Rapid interaction profiling of 2019-nCoV for network-based deep drug-repurpose learning (DDRL)

Deliverables

MimicINT computational pipeline - webserver integration

Deliverable-1-2, -CoV ORFeome, ORF reagents for functional experiments by other researchers that require protein expression

Variant ORFs

Deliverable41 fully integrated fully validated coronavirushuman interactome network map

Initial Drug Validation

Deliverable61 test results for at least 10 topranked predicted already approved drugs

Novel small molecules evaluation

Deliverable-6-2, test results for at least 10 top-ranked novel small molecules

Data Sharing Plan

Data Sharing Plan All data relevant combating the current health emergency will be communicated to the commission and policy makers as soon as available.

Update of DPM

First data release and update to DPM

Manuscripts

Primary Interactive Manuscript(s) in month 15/16 and in month 36

CoHIN Manuscript

Publications

Modulation of human kinase activity through direct interaction with SARS-CoV-2 proteins

Author(s): Bettina Halwachs, Christina S. Moesslacher, Johanna M. Kohlmayr, Sandra Fasching, Sarah Masser, Sébastien A. Choteau, Andreas Zanzoni, Natalia Kunowska, Ulrich Stelzl
Published in: BiorXiv, 2023, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.27.568816

<i>mimic</i>INT: a workflow for microbe-host protein interaction inference

Author(s): Sébastien A. Choteau; Marceau Cristianini; Kevin Maldonado; Lilian Drets; Mégane Boujeant; Christine Brun; Lionel Spinelli; Andreas Zanzoni
Published in: https://hal.science/hal-04240079, Issue 6, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.11.04.515250

A map of binary SARS-CoV-2 protein interactions implicates host immune regulation and ubiquitination

Author(s): Dae-Kyum Kim, Benjamin Weller, Chung-Wen Lin, Dayag Sheykhkarimli, Jennifer J. Knapp, Nishka Kishore, Mayra Sauer, Ashyad Rayhan, Veronika Young, Nora Marin-de la Rosa, Oxana Pogoutse, Kerstin Spirohn, Alexandra Strobel, Florent Laval, Patrick Schwehn, Roujia Li, Simin Rothballer, Melina Altmann, Patricia Cassonnet, Guillaume Dugied, Atina G. Cote, Lena Elorduy Vergara, Isaiah Hazelwood, Bingruo B
Published in: bioRxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.03.15.433877

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms.

Author(s): Estelle M.N. Laurent, Yorgos Sofianatos, Anastassia Komarova, Jean-Pascal Gimeno, Payman Samavarchi Tehrani, Dae-Kyum Kim, Hala Abdouni, Marie Duhamel, Patricia Cassonnet, Jennifer J. Knapp, Da Kuang, Aditya Chawla, Dayag Sheykhkarimli, Ashyad Rayhan, Roujia Li, Oxana Pogoutse, David E. Hill, Michael A. Calderwood, Pascal Falter-Braun, Patrick Aloy, Ulrich Stelzl, Marc Vidal, Anne-Claude Gingras,
Published in: bioRxiv, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.08.28.272955

SARS-CoV-2 NSP14 MTase activity is critical for inducing canonical NF-κB activation

Author(s): Marie J Tofaute 1 , Benjamin Weller 2 , Carina Graß 1 , Hridi Halder 2 , Bushra Dohai 2 , Pascal Falter-Braun 2 3 , Daniel Krappmann 1
Published in: Bioscience Reports, 2024, ISSN 1573-4935
Publisher: Portland Press
DOI: 10.1042/bsr20231418

Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs

Author(s): Miquel Duran-Frigola, Martino Bertoni, Roi Blanco, Víctor Martínez, Eduardo Pauls, Víctor Alcalde, Gemma Turon, Núria Villegas, Adrià Fernández-Torras, Carles Pons, Lídia Mateo, Oriol Guitart-Pla, Pau Badia-i-Mompel, Aleix Gimeno, Nicolas Soler, Isabelle Brun-Heath, Hugo Zaragoza, Patrick Aloy
Published in: Journal of Chemical Information and Modeling, Issue 60/12, 2020, Page(s) 5730-5734, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.0c00420

A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection

Author(s): Benjamin Weller 1 , Chung-Wen Lin 1 , Oxana Pogoutse 2 3 4 5 , Mayra Sauer 1 , Nora Marin-de la Rosa 1 , Alexandra Strobel 1 , Veronika Young 1 , Jennifer J Knapp 2 3 4 5 , Ashyad Rayhan 2 3 4 5 , Claudia Falter 1 , Dae-Kyum Kim 2 3 4 5 6 , Frederick P Roth 2 3 4 5 7 , Pascal Falter-Braun 1 8
Published in: G3 - Genes, Genomes, Genetics, 2023, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkad105

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

Author(s): Douglass, Eugene F.; Allaway, Robert J.; Szalai, Bence; Wang, Wenyu; Tian, Tingzhong; Fernández-Torras, Adrià; Realubit, Ron; Karan, Charles; Zheng, Shuyu; Pessia, Alberto; Tanoli, Ziaurrehman; Jafari, Mohieddin; Wan, Fangping; Li, Shuya; Xiong, Yuanpeng; Duran-Frigola, Miquel; Bertoni, Martino; Badia-i-Mompel, Pau; Mateo, Lídia; Guitart-Pla, Oriol; Chung, Verena; Tang, Jing; Zeng, Jianyang; Al
Published in: Cell Reports Medicine, Issue 7, 2022, ISSN 2666-3791
Publisher: Elsevier
DOI: 10.1016/j.xcrm.2021.100492

The intricacy of the viral-human protein interaction networks: resources, data and analyses

Author(s): Saha D, Iannuccielli M, Brun C, Zanzoni A, Licata L
Published in: Frontiers in Microbiology, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.849781

Long-COVID-19: the persisting imprint of SARS-CoV-2 infections on the innate immune system

Author(s): Marianne Boes 1 , Pascal Falter-Braun 2 3
Published in: Signal Transduction and Targeted Therapy, 2023, ISSN 2059-3635
Publisher: Springer Nature
DOI: 10.1038/s41392-023-01717-9

Bioactivity descriptors for uncharacterized compounds

Author(s): Martino Bertoni; Miquel Duran-Frigola; Pau Badia-i-Mompel; Eduardo Pauls; Modesto Orozco-Ruiz; Oriol Guitart-Pla; Víctor Alcalde; Víctor M. Díaz; Antoni Berenguer-Llergo; Antonio García de Herreros; Patrick Aloy
Published in: Nature Communications, Issue 12, 2021, Page(s) 3932, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2020.07.21.214197

BQsupports: systematic assessment of the support and novelty of new biomedical associations.

Author(s): Adrià Fernández-Torras, Martina Locatelli, Martino Bertoni, Patrick Aloy
Published in: Bioinformatics, Issue Volume 39, Issue 9, September 2023, 2023, ISSN 1367-4811
Publisher: Oxford Univeristy Press
DOI: 10.1093/bioinformatics/btad581

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

Author(s): Adrià Fernández-Torras; Miquel Duran-Frigola; Martino Bertoni; Martina Locatelli; Patrick Aloy
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33026-0

Connecting chemistry and biology through molecular descriptors.

Author(s): Adrià Fernández-Torras; Arnau Comajuncosa-Creus; Miquel Duran-Frigola; Patrick Aloy
Published in: Current Opinion in Chemical Biology, Issue 1, 2022, ISSN 1367-5931
Publisher: Elsevier BV
DOI: 10.1016/j.cbpa.2021.09.001

A proteome-scale map of the SARS-CoV-2–human contactome

Author(s): Dae-Kyum Kim, Benjamin Weller, Chung-Wen Lin, Dayag Sheykhkarimli, Jennifer J. Knapp, Guillaume Dugied, Andreas Zanzoni, Carles Pons, Marie J. Tofaute, Sibusiso B. Maseko, Kerstin Spirohn, Florent Laval, Luke Lambourne, Nishka Kishore, Ashyad Rayhan, Mayra Sauer, Veronika Young, Hridi Halder, Nora Marín-de la Rosa, Oxana Pogoutse, Alexandra Strobel, Patrick Schwehn, Roujia Li, Simin T. Rothballer
Published in: Nature Biotechnology, 2023, ISSN 1546-1696
Publisher: Springer Nature
DOI: 10.1038/s41587-022-01475-z

Probing SARS-CoV-2 RNA interactome to unravel post-transcriptional dysregulation associated with COVID-19

Author(s): Saha D, Ribeiro D, Zanzoni A, Brun C.
Published in: Proceeding of JOBIM'22 (Journées Ouvertes Biologie Informatique Mathématiques), Issue Yearly, 2022
Publisher: SFBI (Société Française de Bioinformatique)

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