Publications related to SARS-CoV-2/COVID-19 research

  1. Sauerhering L, Kupke A, Meier L, Dietzel E, Hoppe J, Gruber AD, Gattenloehner S, Witte B, Fink L, Hofmann N, Zimmermann T, Goesmann A, Nist A, Stiewe T, Becker S, Herold S Peteranderl C. Cyclophilin inhibitors restrict middle east respiratory syndrome coronavirus via interferon lambda In vitro and in mice. European Respiratory Journal 2020. DOI: https://doi.org/10.1183/13993003.01826-2019

  2. Korbel JO, Stegle O. Effects of the COVID-19 pandemic on life scientists. Genome Biol. 2020. DOI: https://doi.org/10.1186/s13059-020-02031-1

  3. Lukassen S, Chua RL, Trefzer T, Kahn NC, Schneider MA, Muley T, Winter H, Meister M, Veith C, Boots AW, Hennig BP, Kreuter M, Conrad C, Eils R. SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches. EMBO Journal 2020. DOI: https://doi.org/10.15252/embj.20105114

  4. Mészáros B, Sámano-Sánchez H, Alvarado-Valverde J, Čalyševa J, Martínez-Pérez E, Alves R, Kumar M, Rippmann F, Chemes LB, Gibson TJ. Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. Sci Signal. 2021 Jan 12;14(665):eabd0334. doi: 10.1126/scisignal.abd0334. PMID: 33436497.

  5. Chua, RL, Lukassen S, Trump S, Hennig BP, Wendisch D, Pott F, Debnath O, Thürmann L, Kurth F, Völker MT, Kazmierski J, Timmermann B, Twardziok S, Schneider S, Machleidt F, Müller-Redetzky H, Maier M, Krannich A, Schmidt S, Balzer F, Liebig J, Loske J, Suttorp N, Eils J, Ishaque N, Liebert UG, von Kalle C, Hocke A, Witzenrath M, Goffinet C, Drosten C, Laudi S, Lehmann I, Conrad C, Sander LE, Eils R. COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis. Nature Biotechnology 2020. DOI: https://doi.org/10.1038/s41587-020-0602-4

  6. Wyler E, Mösbauer K, Franke V, Diag A, Gottula LT, Arsie R, Klironomos F, Koppstein D, Ayoub S, Buccitelli C, Richter A, Legnini I, Ivanov A, Mari T, Del GS, Papies JP, Müller MA, Niemeyer D, Selbach M, Akalin A, Rajewsky N, Drosten C, Landthaler M. Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention. bioRxiv 2020. DOI: https://doi.org/10.1101/2020.05.05.079194

  7. Ellinghaus D. et al., for The Severe Covid-19 GWAS Group. Genomewide association study of severe Covid-19 with respiratory failure. N. Engl. J Med. 2020. DOI: https://doi.org/10.1056/NEJMoa2020283

  8. Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier A, Nekrutenko A, Taylor J, Weaver S. (2020) No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS Pathog 16(8): e1008643. https://doi.org/10.1371/journal.ppat.1008643

  9. Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R & Schneider R. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data 2020. DOI: https://doi.org/10.1038/s41597-020-0477-8

  10. Bej S, Wolkenhauer O. The timing of contact restrictions and pro-active testing balances the socio-economic impact of a lockdown with the control of infections. medRxiv 2020. DOI: https://doi.org/10.1101/2020.05.08.20095596

  11. Müller C, Hardt M, Schwudke D, Neuman BW, Pleschka S, Ziebuhr J. Inhibition of cytosolic phospholipase A2α impairs an early step of coronavirus replication in cell culture. J Virol. 2018. DOI: https://doi.org/10.1128/JVI.01463-17

  12. Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, . Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, K J. Lim, McBride T, O’Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The global phosphorylation landscape of SARS-CoV-2 infection. Cell 2020. DOI: https://doi.org/10.1016/j.cell.2020.06.034

  13. Warnat-Herresthal S, et al., and German COVID-19 OMICS Initiative (DeCOI). Swarm Learning as a privacy-preserving machine learning approach for disease classification, German COVID-19 OMICS Initiative (DeCOI), bioRxiv 2020, DOI: https://doi.org/10.1101/2020.06.25.171009

  14. Schulte-Schrepping J, et al., and Deutsche COVID-19 OMICS Initiative (DeCOI). Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment, DOI: 10.1016/j.cell.2020.08.001

  15. Voelkel G, Fuerstberger A, Schwab JD, Kuehlwein DS, Gscheidmeier T, Kraus JM, Gross A, Kohlmayer F, Kuhn P, Kuhn KA, Kohlbacher O, Seufferlein T, Kestler HA. A secure and rapid query-software for COVID-19 test results that can easily be integrated into the clinical workflow to avoid communication overload. medRxiv 2020, Doi: https://doi.org/10.1101/2020.04.07.20056887

  16. Trump S, Lukassen S, Anker MS, Chua RL, Liebig J, Thürmann L, Corman VM, Binder M, Loske J, Klasa C, Krieger TG, Hennig BP, Messingschlager M, Pott F, Kazmierski J, Twardziok S, Albrecht JP, Eils J, Hadzibegovic S, Lena A, Heidecker B, Bürgel T, Steinfeldt J, Goffinet C, Kurth F, Witzenrat M, Völker MT, Müller SD, Liebert UG, Ishaque N, Kaderali L, Sander LE, Drosten C, Laudi S, Eils R, Conrad C, Landmesser U, Lehmann I. Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-191, Nature Biotechnology DOI: 10.1038/s41587-020-00796-1

  17. Wittig A, Miranda F, Tang M, Hölzer M, Renard BY, Fuchs S. CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance,  bioRxiv 2021.02.03.429146; doi: https://doi.org/10.1101/2021.02.03.429146

  18. Guerler A, Baker D, van den Beek M, Grüning B, Bouvier B, Coraor N, Shank SD, Zehr JD, Schatz MC, Nekrutenko A. Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy,  bioRxiv 2021.03.17.435706v2; doi: https://doi.org/10.1101/2021.03.17.435706

  19. Gallardo-Alba C, Grüning B, Serrano-Solano B. A constructivist-based proposal for bioinformatics teaching practices during lockdown,  PLoS Comput Biol 17(5): e1008922; doi: https://doi.org/10.1371/journal.pcbi.1008922

  20. Serrano-Solano BC, Föll MC, Gallardo-Alba C, Erxleben A , Rasche H, Hiltemann S, Fahrner M, Dunning MJ, Schulz MH, Scholtz B, Clements D, Nekrutenko A, Batut B, Grüning B. Fostering accessible online education using Galaxy as an e-learning platform,  PLoS Comput Biol 17(5): e1008923; doi: https://doi.org/10.1371/journal.pcbi.1008923

  21. Brandt D, Simunovic M, Busche T, Haak M, Belmann P, Jünemann S, Schulz T, Klages LJ, Vinke S, Beckstette M, Pohl E, Scherer C, Sczyrba A, Kalinowski J. Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines. Viruses 2021, 13, 1870.https://doi.org/10.3390/v130918

  22. Mayer W, Bray S, Van den Beek M, Bouvier D, Coraor N, Miladi M, Singh B, Rambla De Argila J, Baker D,  Roach N, Gladman S, Coppens F, Martin D, Lonie A, Grüning B, Kosakovsky Pond SL & Nekrutenko A. Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-01069-1

  23. Loske J, Röhmel J, Lukassen S, Stricker S, Magalhães VG,  Liebig J, Chua RL, Thürmann L, Messingschlager M, Seegebarth A, Timmermann B, Klages S, Ralser M, Sawitzki B, Sander LE, Corman VM, Conrad C, Laudi S, Binder M, Trump S, Eils R, Mall MA & Lehmann I. Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-01037-9

  24. Schuhenn J, Meister TL, Todt D, Bracht T, Schork K, Billaud JN, Elsner C, Heinen N, Karakoese Z, Haid S, Kumar S, Brunotte L, Eisenacher M, Di Y, Lew J, Falzarano D, Chen J, Yuan Z, Pietschmann T, Wiegmann B, Uebner H, Taube C, Le-Trilling VTK, Trilling M, Krawczyk A, Ludwig S, Sitek B, Steinmann E, Dittmer U,  Lavender KJ, Sutter K and Pfaender. Differential interferon-α subtype induced immune signatures are associated with suppression of SARS-CoV-2 infection. https://doi.org/10.1073/pnas.2111600119

 Publications that cite use of de.NBI Cloud for SARS-CoV-2 / COVID-19 research

  1. Bartoszewicz JM, Seidel A, Renard BY. Interpretable detection of novel human viruses from genome sequencing data. bioRxiv 2020. DOI: https://doi.org/10.1101/2020.01.29.925354