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, View ORCID ProfileSara Sadat Aghamiri, View ORCID ProfileMarcio Luis Acencio, View ORCID ProfileEnrico Glaab, View ORCID ProfileAndreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, View ORCID ProfileLuis Cristóbal Monraz Gómez, View ORCID ProfileJulia Somers, View ORCID ProfileMatti Hoch, View ORCID ProfileShailendra Kumar Gupta, View ORCID ProfileJulia Scheel, Hanna Borlinghaus, View ORCID ProfileTobias Czauderna, View ORCID ProfileFalk 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, View ORCID ProfileMarius Rameil, Vanessa Nakonecnij, View ORCID ProfileJakob Vanhoefer, View ORCID ProfileLeonard Schmiester, Muying Wang, View ORCID ProfileEmily E. Ackerman, View ORCID ProfileJason 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 ProfileNhung Pham, 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, View ORCID ProfileSilvia Marchesi, View ORCID ProfilePiotr Gawron, View ORCID ProfileEwa 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, View ORCID ProfileDieter 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, View ORCID ProfileFrancesca Sacco, View ORCID ProfileAnastasia Nesterova, View ORCID ProfileAnton 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 ProfileKinza Rian, 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 ProfileAurélien Naldi, View ORCID ProfileVincent Noë, View ORCID ProfileLaurence Calzone, View ORCID ProfileChris Sander, View ORCID ProfileEmek Demir, View ORCID ProfileTamas Korcsmaros, View ORCID ProfileTom C. Freeman, View ORCID ProfileFranck 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, View ORCID ProfileHiroaki 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
5INSERM, U900, Paris, France
6MINES ParisTech, PSL Research University, Paris, France
Robert Phair
7Integrative Bioinformatics, Inc., 346 Paul Ave, Mountain View, CA, USA
Aurelio Orta-Resendiz
8Institut Pasteur, HIV, Inflammation and Persistence Unit, Paris, France
9Bio 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
10Inserm- 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
11Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Gisela Fobo
11Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Corinna Montrone
11Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Barbara Brauner
11Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
Goar Frishman
11Institute 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
5INSERM, U900, Paris, France
6MINES ParisTech, PSL Research University, Paris, France
Julia Somers
12Oregon Health & Sciences University; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239
Matti Hoch
13Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Shailendra Kumar Gupta
13Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Julia Scheel
13Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Hanna Borlinghaus
14Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
Tobias Czauderna
15Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, Australia
Falk Schreiber
14Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
15Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, Australia
Arnau Montagud
16Barcelona Supercomputing Center (BSC), Barcelona, Spain
Miguel Ponce de Leon
16Barcelona Supercomputing Center (BSC), Barcelona, Spain
Akira Funahashi
17Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
Yusuke Hiki
17Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
Noriko Hiroi
17Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
18Sanyo-Onoda City University, Faculty of Pharmaceutical Sciences, University St.1-1-1, Yamaguchi, Japan 756-0884
Takahiro G. Yamada
17Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
Andreas Dräger
19Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
20Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
21German Center for Infection Research (DZIF), partner site Tübingen, Germany
Alina Renz
19Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
20Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
Muhammad Naveez
13Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
22Riga Technical University, Institute of Applied Computer Systems,1 Kalku Street, LV-1658 Riga, Latvia
Zsolt Bocskei
23Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France
Francesco Messina
24Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases ’Lazzaro Spallanzani’ I.R.C.C.S., Rome, Italy
25COVID 19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases ’Lazzaro Spallanzani’ I.R.C.C.S., Rome, Italy
Daniela Börnigen
26Bioinformatics Core Facility, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
Liam Fergusson
27The University of Edinburgh, Royal (Dick) School of Veterinary Medicine, Easter Bush Campus, Midlothian, EH25 9RG
Marta Conti
28Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Marius Rameil
28Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Vanessa Nakonecnij
28Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Jakob Vanhoefer
28Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Leonard Schmiester
28Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
30Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Garching, Germany
Muying Wang
31Department of Chemical and Petroleum Engineering, University of Pittsburgh
Emily E. Ackerman
31Department of Chemical and Petroleum Engineering, University of Pittsburgh
Jason Shoemaker
31Department of Chemical and Petroleum Engineering, University of Pittsburgh
32Department of Computational and Systems Biology, University of Pittsburgh
Jeremy Zucker
33Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, US
Kristie Oxford
33Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, US
Jeremy Teuton
33Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, US
Ebru Kocakaya
34Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere, Ankara, Turkey
Gökçe Yağmur Summak
34Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere, Ankara, Turkey
Kristina Hanspers
35Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, US
Martina Kutmon
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
37Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
Susan Coort
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Lars Eijssen
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
38Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
Friederike Ehrhart
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
38Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
D. A. B. Rex
39Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
Denise Slenter
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Marvin Martens
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Nhung Pham
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Robin Haw
40Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Bijay Jassal
40Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Lisa Matthews
41NYU Grossman School of Medicine, New York NY 10016, US
Marija Orlic-Milacic
40Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Andrea Senff Ribeiro
40Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
42Universidade Federal do Paraná, Brasil
Karen Rothfels
40Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
Veronica Shamovsky
41NYU Grossman School of Medicine, New York NY 10016, US
Ralf Stephan
40Ontario 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
48Department of Surgical Science, Uppsala 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
35Institute 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
16Barcelona Supercomputing Center (BSC), Barcelona, Spain
Pablo Porras
43EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
57Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
Luana Licata
58University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
Marta Iannuccelli
58University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
Francesca Sacco
58University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
Anastasia Nesterova
59Elsevier, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103, US
Anton Yuryev
59Elsevier, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103, US
Anita de Waard
60Elsevier, Research Collaborations Unit, 71 Hanley Lane, Jericho, VT 05465, US
Denes Turei
61Heidelberg University, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Augustin Luna
62cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, US
63Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, US
Ozgun Babur
64University 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
61Heidelberg University, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Marina Esteban- Medina
65Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
66Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS). Hospital Virgen del Rocio, Sevilla 41013, Spain
Maria Peña-Chilet
65Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
66Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS). Hospital Virgen del Rocio, Sevilla 41013, Spain
67Bioinformatics in Rare Diseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain
Kinza Rian
65Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
66Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS). Hospital Virgen del Rocio, Sevilla 41013, Spain
Tomáš Helikar
68University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, US
Bhanwar Lal Puniya
68University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, US
Dezso Modos
69Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
70Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Agatha Treveil
69Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
70Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Marton Olbei
69Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
70Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Bertrand De Meulder
71European Institute for Systems Biology and Medicine (EISBM), Vourles, France
Aurélien Dugourd
61Heidelberg University, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
72Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH, Aachen University, Aachen, Germany
Aurélien Naldi
3Lifeware Group, Inria Saclay-Ile de France, Palaiseau 91120, France
Vincent Noë
4Institut Curie, PSL Research University, Paris, France
5INSERM, U900, Paris, France
6MINES ParisTech, PSL Research University, Paris, France
Laurence Calzone
4Institut Curie, PSL Research University, Paris, France
5INSERM, U900, Paris, France
6MINES ParisTech, PSL Research University, Paris, France
Chris Sander
62cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, US
63Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, US
Emek Demir
12Oregon Health & Sciences University; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239
Tamas Korcsmaros
69Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
70Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Tom C. Freeman
73The Roslin Institute, University of Edinburgh EH25 9RG
Franck Augé
23Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France
Jacques S. Beckmann
74University of Lausanne, Lausanne, Switzerland
Jan Hasenauer
29Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany
75Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Germany
Olaf Wolkenhauer
13Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
Egon L. Wilighagen
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
Alexander R. Pico
35Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, US
Chris T. Evelo
36Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
37Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
Marc E. Gillespie
40Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
76StJohn’s University College of Pharmacy and Health Sciences, Queens, NY USA
Lincoln D. Stein
40Ontario 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
41NYU Grossman School of Medicine, New York NY 10016, US
Julio Saez-Rodriguez
61Heidelberg University, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Joaquin Dopazo
65Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
66Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS). Hospital Virgen del Rocio, Sevilla 41013, Spain
67Bioinformatics in Rare Diseases (BiER). Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain
77FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, 42013, Spain
Alfonso Valencia
16Barcelona Supercomputing Center (BSC), Barcelona, Spain
78Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
Hiroaki Kitano
79Systems Biology Institute, Tokyo Japan
80Okinawa Institute of Science and Technology Graduate School
Emmanuel Barillot
4Institut Curie, PSL Research University, Paris, France
5INSERM, U900, Paris, France
6MINES ParisTech, PSL Research University, Paris, France
Charles Auffray
71European 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
Abstract
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. 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 for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.
Competing Interest Statement
D. Maier and A. Bauch 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.
Footnotes
↵81 FAIRDOMHub: https://fairdomhub.org/projects/190
This version introduces small revisions of the authors' affiliations and ORCIDs
6 https://www.wikipathways.org/index.php/Help:Editing_Pathways
12 https://www.ebi.ac.uk/intact/imex/main.xhtml?query=annot:“dataset:coronavirus”
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 February 26, 2021.
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 Frishman, 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, Nhung Pham, 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, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurélien Dugourd, Aurélien Naldi, Vincent Noë, 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 Frishman, 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, Nhung Pham, 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, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurélien Dugourd, Aurélien Naldi, Vincent Noë, 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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