Wenchao Zhang

Bioinformatics Software Engineer(DevOps)
St. Jude Profile
z/wenchao-zhang
ORCID
0000-0003-4478-8410
Google Scholar
Wenchao Zhang
LinkedIn
Wenchao Zhang
Email
wenchao.zhangobfuscate#stjude.org

Overview

Dr. Wenchao Zhang is a bioinformatics software engineer in the Center for Applied Bioinformatics (CAB) in the St Jude Children’s Research Hospital (SJCRH). He worked as an electronics engineer in his early career time and later on switched to Bioinformatics. He has since been accumulated knowledge and skills in bioinformatics software/pipeline development, including computational mass-spectrometry for proteomics and metabolomics, statistical genomics with a focus on polygenic variant analysis, epistatic GWAS mapping, NGS and HiC data analysis. He is particularly interested in utilizing HPC skills (task driven CPU parallel computing such as MPI, and data driven parallel computing such as CUDA GPU) to accelerate the bioinformatics analysis.

Education

  • PhD, Communication & Information System, Institute of Electronics, Chinese Academy of Science, Beijing, China (2008)
  • MS, Communication & Information System, Jilin University, Changchun, China (2004)
  • BS, Electronics Engineering, Jilin University, Changchun, China (2001)

Professional Experience

Time Position PI/Supervisor Institution  
2021- Bioinformatics Software Engineer Yawei Hui St. Jude Children’s Research Hospital  
2020-2021 Computational Biologist II Chao Xing UT Southwestern Medical Center  
2017-2020 Computational Biologist Patrick Zhao Noble Research Institute  
2012-2017 Bioinformatics Research Analyst Patrick Zhao The Samuel Roberts Noble Foundation  
2010-2012 Postdoc. Res. Associate Xiuxia Du UNC-Charlotte & NC Research Campus  
2007-2010 Algorithm Engineer Xiaoxu Guo Analogix SemiConductor Inc.  

Publications

For a full list (GEO|SRA|Browser|Code) see below , or Google Scholar

Full List

*denotes equal contribution, #denotes corresponding

2021:2

  1. Frontiers in plant s
    Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees
    Zhang W, Kang Y, Cheng X, Wen J, Zhang H, Torres-Jerez I, Krom N, Udvardi MK, Scheible WR., Zhao PX
    Frontiers in plant science 2021
  2. NAR genomics and bio
    PIP-SNP: a pipeline for processing SNP data featured as linkage disequilibrium bin mapping, genotype imputing and marker synthesizing
    Zhang W, Kang Y, Dai X, Xu S., Zhao PX
    NAR genomics and bioinformatics 2021

2020:2

  1. NAR genomics and bio
    GPU empowered pipelines for calculating genome-wide kinship matrices with ultra-high dimensional genetic variants and facilitating 1D and 2D GWAS
    Zhang W, Dai X, Xu S, Zhao PX
    NAR genomics and bioinformatics 2020
  2. The Plant Journal
    Insertional mutagenesis of Brachypodium distachyon using the Tnt1 retrotransposable element
    Nandety RS, Serrani‐Yarce JC, Gill U.S, Oh S, Lee HK, Zhang X, Dai X, Zhang W, Krom N, Wen J., Zhao PX
    The Plant Journal 2020

2019:1

  1. Bioinformatics
    GWASpro: a high-performance genome-wide association analysis server
    Kim B, Dai X, Zhang W, Zhuang Z, Sanchez DL, Lübberstedt T, Kang Y, Udvardi MK, Beavis WD, Xu S, Zhao PX
    Bioinformatics 2019

2018:1

  1. Communications biolo
    2D association and integrative omics analysis in rice provides systems biology view in trait analysis
    Zhang W, Dai X, Xu S, Zhao PX
    Communications biology 2018

2016:1

  1. PLoS computational b
    PEPIS: a pipeline for estimating epistatic effects in quantitative trait locus mapping and genome-wide association studies
    Zhang W, Dai X, Wang Q, Xu S, Zhao PX
    PLoS computational biology 2016

2015:1

  1. Analytical chemistry
    MET-XAlign: a metabolite cross-alignment tool for LC/MS-based comparative metabolomics
    Zhang W, Lei Z, Huhman D, Sumner LW, Zhao PX
    Analytical chemistry 2015

2014:2

  1. Analytical chemistry
    MET-COFEA: a liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation
    Zhang W, Chang J, Lei Z, Huhman D, Sumner LW, Zhao PX
    Analytical chemistry 2014
  2. BMC bioinformatics
    Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data
    Zhang W, Zhao PX
    BMC bioinformatics 2014

2012:2

  1. Journal of molecular
    The PHD and chromo domains regulate the ATPase activity of the human chromatin remodeler CHD4
    Watson AA, Mahajan P, Mertens HD, Deery MJ, Zhang W, Pham P, Du X, Bartke T, Zhang W, Edlich C, G Berridge
    Journal of molecular biology 2012
  2. Analytical chemistry
    ADAP-GC 2.0: deconvolution of coeluting metabolites from GC/TOF-MS data for metabolomics studies
    Ni Y, Qiu Y, Jiang W, Suttlemyre K, Su M, Zhang W, Jia W., Du X
    Analytical chemistry 2012

2011:1

  1. BookChapter
    Several Kinds of Modified SPIHT Codec
    Zhang Wenchao
    In Discrete Wavelet Transforms - Algorithms and Applications 2011

2008:1

  1. IET Image Processing
    Compression of multi-polarimetric SAR intensity images based on 3D-matrix transform
    Zhang W, Wang YF, Hu GH
    IET Image Processing 2008