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description Publicationkeyboard_double_arrow_right Preprint 2022 FranceCenter for Open Science Mariana Galvão Ferrarini; Aguiar-Pulido; Eric T. Dawson; Andrea Guarracino; Andreas Gruber; Lukas Heumos; Alexander Kanitz; Amit Kumar Lal; Brett E. Pickett; Rita Rebollo; Ruiz-Arenas C; Olaitan Igbagbo Awe; Sarbjit Singh Bedi; Ben Busby; Georgaki M; James C; Itziar Martinez Gonzalez; Meldal B; Scheila G. Mucha; Noushin Nabavi; Neiro J; Núria Queralt-Rosinach; Philippe Rocca-Serra; de Oliveira Ds; Tsagiopoulou M;As part of the virtual BioHackathon 2020, we formed a working group that focused on the analysis of gene expression in the context of COVID-19. More specifically, we performed transcriptome analyses on published datasets in order to better understand the interaction between the human host and the SARS-CoV-2 virus.The ideas proposed during this hackathon were divided into five projects. Projects 1 and 2 aimed to identify human genes that are important in the process of viral infection of human cells. Projects 3 and 4 aimed to take the candidate genes identified in projects 1 and 2, as well as by independent studies, and relate them to clinical information and to possible therapeutic interventions. Finally, Project 5 aimed to package and containerize software and workflows used and generated here in a reusable manner, ultimately providing scalable and reproducible workflows.
http://biohackrxiv.o... arrow_drop_down add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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You have already added works in your ORCID record related to the merged Research product.Do the share buttons not appear? Please make sure, any blocking addon is disabled, and then reload the page.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.37044/osf.io/b4zkp&type=result"></script>'); --> </script>For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average 
Powered by BIP!Research data keyboard_double_arrow_right Dataset 2020 EnglishZenodo Aguiar-Pulido, Vanessa; Ferrarini, Mariana G.; Guarracino, Andrea; Ruiz-Arenas, Carlos;Aguiar-Pulido, Vanessa; Ferrarini, Mariana G.; Guarracino, Andrea; Ruiz-Arenas, Carlos;These data represent results from: Processing reads from 20 experiments (part of GSE147507) by following a standard approach, which includes using STAR to align the reads to GRCh38 and StringTie to calculate the (raw) counts per experiment. These results depict the transcriptomic response of human cells to SARS-CoV-2, RSV and H1N1, and enrichment analyses based on genes differentially expressed in SARS-CoV-2 but not in RSV or H1N1. (Authors: V.A.-P., M.G.F. and A.G.) Aligning to SARS-CoV-2 and quantifying reads by using HISAT2 and StringTie. (Author: C.R.-A.) Disclaimer: These results were obtained during the virtual BioHackathon 2020. As such, they are subject to ongoing research and have thus NOT yet undergone any scientific peer-review. That is, none of the contents can be considered to be free of errors and must be taken with caution! {"references": ["Ferrarini, Aguiar-Pulido et al. (2020). Global analysis of human SARS-CoV-2 infection and host-virus interaction. BioHackrXiv. https://doi.org/10.37044/osf.io/b4zkp"]} Data uploaded here are licensed under the CC0 1.0 Universal license
ZENODO arrow_drop_down add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.Do the share buttons not appear? Please make sure, any blocking addon is disabled, and then reload the page.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.3749901&type=result"></script>'); --> </script>For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!visibility 928visibility views 928 download downloads 239 Powered by
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description Publicationkeyboard_double_arrow_right Preprint 2022 FranceCenter for Open Science Mariana Galvão Ferrarini; Aguiar-Pulido; Eric T. Dawson; Andrea Guarracino; Andreas Gruber; Lukas Heumos; Alexander Kanitz; Amit Kumar Lal; Brett E. Pickett; Rita Rebollo; Ruiz-Arenas C; Olaitan Igbagbo Awe; Sarbjit Singh Bedi; Ben Busby; Georgaki M; James C; Itziar Martinez Gonzalez; Meldal B; Scheila G. Mucha; Noushin Nabavi; Neiro J; Núria Queralt-Rosinach; Philippe Rocca-Serra; de Oliveira Ds; Tsagiopoulou M;As part of the virtual BioHackathon 2020, we formed a working group that focused on the analysis of gene expression in the context of COVID-19. More specifically, we performed transcriptome analyses on published datasets in order to better understand the interaction between the human host and the SARS-CoV-2 virus.The ideas proposed during this hackathon were divided into five projects. Projects 1 and 2 aimed to identify human genes that are important in the process of viral infection of human cells. Projects 3 and 4 aimed to take the candidate genes identified in projects 1 and 2, as well as by independent studies, and relate them to clinical information and to possible therapeutic interventions. Finally, Project 5 aimed to package and containerize software and workflows used and generated here in a reusable manner, ultimately providing scalable and reproducible workflows.
http://biohackrxiv.o... arrow_drop_down add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.Do the share buttons not appear? Please make sure, any blocking addon is disabled, and then reload the page.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.37044/osf.io/b4zkp&type=result"></script>'); --> </script>For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!Research data keyboard_double_arrow_right Dataset 2020 EnglishZenodo Aguiar-Pulido, Vanessa; Ferrarini, Mariana G.; Guarracino, Andrea; Ruiz-Arenas, Carlos;Aguiar-Pulido, Vanessa; Ferrarini, Mariana G.; Guarracino, Andrea; Ruiz-Arenas, Carlos;These data represent results from: Processing reads from 20 experiments (part of GSE147507) by following a standard approach, which includes using STAR to align the reads to GRCh38 and StringTie to calculate the (raw) counts per experiment. These results depict the transcriptomic response of human cells to SARS-CoV-2, RSV and H1N1, and enrichment analyses based on genes differentially expressed in SARS-CoV-2 but not in RSV or H1N1. (Authors: V.A.-P., M.G.F. and A.G.) Aligning to SARS-CoV-2 and quantifying reads by using HISAT2 and StringTie. (Author: C.R.-A.) Disclaimer: These results were obtained during the virtual BioHackathon 2020. As such, they are subject to ongoing research and have thus NOT yet undergone any scientific peer-review. That is, none of the contents can be considered to be free of errors and must be taken with caution! {"references": ["Ferrarini, Aguiar-Pulido et al. (2020). Global analysis of human SARS-CoV-2 infection and host-virus interaction. BioHackrXiv. https://doi.org/10.37044/osf.io/b4zkp"]} Data uploaded here are licensed under the CC0 1.0 Universal license
ZENODO arrow_drop_down add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.Do the share buttons not appear? Please make sure, any blocking addon is disabled, and then reload the page.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.3749901&type=result"></script>'); --> </script>For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!visibility 928visibility views 928 download downloads 239 Powered by