Publications by SIB Members published in 2020

Listed in Europe PMC, latest update: 2020-07-01.

Peer-reviewed articles and conference proceedings

Search

  1. Abriata LA, Dal Peraro M. Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction? J Chem Inf Model 2020;60(5):2443-2447
  2. Abriata LA, Lepore R, Dal Peraro M. About the need to make computational models of biological macromolecules available and discoverable. Bioinformatics 2020;36(9):2952-2954
  3. Agüero JA, Akarsu H, Aguilar-Bultet L, Oevermann A, Falquet L. Large-Scale Comparison of Toxin and Antitoxins in Listeria monocytogenes. Toxins (Basel) 2020;12(1)
  4. Alijevic O, Bignucolo O, Hichri E, Peng Z, Kucera JP, Kellenberger S. Slowing of the Time Course of Acidification Decreases the Acid-Sensing Ion Channel 1a Current Amplitude and Modulates Action Potential Firing in Neurons. Front Cell Neurosci 2020;14:41
  5. Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, For Orthologs Consortium TQ, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C. The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res 2020;48(w1):W538-W545
  6. Ambrosini G, Vorontsov I, Penzar D, Groux R, Fornes O, Nikolaeva DD, Ballester B, Grau J, Grosse I, Makeev V, Kulakovskiy I, Bucher P. Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. Genome Biol 2020;21(1):114
  7. Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC. Publisher Correction: Orchestrating single-cell analysis with Bioconductor. Nat Methods 2020;17(2):242
  8. Amini P, Nassiri S, Malbon A, Markkanen E. Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components. Sci Rep 2020;10(1):5506
  9. Ansar M, Ebstein F, Özkoç H, Paracha SA, Iwaszkiewicz J, Gesemann M, Zoete V, Ranza E, Santoni FA, Sarwar MT, Ahmed J, Krüger E, Bachmann-Gagescu R, Antonarakis SE. Biallelic variants in PSMB1 encoding the proteasome subunit β6 cause impairment of proteasome function, microcephaly, intellectual disability, developmental delay and short stature. Hum Mol Genet 2020;29(7):1132-1143
  10. Ansar M, Ranza E, Shetty M, Paracha SA, Azam M, Kern I, Iwaszkiewicz J, Farooq O, Pournaras CJ, Malcles A, Kecik M, Rivolta C, Muzaffar W, Qurban A, Ali L, Aggoun Y, Santoni FA, Makrythanasis P, Ahmed J, Qamar R, Sarwar MT, Henry LK, Antonarakis SE. Taurine treatment of retinal degeneration and cardiomyopathy in a consanguineous family with SLC6A6 taurine transporter deficiency. Hum Mol Genet 2020;29(4):618-623
  11. Aoki-Kinoshita KF, Lisacek F, Mazumder R, York WS, Packer NH. The GlySpace Alliance: toward a collaborative global glycoinformatics community. Glycobiology 2020;30(2):70-71
  12. Archibald J, MacMillan EL, Enzler A, Jutzeler CR, Schweinhardt P, Kramer JLK. Excitatory and inhibitory responses in the brain to experimental pain: A systematic review of MR spectroscopy studies. Neuroimage 2020;215:116794
  13. Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL. HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation. Mol Biol Evol 2020;37(3):639-650
  14. Atabaki-Pasdar N, Ohlsson M, Viñuela A, Frau F, Pomares-Millan H, Haid M, Jones AG, Thomas EL, Koivula RW, Kurbasic A, Mutie PM, Fitipaldi H, Fernandez J, Dawed AY, Giordano GN, Forgie IM, McDonald TJ, Rutters F, Cederberg H, Chabanova E, Dale M, Masi F, Thomas CE, Allin KH, Hansen TH, Heggie A, Hong MG, Elders PJM, Kennedy G, Kokkola T, Pedersen HK, Mahajan A, McEvoy D, Pattou F, Raverdy V, Häussler RS, Sharma S, Thomsen HS, Vangipurapu J, Vestergaard H, 't Hart LM, Adamski J, Musholt PB, Brage S, Brunak S, Dermitzakis E, Frost G, Hansen T, Laakso M, Pedersen O, Ridderstråle M, Ruetten H, Hattersley AT, Walker M, Beulens JWJ, Mari A, Schwenk JM, Gupta R, McCarthy MI, Pearson ER, Bell JD, Pavo I, Franks PW. Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts. PLoS Med 2020;17(6):e1003149
  15. Ataca D, Aouad P, Constantin C, Laszlo C, Beleut M, Shamseddin M, Rajaram RD, Jeitziner R, Mead TJ, Caikovski M, Bucher P, Ambrosini G, Apte SS, Brisken C. The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche. Nat Commun 2020;11(1):1571
  16. Aynaud MM, Mirabeau O, Gruel N, Grossetête S, Boeva V, Durand S, Surdez D, Saulnier O, Zaïdi S, Gribkova S, Fouché A, Kairov U, Raynal V, Tirode F, Grünewald TGP, Bohec M, Baulande S, Janoueix-Lerosey I, Vert JP, Barillot E, Delattre O, Zinovyev A. Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution. Cell Rep 2020;30(6):1767-1779.e6
  17. Azpeitia E, Wagner A. Short Residence Times of DNA-Bound Transcription Factors Can Reduce Gene Expression Noise and Increase the Transmission of Information in a Gene Regulation System. Front Mol Biosci 2020;7:67
  18. Barbensi A, Celoria D, Harrington HA, Stasiak A, Buck D. Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology. Sci Adv 2020;6(9):eaay1458
  19. Barceló C, Guidi M, Thorball CW, Hammer C, Chaouch A, Scherrer AU, Hasse B, Cavassini M, Furrer H, Calmy A, Haubitz S, Bernasconi E, Buclin T, Fellay J, Tarr PE, Csajka C, Swiss HIV Cohort Study . Impact of Genetic and Nongenetic Factors on Body Mass Index and Waist-Hip Ratio Change in HIV-Infected Individuals Initiating Antiretroviral Therapy. Open Forum Infect Dis 2020;7(1):ofz464
  20. Barido-Sottani J, Vaughan TG, Stadler T. A Multi-Type Birth-Death model for Bayesian inference of lineage-specific birth and death rates. Syst Biol 2020
  21. Barut GT, Lischer HEL, Bruggmann R, Summerfield A, Talker SC. Transcriptomic profiling of bovine blood dendritic cells and monocytes following toll-like receptor stimulation. Eur J Immunol 2020
  22. Bekkar A, Nasrallah A, Guex N, Fajas L, Xenarios I, Lopez-Mejia IC. PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. Bioinformatics 2020
  23. Bellenberg S, Buetti-Dinh A, Galli V, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, Vera M, Dopson M. Correction for Bellenberg et al., "Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms". Appl Environ Microbiol 2020;86(3)
  24. Berdous D, Berney X, Sanchez-Archidona AR, Jan M, Roujeau C, Lopez-Mejia IC, Mynatt R, Thorens B. A genetic screen identifies Crat as a regulator of pancreatic beta-cell insulin secretion. Mol Metab 2020;37:100993
  25. Bignucolo O, Vullo S, Ambrosio N, Gautschi I, Kellenberger S. Structural and Functional Analysis of Gly212 Mutants Reveals the Importance of Intersubunit Interactions in ASIC1a Channel Function. Front Mol Biosci 2020;7:58
  26. Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Res 2020;30(2):250-262
  27. Boettcher S, Wilk CM, Singer J, Beier F, Burcklen E, Beisel C, Ventura Ferreira MS, Gourri E, Gassner C, Frey BM, Schanz U, Skoda RC, Ebert BL, Brummendorf TH, Beerenwinkel N, Manz MG. Clonal hematopoiesis in donors and long-term survivors of related allogeneic hematopoietic stem cell transplantation. Blood 2020;135(18):1548-1559
  28. Bolis M, Paroni G, Fratelli M, Vallerga A, Guarrera L, Zanetti A, Kurosaki M, Garattini SK, Gianni' M, Lupi M, Pattini L, Barzago MM, Terao M, Garattini E. All-Trans Retinoic Acid Stimulates Viral Mimicry, Interferon Responses and Antigen Presentation in Breast-Cancer Cells. Cancers (Basel) 2020;12(5)
  29. Bolleman J, de Castro E, Baratin D, Gehant S, Cuche BA, Auchincloss AH, Coudert E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Xenarios I, Redaschi N, Bridge A. HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. Gigascience 2020;9(2)
  30. Bonnardel F, Perez S, Lisacek F, Imberty A. Structural Database for Lectins and the UniLectin Web Platform. Methods Mol Biol 2020;2132:1-14
  31. Borghesi A, Trück J, Asgari S, Sancho-Shimizu V, Agyeman PKA, Bellos E, Giannoni E, Stocker M, Posfay-Barbe KM, Heininger U, Bernhard-Stirnemann S, Niederer-Loher A, Kahlert CR, Natalucci G, Relly C, Riedel T, Kuehni CE, Thorball CW, Chaturvedi N, Martinon-Torres F, Kuijpers TW, Coin L, Wright V, Herberg J, Levin M, Aebi C, Berger C, Fellay J, Schlapbach LJ, EUCLIDS consortium and the Swiss Paediatric Sepsis Study. Whole-exome sequencing for the identification of rare variants in primary immunodeficiency genes in children with sepsis - a prospective population-based cohort study. Clin Infect Dis 2020
  32. Borgsmüller N, Bonet J, Marass F, Gonzalez-Perez A, Lopez-Bigas N, Beerenwinkel N. BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. Bioinformatics 2020
  33. Boskova V, Stadler T. PIQMEE: Bayesian phylodynamic method for analysis of large datasets with duplicate sequences. Mol Biol Evol 2020
  34. Bosmani C, Leuba F, Hanna N, Bach F, Burdet F, Pagni M, Hagedorn M, Soldati T. Vacuolins and myosin VII are required for phagocytic uptake and phagosomal membrane recycling in Dictyostelium discoideum. J Cell Sci 2020
  35. Bosshard L, Peischl S, Ackermann M, Excoffier L. Dissection of the mutation accumulation process during bacterial range expansions. BMC Genomics 2020;21(1):253
  36. Bou Sleiman M, Frochaux MV, Andreani T, Osman D, Guigo R, Deplancke B. Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes. Genome Biol 2020;21(1):4
  37. Bovay A, Nassiri S, Maby-El Hajjami H, Marcos Mondéjar P, Akondy RS, Ahmed R, Lawson B, Speiser DE, Fuertes Marraco SA. Minimal immune response to booster vaccination against Yellow Fever associated with pre-existing antibodies. Vaccine 2020;38(9):2172-2182
  38. Bresadola L, Link V, Buerkle CA, Lexer C, Wegmann D. Estimating and accounting for genotyping errors in RAD-seq experiments. Mol Ecol Resour 2020
  39. Buetti-Dinh A, Herold M, Christel S, El Hajjami M, Delogu F, Ilie O, Bellenberg S, Wilmes P, Poetsch A, Sand W, Vera M, Pivkin IV, Friedman R, Dopson M. Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. BMC Bioinformatics 2020;21(1):23
  40. Bye-A-Jee H, Zaru R, Magrane M, Orchard S, UniProt Consortium. Caenorhabditis elegans phosphatase complexes in UniProtKB and Complex Portal. FEBS J 2020
  41. Caputo T, Tran VDT, Bararpour N, Winkler C, Aguileta G, Trang KB, Giordano Attianese GMP, Wilson A, Thomas A, Pagni M, Guex N, Desvergne B, Gilardi F. Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue. Cell Mol Life Sci 2020
  42. Cardner M, Yalcinkaya M, Goetze S, Luca E, Balaz M, Hunjadi M, Hartung J, Shemet A, Kränkel N, Radosavljevic S, Keel M, Othman A, Karsai G, Hornemann T, Claassen M, Liebisch G, Carreira E, Ritsch A, Landmesser U, Krützfeldt J, Wolfrum C, Wollscheid B, Beerenwinkel N, Rohrer L, von Eckardstein A. Structure-function relationships of HDL in diabetes and coronary heart disease. JCI Insight 2020;5(1)
  43. Carl SH, Duempelmann L, Shimada Y, Bühler M. A fully automated deep learning pipeline for high-throughput colony segmentation and classification. Biol Open 2020;9(6)
  44. Carmona SJ, Siddiqui I, Bilous M, Held W, Gfeller D. Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. Oncoimmunology 2020;9(1):1737369
  45. Carrio-Cordo P, Acheson E, Huang Q, Baudis M. Geographic assessment of cancer genome profiling studies. Database (Oxford) 2020;2020
  46. Castro-Giner F, Aceto N. Tracking cancer progression: from circulating tumor cells to metastasis. Genome Med 2020;12(1):31
  47. Caucheteur D, Gobeill J, Mottaz A, Pasche E, Michel PA, Mottin L, Stekhoven DJ, Barbié V, Ruch P. Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. Stud Health Technol Inform 2020;270:884-888
  48. Ceriani L, Gritti G, Cascione L, Pirosa MC, Polino A, Ruberto T, Stathis A, Bruno A, Moccia AA, Giovanella L, Hayoz S, Schär S, Dirnhofer S, Rambaldi A, Martinelli G, Mamot C, Zucca E. SAKK38/07 study: integration of baseline metabolic heterogeneity and metabolic tumor volume in DLBCL prognostic model. Blood Adv 2020;4(6):1082-1092
  49. Chong C, Müller M, Pak H, Harnett D, Huber F, Grun D, Leleu M, Auger A, Arnaud M, Stevenson BJ, Michaux J, Bilic I, Hirsekorn A, Calviello L, Simó-Riudalbas L, Planet E, Lubiński J, Bryśkiewicz M, Wiznerowicz M, Xenarios I, Zhang L, Trono D, Harari A, Ohler U, Coukos G, Bassani-Sternberg M. Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nat Commun 2020;11(1):1293
  50. Chowdhury S, Happonen L, Khakzad H, Malmström L, Malmström J. Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria-human protein interactions. Med Microbiol Immunol 2020;209(3):265-275
  51. Coman Schmid D, Crameri K, Oesterle S, Rinn B, Sengstag T, Stockinger H, BioMedIT network team . SPHN - The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data. Stud Health Technol Inform 2020;270:1170-1174
  52. Contat C, Ancey PB, Zangger N, Sabatino S, Pascual J, Escrig S, Jensen L, Goepfert C, Lanz B, Lepore M, Gruetter R, Rossier A, Berezowska S, Neppl C, Zlobec I, Clerc-Rosset S, Knott GW, Rathmell JC, Abel ED, Meibom A, Meylan E. Combined deletion of Glut1 and Glut3 impairs lung adenocarcinoma growth. Elife 2020;9
  53. Cvitas I, Oberhänsli S, Leeb T, Dettwiler M, Müller E, Bruggman R, Marti EI. Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity. PLoS One 2020;15(4):e0232189
  54. Dąbrowska J, Keller I, Karamon J, Kochanowski M, Gottstein B, Cencek T, Frey CF, Müller N. Whole genome sequencing of a feline strain of Tritrichomonas foetus reveals massive genetic differences to bovine and porcine isolates. Int J Parasitol 2020;50(3):227-233
  55. Dainese R, Gardeux V, Llimos G, Alpern D, Jiang JY, Meireles-Filho ACA, Deplancke B. A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors. Proc Natl Acad Sci U S A 2020;117(24):13828-13838
  56. David FPA, Litovchenko M, Deplancke B, Gardeux V. ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. Nucleic Acids Res 2020;48(w1):W403-W414
  57. de Galan BE, McCrimmon RJ, Ibberson M, Heller SR, Choudhary P, Pouwer F, Speight J, Carlton J, Pieber TR, Rosilio M, Tack CJ, Müllenborn M, Hypo-RESOLVE Consortium. Reducing the burden of hypoglycaemia in people with diabetes through increased understanding: design of the Hypoglycaemia REdefining SOLutions for better liVEs (Hypo-RESOLVE) project. Diabet Med 2020;37(6):1066-1073
  58. de La Harpe R, Rüeger S, Kutalik Z, Ballabeni P, Suter M, Vionnet N, Laferrère B, Pralong F. Weight Loss Directly Influences Intermediate-Term Remission of Diabetes Mellitus After Bariatric Surgery: A Retrospective Case-Control Study. Obes Surg 2020;30(4):1332-1338
  59. de Las Fuentes L, Sung YJ, Noordam R, Winkler T, Feitosa MF, Schwander K, Bentley AR, Brown MR, Guo X, Manning A, Chasman DI, Aschard H, Bartz TM, Bielak LF, Campbell A, Cheng CY, Dorajoo R, Hartwig FP, Horimoto ARVR, Li C, Li-Gao R, Liu Y, Marten J, Musani SK, Ntalla I, Rankinen T, Richard M, Sim X, Smith AV, Tajuddin SM, Tayo BO, Vojinovic D, Warren HR, Xuan D, Alver M, Boissel M, Chai JF, Chen X, Christensen K, Divers J, Evangelou E, Gao C, Girotto G, Harris SE, He M, Hsu FC, Kühnel B, Laguzzi F, Li X, Lyytikäinen LP, Nolte IM, Poveda A, Rauramaa R, Riaz M, Rueedi R, Shu XO, Snieder H, Sofer T, Takeuchi F, Verweij N, Ware EB, Weiss S, Yanek LR, Amin N, Arking DE, Arnett DK, Bergmann S, Boerwinkle E, Brody JA, Broeckel U, Brumat M, Burke G, Cabrera CP, Canouil M, Chee ML, Chen YI, Cocca M, Connell J, de Silva HJ, de Vries PS, Eiriksdottir G, Faul JD, Fisher V, Forrester T, Fox EF, Friedlander Y, Gao H, Gigante B, Giulianini F, Gu CC, Gu D, Harris TB, He J, Heikkinen S, Heng CK, Hunt S, Ikram MA, Irvin MR, Kähönen M, Kavousi M, Khor CC, Kilpeläinen TO, Koh WP, Komulainen P, Kraja AT, Krieger JE, Langefeld CD, Li Y, Liang J, Liewald DCM, Liu CT, Liu J, Lohman KK, Mägi R, McKenzie CA, Meitinger T, Metspalu A, Milaneschi Y, Milani L, Mook-Kanamori DO, Nalls MA, Nelson CP, Norris JM, O'Connell J, Ogunniyi A, Padmanabhan S, Palmer ND, Pedersen NL, Perls T, Peters A, Petersmann A, Peyser PA, Polasek O, Porteous DJ, Raffel LJ, Rice TK, Rotter JI, Rudan I, Rueda-Ochoa OL, Sabanayagam C, Salako BL, Schreiner PJ, Shikany JM, Sidney SS, Sims M, Sitlani CM, Smith JA, Starr JM, Strauch K, Swertz MA, Teumer A, Tham YC, Uitterlinden AG, Vaidya D, van der Ende MY, Waldenberger M, Wang L, Wang YX, Wei WB, Weir DR, Wen W, Yao J, Yu B, Yu C, Yuan JM, Zhao W, Zonderman AB, Becker DM, Bowden DW, Deary IJ, Dörr M, Esko T, Freedman BI, Froguel P, Gasparini P, Gieger C, Jonas JB, Kammerer CM, Kato N, Lakka TA, Leander K, Lehtimäki T, Lifelines Cohort Study, Magnusson PKE, Marques-Vidal P, Penninx BWJH, Samani NJ, van der Harst P, Wagenknecht LE, Wu T, Zheng W, Zhu X, Bouchard C, Cooper RS, Correa A, Evans MK, Gudnason V, Hayward C, Horta BL, Kelly TN, Kritchevsky SB, Levy D, Palmas WR, Pereira AC, Province MM, Psaty BM, Ridker PM, Rotimi CN, Tai ES, van Dam RM, van Duijn CM, Wong TY, Rice K, Gauderman WJ, Morrison AC, North KE, Kardia SLR, Caulfield MJ, Elliott P, Munroe PB, Franks PW, Rao DC, Fornage M. Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci. Mol Psychiatry 2020
  60. De Vrieze M, Varadarajan AR, Schneeberger K, Bailly A, Rohr RP, Ahrens CH, Weisskopf L. Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight. Front Microbiol 2020;11:857
  61. Dehaene H, Praz V, Lhôte P, Lopes M, Herr W. THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation. PLoS One 2020;15(1):e0224646
  62. Dehasque M, Ávila-Arcos MC, Díez-Del-Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas AS, Marques-Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. Inference of natural selection from ancient DNA. Evol Lett 2020;4(2):94-108
  63. Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D, Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz S, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. Bioinformatics 2020;36(7):2098-2104
  64. Delucchi M, Schaper E, Sachenkova O, Elofsson A, Anisimova M. A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. Genes (Basel) 2020;11(4)
  65. Dheilly E, Battistello E, Katanayeva N, Sungalee S, Michaux J, Duns G, Wehrle S, Sordet-Dessimoz J, Mina M, Racle J, Farinha P, Coukos G, Gfeller D, Mottok A, Kridel R, Correia BE, Steidl C, Bassani-Sternberg M, Ciriello G, Zoete V, Oricchio E. Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma. Cancer Cell 2020;37(5):674-689.e12
  66. Dietrich LG, Barceló C, Thorball CW, Ryom L, Burkhalter F, Hasse B, Furrer H, Weisser M, Steffen A, Bernasconi E, Cavassini M, de Seigneux S, Csajka C, Fellay J, Ledergerber B, Tarr PE. Contribution of Genetic Background and Data Collection on Adverse Events of Anti-human Immunodeficiency Virus (HIV) Drugs (D:A:D) Clinical Risk Score to Chronic Kidney Disease in Swiss HIV-infected Persons With Normal Baseline Estimated Glomerular Filtration Rate. Clin Infect Dis 2020;70(5):890-897
  67. Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform 2020;4:210-220
  68. Dirmeier S, Dächert C, van Hemert M, Tas A, Ogando NS, van Kuppeveld F, Bartenschlager R, Kaderali L, Binder M, Beerenwinkel N. Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. PLoS Comput Biol 2020;16(2):e1007587
  69. Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Elixir Core Data Resource Forum , Blomberg N, Durinx C, McEntyre J. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinformatics 2020;36(8):2636-2642
  70. Du K, Stöck M, Kneitz S, Klopp C, Woltering JM, Adolfi MC, Feron R, Prokopov D, Makunin A, Kichigin I, Schmidt C, Fischer P, Kuhl H, Wuertz S, Gessner J, Kloas W, Cabau C, Iampietro C, Parrinello H, Tomlinson C, Journot L, Postlethwait JH, Braasch I, Trifonov V, Warren WC, Meyer A, Guiguen Y, Schartl M. The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol 2020;4(6):841-852
  71. Ducrest AL, Neuenschwander S, Schmid-Siegert E, Pagni M, Train C, Dylus D, Nevers Y, Warwick Vesztrocy A, San-Jose LM, Dupasquier M, Dessimoz C, Xenarios I, Roulin A, Goudet J. New genome assembly of the barn owl (Tyto alba alba). Ecol Evol 2020;10(5):2284-2298
  72. Duguet TB, Soichot J, Kuzyakiv R, Malmström L, Tritten L. Extracellular Vesicle-Contained microRNA of C. elegans as a Tool to Decipher the Molecular Basis of Nematode Parasitism. Front Cell Infect Microbiol 2020;10:217
  73. Dumayne C, Tarussio D, Sanchez-Archidona AR, Picard A, Basco D, Berney XP, Ibberson M, Thorens B. Klf6 protects β-cells against insulin resistance-induced dedifferentiation. Mol Metab 2020;35:100958
  74. Faiss R, Saugy J, Zollinger A, Robinson N, Schuetz F, Saugy M, Garnier PY. Prevalence Estimate of Blood Doping in Elite Track and Field Athletes During Two Major International Events. Front Physiol 2020;11:160
  75. Fassan M, Realdon S, Cascione L, Hahne JC, Munari G, Guzzardo V, Arcidiacono D, Lampis A, Brignola S, Dal Santo L, Agostini M, Bracon C, Maddalo G, Scarpa M, Farinati F, Zaninotto G, Valeri N, Rugge M. Circulating microRNA expression profiling revealed miR-92a-3p as a novel biomarker of Barrett's carcinogenesis. Pathol Res Pract 2020;216(5):152907
  76. Faurby S, Silvestro D, Werdelin L, Antonelli A. Brain expansion in early hominins predicts carnivore extinctions in East Africa. Ecol Lett 2020;23(3):537-544
  77. Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell 2020;181(5):990-996.e5
  78. Feron R, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Eché C, Valière S, Donnadieu C, Haffray P, Bestin A, Morvezen R, Acloque H, Euclide PT, Wen M, Jouano E, Schartl M, Postlethwait JH, Schraidt C, Christie MR, Larson WA, Herpin A, Guiguen Y. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. Mol Ecol Resour 2020;20(2):531-543
  79. Ferrario C, Czarkwiani A, Dylus DV, Piovani L, Candia Carnevali MD, Sugni M, Oliveri P. Extracellular matrix gene expression during arm regeneration in Amphiura filiformis. Cell Tissue Res 2020
  80. Fisch U, Brégère C, Geier F, Chicha L, Guzman R. Neonatal hypoxia-ischemia in rat elicits a region-specific neurotrophic response in SVZ microglia. J Neuroinflammation 2020;17(1):26
  81. Flissi A, Ricart E, Campart C, Chevalier M, Dufresne Y, Michalik J, Jacques P, Flahaut C, Lisacek F, Leclère V, Pupin M. Norine: update of the nonribosomal peptide resource. Nucleic Acids Res 2020;48(d1):D465-D469
  82. Fontana P, Ibberson M, Stevenson B, Wigger L, Daali Y, Niknejad A, Mach F, Docquier M, Xenarios I, Cuisset T, Alessi MC, Reny JL. Contribution of exome sequencing to the identification of genes involved in the response to clopidogrel in cardiovascular patients. J Thromb Haemost 2020;18(6):1425-1434
  83. Frochaux MV, Bou Sleiman M, Gardeux V, Dainese R, Hollis B, Litovchenko M, Braman VS, Andreani T, Osman D, Deplancke B. cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel. Genome Biol 2020;21(1):6
  84. Fujita S, De Bellis D, Edel KH, Köster P, Andersen TG, Schmid-Siegert E, Dénervaud Tendon V, Pfister A, Marhavý P, Ursache R, Doblas VG, Barberon M, Daraspe J, Creff A, Ingram G, Kudla J, Geldner N. SCHENGEN receptor module drives localized ROS production and lignification in plant roots. EMBO J 2020;39(9):e103894
  85. Gao B, Baudis M. Minimum error calibration and normalization for genomic copy number analysis. Genomics 2020
  86. Garcia L, Batut B, Burke ML, Kuzak M, Psomopoulos F, Arcila R, Attwood TK, Beard N, Carvalho-Silva D, Dimopoulos AC, Del Angel VD, Dumontier M, Gurwitz KT, Krause R, McQuilton P, Le Pera L, Morgan SL, Rauste P, Via A, Kahlem P, Rustici G, van Gelder CWG, Palagi PM. Ten simple rules for making training materials FAIR. PLoS Comput Biol 2020;16(5):e1007854
  87. Garofalo M, Grazioso G, Cavalli A, Sgrignani J. How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs. Molecules 2020;25(7)
  88. Gauthier J, Pajkovic M, Neuenschwander S, Kaila L, Schmid S, Orlando L, Alvarez N. Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland. Mol Ecol Resour 2020
  89. Geiger KM, Guignard D, Yang C, Bikorimana JP, Correia BE, Houard S, Mkindi C, Daubenberger CA, Spertini F, Corradin G, Audran R. Epitope Mapping and Fine Specificity of Human T and B Cell Responses for Novel Candidate Blood-Stage Malaria Vaccine P27A. Front Immunol 2020;11:412
  90. Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity. Nat Commun 2020;11(1):2680
  91. Giordano-Attianese G, Gainza P, Gray-Gaillard E, Cribioli E, Shui S, Kim S, Kwak MJ, Vollers S, Corria Osorio AJ, Reichenbach P, Bonet J, Oh BH, Irving M, Coukos G, Correia BE. A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy. Nat Biotechnol 2020;38(4):426-432
  92. Giordano-Attianese G, Gainza P, Gray-Gaillard E, Cribioli E, Shui S, Kim S, Kwak MJ, Vollers S, Corria Osorio AJ, Reichenbach P, Bonet J, Oh BH, Irving M, Coukos G, Correia BE. Author Correction: A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy. Nat Biotechnol 2020;38(4):503
  93. Gobeill J, Caucheteur D, Michel PA, Mottin L, Pasche E, Ruch P. SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. Nucleic Acids Res 2020;48(w1):W12-W16
  94. Gobeill J, Ruch P, Meyer R. Machine Learning for Automatic Encoding of French Electronic Medical Records: Is More Data Better? Stud Health Technol Inform 2020;270:312-316
  95. Gooding KM, Lienczewski C, Papale M, Koivuviita N, Maziarz M, Dutius Andersson AM, Sharma K, Pontrelli P, Garcia Hernandez A, Bailey J, Tobin K, Saunavaara V, Zetterqvist A, Shelley D, Teh I, Ball C, Puppala S, Ibberson M, Karihaloo A, Metsärinne K, Banks RE, Gilmour PS, Mansfield M, Gilchrist M, de Zeeuw D, Heerspink HJL, Nuutila P, Kretzler M, Welberry Smith M, Gesualdo L, Andress D, Grenier N, Shore AC, Gomez MF, Sourbron S, BEAt-DKD consortium. Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol. BMC Nephrol 2020;21(1):242
  96. Goulooze SC, Zwep LB, Vogt JE, Krekels EHJ, Hankemeier T, van den Anker JN, Knibbe CAJ. Beyond the Randomized Clinical Trial: Innovative Data Science to Close the Pediatric Evidence Gap. Clin Pharmacol Ther 2020;107(4):786-795
  97. Gouy A, Excoffier L. Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens. Mol Biol Evol 2020;37(5):1420-1433
  98. Graciotti M, Marino F, Pak H, Baumgaertner P, Thierry AC, Chiffelle J, Perez MAS, Zoete V, Harari A, Bassani-Sternberg M, Kandalaft LE. Deciphering the Mechanisms of Improved Immunogenicity of Hypochlorous Acid-Treated Antigens in Anti-Cancer Dendritic Cell-Based Vaccines. Vaccines (Basel) 2020;8(2)
  99. Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020;6(1):veaa004
  100. Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic Encryption of Digital Data Stored in Synthetic DNA. Angew Chem Int Ed Engl 2020;59(22):8476-8480
  101. Gumpinger AC, Rieck B, Grimm DG, International Headache Genetics Consortium, Borgwardt K. Network-guided search for genetic heterogeneity between gene pairs. Bioinformatics 2020
  102. Hanna N, Kicka S, Chiriano G, Harrison C, Sakouhi HO, Trofimov V, Kranjc A, Nitschke J, Pagni M, Cosson P, Hilbi H, Scapozza L, Soldati T. Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models. Front Microbiol 2020;11:266
  103. Hassan M, Moghadamrad S, Sorribas M, Muntet SG, Kellmann P, Trentesaux C, Fraudeau M, Nanni P, Wolski W, Keller I, Hapfelmeier S, Shroyer NF, Wiest R, Romagnolo B, De Gottardi A. Paneth cells promote angiogenesis and regulate portal hypertension in response to microbial signals. J Hepatol 2020
  104. Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res 2020;48(d1):D269-D276
  105. Hernandez-Valdes JA, van Gestel J, Kuipers OP. A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium. Nat Commun 2020;11(1):1203
  106. Herndon N, Shelton J, Gerischer L, Ioannidis P, Ninova M, Dönitz J, Waterhouse RM, Liang C, Damm C, Siemanowski J, Kitzmann P, Ulrich J, Dippel S, Oberhofer G, Hu Y, Schwirz J, Schacht M, Lehmann S, Montino A, Posnien N, Gurska D, Horn T, Seibert J, Vargas Jentzsch IM, Panfilio KA, Li J, Wimmer EA, Stappert D, Roth S, Schröder R, Park Y, Schoppmeier M, Chung HR, Klingler M, Kittelmann S, Friedrich M, Chen R, Altincicek B, Vilcinskas A, Zdobnov E, Griffiths-Jones S, Ronshaugen M, Stanke M, Brown SJ, Bucher G. Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC Genomics 2020;21(1):47
  107. Herrmann CJ, Schmidt R, Kanitz A, Artimo P, Gruber AJ, Zavolan M. PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing. Nucleic Acids Res 2020;48(d1):D174-D179
  108. Huang Q, Baudis M. Enabling population assignment from cancer genomes with SNP2pop. Sci Rep 2020;10(1):4846
  109. Kapheim KM, Jones BM, Pan H, Li C, Harpur BA, Kent CF, Zayed A, Ioannidis P, Waterhouse RM, Kingwell C, Stolle E, Avalos A, Zhang G, McMillan WO, Wcislo WT. Developmental plasticity shapes social traits and selection in a facultatively eusocial bee. Proc Natl Acad Sci U S A 2020;117(24):13615-13625
  110. Kieser S, Brown J, Zdobnov EM, Trajkovski M, McCue LA. ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. BMC Bioinformatics 2020;21(1):257
  111. Klemm F, Maas RR, Bowman RL, Kornete M, Soukup K, Nassiri S, Brouland JP, Iacobuzio-Donahue CA, Brennan C, Tabar V, Gutin PH, Daniel RT, Hegi ME, Joyce JA. Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells. Cell 2020;181(7):1643-1660.e17
  112. Knop J, Spilgies LM, Rufli S, Reinhart R, Vasilikos L, Yabal M, Owsley E, Jost PJ, Marsh RA, Wajant H, Robinson MD, Kaufmann T, Wong WW. Correction: TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP. Cell Death Dis 2020;11(1):56
  113. Koivula RW, Atabaki-Pasdar N, Giordano GN, White T, Adamski J, Bell JD, Beulens J, Brage S, Brunak S, De Masi F, Dermitzakis ET, Forgie IM, Frost G, Hansen T, Hansen TH, Hattersley A, Kokkola T, Kurbasic A, Laakso M, Mari A, McDonald TJ, Pedersen O, Rutters F, Schwenk JM, Teare HJA, Thomas EL, Vinuela A, Mahajan A, McCarthy MI, Ruetten H, Walker M, Pearson E, Pavo I, Franks PW, IMI DIRECT Consortium. The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes: an IMI DIRECT study. Diabetologia 2020;63(4):744-756
  114. Kong XD, Moriya J, Carle V, Pojer F, Abriata LA, Deyle K, Heinis C. De novo development of proteolytically resistant therapeutic peptides for oral administration. Nat Biomed Eng 2020;4(5):560-571
  115. Krauss J, Vikuk V, Young CA, Krischke M, Mueller MJ, Baerenfaller K. Epichloë Endophyte Infection rates and Alkaloid Content in Commercially Available Grass Seed Mixtures in Europe. Microorganisms 2020;8(4)
  116. Krempaska K, Barnowski S, Gavini J, Hobi N, Ebener S, Simillion C, Stokes A, Schliep R, Knudsen L, Geiser TK, Funke-Chambour M. Azithromycin has enhanced effects on lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients compared to controls [corrected]. Respir Res 2020;21(1):25
  117. Krempaska K, Barnowski S, Gavini J, Hobi N, Ebener S, Simillion C, Stokes A, Schliep R, Knudsen L, Geiser TK, Funke-Chambour M. Correction to: Azithromycin has enhanced effects on lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients compared to controls. Respir Res 2020;21(1):29
  118. Künzli M, Schreiner D, Pereboom TC, Swarnalekha N, Litzler LC, Lötscher J, Ertuna YI, Roux J, Geier F, Jakob RP, Maier T, Hess C, Taylor JJ, King CG. Long-lived T follicular helper cells retain plasticity and help sustain humoral immunity. Sci Immunol 2020;5(45)
  119. Kuo TCY, Hatakeyama M, Tameshige T, Shimizu KK, Sese J. Homeolog expression quantification methods for allopolyploids. Brief Bioinform 2020;21(2):395-407
  120. Kutalik Z. Commentary on: "the contribution of tissue-specific BMI-associated gene sets to cardiometabolic disease risk: a Mendelian randomization study". Int J Epidemiol 2020
  121. Labroussaa F, Thomann A, Nicholson P, Falquet L, Jores J. Complete Genome Sequence of Mycoplasma feriruminatoris Strain IVB14/OD_0535, Isolated from an Alpine Ibex in a Swiss Zoo. Microbiol Resour Announc 2020;9(12)
  122. Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Eleven grand challenges in single-cell data science. Genome Biol 2020;21(1):31
  123. Laloum D, Robinson-Rechavi M. Methods detecting rhythmic gene expression are biologically relevant only for strong signal. PLoS Comput Biol 2020;16(3):e1007666
  124. Lamrabet O, Melotti A, Burdet F, Hanna N, Perrin J, Nitschke J, Pagni M, Hilbi H, Soldati T, Cosson P. Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria. Front Microbiol 2020;11:410
  125. Lang BM, Kuipers J, Misselwitz B, Beerenwinkel N. Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. PLoS Comput Biol 2020;16(2):e1007552
  126. Lee HO, Hong Y, Etlioglu HE, Cho YB, Pomella V, Van den Bosch B, Vanhecke J, Verbandt S, Hong H, Min JW, Kim N, Eum HH, Qian J, Boeckx B, Lambrechts D, Tsantoulis P, De Hertogh G, Chung W, Lee T, An M, Shin HT, Joung JG, Jung MH, Ko G, Wirapati P, Kim SH, Kim HC, Yun SH, Tan IBH, Ranjan B, Lee WY, Kim TY, Choi JK, Kim YJ, Prabhakar S, Tejpar S, Park WY. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nat Genet 2020;52(6):594-603
  127. Lehal R, Zaric J, Vigolo M, Urech C, Frismantas V, Zangger N, Cao L, Berger A, Chicote I, Loubéry S, Choi SH, Koch U, Blacklow SC, Palmer HG, Bornhauser B, González-Gaitán M, Arsenijevic Y, Zoete V, Aster JC, Bourquin JP, Radtke F. Pharmacological disruption of the Notch transcription factor complex. Proc Natl Acad Sci U S A 2020
  128. Lehmann FM, von Burg N, Ivanek R, Teufel C, Horvath E, Peter A, Turchinovich G, Staehli D, Eichlisberger T, Gomez de Agüero M, Coto-Llerena M, Prchal-Murphy M, Sexl V, Bentires-Alj M, Mueller C, Finke D. Microbiota-induced tissue signals regulate ILC3-mediated antigen presentation. Nat Commun 2020;11(1):1794
  129. Leisle L, Xu Y, Fortea E, Lee S, Galpin JD, Vien M, Ahern CA, Accardi A, Bernèche S. Divergent Cl- and H+ pathways underlie transport coupling and gating in CLC exchangers and channels. Elife 2020;9
  130. Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 2020
  131. Liko D, Rzepiela A, Vukojevic V, Zavolan M, Hall MN. Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs. Proc Natl Acad Sci U S A 2020;117(3):1524-1532
  132. Lima WC, Gasteiger E, Marcatili P, Duek P, Bairoch A, Cosson P. The ABCD database: a repository for chemically defined antibodies. Nucleic Acids Res 2020;48(d1):D261-D264
  133. Logares R, Deutschmann IM, Junger PC, Giner CR, Krabberød AK, Schmidt TSB, Rubinat-Ripoll L, Mestre M, Salazar G, Ruiz-González C, Sebastián M, de Vargas C, Acinas SG, Duarte CM, Gasol JM, Massana R. Disentangling the mechanisms shaping the surface ocean microbiota. Microbiome 2020;8(1):55
  134. Love MI, Soneson C, Hickey PF, Johnson LK, Pierce NT, Shepherd L, Morgan M, Patro R. Tximeta: Reference sequence checksums for provenance identification in RNA-seq. PLoS Comput Biol 2020;16(2):e1007664
  135. MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin M, UniProt Consortium. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. Bioinformatics 2020
  136. Mahul-Mellier AL, Burtscher J, Maharjan N, Weerens L, Croisier M, Kuttler F, Leleu M, Knott GW, Lashuel HA. The process of Lewy body formation, rather than simply α-synuclein fibrillization, is one of the major drivers of neurodegeneration. Proc Natl Acad Sci U S A 2020;117(9):4971-4982
  137. Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. ISME J 2020;14(5):1247-1259
  138. Majic P, Payne JL. Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks. Mol Biol Evol 2020;37(4):1165-1178
  139. Malan-Müller S, de Souza VBC, Daniels WMU, Seedat S, Robinson MD, Hemmings SMJ. Shedding Light on the Transcriptomic Dark Matter in Biological Psychiatry: Role of Long Noncoding RNAs in D-cycloserine-Induced Fear Extinction in Posttraumatic Stress Disorder. OMICS 2020;24(6):352-369
  140. Manni M, Simao FA, Robertson HM, Gabaglio MA, Waterhouse RM, Misof B, Niehuis O, Szucsich NU, Zdobnov EM. The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations. Genome Biol Evol 2020;12(1):3534-3549
  141. Mapelli SN, Albino D, Mello-Grand M, Shinde D, Scimeca M, Bonfiglio R, Bonanno E, Chiorino G, Garcia-Escudero R, Catapano CV, Carbone GM. A Novel Prostate Cell Type-Specific Gene Signature to Interrogate Prostate Tumor Differentiation Status and Monitor Therapeutic Response (Running Title: Phenotypic Classification of Prostate Tumors). Cancers (Basel) 2020;12(1)
  142. Marass F, Castro-Giner F, Szczerba BM, Jahn K, Kuipers J, Aceto N, Beerenwinkel N. Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies. Recent Results Cancer Res 2020;215:347-368
  143. Marass F, Stephens D, Ptashkin R, Zehir A, Berger MF, Solit DB, Diaz LA, Tsui DWY. Fragment Size Analysis May Distinguish Clonal Hematopoiesis from Tumor-Derived Mutations in Cell-Free DNA. Clin Chem 2020;66(4):616-618
  144. Marazza A, Galli C, Fasana E, Sgrignani J, Burda P, Fassi EMA, Baumgartner M, Cavalli A, Molinari M. Endoplasmic Reticulum and Lysosomal Quality Control of Four Nonsense Mutants of Iduronate 2-Sulfatase Linked to Hunter's Syndrome. DNA Cell Biol 2020;39(2):226-234
  145. Mastelic-Gavillet B, Sarivalasis A, Lozano LE, Wyss T, Inoges S, de Vries IJM, Dartiguenave F, Jichlinski P, Derrè L, Coukos G, Melero I, Harari A, Romero P, Viganó S, Kandalaft LE. Quantitative and qualitative impairments in dendritic cell subsets of patients with ovarian or prostate cancer. Eur J Cancer 2020;135:173-182
  146. Mathony J, Harteveld Z, Schmelas C, Upmeier Zu Belzen J, Aschenbrenner S, Sun W, Hoffmann MD, Stengl C, Scheck A, Georgeon S, Rosset S, Wang Y, Grimm D, Eils R, Correia BE, Niopek D. Computational design of anti-CRISPR proteins with improved inhibition potency. Nat Chem Biol 2020;16(7):725-730
  147. Mattout A, Gaidatzis D, Padeken J, Schmid CD, Aeschimann F, Kalck V, Gasser SM. LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay. Nat Cell Biol 2020;22(5):579-590
  148. McCuaig S, Barras D, Mann EH, Friedrich M, Bullers SJ, Janney A, Garner LC, Domingo E, Koelzer VH, Delorenzi M, Tejpar S, Maughan TS, West NR, Powrie F. The Interleukin 22 Pathway Interacts with Mutant KRAS to Promote Poor Prognosis in Colon Cancer. Clin Cancer Res 2020
  149. Melior H, Maaß S, Li S, Förstner KU, Azarderakhsh S, Varadarajan AR, Stötzel M, Elhossary M, Barth-Weber S, Ahrens CH, Becher D, Evguenieva-Hackenberg E. The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes. mBio 2020;11(3)
  150. Meyer-Schaller N, Tiede S, Ivanek R, Diepenbruck M, Christofori G. A dual role of Irf1 in maintaining epithelial identity but also enabling EMT and metastasis formation of breast cancer cells. Oncogene 2020;39(24):4728-4740
  151. Meylan P, Dreos R, Ambrosini G, Groux R, Bucher P. EPD in 2020: enhanced data visualization and extension to ncRNA promoters. Nucleic Acids Res 2020;48(d1):D65-D69
  152. Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science 2020;368(6498):1460-1465
  153. Midgley SE, Benschop K, Dyrdak R, Mirand A, Bailly JL, Bierbaum S, Buderus S, Böttcher S, Eis-Hübinger AM, Hönemann M, Jensen VV, Hartling UB, Henquell C, Panning M, Thomsen MK, Hodcroft EB, Meijer A. Co-circulation of multiple enterovirus D68 subclades, including a novel B3 cluster, across Europe in a season of expected low prevalence, 2019/20. Euro Surveill 2020;25(2)
  154. Moerman F, Arquint A, Merkli S, Wagner A, Altermatt F, Fronhofer EA. Evolution under pH stress and high population densities leads to increased density-dependent fitness in the protist Tetrahymena thermophila. Evolution 2020;74(3):573-586
  155. Moerman F, Fronhofer EA, Wagner A, Altermatt F. Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila. Biol Lett 2020;16(6):20200244
  156. Moreno-Mayar JV, Korneliussen TS, Dalal J, Renaud G, Albrechtsen A, Nielsen R, Malaspinas AS. A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. Bioinformatics 2020;36(3):828-841
  157. Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, Bansal P, Bolleman J, Gasteiger E, de Castro E, Baratin D, Pozzato M, Xenarios I, Poux S, Redaschi N, Bridge A, UniProt Consortium. Enzyme annotation in UniProtKB using Rhea. Bioinformatics 2020;36(6):1896-1901
  158. Mounier N, Kutalik Z. bGWAS: an R package to perform Bayesian Genome Wide Association Studies. Bioinformatics 2020
  159. Mukhtar T, Breda J, Grison A, Karimaddini Z, Grobecker P, Iber D, Beisel C, van Nimwegen E, Taylor V. Tead transcription factors differentially regulate cortical development. Sci Rep 2020;10(1):4625
  160. Neher RA, Dyrdak R, Druelle V, Hodcroft EB, Albert J. Potential impact of seasonal forcing on a SARS-CoV-2 pandemic. Swiss Med Wkly 2020;150:w20224
  161. Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, Marcus von Reumont B, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera. Genome Biol Evol 2020
  162. Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Res 2020;9
  163. Orjuela S, Machlab D, Menigatti M, Marra G, Robinson MD. DAMEfinder: a method to detect differential allele-specific methylation. Epigenetics Chromatin 2020;13(1):25
  164. Orjuela S, Menigatti M, Schraml P, Kambakamba P, Robinson MD, Marra G. The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers. BMC Cancer 2020;20(1):290
  165. Øyås O, Borrell S, Trauner A, Zimmermann M, Feldmann J, Liphardt T, Gagneux S, Stelling J, Sauer U, Zampieri M. Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2020;117(15):8494-8502
  166. Paladin L, Schaeffer M, Gaudet P, Zahn-Zabal M, Michel PA, Piovesan D, Tosatto SCE, Bairoch A. The Feature-Viewer: a visualization tool for positional annotations on a sequence. Bioinformatics 2020;36(10):3244-3245
  167. Papili Gao N, Hartmann T, Fang T, Gunawan R. CALISTA: Clustering and LINEAGE Inference in Single-Cell Transcriptional Analysis. Front Bioeng Biotechnol 2020;8:18
  168. 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. Genomic basis for RNA alterations in cancer. Nature 2020;578(7793):129-136
  169. Pietrzak K, Kuzyakiv R, Simon R, Bolis M, Bär D, Aprigliano R, Theurillat JP, Sauter G, Santoro R. TIP5 primes prostate luminal cells for the oncogenic transformation mediated by PTEN-loss. Proc Natl Acad Sci U S A 2020;117(7):3637-3647
  170. Plank M, Perepelkina M, Müller M, Vaga S, Zou X, Bourgoint C, Berti M, Saarbach J, Haesendonckx S, Winssinger N, Aebersold R, Loewith R. Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9. Mol Cell Proteomics 2020;19(4):655-671
  171. Pondeville E, Puchot N, Parvy JP, Carissimo G, Poidevin M, Waterhouse RM, Marois E, Bourgouin C. Hemocyte-targeted gene expression in the female malaria mosquito using the hemolectin promoter from Drosophila. Insect Biochem Mol Biol 2020;120:103339
  172. Prieto-Godino LL, Silbering AF, Khallaf MA, Cruchet S, Bojkowska K, Pradervand S, Hansson BS, Knaden M, Benton R. Functional integration of "undead" neurons in the olfactory system. Sci Adv 2020;6(11):eaaz7238
  173. Putora PM, Baudis M, Beadle BM, El Naqa I, Giordano FA, Nicolay NH. Oncology Informatics: Status Quo and Outlook. Oncology 2020;98(6):329-331
  174. Racle J, Gfeller D. EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data. Methods Mol Biol 2020;2120:233-248
  175. Ragusa S, Prat-Luri B, González-Loyola A, Nassiri S, Squadrito ML, Guichard A, Cavin S, Gjorevski N, Barras D, Marra G, Lutolf MP, Perentes J, Corse E, Bianchi R, Wetterwald L, Kim J, Oliver G, Delorenzi M, De Palma M, Petrova TV. Antiangiogenic immunotherapy suppresses desmoplastic and chemoresistant intestinal tumors in mice. J Clin Invest 2020;130(3):1199-1216
  176. Rambousek L, Gschwind T, Lafourcade C, Paterna JC, Dib L, Fritschy JM, Fontana A. Aberrant expression of PAR bZIP transcription factors is associated with epileptogenesis, focus on hepatic leukemia factor. Sci Rep 2020;10(1):3760
  177. Ranallo-Benavidez TR, Jaron KS, Schatz MC. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun 2020;11(1):1432
  178. Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ, PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun 2020;11(1):729
  179. 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. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020;578(7793):102-111
  180. Riether C, Pabst T, Höpner S, Bacher U, Hinterbrandner M, Banz Y, Müller R, Manz MG, Gharib WH, Francisco D, Bruggmann R, van Rompaey L, Moshir M, Delahaye T, Gandini D, Erzeel E, Hultberg A, Fung S, de Haard H, Leupin N, Ochsenbein AF. Targeting CD70 with cusatuzumab eliminates acute myeloid leukemia stem cells in patients treated with hypomethylating agents. Nat Med 2020
  181. Roberts TM, Kaltenbach HM, Rudolf F. Development and optimisation of a defined high cell density yeast medium. Yeast 2020;37(5-6):336-347
  182. Rodius S, de Klein N, Jeanty C, Sánchez-Iranzo H, Crespo I, Ibberson M, Xenarios I, Dittmar G, Mercader N, Niclou SP, Azuaje F. Fisetin protects against cardiac cell death through reduction of ROS production and caspases activity. Sci Rep 2020;10(1):2896
  183. Rodríguez-Lorenzo S, Ferreira Francisco DM, Vos R, van Het Hof B, Rijnsburger M, Schroten H, Ishikawa H, Beaino W, Bruggmann R, Kooij G, de Vries HE. Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis. Acta Neuropathol Commun 2020;8(1):35
  184. Ruiz-González C, Mestre M, Estrada M, Sebastián M, Salazar G, Agustí S, Moreno-Ostos E, Reche I, Álvarez-Salgado XA, Morán XAG, Duarte CM, Sala MM, Gasol JM. Major imprint of surface plankton on deep ocean prokaryotic structure and activity. Mol Ecol 2020;29(10):1820-1838
  185. Rybiński M, Möller S, Sunnåker M, Lormeau C, Stelling J. TopoFilter: a MATLAB package for mechanistic model identification in systems biology. BMC Bioinformatics 2020;21(1):34
  186. Santos-Moreno J, Tasiudi E, Stelling J, Schaerli Y. Multistable and dynamic CRISPRi-based synthetic circuits. Nat Commun 2020;11(1):2746
  187. Sarah B, Laurent F, Heinz MS. Genome assembly of the ragweed leaf beetle: a step forward to better predict rapid evolution of a weed biocontrol agent to environmental novelties. Genome Biol Evol 2020
  188. Savary R, Dupuis C, Masclaux FG, Mateus ID, Rojas EC, Sanders IR. Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava. ISME J 2020;14(6):1333-1344
  189. Schairer R, Hall G, Zhang M, Cowan R, Baravalle R, Muskett FW, Coombs PJ, Mpamhanga C, Hale LR, Saxty B, Iwaszkiewicz J, Décaillet C, Perroud M, Carr MD, Thome M. Allosteric activation of MALT1 by its ubiquitin-binding Ig3 domain. Proc Natl Acad Sci U S A 2020;117(6):3093-3102
  190. Schmid-Siegert E, Richard S, Luraschi A, Mühlethaler K, Pagni M, Hauser PM. Expression pattern of the Pneumocystis jirovecii major surface glycoprotein superfamily in patients with pneumonia. J Infect Dis 2020
  191. Scire J, Nadeau S, Vaughan T, Brupbacher G, Fuchs S, Sommer J, Koch KN, Misteli R, Mundorff L, Götz T, Eichenberger T, Quinto C, Savic M, Meienberg A, Burkard T, Mayr M, Meier CA, Widmer A, Kuehl R, Egli A, Hirsch HH, Bassetti S, Nickel CH, Rentsch KS, Kübler W, Bingisser R, Battegay M, Tschudin-Sutter S, Stadler T. Reproductive number of the COVID-19 epidemic in Switzerland with a focus on the Cantons of Basel-Stadt and Basel-Landschaft. Swiss Med Wkly 2020;150:w20271
  192. Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Building an international consortium for tracking coronavirus health status. Nat Med 2020
  193. Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Publisher Correction: Building an international consortium for tracking coronavirus health status. Nat Med 2020
  194. Selmoni OM, Maitre D, Roux J, Wilkins LGE, Marques da Cunha L, Vermeirssen ELM, Knörr S, Robinson-Rechavi M, Wedekind C. Correction to: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae). BMC Genomics 2020;21(1):371
  195. Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang CI, Abriata LA, Kucharska I, Castoro G, Vollers SS, Galloux M, Dheilly E, Rosset S, Corthésy P, Georgeon S, Villard M, Richard CA, Descamps D, Delgado T, Oricchio E, Rameix-Welti MA, Más V, Ervin S, Eléouët JF, Riffault S, Bates JT, Julien JP, Li Y, Jardetzky T, Krey T, Correia BE. De novo protein design enables the precise induction of RSV-neutralizing antibodies. Science 2020;368(6492)
  196. Shaul ME, Eyal O, Guglietta S, Aloni P, Zlotnik A, Forkosh E, Levy L, Weber LM, Levin Y, Pomerantz A, Nechushtan H, Eruslanov E, Singhal S, Robinson MD, Krieg C, Fridlender ZG. Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis. FASEB J 2020;34(3):4204-4218
  197. Shaw LP, Wang AD, Dylus D, Meier M, Pogacnik G, Dessimoz C, Balloux F. The phylogenetic range of bacterial and viral pathogens of vertebrates. Mol Ecol 2020
  198. Sigrist CJ, Bridge A, Le Mercier P. A potential role for integrins in host cell entry by SARS-CoV-2. Antiviral Res 2020;177:104759
  199. Simon R, Lischer HEL, Pieńkowska-Schelling A, Keller I, Häfliger IM, Letko A, Schelling C, Lühken G, Drögemüller C. New genomic features of the polled intersex syndrome variant in goats unraveled by long-read whole-genome sequencing. Anim Genet 2020;51(3):439-448
  200. Sjaarda J, Gerstein HC, Kutalik Z, Mohammadi-Shemirani P, Pigeyre M, Hess S, Paré G. Influence of Genetic Ancestry on Human Serum Proteome. Am J Hum Genet 2020;106(3):303-314
  201. Spaltenstein J, van Dooren N, Pasquier G, Roduit N, Brenet M, Pasquier G, Gibaud B, Mildenberger P, Ratib O. A multicentric IT platform for storage and sharing of imaging-based radiation dosimetric data. Int J Comput Assist Radiol Surg 2020
  202. Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, Chen M, Cheng S, Childers C, Dinh H, Doddapaneni HV, Dugan S, Elpidina EN, Farrow DW, Friedrich M, Gibbs RA, Hall B, Han Y, Hardy RW, Holmes CJ, Hughes DST, Ioannidis P, Cheatle Jarvela AM, Johnston JS, Jones JW, Kronmiller BA, Kung F, Lee SL, Martynov AG, Masterson P, Maumus F, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Nelson DR, Oppert B, Panfilio KA, Paula DP, Pick L, Poelchau MF, Qu J, Reding K, Rhoades JH, Rhodes A, Richards S, Richter R, Robertson HM, Rosendale AJ, Tu ZJ, Velamuri AS, Waterhouse RM, Weirauch MT, Wells JT, Werren JH, Worley KC, Zdobnov EM, Gundersen-Rindal DE. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics 2020;21(1):227
  203. Spodzieja M, Kuncewicz K, Sieradzan A, Karczyńska A, Iwaszkiewicz J, Cesson V, Węgrzyn K, Zhukov I, Maszota-Zieleniak M, Michielin O, Speiser DE, Zoete V, Derré L, Rodziewicz-Motowidło S. Disulfide-Linked Peptides for Blocking BTLA/HVEM Binding. Int J Mol Sci 2020;21(2)
  204. Starikova EV, Tikhonova PO, Prianichnikov NA, Rands CM, Zdobnov EM, Ilina EN, Govorun VM. Phigaro: high-throughput prophage sequence annotation. Bioinformatics 2020;36(12):3882-3884
  205. Stibal M, Bradley JA, Edwards A, Hotaling S, Zawierucha K, Rosvold J, Lutz S, Cameron KA, Mikucki JA, Kohler TJ, Šabacká M, Anesio AM. Glacial ecosystems are essential to understanding biodiversity responses to glacier retreat. Nat Ecol Evol 2020;4(5):686-687
  206. Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T. QMEANDisCo-distance constraints applied on model quality estimation. Bioinformatics 2020;36(8):2647
  207. Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T. QMEANDisCo-distance constraints applied on model quality estimation. Bioinformatics 2020;36(6):1765-1771
  208. Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. Quantification of the overall contribution of gene-environment interaction for obesity-related traits. Nat Commun 2020;11(1):1385
  209. Sulc J, Winkler TW, Heid IM, Kutalik Z. Heterogeneity in Obesity: Genetic Basis and Metabolic Consequences. Curr Diab Rep 2020;20(1):1
  210. Sunagawa S, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 2020
  211. Tarantelli C, Lange M, Gaudio E, Cascione L, Spriano F, Kwee I, Arribas AJ, Rinaldi A, Jourdan T, Berthold M, Sturz A, Sperl C, Margheriti F, Scalise L, Gritti G, Rossi D, Stathis A, Liu N, Zucca E, Politz O, Bertoni F. Copanlisib synergizes with conventional and targeted agents including venetoclax in B- and T-cell lymphoma models. Blood Adv 2020;4(5):819-829
  212. Tavridou E, Schmid-Siegert E, Fankhauser C, Ulm R. UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis. PLoS Genet 2020;16(5):e1008797
  213. Teodoro D, Knafou J, Naderi N, Pasche E, Gobeill J, Arighi CN, Ruch P. UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database (Oxford) 2020;2020
  214. Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE, Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B, Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann M, Perry T, Peters RS, Poynton HC, Prpic NM, Qu J, Rotenberg D, Schal C, Schoville SD, Scully ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S. Gene content evolution in the arthropods. Genome Biol 2020;21(1):15
  215. Tiberi S, Robinson MD. BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty. Genome Biol 2020;21(1):69
  216. Tissières V, Geier F, Kessler B, Wolf E, Zeller R, Lopez-Rios J. Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits. Cell Rep 2020;31(1):107490
  217. Togninalli M, Seren Ü, Freudenthal JA, Monroe JG, Meng D, Nordborg M, Weigel D, Borgwardt K, Korte A, Grimm DG. AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. Nucleic Acids Res 2020;48(d1):D1063-D1068
  218. Tomasoni M, Gómez S, Crawford J, Zhang W, Choobdar S, Marbach D, Bergmann S. MONET: a toolbox integrating top-performing methods for network modularization. Bioinformatics 2020;36(12):3920-3921
  219. van Gestel J. Slow lane to collectivity. Nat Ecol Evol 2020;4(3):292-293
  220. Varadarajan AR, Goetze S, Pavlou MP, Grosboillot V, Shen Y, Loessner MJ, Ahrens CH, Wollscheid B. A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships. J Proteome Res 2020;19(4):1647-1662
  221. Vega-Rúa A, Marconcini M, Madec Y, Manni M, Carraretto D, Gomulski LM, Gasperi G, Failloux AB, Malacrida AR. Vector competence of Aedes albopictus populations for chikungunya virus is shaped by their demographic history. Commun Biol 2020;3(1):326
  222. Villaseñor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T. ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 2020;38(6):728-736
  223. Villaseñor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T. Publisher Correction: ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 2020;38(6):757
  224. Volery M, Scherz V, Jakob W, Bandeira D, Deggim-Messmer V, Lauber-Biason A, Wildhaber J, Falquet L, Curtis N, Zimmermann P. Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term. BMJ Open 2020;10(6):e036275
  225. Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Res 2020;9:136
  226. Walter J, Monthoux C, Fortes C, Grossmann J, Roschitzki B, Meili T, Riond B, Hofmann-Lehmann R, Naegeli H, Bleul U. The bovine cumulus proteome is influenced by maturation condition and maturational competence of the oocyte. Sci Rep 2020;10(1):9880
  227. Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, Feron R, Bérard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, Peery A, Phillippy AM, Sharakhova MV, Tannier E, Unger MF, Zhang SV, Alekseyev MA, Besansky NJ, Chauve C, Emrich SJ, Sharakhov IV. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biol 2020;18(1):1
  228. Weis CV, Jutzeler CR, Borgwardt K. Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review. Clin Microbiol Infect 2020
  229. Wuggenig P, Kaya B, Melhem H, Ayata CK, Swiss IBD Cohort Investigators, Hruz P, Sayan AE, Tsumura H, Ito M, Roux J, Niess JH. Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice. Commun Biol 2020;3(1):130
  230. Yordanov P, Stelling J, Otero-Muras I. BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks. Bioinformatics 2020;36(5):1640-1641
  231. Yordanov P, Stelling J. Efficient manipulation and generation of Kirchhoff polynomials for the analysis of non-equilibrium biochemical reaction networks. J R Soc Interface 2020;17(165):20190828
  232. Zahn-Zabal M, Dessimoz C, Glover NM. Identifying orthologs with OMA: A primer. F1000Res 2020;9:27
  233. Zahn-Zabal M, Lane L. What will neXtProt help us achieve in 2020 and beyond? Expert Rev Proteomics 2020;17(2):95-98
  234. Zahn-Zabal M, Michel PA, Gateau A, Nikitin F, Schaeffer M, Audot E, Gaudet P, Duek PD, Teixeira D, Rech de Laval V, Samarasinghe K, Bairoch A, Lane L. The neXtProt knowledgebase in 2020: data, tools and usability improvements. Nucleic Acids Res 2020;48(d1):D328-D334
  235. Zancolli G, Casewell NR. Venom systems as models for studying the origin and regulation of evolutionary novelties. Mol Biol Evol 2020
  236. Zhang S, Reljić B, Liang C, Kerouanton B, Francisco JC, Peh JH, Mary C, Jagannathan NS, Olexiouk V, Tang C, Fidelito G, Nama S, Cheng RK, Wee CL, Wang LC, Duek Roggli P, Sampath P, Lane L, Petretto E, Sobota RM, Jesuthasan S, Tucker-Kellogg L, Reversade B, Menschaert G, Sun L, Stroud DA, Ho L. Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly. Nat Commun 2020;11(1):1312
  237. Zile K, Dessimoz C, Wurm Y, Masel J. Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence. Genome Biol Evol 2020