Peer-reviewed articles and conference proceedings

Listed in Europe PMC, latest update: 2020-10-08.
Discover the SIB Remarkable Outputs 2019

In 2019, the SIB Remarkable Outputs were launched to provide the global bioinformatics community with the 'must-reads' of the year by SIB Scientists. See here the last selection. The next edition of the SIB remarkable Output will be announced early next year.

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  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. Aguilar-Bultet L, Bagutti C, Egli A, Alt M, Maurer Pekerman L, Schindler R, Furger R, Eichenberger L, Roloff T, Steffen I, Huebner P, Stadler T, Tschudin-Sutter S. Identification of a cluster of Extended-Spectrum Beta-Lactamase producing Klebsiella pneumoniae sequence type 101 isolated from food and humans. Clin Infect Dis 2020
  5. Ahmed R, Crespo I, Tuyaerts S, Bekkar A, Graciotti M, Xenarios I, Kandalaft LE. Predicting combinations of immunomodulators to enhance dendritic cell-based vaccination based on a hybrid experimental and computational platform. Comput Struct Biotechnol J 2020;18:2217-2227
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. Arpat AB, Liechti A, De Matos M, Dreos R, Janich P, Gatfield D. Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing. Genome Res 2020;30(7):985-999
  17. 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
  18. 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
  19. Auray G, Talker SC, Keller I, Python S, Gerber M, Liniger M, Ganges L, Bruggmann R, Ruggli N, Summerfield A. High-Resolution Profiling of Innate Immune Responses by Porcine Dendritic Cell Subsets in vitro and in vivo. Front Immunol 2020;11:1429
  20. 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
  21. 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
  22. 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
  23. 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
  24. Barido-Sottani J, Vaughan TG, Stadler T. A Multitype Birth-Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates. Syst Biol 2020;69(5):973-986
  25. Bartel J, Varadarajan AR, Sura T, Ahrens CH, Maaß S, Becher D. Optimized Proteomics Workflow for the Detection of Small Proteins. J Proteome Res 2020
  26. Barut GT, Lischer HEL, Bruggmann R, Summerfield A, Talker SC. Transcriptomic profiling of bovine blood dendritic cells and monocytes following TLR stimulation. Eur J Immunol 2020
  27. Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Seattle Flu Study Investigators, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington state. Science 2020
  28. Bekkar A, Nasrallah A, Guex N, Fajas L, Xenarios I, Lopez-Mejia IC. PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. Bioinformatics 2020
  29. 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)
  30. 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
  31. Bignucolo O, Bernèche S. The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix. Front Mol Biosci 2020;7:162
  32. 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
  33. 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
  34. Boesch M, Baty F, Brutsche MH, Tamm M, Roux J, Knudsen L, Gazdhar A, Geiser T, Khan P, Hostettler KE. Transcriptomic profiling reveals disease-specific characteristics of epithelial cells in idiopathic pulmonary fibrosis. Respir Res 2020;21(1):165
  35. 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
  36. 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)
  37. 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)
  38. Bonhoure N, Praz V, Moir RD, Willemin G, Mange F, Moret C, Willis IM, Hernandez N. MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse. Sci Rep 2020;10(1):11956
  39. Bonnardel F, Perez S, Lisacek F, Imberty A. Structural Database for Lectins and the UniLectin Web Platform. Methods Mol Biol 2020;2132:1-14
  40. 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
  41. 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
  42. Boskova V, Stadler T. PIQMEE: Bayesian phylodynamic method for analysis of large datasets with duplicate sequences. Mol Biol Evol 2020
  43. 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;133(13)
  44. Bosshard L, Peischl S, Ackermann M, Excoffier L. Dissection of the mutation accumulation process during bacterial range expansions. BMC Genomics 2020;21(1):253
  45. 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
  46. Bouchemousse S, Falquet L, Müller-Schärer H, Eyre-Walker A. 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;12(7):1167-1173
  47. Bouchemousse S, Falquet L, Müller-Schärer H. 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;12(7):1167-1173
  48. 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
  49. Bovay A, Zoete V, Rizkallah PJ, Beck K, Delbreil P, Speiser DE, Cole DK, Fuertes Marraco SA. Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b 214-222 by combinatorial peptide library screening. Mol Immunol 2020;125:43-50
  50. Bresadola L, Link V, Buerkle CA, Lexer C, Wegmann D. Estimating and accounting for genotyping errors in RAD-seq experiments. Mol Ecol Resour 2020;20(4):856-870
  51. Breuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti ML, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, Wang LS, Wu E, Orchard S, IMEx Consortium, UniProt Consortium. A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. J Alzheimers Dis 2020;77(1):257-273
  52. 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
  53. Buetti-Dinh A, Herold M, Christel S, Hajjami ME, Bellenberg S, Ilie O, Wilmes P, Poetsch A, Sand W, Vera M, Pivkin IV, Dopson M. Systems biology of acidophile biofilms for efficient metal extraction. Sci Data 2020;7(1):215
  54. Burger J, Link V, Blöcher J, Schulz A, Sell C, Pochon Z, Diekmann Y, Žegarac A, Hofmanová Z, Winkelbach L, Reyna-Blanco CS, Bieker V, Orschiedt J, Brinker U, Scheu A, Leuenberger C, Bertino TS, Bollongino R, Lidke G, Stefanović S, Jantzen D, Kaiser E, Terberger T, Thomas MG, Veeramah KR, Wegmann D. Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years. Curr Biol 2020
  55. Bye-A-Jee H, Zaru R, Magrane M, Orchard S, UniProt Consortium. Caenorhabditis elegans phosphatase complexes in UniProtKB and Complex Portal. FEBS J 2020;287(13):2664-2684
  56. Cano AV, Payne JL. Mutation bias interacts with composition bias to influence adaptive evolution. PLoS Comput Biol 2020;16(9):e1008296
  57. 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
  58. 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)
  59. 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)
  60. 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
  61. Carrio-Cordo P, Acheson E, Huang Q, Baudis M. Geographic assessment of cancer genome profiling studies. Database (Oxford) 2020;2020
  62. Carroll LM, Huisman JS, Wiedmann M. Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State. Sci Rep 2020;10(1):14428
  63. Cassotta A, Paparoditis P, Geiger R, Mettu RR, Landry SJ, Donati A, Benevento M, Foglierini M, Lewis DJM, Lanzavecchia A, Sallusto F. Deciphering and predicting CD4+ T cell immunodominance of influenza virus hemagglutinin. J Exp Med 2020;217(10)
  64. Castanon I, Hannich JT, Abrami L, Huber F, Dubois M, Müller M, van der Goot FG, Gonzalez-Gaitan M. Wnt-controlled sphingolipids modulate Anthrax Toxin Receptor palmitoylation to regulate oriented mitosis in zebrafish. Nat Commun 2020;11(1):3317
  65. Castro-Giner F, Aceto N. Tracking cancer progression: from circulating tumor cells to metastasis. Genome Med 2020;12(1):31
  66. 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
  67. 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
  68. Ceriani L, Milan L, Virili C, Cascione L, Paone G, Trimboli P, Giovanella L. Radiomics Analysis of [18F]-Fluorodeoxyglucose-Avid Thyroid Incidentalomas Improves Risk Stratification and Selection for Clinical Assessment. Thyroid 2020
  69. Chartoumpekis DV, Ziros PG, Georgakopoulos-Soares I, Smith AAT, Marques AC, Ibberson M, A Kopp P, Habeos I, Trougakos IP, Khoo NKH, Sykiotis GP. The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System. Antioxidants (Basel) 2020;9(9)
  70. Chen Q, Britto R, Erill I, Jeffery CJ, Liberzon A, Magrane M, Onami JI, Robinson-Rechavi M, Sponarova J, Zobel J, Verspoor K. Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genomics Proteomics Bioinformatics 2020
  71. Chiffelle J, Genolet R, Perez MA, Coukos G, Zoete V, Harari A. T-cell repertoire analysis and metrics of diversity and clonality. Curr Opin Biotechnol 2020;65:284-295
  72. Choi M, Carver J, Chiva C, Tzouros M, Huang T, Tsai TH, Pullman B, Bernhardt OM, Hüttenhain R, Teo GC, Perez-Riverol Y, Muntel J, Müller M, Goetze S, Pavlou M, Verschueren E, Wollscheid B, Nesvizhskii AI, Reiter L, Dunkley T, Sabidó E, Bandeira N, Vitek O. MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nat Methods 2020
  73. 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
  74. 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
  75. 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
  76. 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
  77. Cowan CS, Renner M, De Gennaro M, Gross-Scherf B, Goldblum D, Hou Y, Munz M, Rodrigues TM, Krol J, Szikra T, Cuttat R, Waldt A, Papasaikas P, Diggelmann R, Patino-Alvarez CP, Galliker P, Spirig SE, Pavlinic D, Gerber-Hollbach N, Schuierer S, Srdanovic A, Balogh M, Panero R, Kusnyerik A, Szabo A, Stadler MB, Orgül S, Picelli S, Hasler PW, Hierlemann A, Scholl HPN, Roma G, Nigsch F, Roska B. Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution. Cell 2020;182(6):1623-1640.e34
  78. 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
  79. 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
  80. 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
  81. 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
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