Xun Zhu

Bioinformatics Resch Scientist
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xun.zhuobfuscate#stjude.org

Overview

Dr. Xun Zhu is a Bioinformatics Research Scientist in the Center for Applied Bioinformatics at St Jude Children’s Research Hospital. His work focuses on the design and development of a next-generation bioinformatics workflow platform that would enable streamlined, collaborative, and reproducible biological data analysis.

Education

  • PhD, Molecular Biosciences and Bioengineering, University of Hawaii at Manoa
  • MS, Applied Mathematics, University of Southern California
  • BS, Mathematics and Applied Mathematics, Tianjin Polytechnic University

Professional Experience

Time Position PI/Supervisor Institution
2019 - Current Bioinformatics Research Scientist Gang Wu St. Jude Children’s Research Hospital, Memphis, TN
2019 Postdoctoral Researcher John Shepherd 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

2020:5

  1. 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. 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. 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. 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. 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. 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. 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. Data Analysis in Single-Cell RNA-Seq
    Zhu Xun, Garmire Lana X
    2019
  4. 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. 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. 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. 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. 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. 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. 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. 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. Single-cell transcriptomics bioinformatics and computational challenges
    Poirion Olivier B, Zhu Xun, Ching Travers, Garmire Lana
    Frontiers in genetics 2016
  2. 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. 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. 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. 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. 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