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

Resultado final

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

Publicaciones

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

Autores: Bettina Halwachs, Christina S. Moesslacher, Johanna M. Kohlmayr, Sandra Fasching, Sarah Masser, Sébastien A. Choteau, Andreas Zanzoni, Natalia Kunowska, Ulrich Stelzl
Publicado en: BiorXiv, 2023, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.27.568816

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

Autores: Sébastien A. Choteau; Marceau Cristianini; Kevin Maldonado; Lilian Drets; Mégane Boujeant; Christine Brun; Lionel Spinelli; Andreas Zanzoni
Publicado en: https://hal.science/hal-04240079, Edición 6, 2022, ISSN 2692-8205
Editor: 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

Autores: 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
Publicado en: bioRxiv, 2021
Editor: 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.

Autores: 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,
Publicado en: bioRxiv, 2020
Editor: 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

Autores: Marie J Tofaute 1 , Benjamin Weller 2 , Carina Graß 1 , Hridi Halder 2 , Bushra Dohai 2 , Pascal Falter-Braun 2 3 , Daniel Krappmann 1
Publicado en: Bioscience Reports, 2024, ISSN 1573-4935
Editor: Portland Press
DOI: 10.1042/bsr20231418

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

Autores: 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
Publicado en: Journal of Chemical Information and Modeling, Edición 60/12, 2020, Página(s) 5730-5734, ISSN 1549-9596
Editor: 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

Autores: 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
Publicado en: G3 - Genes, Genomes, Genetics, 2023, ISSN 2160-1836
Editor: Genetics Society of America
DOI: 10.1093/g3journal/jkad105

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

Autores: 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
Publicado en: Cell Reports Medicine, Edición 7, 2022, ISSN 2666-3791
Editor: Elsevier
DOI: 10.1016/j.xcrm.2021.100492

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

Autores: Saha D, Iannuccielli M, Brun C, Zanzoni A, Licata L
Publicado en: Frontiers in Microbiology, 2022, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2022.849781

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

Autores: Marianne Boes 1 , Pascal Falter-Braun 2 3
Publicado en: Signal Transduction and Targeted Therapy, 2023, ISSN 2059-3635
Editor: Springer Nature
DOI: 10.1038/s41392-023-01717-9

Bioactivity descriptors for uncharacterized compounds

Autores: 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
Publicado en: Nature Communications, Edición 12, 2021, Página(s) 3932, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2020.07.21.214197

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

Autores: Adrià Fernández-Torras, Martina Locatelli, Martino Bertoni, Patrick Aloy
Publicado en: Bioinformatics, Edición Volume 39, Edición 9, September 2023, 2023, ISSN 1367-4811
Editor: Oxford Univeristy Press
DOI: 10.1093/bioinformatics/btad581

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

Autores: Adrià Fernández-Torras; Miquel Duran-Frigola; Martino Bertoni; Martina Locatelli; Patrick Aloy
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-33026-0

Connecting chemistry and biology through molecular descriptors.

Autores: Adrià Fernández-Torras; Arnau Comajuncosa-Creus; Miquel Duran-Frigola; Patrick Aloy
Publicado en: Current Opinion in Chemical Biology, Edición 1, 2022, ISSN 1367-5931
Editor: Elsevier BV
DOI: 10.1016/j.cbpa.2021.09.001

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

Autores: 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
Publicado en: Nature Biotechnology, 2023, ISSN 1546-1696
Editor: Springer Nature
DOI: 10.1038/s41587-022-01475-z

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

Autores: Saha D, Ribeiro D, Zanzoni A, Brun C.
Publicado en: Proceeding of JOBIM'22 (Journées Ouvertes Biologie Informatique Mathématiques), Edición Yearly, 2022
Editor: SFBI (Société Française de Bioinformatique)

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Resultado final

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