The paper introduces the GA4GH Workflow Execution Service API, which standardizes workflow execution across different compute environments and demonstrates its cross-site functionality.

bioRxiv · Oct 24, 2026 · 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

A user's guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

Mary J. Goldman, Junjun Zhang, Nuno A. Fonseca, Isidro Cortés‐Ciriano, Qian Xiang, Brian Craft, Elena Piñeiro-Yáñez, Brian D. O’Connor, Wojciech Bażant, Elisabet Barrera, Alfonso Muñoz-Pomer Fuentes, Robert Petryszak, Anja Füllgrabe, Fátima Al‐Shahrour, Maria Keays, , Miguél Vázquez

The paper provides a user guide to five online tools for exploring and visualizing PCAWG data, demonstrating their integration with external resources to enhance cancer genomics research.

Nature Communications · Jul 7, 2020Peer-reviewedBioinformatics

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

Yiqun Zhang, Fengju Chen, Nuno A. Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brāzma, PCAWG Transcriptome Working Group, Samirkumar B. Amin, Philip Awadalla, Peter J. Bailey, Alvis Brazma, Angela Norie Brooks, Claudia Calabrese, , Paul Alan Edwards

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Nature Communications · Feb 5, 2020Peer-reviewedGenomics

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

PCAWG Transcriptome Core Group, Claudia Calabrese, Natalie R. Davidson, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Deniz Demircioğlu, Liliana Greger, Siliang Li, Dongbing Liu, , Zemin Zhang

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.

bioRxiv · Mar 12, 2018 · PreprintGenomics

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

Christina K. Yung, Brian D. O’Connor, Sergei Yakneen, Junjun Zhang, Kyle Ellrott, Kortine Kleinheinz, Naoki Miyoshi, Keiran M. Raine, Romina Royo, Gordon Saksena, Matthias Schlesner, Solomon I. Shorser, Miguel Vazquez, Joachim Weischenfeldt, Denis Yuen, , Charles L. Short

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.

bioRxiv · Jul 10, 2017 · PreprintGenomics