| Title: |
A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms |
| Authors: |
Niarakis, Anna; Ostaszewski, Marek; Mazein, Alexander; Kuperstein, Inna; Kutmon, Martina; Gillespie, Marc, E; Funahashi, Akira; Acencio, Marcio, Luis; Hemedan, Ahmed; Aichem, Michael; Klein, Karsten; Czauderna, Tobias; Burtscher, Felicia; Yamada, Takahiro, G; Hiki, Yusuke; Hiroi, Noriko, F; Hu, Finterly; Pham, Nhung; Ehrhart, Friederike; Willighagen, Egon, L; Valdeolivas, Alberto; Dugourd, Aurelien; Messina, Francesco; Esteban-Medina, Marina; Pena-Chilet, Maria; Rian, Kinza; Soliman, Sylvain; Aghamiri, Sara, Sadat; Puniya, Bhanwar, Lal; Naldi, Aurelien; Helikar, Tomas; Singh, Vidisha; Farinas Fernandez, Marco; Bermudez, Viviam; Tsirvouli, Eirini; Montagud, Arnau; Noel, Vincent; Ponce de Leon, Miguel; Maier, Dieter; Bauch, Angela; Gyori, Benjamin, M; Bachman, John, A; Luna, Agustin; Pinero, Janet; Furlong, Laura, I; Balaur, Irina; Rougny, Adrien; Jarosz, Yohan; Overall, Rupert, W; Phair, Robert; Perfetto, Livia; Matthews, Lisa; Rex, Devasahayam, Arokia Balaya; Orlic-Milacic, Marija; Monraz Gomez, Luis, Cristobal; de Meulder, Bertrand; Ravel, Jean, Marie; Jassal, Bijay; Satagopam, Venkata, P; Wu, Guanming; Golebiewski, Martin; Gawron, Piotr; Calzone, Laurence; Beckmann, Jacques, S; Evelo, Chris, T; d'Eustachio, Peter; Schreiber, Falk; Saez-Rodriguez, Julio; Dopazo, Joaquin; Kuiper, Martin; Valencia, Alfonso; Wolkenhauer, Olaf; Kitano, Hiroaki; Barillot, Emmanuel; Auffray, Charles; Balling, Rudi; Schneider, Reinhard |
| Contributors: |
Computational systems biology and optimization (Lifeware); Centre Inria de Saclay; Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria); Laboratoire de recherche européen pour la polyarthrite rhumatoïde (GenHotel); Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay; Université du Luxembourg = University of Luxembourg = Universität Luxemburg (uni.lu); Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe; Mines Paris - PSL (École nationale supérieure des mines de Paris); Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut Curie Paris -Institut National de la Santé et de la Recherche Médicale (INSERM); Université Paris Sciences et Lettres (PSL); Maastricht Centre for Systems Biology Maastricht (MaCSBio); Maastricht University Maastricht; Ontario Institute for Cancer Research Canada (OICR); Ontario Institute for Cancer Research; Keio University Tokyo = Keiō Gijuku Daigaku = 慶應義塾大学; Luxembourg Centre For Systems Biomedicine (LCSB); University of Konstanz; Hochschule Mittweida - University of Applied Sciences; Kanagawa Institute of Technology; Heidelberg University Hospital Heidelberg; National Institute for Infectious Diseases "Lazzaro Spallanzani"; Hospital Universitario Virgen del Rocío Sevilla (HUVR); Biomedicine Institute of Sevilla Seville, Spain; University of Nebraska–Lincoln; University of Nebraska System; Norwegian University of Science and Technology Trondheim (NTNU); Norwegian University of Science and Technology = Norges Teknisk-Naturvitenskapelige Universitet = Norjan teknis-luonnontieteellinen yliopisto (NTNU); Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC-CNS); Harvard Medical School Boston (HMS); Universitat Pompeu Fabra Barcelona (UPF); National Institute of Advanced Industrial Science and Technology (AIST); Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin (HU Berlin); Integrative Bioinformatics Inc Mountain View; Department of Informatics and System Sciences (Sapienza University of Rome); Università degli Studi di Roma "La Sapienza" = Sapienza University Rome (UNIROMA); New York University Langone Medical Center (NYU Langone Medical Center); NYU System (NYU); Yenepoya University; Janet Piñero, Laura I. Furlong: IMI2-JU grants, resources which are composed of financial contributions from the European Union’s Horizon 2020 Research and Innovation Programme and EFPIA GA: 777365 eTRANSAFE , and the EU H2020 Programme GA:964537 RISKHUNT3R; Project 001-P-001647—Valorisation of EGA for Industry and Society funded by the European Regional Development Fund (ERDF) and Generalitat de Catalunya; Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”). |
| Source: |
https://inria.hal.science/hal-03907738 ; 2022. |
| Publisher Information: |
CCSD |
| Publication Year: |
2022 |
| Subject Terms: |
SARS-CoV-2; systems biology; disease maps; mechanistic models; dynamic models; systems medicine; large-scale community effort; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] |
| Description: |
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. |
| Document Type: |
report |
| Language: |
English |
| Relation: |
BIORXIV: 2022.12.17.520865 |
| DOI: |
10.1101/2022.12.17.520865 |
| Availability: |
https://inria.hal.science/hal-03907738; https://inria.hal.science/hal-03907738v1/document; https://inria.hal.science/hal-03907738v1/file/2022.12.17.520865v1.full.pdf; https://doi.org/10.1101/2022.12.17.520865 |
| Rights: |
https://about.hal.science/hal-authorisation-v1/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.10B42F5F |
| Database: |
BASE |