van Maldergem L, Lupski JR, Roscioli T, Dawson VL, Dawson TM, Antonarakis SE. Bi-allelic TTI1 variants cause an autosomal-recessive neurodevelopmental disorder with microcephaly. Am J Hum Genet 2023:S0002-9297(23)00006-X
  58. Sianta SA, Peischl S, Moeller DA, Brandvain Y. The efficacy of selection may increase or decrease with selfing depending upon the recombination environment. Evolution 2023;77(2):394-408
  59. Steiner M, Pingel M, Falquet L, Giffard B, Griesser M, Leyer I, Preda C, Uzman D, Bacher S, Reineke A. Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards. PLoS One 2023;18(1):e0280516
  60. Stetka J, Usart M, Kubovcakova L, Rai S, Nageswara Rao T, Sutter J, Hao-Shen H, Dirnhofer S, Geier F, Bader MS, Passweg JR, Manolova V, Dürrenberger F, Ahmed N, Schroeder T, Ganz T, Nemeth E, Silvestri L, Nai A, Camaschella C, Skoda RC. Iron is a modifier of the phenotypes of JAK2-mutant myeloproliferative neoplasms. Blood 2023:blood.2022017976
  61. Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res 2023;51(d1):D638-D646
  62. Tadros DM, Eggenschwiler S, Racle J, Gfeller D. The MHC Motif Atlas: a database of MHC binding specificities and ligands. Nucleic Acids Res 2023;51(d1):D428-D437
  63. Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J, European Reference Genome Atlas Consortium. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3
  64. Tichet M, Wullschleger S, Chryplewicz A, Fournier N, Marcone R, Kauzlaric A, Homicsko K, Deak LC, Umaña P, Klein C, Hanahan D. Bispecific PD1-IL2v and anti-PD-L1 break tumor immunity resistance by enhancing stem-like tumor-reactive CD8+ T cells and reprogramming macrophages. Immunity 2023;56(1):162-179.e6
  65. Trefny MP, Kirchhammer N, Auf der Maur P, Natoli M, Schmid D, Germann M, Fernandez Rodriguez L, Herzig P, Lötscher J, Akrami M, Stinchcombe JC, Stanczak MA, Zingg A, Buchi M, Roux J, Marone R, Don L, Lardinois D, Wiese M, Jeker LT, Bentires-Alj M, Rossy J, Thommen DS, Griffiths GM, Läubli H, Hess C, Zippelius A. Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy. Nat Commun 2023;14(1):86
  66. Valentin JDP, Altenried S, Varadarajan AR, Ahrens CH, Schreiber F, Webb JS, van der Mei HC, Ren Q. Identification of Potential Antimicrobial Targets of Pseudomonas aeruginosa Biofilms through a Novel Screening Approach. Microbiol Spectr 2023:e0309922
  67. Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. J Mol Biol 2023:168021
  68. Vora J, Navelkar R, Vijay-Shanker K, Edwards N, Martinez K, Ding X, Wang T, Su P, Ross K, Lisacek F, Hayes C, Kahsay R, Ranzinger R, Tiemeyer M, Mazumder R. The glycan structure dictionary-a dictionary describing commonly used glycan structure terms. Glycobiology 2023:cwad014
  69. Weiler P, Van den Berge K, Street K, Tiberi S. A Guide to Trajectory Inference and RNA Velocity. Methods Mol Biol 2023;2584:269-292
  70. Wolfe AJ, Rademacher DJ, Mores CR, Evans RJ, Overholt T, Halverson T, Limeira R, Matthews C, Badlani G, Brubaker L, Walker SJ. Detection of Bacteria in Bladder Mucosa of Adult Females. J Urol 2023:101097JU0000000000003189
  71. Yang L, Sadler MC, Altman RB. Genetic association studies using disease liabilities from deep neural networks 2023
  72. Zamariolli M, Auwerx C, Sadler MC, van der Graaf A, Lepik K, Schoeler T, Moysés-Oliveira M, Dantas AG, Melaragno MI, Kutalik Z. The impact of 22q11.2 copy-number variants on human traits in the general population. Am J Hum Genet 2023;110(2):300-313