COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Autor: Ostaszewski M; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Niarakis A; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.; Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France., Mazein A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Kuperstein I; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France., Phair R; Integrative Bioinformatics, Inc., Mountain View, CA, USA., Orta-Resendiz A; Institut Pasteur, Université de Paris, Unité HIV, Inflammation et Persistance, Paris, France.; Bio Sorbonne Paris Cité, Université de Paris, Paris, France., Singh V; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France., Aghamiri SS; Inserm- Institut national de la santé et de la recherche médicale, Paris, France., Acencio ML; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Glaab E; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Ruepp A; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany., Fobo G; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany., Montrone C; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany., Brauner B; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany., Frishman G; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany., Monraz Gómez LC; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France., Somers J; Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR, USA., Hoch M; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany., Kumar Gupta S; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany., Scheel J; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany., Borlinghaus H; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany., Czauderna T; Faculty of Information Technology, Department of Human-Centred Computing, Monash University, Clayton, Vic., Australia., Schreiber F; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; Faculty of Information Technology, Department of Human-Centred Computing, Monash University, Clayton, Vic., Australia., Montagud A; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Ponce de Leon M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Funahashi A; Department of Biosciences and Informatics, Keio University, Yokohama, Japan., Hiki Y; Department of Biosciences and Informatics, Keio University, Yokohama, Japan., Hiroi N; Graduate School of Media and Governance, Research Institute at SFC, Keio University, Kanagawa, Japan., Yamada TG; Department of Biosciences and Informatics, Keio University, Yokohama, Japan., Dräger A; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.; Department of Computer Science, University of Tübingen, Tübingen, Germany.; German Center for Infection Research (DZIF), partner site, Tübingen, Germany., Renz A; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.; Department of Computer Science, University of Tübingen, Tübingen, Germany., Naveez M; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.; Institute of Applied Computer Systems, Riga Technical University, Riga, Latvia., Bocskei Z; Sanofi R&D, Translational Sciences, Chilly-Mazarin, France., Messina F; Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S., Rome, Italy.; COVID-19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S, Rome, Italy., Börnigen D; Bioinformatics Core Facility, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany., Fergusson L; Royal (Dick) School of Veterinary Medicine, The University of Edinburgh, Edinburgh, UK., Conti M; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany., Rameil M; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany., Nakonecnij V; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany., Vanhoefer J; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany., Schmiester L; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.; Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany., Wang M; Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA., Ackerman EE; Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA., Shoemaker JE; Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA.; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA., Zucker J; Pacific Northwest National Laboratory, Richland, WA, USA., Oxford K; Pacific Northwest National Laboratory, Richland, WA, USA., Teuton J; Pacific Northwest National Laboratory, Richland, WA, USA., Kocakaya E; Stem Cell Institute, Ankara University, Ankara, Turkey., Summak GY; Stem Cell Institute, Ankara University, Ankara, Turkey., Hanspers K; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA., Kutmon M; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands., Coort S; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands., Eijssen L; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht University Medical Centre, Maastricht, The Netherlands., Ehrhart F; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht University Medical Centre, Maastricht, The Netherlands., Rex DAB; Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India., Slenter D; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands., Martens M; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands., Pham N; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands., Haw R; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada., Jassal B; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada., Matthews L; NYU Grossman School of Medicine, New York, NY, USA., Orlic-Milacic M; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada., Senff Ribeiro A; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.; Universidade Federal do Paraná, Curitiba, Brasil., Rothfels K; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada., Shamovsky V; NYU Grossman School of Medicine, New York, NY, USA., Stephan R; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada., Sevilla C; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK., Varusai T; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK., Ravel JM; INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, Nancy, France.; Laboratoire de génétique médicale, CHRU Nancy, Nancy, France., Fraser R; Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK., Ortseifen V; Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany., Marchesi S; Department of Surgical Science, Uppsala University, Uppsala, Sweden., Gawron P; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.; Institute of Computing Science, Poznan University of Technology, Poznan, Poland., Smula E; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Heirendt L; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Satagopam V; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Wu G; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA., Riutta A; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA., Golebiewski M; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany., Owen S; Department of Computer Science, The University of Manchester, Manchester, UK., Goble C; Department of Computer Science, The University of Manchester, Manchester, UK., Hu X; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany., Overall RW; German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany.; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.; Institute for Biology, Humboldt University of Berlin, Berlin, Germany., Maier D; Biomax Informatics AG, Planegg, Germany., Bauch A; Biomax Informatics AG, Planegg, Germany., Gyori BM; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, USA., Bachman JA; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, USA., Vega C; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Grouès V; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Vazquez M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Porras P; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK., Licata L; Department of Biology, University of Rome Tor Vergata, Rome, Italy., Iannuccelli M; Department of Biology, University of Rome Tor Vergata, Rome, Italy., Sacco F; Department of Biology, University of Rome Tor Vergata, Rome, Italy., Nesterova A; Elsevier, Philadelphia, PA, USA., Yuryev A; Elsevier, Philadelphia, PA, USA., de Waard A; Research Collaborations Unit, Elsevier, Jericho, VT, USA., Turei D; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany., Luna A; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Cell Biology, Harvard Medical School, Boston, MA, USA., Babur O; Computer Science Department, University of Massachusetts Boston, Boston, MA, USA., Soliman S; Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France., Valdeolivas A; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany., Esteban-Medina M; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain., Peña-Chilet M; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla, Spain., Rian K; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain., Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA., Puniya BL; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA., Modos D; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK., Treveil A; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK., Olbei M; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK., De Meulder B; European Institute for Systems Biology and Medicine (EISBM), Vourles, France., Ballereau S; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK., Dugourd A; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.; Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH, Aachen University, Aachen, Germany., Naldi A; Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France., Noël V; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France., Calzone L; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France., Sander C; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Cell Biology, Harvard Medical School, Boston, MA, USA., Demir E; Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR, USA., Korcsmaros T; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK., Freeman TC; The Roslin Institute, University of Edinburgh, Edinburgh, UK., Augé F; Sanofi R&D, Translational Sciences, Chilly-Mazarin, France., Beckmann JS; University of Lausanne, Lausanne, Switzerland., Hasenauer J; Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.; Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Bonn, Germany., Wolkenhauer O; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany., Wilighagen EL; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands., Pico AR; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA., Evelo CT; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands., Gillespie ME; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.; St. John's University College of Pharmacy and Health Sciences, Queens, NY, USA., Stein LD; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada., Hermjakob H; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK., D'Eustachio P; NYU Grossman School of Medicine, New York, NY, USA., Saez-Rodriguez J; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany., Dopazo J; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla, Spain.; FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain., Valencia A; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain., Kitano H; Systems Biology Institute, Tokyo, Japan.; Okinawa Institute of Science and Technology Graduate School, Okinawa, Japan., Barillot E; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France., Auffray C; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK., Balling R; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Schneider R; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
Jazyk: angličtina
Zdroj: Molecular systems biology [Mol Syst Biol] 2021 Oct; Vol. 17 (10), pp. e10387.
DOI: 10.15252/msb.202110387
Abstrakt: We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
(© 2021 The Authors. Published under the terms of the CC BY 4.0 license.)
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje