Xun Zhu

Tech Lead Manager
St. Jude Profile
z/xun-zhu
ORCID
0000-0001-9097-7824
GitHub
xz-stjude
Google Scholar
Xun Zhu
LinkedIn
Xun Zhu
Email
xun.zhuobfuscate#stjude.org

Overview

Dr. Xun Zhu is a Manager of Software Engineering in the Center for Applied Bioinformatics at St. Jude Children’s Research Hospital. He leads the team behind Planet9, a HIPAA-aligned cloud platform where St. Jude Global partner hospitals run biomedical analyses. He built the original prototype for Planet9, and has grown the project into a global platform serving 10+ state-of-the-art analysis applications to partner hospitals in Asia, Africa, North America, South America, and Europe.

Before St. Jude, he developed the single-cell RNA-Seq analysis platforms Granatum and GranatumX, and published machine learning methods for omics and medical imaging data.

Education

  • PhD, Molecular Biosciences and Bioengineering, University of Hawaii at Manoa
  • MS, Computer Science, University of Illinois Urbana-Champaign
  • MS, Applied Mathematics, University of Southern California
  • BS, Mathematics and Applied Mathematics, Tianjin Polytechnic University

Professional Experience

Time Position PI/Supervisor Institution
2023 - Current Manager of Software Engineering Gang Wu St. Jude Children’s Research Hospital, Memphis, TN
2023 Staff Software Engineer Gang Wu St. Jude Children’s Research Hospital, Memphis, TN
2022 - 2023 Sr. Bioinformatics Software Engineer Gang Wu St. Jude Children’s Research Hospital, Memphis, TN
2020 - 2022 Bioinformatics Research Scientist Gang Wu St. Jude Children’s Research Hospital, Memphis, TN
2019 - 2020 Postdoctoral Researcher John Shepherd University of Hawaii Cancer Center, Honolulu, HI
2014 - 2019 Research Assistant Lana Garmire University of Hawaii Cancer Center, Honolulu, HI

Publications

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

Full List

*denotes equal contribution, #denotes corresponding

2020:5

  1. Nature methods
    Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition
    Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Åkesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others
    Nature methods 2020
  2. NATURE METHODS
    Analysis of the Human Protein Atlas Image Classification competition (vol 54, pg 2112, 2019)
    Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Akesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others
    NATURE METHODS 2020
  3. Nature Methods
    Author Correction: Analysis of the Human Protein Atlas Image Classification competition
    Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Åkesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others
    Nature Methods 2020
  4. NATURE METHODS
    Analysis of the Human Protein Atlas Image Classification competition (vol 53, pg 961, 2019)
    Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Akesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others
    NATURE METHODS 2020
  5. NATURE METHODS
    Analysis of the Human Protein Atlas Image Classification competition (vol 16, pg 1254, 2019)
    Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Akesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others
    NATURE METHODS 2020

2019:5

  1. Genome biology
    DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data
    Arisdakessian Cédric, Poirion Olivier, Yunits Breck, Zhu Xun, Garmire Lana X
    Genome biology 2019
  2. bioRxiv
    GranatumX: A community engaging and flexible software environment for single-cell analysis
    Zhu Xun, Yunits Breck, Wolfgruber Thomas, Liu Yu, Huang Qianhui, Poirion Olivier, Arisdakessian Cédric, Zhao Tianying, Garmire David, Garmire Lana
    bioRxiv 2019
  3. BookChapter
    Data Analysis in Single-Cell RNA-Seq
    Zhu Xun, Garmire Lana X
    2019
  4. PloS one
    Maternal cardiovascular-related single nucleotide polymorphisms, genes, and pathways associated with early-onset preeclampsia
    Benny Paula, Yamasato Kelly, Yunits Breck, Zhu Xun, Ching Travers, Garmire Lana X, Berry Marla J, Towner Dena
    PloS one 2019
  5. Nature methods
    Analysis of the human protein atlas image classification competition
    Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Åkesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others
    Nature methods 2019

2018:2

  1. PLoS computational b
    Cox-nnet: an artificial neural network method for prognosis prediction of high-throughput omics data
    Ching Travers, Zhu Xun, Garmire Lana X
    PLoS computational biology 2018
  2. Nature communication
    Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage
    Poirion Olivier, Zhu Xun, Ching Travers, Garmire Lana X
    Nature communications 2018

2017:4

  1. Genome medicine
    Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
    Zhu Xun, Wolfgruber Thomas K, Tasato Austin, Arisdakessian Cédric, Garmire David G, Garmire Lana X
    Genome medicine 2017
  2. PeerJ
    Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
    Zhu Xun, Ching Travers, Pan Xinghua, Weissman Sherman M, Garmire Lana
    PeerJ 2017
  3. Nucleic acids resear
    Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors
    Yang Jennifer, Tanaka Yoshiaki, Seay Montrell, Li Zhen, Jin Jiaqi, Garmire Lana Xia, Zhu Xun, Taylor Ashley, Li Weidong, Euskirchen Ghia, others
    Nucleic acids research 2017
  4. Clinical and transla
    Using single-cell multiple omics approaches to resolve tumor heterogeneity
    Ortega Michael A, Poirion Olivier, Zhu Xun, Huang Sijia, Wolfgruber Thomas K, Sebra Robert, Garmire Lana X
    Clinical and translational medicine 2017

2016:6

  1. Frontiers in genetic
    Single-cell transcriptomics bioinformatics and computational challenges
    Poirion Olivier B, Zhu Xun, Ching Travers, Garmire Lana
    Frontiers in genetics 2016
  2. Oncotarget
    Meta-dimensional data integration identifies critical pathways for susceptibility, tumorigenesis and progression of endometrial cancer
    Wei Runmin, De Vivo Immaculata, Huang Sijia, Zhu Xun, Risch Harvey, Moore Jason H, Yu Herbert, Garmire Lana X
    Oncotarget 2016
  3. EBioMedicine
    Pan-cancer analyses reveal long intergenic non-coding RNAs relevant to tumor diagnosis, subtyping and prognosis
    Ching Travers, Peplowska Karolina, Huang Sijia, Zhu Xun, Shen Yi, Molnar Janos, Yu Herbert, Tiirikainen Maarit, Fogelgren Ben, Fan Rong, others
    EBioMedicine 2016
  4. Scientific reports
    Time Series miRNA-mRNA integrated analysis reveals critical miRNAs and targets in macrophage polarization
    Lu Liangqun, McCurdy Sara, Huang Sijia, Zhu Xun, Peplowska Karolina, Tiirikainen Maarit, Boisvert William A, Garmire Lana X
    Scientific reports 2016
  5. bioRxiv
    Using Single Nucleotide Variations in Cancer Single-Cell RNA-Seq Data for Subpopulation Identification and Genotype-phenotype Linkage Analysis
    Poirion Olivier, Zhu Xun, Ching Travers, Garmire Lana
    bioRxiv 2016
  6. bioRxiv
    Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Tumor Subpopulations and Genotype-phenotype Linkage
    Poirion Olivier, Zhu Xun, Ching Travers, Garmire Lana X
    bioRxiv 2016