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The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions [article]

Livia Perfetto, Chiara Pastrello, Noemi Del-Toro, Margaret Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, Kalpana Panneerselvam, Simona Panni, Negin Rahimzadeh, Sylvie Ricard-Blum (+8 others)
2020 biorxiv/medrxiv  
Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae  ...  Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the  ...  Acknowledgements The authors would like to thank Dr Yun Niu for assistance in pathway reduction analysis and Dr Serene Wong for useful discussion.  ... 
doi:10.1101/2020.06.16.153817 pmid:32587962 pmcid:PMC7310617 fatcat:xgzjcgg6m5gnvezhkllhkyivgu

The IMEx coronavirus interactome: an evolving map of Coronaviridae–host molecular interactions

L Perfetto, C Pastrello, N del-Toro, M Duesbury, M Iannuccelli, M Kotlyar, L Licata, B Meldal, K Panneerselvam, S Panni, N Rahimzadeh, S Ricard-Blum (+8 others)
2020 Database: The Journal of Biological Databases and Curation  
We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International  ...  Molecular Exchange (IMEx) Consortium curators.  ...  Funding The IntAct and Complex Portal databases and EMBL-EBI-based authors received funding from EMBL core funding, Open Targets  ... 
doi:10.1093/database/baaa096 pmid:33206959 pmcid:PMC7673336 fatcat:qnjvamhnzvhd7npua4moujnnau

Comprehensive pathway enrichment analysis workflows: COVID-19 case study

Giuseppe Agapito, Chiara Pastrello, Igor Jurisica
2020 Briefings in Bioinformatics  
The coronavirus disease 2019 (COVID-19) outbreak due to the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been classified as a pandemic disease by the World Health  ...  One class of such tools, pathway enrichment analysis (PEA) methods, helps researchers to find possible key targets present in biological pathways of host cells that are targeted by SARS-CoV-2.  ...  Evidence obtained using related human coronaviruses diseases such as SARS and MERS is also mapped to the networks.  ... 
doi:10.1093/bib/bbaa377 fatcat:aa2xtbxb55g4xp3zav3veu2m4y

COVID19 Disease Map, a computational knowledge repository of 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 (+129 others)
2021
The COVID‐19 Disease Map (C19DMap) is a graphical, interactive representation of disease‐relevant molecular mechanisms linking many knowledge sources.  ...  The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases.  ...  Acknowledgements We would like to thank Andjela Tatarovic, architect, and Gina Crovetto, a researcher in the field of cancer, for their help with the design of the top-level view diagrams.  ... 
doi:10.17863/cam.77076 fatcat:xwr7r73ocrgfbaqfdiqxw5tj6m

COVID19 Disease Map, a computational knowledge repository of 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 (+128 others)
2021
The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources.  ...  The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases.  ...  Acknowledgements We would like to thank Andjela Tatarovic, architect, and Gina Crovetto, a researcher in the field of cancer, for their help with the design of the top-level view diagrams.  ... 
doi:10.15252/msb.202110387 pmid:34664389 pmcid:PMC8524328 fatcat:3di2t3nc3zhq7mdmi7sk4h5s24