The paper predicts functional interactions of dark proteins with Reactome pathways using a random forest classifier and develops a web portal to visualize these interactions.

bioRxiv · Jun 5, 2023 · PreprintBioinformatics

JBrowse 2: A modular genome browser with views of synteny and structural variation

Colin M. Diesh, Garrett Stevens, Peter Xie, Teresa De Jesus Martinez, Elliot A. Hershberg, Angel Leung, Emma Guo, Shihab Dider, Junjun Zhang, Caroline Bridge, Gregory F J Hogue, Andrew Duncan, Matthew Morgan, Tia Flores, Benjamin N. Bimber, , Ian H Holmes

JBrowse 2 is a genome browser with enhanced views for structural variation and synteny, offering modular design and multiple usage options.

Genome biology · Apr 17, 2023Peer-reviewedBioinformatics

JBrowse Jupyter: A Python interface to JBrowse 2

Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett Stevens, Colin M. Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert Buels, Lincoln David Stein, Ian H Holmes

JBrowse Jupyter provides a Python interface to JBrowse 2 for interactive genomic visualization within Jupyter notebooks.

Bioinformatics · Jan 1, 2023Peer-reviewedBioinformatics

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert D. Phair, Aurelio Orta Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Márcio Luís Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, , Özgün Babur

The paper describes the development of a computational knowledge repository, the COVID-19 Disease Map, which curates SARS-CoV-2 virus-host interaction mechanisms and provides tools for their analysis and application.

Molecular Systems Biology · Oct 1, 2021Peer-reviewedSystems Biology