Author

Jingchun Zhu

BGI Group (China)ORCID 0000-0003-4075-431XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Assay:bulk RNA-seq· 2 Assay:whole-genome sequencing· 2 Research Focus:batch correction / integration· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1

Frequent Co-Authors

Brian CraftiD· 3 shared Isidro Cortés‐CirianoiD· 2 shared Junjun ZhangiD· 2 shared Mary J. GoldmaniD· 2 shared Nuno A. FonsecaiD· 2 shared Peter J. ParkiD· 2 shared Qian XiangiD· 2 shared Adam Novak· 1 shared

Activity by Year

2016-2020 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Brian CraftORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

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

Rapid and efficient analysis of 20,000 RNA-seq samples with Toil

John Vivian, Arjun Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian, Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, , Benedict Paten

The paper demonstrates Toil's ability to efficiently process 20,000 RNA-seq samples to create a batch-effect-free meta-analysis across five datasets.

bioRxiv · Jul 7, 2016Bioinformatics