Software available at: https://github.com/jin-wash-u

HPV-EM: an accurate HPV detection and genotyping tool

Download Now

Inkman MJ, Jayachandran K, Ellis TM, Ruiz F, McLellan MD, Miller CA, Wu Y, Ojesina AI, Schwarz JK, Zhang J. HPV-EM: an accurate HPV detection and genotyping EM algorithm. Sci Rep. 2020 Aug 31;10(1):14340. doi: 10.1038/s41598-020-71300-7. PMID: 32868873; PMCID: PMC7459114.

INTEGRATE: A tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.

Download Now

Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA. INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PubMed PMID: 26556708; PubMed Central PMCID: PMC4691743.

Best paper in Bioinformatics and Translational Informatics – IMIA Yearbook of Medical Informatics 2017

INTEGRATE-Neo: A tool for gene fusion neoantigen discovering tool using next-generation sequencing data. 

Download Now

Zhang J, Mardis ER, Maher CA. INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. Bioinformatics. 2016 Oct 24. pii: btw674. [Epub ahead of print] PubMed PMID: 27797777.

INTEGRATE-Vis: A tool for comprehensive gene fusion visualization using next-generation sequencing data

Download Now

Zhang J, Gao T, Maher CA. INTEGRATE-Vis: a tool for comprehensive gene fusion visualization. Sci Rep. 2017 Dec 19;7(1):17808. doi: 10.1038/s41598-017-18257-2. PMID: 29259323; PMCID: PMC5736641.

SVSeq2: Accurate and efficient detection of structural variations with low-coverage sequencing data

Download Now

Zhang J, Wang J, Wu Y. An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. BMC Bioinformatics. 2012 Apr 19;13 Suppl 6(Suppl 6):S6. doi: 10.1186/1471-2105-13-S6-S6. PMID: 22537045; PMCID: PMC3358659.

SVseq: Detection of exact breakpoints with low-coverage sequencing data

Download Now

Zhang J, Wu Y. SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data. Bioinformatics. 2011 Dec 1;27(23):3228-34. doi: 10.1093/bioinformatics/btr563. Epub 2011 Oct 12. PMID: 21994222.

HapReads: Haplotype inference from short sequence reads using a population genealogical history model

Download Now

Zhang J, Wu Y. Haplotype inference from short sequence reads using a population genealogical history model. Pac Symp Biocomput. 2011:288-99. doi: 10.1142/9789814335058_0030. PMID: 21121056.

Book chapter on SVseq 1 and 2: 

Computational approaches for finding long insertions and deletions with next generation sequencing data

J Zhang, C Chu, Y Wu
Computational Methods for Next Generation Sequencing Data Analysis, 175-195

Book chapter on INTEGRATE tools: 

Gene Fusion Discovery with INTEGRATE

J Zhang, C Maher
Methods in Molecular Biology, 41-68
PMID: 31728961

ICGC-TCGA DREAM Somatic Mutation Calling – RNA Challenge

https://www.synapse.org/#!Synapse:syn2813589

https://github.com/Sage-Bionetworks-Challenges/SMC-RNA-Challenge