A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms - Inria - Institut national de recherche en sciences et technologies du numérique
Pré-Publication, Document De Travail Année : 2022

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Anna Niarakis (1, 2) , Marek Ostaszewski (3) , Alexander Mazein (3) , Inna Kuperstein (4, 5) , Martina Kutmon (6) , Marc E Gillespie (7) , Akira Funahashi (8) , Marcio Luis Acencio (9) , Ahmed Hemedan (9) , Michael Aichem (10) , Karsten Klein (10) , Tobias Czauderna (11) , Felicia Burtscher (3) , Takahiro G Yamada (8) , Yusuke Hiki (8) , Noriko F Hiroi (8, 12) , Finterly Hu (6) , Nhung Pham (6) , Friederike Ehrhart (13) , Egon L Willighagen (13) , Alberto Valdeolivas (14) , Aurelien Dugourd (14) , Francesco Messina (15) , Marina Esteban-Medina (16) , Maria Pena-Chilet (17, 16) , Kinza Rian , Sylvain Soliman (1) , Sara Sadat Aghamiri (18) , Bhanwar Lal Puniya (18) , Aurelien Naldi (1) , Tomas Helikar (18) , Vidisha Singh (2) , Marco Farinas Fernandez (19) , Viviam Bermudez (19) , Eirini Tsirvouli (19) , Arnau Montagud (20) , Vincent Noel (4, 5) , Miguel Ponce de Leon (20) , Dieter Maier , Angela Bauch , Benjamin M Gyori (21) , John A Bachman (21) , Agustin Luna (21) , Janet Pinero (22) , Laura I Furlong (22) , Irina Balaur (3) , Adrien Rougny (23) , Yohan Jarosz (3) , Rupert W Overall (24) , Robert Phair (25) , Livia Perfetto (26) , Lisa Matthews (27) , Devasahayam Arokia Balaya Rex (28) , Marija Orlic-Milacic , Luis Cristobal Monraz Gomez , Bertrand de Meulder , Jean Marie Ravel , Bijay Jassal , Venkata P Satagopam , Guanming Wu , Martin Golebiewski , Piotr Gawron , Laurence Calzone , Jacques S Beckmann , Chris T Evelo , Peter d'Eustachio , Falk Schreiber , Julio Saez-Rodriguez , Joaquin Dopazo , Martin Kuiper , Alfonso Valencia , Olaf Wolkenhauer , Hiroaki Kitano , Emmanuel Barillot , Charles Auffray , Rudi Balling , Reinhard Schneider
1 Lifeware - Computational systems biology and optimization
2 GenHotel - Laboratoire de recherche européen pour la polyarthrite rhumatoïde
3 uni.lu - Université du Luxembourg = University of Luxembourg = Universität Luxemburg
4 Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe
5 PSL - Université Paris Sciences et Lettres
6 MaCSBio - Maastricht Centre for Systems Biology [Maastricht]
7 OICR - Ontario Institute for Cancer Research [Canada]
8 Keio University [Tokyo]
9 LCSB - Luxembourg Centre For Systems Biomedicine
10 University of Konstanz
11 Hochschule Mittweida - University of Applied Sciences
12 Kanagawa Institute of Technology
13 Maastricht University [Maastricht]
14 Heidelberg University Hospital [Heidelberg]
15 National Institute for Infectious Diseases "Lazzaro Spallanzani"
16 Hospital Universitario Virgen del Rocío [Sevilla]
17 Biomedicine Institute of Sevilla [Seville, Spain]
18 University of Nebraska–Lincoln
19 NTNU - Norwegian University of Science and Technology [Trondheim]
20 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
21 HMS - Harvard Medical School [Boston]
22 UPF - Universitat Pompeu Fabra [Barcelona]
23 AIST - National Institute of Advanced Industrial Science and Technology
24 HU Berlin - Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
25 Integrative Bioinformatics Inc [Mountain View]
26 Sapienza University of Rome - Department of Informatics and System Sciences
27 NYU Langone Medical Center - New York University Langone Medical Center
28 Yenepoya University
Anna Niarakis
Computational systems biology and optimization
Laboratoire de recherche européen pour la polyarthrite rhumatoïde
CV
Marek Ostaszewski
Université du Luxembourg = University of Luxembourg = Universität Luxemburg
Alexander Mazein
Université du Luxembourg = University of Luxembourg = Universität Luxemburg
Inna Kuperstein
Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe
Université Paris Sciences et Lettres
Martina Kutmon
Maastricht Centre for Systems Biology [Maastricht]
Marc E Gillespie
Ontario Institute for Cancer Research [Canada]
Akira Funahashi
Keio University [Tokyo]
Marcio Luis Acencio
Luxembourg Centre For Systems Biomedicine
Ahmed Hemedan
Luxembourg Centre For Systems Biomedicine
Michael Aichem
University of Konstanz
Karsten Klein
University of Konstanz
Tobias Czauderna
Hochschule Mittweida - University of Applied Sciences
Felicia Burtscher
Université du Luxembourg = University of Luxembourg = Universität Luxemburg
Takahiro G Yamada
Keio University [Tokyo]
Yusuke Hiki
Keio University [Tokyo]
Noriko F Hiroi
Keio University [Tokyo]
Kanagawa Institute of Technology
Finterly Hu
Maastricht Centre for Systems Biology [Maastricht]
Nhung Pham
Maastricht Centre for Systems Biology [Maastricht]
Friederike Ehrhart
Maastricht University [Maastricht]
Egon L Willighagen
Maastricht University [Maastricht]
Alberto Valdeolivas
Heidelberg University Hospital [Heidelberg]
Aurelien Dugourd
  • Fonction : Auteur
Heidelberg University Hospital [Heidelberg]
Francesco Messina
National Institute for Infectious Diseases "Lazzaro Spallanzani"
Marina Esteban-Medina
Hospital Universitario Virgen del Rocío [Sevilla]
Maria Pena-Chilet
Biomedicine Institute of Sevilla [Seville, Spain]
Hospital Universitario Virgen del Rocío [Sevilla]
Kinza Rian
Sylvain Soliman
Computational systems biology and optimization
CV
Sara Sadat Aghamiri
University of Nebraska–Lincoln
Bhanwar Lal Puniya
  • Fonction : Auteur
University of Nebraska–Lincoln
Aurelien Naldi
Computational systems biology and optimization
Tomas Helikar
University of Nebraska–Lincoln
Vidisha Singh
Laboratoire de recherche européen pour la polyarthrite rhumatoïde
Marco Farinas Fernandez
Norwegian University of Science and Technology [Trondheim]
Viviam Bermudez
  • Fonction : Auteur
Norwegian University of Science and Technology [Trondheim]
Eirini Tsirvouli
Norwegian University of Science and Technology [Trondheim]
Arnau Montagud
Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
Vincent Noel
Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe
Université Paris Sciences et Lettres
Miguel Ponce de Leon
Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
Dieter Maier
Angela Bauch
Benjamin M Gyori
Harvard Medical School [Boston]
John A Bachman
Harvard Medical School [Boston]
Agustin Luna
  • Fonction : Auteur
Harvard Medical School [Boston]
Janet Pinero
  • Fonction : Auteur
Universitat Pompeu Fabra [Barcelona]
Laura I Furlong
Universitat Pompeu Fabra [Barcelona]
Irina Balaur
Université du Luxembourg = University of Luxembourg = Universität Luxemburg
Adrien Rougny
National Institute of Advanced Industrial Science and Technology
Yohan Jarosz
Université du Luxembourg = University of Luxembourg = Universität Luxemburg
Rupert W Overall
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
Robert Phair
Integrative Bioinformatics Inc [Mountain View]
Livia Perfetto
Department of Informatics and System Sciences
Lisa Matthews
  • Fonction : Auteur
New York University Langone Medical Center
Devasahayam Arokia Balaya Rex
Yenepoya University
Marija Orlic-Milacic
Luis Cristobal Monraz Gomez
Bertrand de Meulder
Jean Marie Ravel
CV
Bijay Jassal
Venkata P Satagopam
Guanming Wu
Martin Golebiewski
Piotr Gawron
Laurence Calzone
Jacques S Beckmann
Chris T Evelo
Peter d'Eustachio
Falk Schreiber
Julio Saez-Rodriguez
Joaquin Dopazo
Martin Kuiper
Alfonso Valencia
Olaf Wolkenhauer
Hiroaki Kitano
Emmanuel Barillot
Charles Auffray
Rudi Balling
Reinhard Schneider

Résumé

The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.

Domaines

Bio-informatique [q-bio.QM]
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https://inria.hal.science/hal-03907738

Soumis le : mardi 20 décembre 2022-11:20:57

Dernière modification le : mercredi 25 septembre 2024-09:56:03

Archivage à long terme le : mercredi 22 mars 2023-16:18:49

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hal-03907738 , version 1 (20-12-2022)

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Anna Niarakis, Marek Ostaszewski, Alexander Mazein, Inna Kuperstein, Martina Kutmon, et al.. A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms. 2022. ⟨hal-03907738⟩

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