Computational Bioinformatics and Bioimaging Laboratory (CBIL)


 
 

Internal Use

 

 

  • (Henry) Xu Shi, Ph.D. Postdoctoral Associate, Yale University

    (GRA at CBIL, Fall 2012 - Fall 2017; Dissertation: Bayesian Modeling for Isoform Identification and Phenotype-specific Transcript Assembly)

  • Xiao Wang, Ph.D., Senior Scientist, Rinat-Pfizer Inc.

    (GRA at CBIL, Fall 2011 - Summer 2016; Dissertation: Computational Modeling for Differential Analysis of RNA-seq and Methylation Data)

  • Xi Chen, Ph.D., Research Fellow, Simons Foundation

    (GRA at CBIL, Fall 2011 - Spring 2016; Dissertation: Bayesian Integration and Modeling for Next-generation Sequencing Data Analysis)

  • Chen Wang, Ph.D., Assistant Professor of Medical Informatics, Mayo College of Medicine (Mayo Clinic)

    (GRA at CBIL, Fall 2006 - Summer 2011; Dissertation: From network to pathway - integrative network analysis of genomic data)

  • (Julia) Yuji Zhang, Ph.D., Assistant Professor, Division of Biostatistics and Bioinformatics, Department of Epidemiology & Public Heath, School of Medicine, University of Maryland at Baltimore

    (GRA at CBIL: Fall 2005 - Summer 2010; Dissertation: Module-based analysis of biological data for network inference and biomarker discovery)

    Ting Gong, Ph.D., Data Scientist, Intel Corp.

    [Assistant Professor of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 2012-2016]

    [Postdoc at Novartis Institutes for Biomedical Research (NIBR), 2010 - 2012]

    (GRA at CBIL: Fall 2004 - Fall 2009; Dissertation: Computational dissection of composite molecular signatures and transcriptional modules)

    Sook S. Ha, Ph.D., Assistant Professor, Dept. of Computer and Information Sciences, Virginia Military Institute

    [Postdoctoral Associate & Computational Biologist, Virginia Bioinformatics Institute, Virginia Tech, 2012-2015]

    (Doctoral graduate student, Fall 2006 - Summer 2012; Dissertation: Statistical learning and informational visualization for bioinformatics )

  • Jun Ruan, Ph.D., Wuhan University of Technology, Software development

  • Liang Zhao, Ph.D., Xian University of Technology, Software development

  • Ibrahim Mohamed Ibrahim, PhD (doctoral graduate student, Fall 2012 - Fall 2016): DCE-MRI data modeling, DNA copy number data modeling and analysis, clinical prediction

  • Niya Wang (doctoral graduate research assistant, Fall 2010 - May 2015)(MS; Tsinghua U)(e-mail: wangny@vt.edu): CAM-nICA/nWCA/NMF-MDL for tissue heterogeneity deconvolution (imaging, mRNA, methylation, CNAs, protein), SIGH-based intratumor/intra-tissue genomic heterogeneity via NGS modeling and analysis.

  • Mohammad R. Nezami Ranjbar (doctoral graduate research assistant, Fall 2010 - May 2015)(MS; Sharif U Technology)(e-mail: nranjbar@vt.edu): Experimental design, quality assessment, data normalization, and data analysis for LC-MS based metabolamics and proteomics with application to biomarker discovery.

  •  
    Zuyi Wang, Ph.D. (1998-2003, GRA), Assistant Professor, Department of Integrative Systems Biology, George Washington University.
     
  • Ye Tian, Ph.D., Google Corporation (doctoral graduate research assistant, Fall 2009 - August 2014)(BS&MS; Tsinghua U)(e-mail: tianye@vt.edu): Genotype/phenotype-defined differential dependence network (DDN), identifying condition-specific significant rewiring of dependencies in biological networks (knowledge-guided and multiplatform), nBTL (network Binary Trait Loci, network-attacking mutations), prioritization of networked biomarkers (CPTAC), origin of tumor.

  • Tsung-Heng Tsai, Ph.D., (doctoral graduate research assistant, Fall 2009 - Dec. 2013)(MS Tsinghua U)(e-mail: thtsai@vt.edu): LC-MS data alignment using Bayesian approaches, variability assessment for LC-MS experiments.

  • Sharmi Benerjee (doctoral graduate research assistant, Summer 2014 - present; GTA, Fall 2013 - Spring 2014)(B-Tech, St. Thomas College of Engg & Tech, India; MS, Texas Tech University)(e-mail: bsharmi6@vt.edu): Analysis of next-gen sequencing data, proteomics, etc.

  • (Bella) Xuchu Hou (master graduate research assistant, Fall 2010 - Winter 2012)(MS; Tsinghua U)(e-mail: bella@vt.edu): Significant aberrations in cancer (BACOM+SAIC).

  • Steven Lin, Ph.D. (Summer 2015 - Summer 2016), National Tsinghua University, Convex analysis of mixtures, complex network, multivariate association network

  • Bai Zhang, PhD, Research Associate, Johns Hopkins University (doctoral graduate research assistant, Fall 2006 - Summer 2011)(MS; Tsinghua U)(e-mail: baizhang@vt.edu): Differential dependence network for differential analysis of biological network, graphic model learning, echo state network characterization and learning, CNA characterization of tumor progression as determinants of phenotypic biological network, in silico correction of normal cell contamination in copy number data

    Guoqiang Yu, PhD, Postdoc, Stanford University (doctoral graduate research assistant, Fall 2006 - Summer 2011)(MS; Tsinghua U)(e-mail: yug@vt.edu): PUG-OVRSVM for multiclass gene selection and predictive classification, SCA-HCIG for detecting interactive SNPs, in silico correction of normal cell contamination in copy number data, significance approximation of dependent genotype in multiple testing, tumor clonality analysis, inference of complex SNP interaction modules

  • (Frank) Jinghua Gu, Ph.D., Research Associate II at The Baylor Institute for Immunology Research (BIIR) of Baylor Heath Care System

    (GRA at CBIL: Fall 2009 - Summer 2013; Dissertation: Novel Monte Carlo approaches to identify aberrant pathways in cancer)

  • Otto Barnes, M.S. SAIC

    (Part-time master graduate student, Fall 2012 - Spring 2013; Thesis: Concurrency optimization for integrative network analysis )

  • (Mike) Yiming Zuo, PhD (Fall 2012 - Spring 2017)(BS, U Zhejiang)(e-mail: zyiming@vt.edu): Biological signaling network inference

  • (Kevin) Minkun Wang, PhD (Fall 2012 - Spring 2017)(BS, USTC)(e-mail: minkunwang@vt.edu): Proteomics data analysis

  • Qing Sun (doctoral graduate research assistant, Fall 2012 - Summer 2013)(BS&MS; Tianjin U)(e-mail: qingsun@vt.edu): Genome/pathway-wide detection of interacting genomic/epigenetic loci and environment variables, fMRI-GWAS

  • Li Chen, PhD, Research Scientist (Bioinformatics), National Cancer Institute (doctoral graduate research assistant, Fall 2006 - Summer 2011)(MS; Shanghai Jiaotong U)(e-mail: chen2000@vt.edu): DCE-MRI (CAM-nWCA blind source separation), sparse multiplicative linear regression (lasso, matrix completion) for detecting interactive SNPs and high dimensional clinical decision making, comparative analysis of interactive SNP detection methods (simulation, etc), tumor clonality analysis and origin of ovarian cancer

  • (Tracey) Ji Wang (doctoral graduate research assistant, Fall 2012)(BS, HIT; MS, UMN)(e-mail: traceyw@vt.edu): Analysis of next-gen sequencing data, Bayesian modeling of epigenetic data, etc.

  • (Lily) Li Chen, Ph.D., Bioinformatics Analyst III, Molecular Characterization & Clinical Assay Development Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research

    [Research Associate, Division of Clinical Chemistry, Dept. of Pathology, Johns Hopkins University, 2010 - 2016]

    (GRA at CBIL: Spring 2007 - Fall 2010; Dissertation: Integrative modeling and analysis of high-throughput biological data)

    Tom (Weidong) Cai, Ph.D., Visiting Scientist, School of Information Technologies, The University of Sydney: Biomedical Imaging

    Xiguo Yuan (visiting GRA, Fall 2009 - Fall 2010)(Spring 2013), Ph.D., Research Scientist, Xidian University: Accurate Identification of Significant Aberrations in Cancer (AISAIC), inter-tumor heterogeneity (subtypes) in copy number space, removal of normal cell contamination (confounding factor), cancer ploidy estimation and feature analysis, Epistatic SNP interaction modeling and simulation, CNA/indel characterization

    Fan Meng, M.S. (Fall 2010 - Summer 2012)(BS&MS; Tsinghua U): Software development for biomedical applications

  • Guo Zhiqiang (July 2012 - June 2013), Ph.D., Visiting Scholar, School of Information Engineering, Wuhan University of Technology: Image Processing

  • (Jack) Shibiao Wan (visiting doctoral student, Spring 2013 - Summer 2013)(Hong Kong PolyU)(e-mail: jackwan2010@gmail.com): Proteomics data analysis

  • Lei Song , M.S., Bioinformatics Engineer, Georgetown University Lombardi Cancer Center (master graduate research assistant, Fall 2008 - May 2011)(MS U Sci Tech U): Practice of real SNP data analysis, CNV detection and CNV-feature extraction, inference of complex interaction models

    Yitan Zhu, Ph.D., Staff Scientist, Boston (Spring 2004 - Summer 2009, GRA)

    Chu-Chuan (JJ) Liu, Ph.D., US Patent Office (GRA, Fall 2003 - Fall 2009): Transmission and reflective ultrasound projection and tomographic imaging

    Yuanjian Feng, Ph.D., Staff Scientist, San Francisco (GRA, Fall 2004 - Spring 2010)(MS Shanghai Jiaotong U)(e-mail: yjfeng@vt.edu): CNV detection, CIN index/feature extraction, tree of phenotype (stability analysis), SNP detection and assessment (SVM-SFFS/RPT)

  • Mohammed Mamdouh Zakaria, M.S. (doctoral graduate student, Fall 2008 - Fall 2013): Copy number signal processing and CNV/CNA characterization

  • Lihua Li, Ph.D., Adjunct Professor of Electrical and Computer Engineering, Director and Chair Professor, Institute for Biomedical Engineering and Instrumentation, Hangzhou Dianzi University

  • Qing Liu, Ph.D., Research Associate Professor: Integrated genomic and epigenetic data modeling and association

  • Yimo Tao, M.S., Microsoft Corporation

    (GRA at CBIL: Fall 2006 - May 2010; Thesis: Multi-Level learning approaches for medical image understanding, computer-aided detection and diagnosis)

  • Guodong Sun, Ph.D., Visiting Scholar, Hubei University of Technology: Computer vision, object recognition, visual learning, medical imaging.

  • Bin Zhou, MS, Georgetown University (Fall 2006 - Fall 2011)(MS; U of Zhejiang): Polarization cellular/tissue imaging (feature extraction and classification); multispectral polarization imaging; motion analysis for adaptive radiation therapy, proteomics data analysis

    Lu Jin, M.S., Bioinformatics Engineer, Georgetown University (GRA, Spring 2008 - May 2010) caBIG bioinformatics software development

    Tsung-Han Chan, Ph.D., Research Associate, National Tsinghua University (Summer 2007, Spring 2008 - Spring 2009, GRA)

  • Xuelin (Nick) Cui (doctoral graduate student, Fall 2013 - present)(BS, Southeast U; MS, Vanderbilt U)(e-mail: xuelincui@gmail.com): Medical imaging reconstruction.

  • Andy Srikanchana, Ph.D. (2003), National Institutes of Health
     
    Hui Zhao, Ph.D. (2003), Kodak
     
    Junying Zhang, Ph.D. (2007; 2001, visiting scholar), Professor of ECE, Xidian University
     
    Su Zhang, Ph.D. (2007, visiting scholar), Associate Professor of Biomedical Eng., Shanghai Jiaotong University
     
    Jianping (James) Lu, M.S. (2007; 2000-2002, visiting scholar), Professor of ECE, Suzhou University
     
    Bin Wang, M.S. (2007), Cornell University
     
    Uwe Klimach, M.S. (2005), Georgetown University Medical Center
    Kun Huang, M.S. (2002), University of South Alabama
     
    Kelvin Woods, Ph.D. (2000), SAIC
     
    Maxine McClain, M.S. (2000), Georgia Tech
     
    Ping Yu, M.S. (2000)

    Lan Luo, M.S. (2000)
     
    Haizhou Ding, M.S. (1998)

     


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    Last Updated: 02/16/2013. Suggestions/Comments - Webmaster