Publications by SIB Members published in 2020

Listed in Europe PMC, latest update: 2020-04-01.

Peer-reviewed articles and conference proceedings

Search

  1. Abriata LA, Lepore R, Dal Peraro M. About the need to make computational models of biological macromolecules available and discoverable. Bioinformatics 2020
  2. 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)
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. Bekkar A, Nasrallah A, Guex N, Fajas L, Xenarios I, Lopez-Mejia IC. PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. Bioinformatics 2020
  13. 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)
  14. 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
  15. 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)
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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)
  21. 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
  22. 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
  23. Cv W, Cr J, K B. Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review. Clin Microbiol Infect 2020
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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 2020:152907
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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:e103894
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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)
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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)
  61. 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
  62. 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
  63. 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)
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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)
  86. 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
  87. 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
  88. 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
  89. 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
  90. Tiberi S, Robinson MD. BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty. Genome Biol 2020;21(1):69
  91. 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
  92. 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
  93. 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
  94. Zahn-Zabal M, Dessimoz C, Glover NM. Identifying orthologs with OMA: A primer. F1000Res 2020;9:27
  95. Zahn-Zabal M, Lane L. What will neXtProt help us achieve in 2020 and beyond? Expert Rev Proteomics 2020;17(2):95-98
  96. 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
  97. 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