New Results
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
View ORCID ProfileMarek Ostaszewski, View ORCID ProfileAnna Niarakis, View ORCID ProfileAlexander Mazein, View ORCID ProfileInna Kuperstein, View ORCID ProfileRobert Phair, View ORCID ProfileAurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, View ORCID ProfileMarcio Luis Acencio, View ORCID ProfileEnrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frischman, Luis Cristóbal Monraz Gómez, Julia Somers, View ORCID ProfileMatti Hoch, View ORCID ProfileShailendra Kumar Gupta, View ORCID ProfileJulia Scheel, Hanna Borlinghaus, View ORCID ProfileTobias Czauderna, Falk Schreiber, View ORCID ProfileArnau Montagud, View ORCID ProfileMiguel Ponce de Leon, View ORCID ProfileAkira Funahashi, View ORCID ProfileYusuke Hiki, View ORCID ProfileNoriko Hiroi, View ORCID ProfileTakahiro G. Yamada, View ORCID ProfileAndreas Dräger, View ORCID ProfileAlina Renz, View ORCID ProfileMuhammad Naveez, View ORCID ProfileZsolt Bocskei, View ORCID ProfileFrancesco Messina, View ORCID ProfileDaniela Börnigen, View ORCID ProfileLiam Fergusson, View ORCID ProfileMarta Conti, Marius Rameil, Vanessa Nakonecnij, View ORCID ProfileJakob Vanhoefer, View ORCID ProfileLeonard Schmiester, Muying Wang, View ORCID ProfileEmily E. Ackerman, Jason Shoemaker, View ORCID ProfileJeremy Zucker, View ORCID ProfileKristie Oxford, View ORCID ProfileJeremy Teuton, View ORCID ProfileEbru Kocakaya, View ORCID ProfileGökçe Yağmur Summak, View ORCID ProfileKristina Hanspers, View ORCID ProfileMartina Kutmon, View ORCID ProfileSusan Coort, View ORCID ProfileLars Eijssen, View ORCID ProfileFriederike Ehrhart, View ORCID ProfileD. A. B. Rex, View ORCID ProfileDenise Slenter, View ORCID ProfileMarvin Martens, View ORCID ProfileRobin Haw, View ORCID ProfileBijay Jassal, View ORCID ProfileLisa Matthews, View ORCID ProfileMarija Orlic-Milacic, View ORCID ProfileAndrea Senff Ribeiro, View ORCID ProfileKaren Rothfels, View ORCID ProfileVeronica Shamovsky, View ORCID ProfileRalf Stephan, View ORCID ProfileCristoffer Sevilla, View ORCID ProfileThawfeek Varusai, View ORCID ProfileJean-Marie Ravel, View ORCID ProfileRupsha Fraser, View ORCID ProfileVera Ortseifen, Silvia Marchesi, View ORCID ProfilePiotr Gawron, Ewa Smula, View ORCID ProfileLaurent Heirendt, View ORCID ProfileVenkata Satagopam, View ORCID ProfileGuanming Wu, View ORCID ProfileAnders Riutta, View ORCID ProfileMartin Golebiewski, View ORCID ProfileStuart Owen, View ORCID ProfileCarole Goble, Xiaoming Hu, View ORCID ProfileRupert W. Overall, Dieter Maier, View ORCID ProfileAngela Bauch, View ORCID ProfileBenjamin M. Gyori, View ORCID ProfileJohn A. Bachman, View ORCID ProfileCarlos Vega, View ORCID ProfileValentin Grouès, View ORCID ProfileMiguel Vazquez, View ORCID ProfilePablo Porras, View ORCID ProfileLuana Licata, View ORCID ProfileMarta Iannuccelli, Francesca Sacco, View ORCID ProfileAnastasia Nesterova, Anton Yuryev, View ORCID ProfileAnita de Waard, View ORCID ProfileDenes Turei, View ORCID ProfileAugustin Luna, View ORCID ProfileOzgun Babur, View ORCID ProfileSylvain Soliman, View ORCID ProfileAlberto Valdeolivas, View ORCID ProfileMarina Esteban-Medina, View ORCID ProfileMaria Peña-Chilet, View ORCID ProfileTomáš Helikar, View ORCID ProfileBhanwar Lal Puniya, View ORCID ProfileDezso Modos, View ORCID ProfileAgatha Treveil, View ORCID ProfileMarton Olbei, View ORCID ProfileBertrand De Meulder, View ORCID ProfileAurélien Dugourd, View ORCID ProfileAurelien Naldi, View ORCID ProfileVincent Noel, View ORCID ProfileLaurence Calzone, View ORCID ProfileChris Sander, View ORCID ProfileEmek Demir, View ORCID ProfileTamas Korcsmaros, View ORCID ProfileTom C. Freeman, Franck Augé, View ORCID ProfileJacques S. Beckmann, View ORCID ProfileJan Hasenauer, View ORCID ProfileOlaf Wolkenhauer, View ORCID ProfileEgon L. Wilighagen, View ORCID ProfileAlexander R. Pico, View ORCID ProfileChris T. Evelo, View ORCID ProfileMarc E. Gillespie, View ORCID ProfileLincoln D. Stein, View ORCID ProfileHenning Hermjakob, View ORCID ProfilePeter D’Eustachio, View ORCID ProfileJulio Saez-Rodriguez, View ORCID ProfileJoaquin Dopazo, View ORCID ProfileAlfonso Valencia, Hiroaki Kitano, View ORCID ProfileEmmanuel Barillot, View ORCID ProfileCharles Auffray, View ORCID ProfileRudi Balling, View ORCID ProfileReinhard Schneider, the COVID-19 Disease Map Community
doi: https://doi.org/10.1101/2020.10.26.356014
Marek Ostaszewski
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Anna Niarakis
2Department of Biology, Univ. Evry, University of Paris-Saclay, GenHotel, Genopole, 91025, Evry, France
3Lifeware Group, Inria Saclay-Ile de France, Palaiseau 91120, France
Alexander Mazein
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Inna Kuperstein
4Institut Curie, PSL Research University, Paris, France. INSERM, U900, Paris, France
5MINES ParisTech, PSL Research University, Paris, France
Robert Phair
6Integrative Bioinformatics, Inc., 346 Paul Ave, Mountain View, CA, USA
Aurelio Orta-Resendiz
7Institut Pasteur, HIV, Inflammation and Persistence Unit, Paris, France
8Bio Sorbonne Paris Cité, Université de Paris, Paris, France
Vidisha Singh
2Department of Biology, Univ. Evry, University of Paris-Saclay, GenHotel, Genopole, 91025, Evry, France
Sara Sadat Aghamiri
9Inserm-Institut national de la santé et de la recherche médicale. Saint-Louis Hospital 1 avenue Claude Vellefaux Pavillon Bazin 75475 Paris
Marcio Luis Acencio
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Enrico Glaab
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Andreas Ruepp
10Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Gisela Fobo
10Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Corinna Montrone
10Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Barbara Brauner
10Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Goar Frischman
10Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Luis Cristóbal Monraz Gómez
4Institut Curie, PSL Research University, Paris, France. INSERM, U900, Paris, France
5MINES ParisTech, PSL Research University, Paris, France
Julia Somers
11Oregon Health & Sciences Univerity; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239
Matti Hoch
12Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Shailendra Kumar Gupta
12Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Julia Scheel
12Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Hanna Borlinghaus
13Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
Tobias Czauderna
14Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, Australia
Falk Schreiber
13Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
14Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, Australia
Arnau Montagud
15Barcelona Supercomputing Center (BSC), Barcelona, Spain
Miguel Ponce de Leon
15Barcelona Supercomputing Center (BSC), Barcelona, Spain
Akira Funahashi
16Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
Yusuke Hiki
16Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
Noriko Hiroi
16Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
17Sanyo-Onoda City University, Faculty of Pharmaceutical Sciences, University St.1-1-1, Yamaguchi, Japan 756-0884
Takahiro G. Yamada
16Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
Andreas Dräger
18Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
19Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
20German Center for Infection Research (DZIF), partner site Tübingen, Germany
Alina Renz
18Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
Muhammad Naveez
12Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
21Riga Technical University, Institute of Applied Computer Systems, 1 Kalku Street, LV-1658 Riga, Latvia
Zsolt Bocskei
22Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France
Francesco Messina
23Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases ‘Lazzaro Spallanzani’ I.R.C.C.S., Rome, Italy
24COVID 19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases ‘Lazzaro Spallanzani’ I.R.C.C.S., Rome, Italy
Daniela Börnigen
25Bioinformatics Core Facility, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
Liam Fergusson
26The University of Edinburgh, Royal (Dick) School of Veterinary Medicine, Easter Bush Campus, Midlothian, EH25 9RG
Marta Conti
27Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Marius Rameil
27Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Vanessa Nakonecnij
27Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Jakob Vanhoefer
27Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Leonard Schmiester
28Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany
29Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Garching, Germany
Muying Wang
30Department of Chemical and Petroleum Engineering, University of Pittsburgh
Emily E. Ackerman
30Department of Chemical and Petroleum Engineering, University of Pittsburgh
Jason Shoemaker
30Department of Chemical and Petroleum Engineering, University of Pittsburgh
31Department of Computational and Systems Biology, University of Pittsburgh
Jeremy Zucker
32Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, US
Kristie Oxford
32Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, US
Jeremy Teuton
32Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, US
Ebru Kocakaya
33Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere, Ankara, Turkey
Gökçe Yağmur Summak
33Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere, Ankara, Turkey
Kristina Hanspers
34Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, US
Martina Kutmon
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
36Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
Susan Coort
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Lars Eijssen
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
37Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
Friederike Ehrhart
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
37Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
D. A. B. Rex
38Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
Denise Slenter
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Marvin Martens
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Robin Haw
39Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Bijay Jassal
39Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Lisa Matthews
40NYU Grossman School of Medicine, New York NY 10016, US
Marija Orlic-Milacic
39Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Andrea Senff Ribeiro
39Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
41Universidade Federal do Paraná, Brasil
Karen Rothfels
39Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Veronica Shamovsky
42NYU Langone Medical Center, New York, USA
Ralf Stephan
39Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Cristoffer Sevilla
43EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
Thawfeek Varusai
43EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
Jean-Marie Ravel
44University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, F-54000 Nancy, France
45Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
Rupsha Fraser
46The University of Edinburgh, Queen’s Medical Research Institute. 47 Little France Crescent, Edinburgh, EH16 4TJ
Vera Ortseifen
47Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
Silvia Marchesi
48Uppsala University, Sweden
Piotr Gawron
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
49Poznan University of Technology, Institute of Computing Science, ul. Piotrowo 2, 60-965 Poznan, Poland
Ewa Smula
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Laurent Heirendt
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Venkata Satagopam
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Guanming Wu
50Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
Anders Riutta
34Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, US
Martin Golebiewski
51Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
Stuart Owen
52The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK
Carole Goble
52The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK
Xiaoming Hu
51Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
Rupert W. Overall
53German Center for Neurodegenerative Diseases (DZNE) Dresden, Tatzberg 41, 01307 Dresden, Germany
54Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
Dieter Maier
55Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany
Angela Bauch
55Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany
Benjamin M. Gyori
56Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA, US
John A. Bachman
56Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA, US
Carlos Vega
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Valentin Grouès
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Miguel Vazquez
15Barcelona Supercomputing Center (BSC), Barcelona, Spain
Pablo Porras
43EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
Luana Licata
57University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
Marta Iannuccelli
57University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
Francesca Sacco
57University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
Anastasia Nesterova
58Elsevier, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103, US
Anton Yuryev
58Elsevier, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103, US
Anita de Waard
59Elsevier, Research Collaborations Unit, 71 Hanley Lane, Jericho, VT 05465, US
Denes Turei
60Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Augustin Luna
61cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, US
62Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, US
Ozgun Babur
63University of Massachusetts Boston, Computer Science Department, 100 William T, Morrissey Blvd, Boston, MA 02125, US
Sylvain Soliman
3Lifeware Group, Inria Saclay-Ile de France, Palaiseau 91120, France
Alberto Valdeolivas
60Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Marina Esteban-Medina
64Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
65Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS). Hospital Virgen del Rocio, Sevilla 41013, Spain
Maria Peña-Chilet
64Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
65Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS). Hospital Virgen del Rocio, Sevilla 41013, Spain
66Bioinformatics in Rare Diseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain
Tomáš Helikar
67University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, US
Bhanwar Lal Puniya
67University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, US
Dezso Modos
68Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
69Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Agatha Treveil
68Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
69Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Marton Olbei
68Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
69Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Bertrand De Meulder
70European Institute for Systems Biology and Medicine (EISBM), Vourles, France
Aurélien Dugourd
60Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
71Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH, Aachen University, Aachen, Germany
Aurelien Naldi
3Lifeware Group, Inria Saclay-Ile de France, Palaiseau 91120, France
Vincent Noel
4Institut Curie, PSL Research University, Paris, France. INSERM, U900, Paris, France
Laurence Calzone
4Institut Curie, PSL Research University, Paris, France. INSERM, U900, Paris, France
5MINES ParisTech, PSL Research University, Paris, France
Chris Sander
61cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, US
62Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, US
Emek Demir
11Oregon Health & Sciences Univerity; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239
Tamas Korcsmaros
68Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
69Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Tom C. Freeman
72The Roslin Institute, University of Edinburgh EH25 9RG
Franck Augé
22Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France
Jacques S. Beckmann
73University of Lausanne, Lausanne, Switzerland
Jan Hasenauer
28Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany
74Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Germany
Olaf Wolkenhauer
12Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Egon L. Wilighagen
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Alexander R. Pico
34Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, US
Chris T. Evelo
35Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
36Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
Marc E. Gillespie
43EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
75St. John’s University College of Pharmacy and Health Sciences, Queens, NY USA
Lincoln D. Stein
39Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Henning Hermjakob
43EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
Peter D’Eustachio
40NYU Grossman School of Medicine, New York NY 10016, US
Julio Saez-Rodriguez
60Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Joaquin Dopazo
64Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
65Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS). Hospital Virgen del Rocio, Sevilla 41013, Spain
66Bioinformatics in Rare Diseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain
76FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, 42013, Spain
Alfonso Valencia
77Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
Hiroaki Kitano
78Systems Biology Institute, Tokyo Japan
79Okinawa Institute of Science and Technology Graduate School
Emmanuel Barillot
4Institut Curie, PSL Research University, Paris, France. INSERM, U900, Paris, France
5MINES ParisTech, PSL Research University, Paris, France
Charles Auffray
70European Institute for Systems Biology and Medicine (EISBM), Vourles, France
Rudi Balling
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Reinhard Schneider
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
80FAIRDOMHub:
Abstract
We hereby 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. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied to the contents of the COVID-19 Disease Map for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases.
Competing Interest Statement
D. Maier and A. Renz are employed at Biomax Informatics AG and will be affected by any effect of this publication on the commercial version of the AILANI software. J.A. Bachman and B. Gyori received consulting fees from Two Six Labs, LLC. T. Helikar has served as a shareholder and/or has consulted for Discovery Collective, Inc. R. Balling and R. Schneider are founders and shareholders of MEGENO S.A. and ITTM S.A. Remaining authors have declared no competing interests.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Posted October 28, 2020.
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frischman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. A. B. Rex, Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurélien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Augé, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D’Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community
bioRxiv 2020.10.26.356014; doi: https://doi.org/10.1101/2020.10.26.356014
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frischman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. A. B. Rex, Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurélien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Augé, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D’Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community
bioRxiv 2020.10.26.356014; doi: https://doi.org/10.1101/2020.10.26.356014
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