biographical sketch - Vanderbilt University School of Medicine

Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
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Zhang, Bing, Ph.D.
eRA COMMONS USER NAME (credential, e.g., agency login)
Associate Professor of Biomedical Informatics
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
(if applicable)
Nanjing University, Nanjing, China
Nanjing University, Nanjing, China
Chinese Academy of Sciences, Shanghai, China
University of Tennessee, Knoxville, TN
Univ Tenn-Oak Ridge National Lab, Oak Ridge, TN
Molecular Genetics
Functional Genomics
A. Personal Statement.
I am an Associate Professor of Biomedical Informatics with a joint appointment in the Department of Cancer
Biology. I have more than 10 years experience in the areas of bioinformatics, proteomics and systems biology,
with more than 50 publications in these areas. The pathway analysis tool WebGestalt developed and
maintained by my group has been serving the biology community for eight years with continuously rising usage
trend (>300 daily usage count as of December 2013). I serve as principal investigator, bioinformatics core
director or co-investigator on several NIH grants. The primary focus of my group is to develop integrative
bioinformatics approaches that help translate experimental data into biological and clinical insights.
B. Positions and Honors.
Positions and Employment
Postdoctoral Research Fellow, Dept. of Microbiology, University of Tennessee, Knoxville, TN
Postdoctoral Research Fellow, Graduate School in Genome Science and Technology,
University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN
Research Scientist, Science Alliance, University of Tennessee-Oak Ridge National Laboratory,
Oak Ridge, TN
Research Assistant Professor, Department of Biomedical Informatics, Vanderbilt University,
Nashville, TN
Assistant Professor, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
2009Visiting Professor, Shanghai Center for Bioinformation Technology, Shanghai, China
2010Assistant Professor (secondary appointment), Department of Cancer Biology, Vanderbilt
University, Nashville, TN
2013Associate Professor, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
Professional Memberships
Member, Chinese Society of Biotechnology
Member, American Society of Plant Physiologists
2003Member, International Society for Computational Biology
2012Member, American Association for Cancer Research
2013Member, American Society for Biochemistry and Molecular Biology
1995 Second Place in the First Academic Works Contest of Nanjing University
1996 Outstanding Graduate Student of Nanjing University
1997 National Prize for Advancements in Science and Technology, Chinese Committee of Science and
2010 High Impact Research Award, Vanderbilt-Ingram Cancer Center
2011 Innovative Uses of NLM Information Award, National Library of Medicine (NLM)
Excellent Young Scientist Award, 3rd International Conference on Computational and Systems Biology
(ICCSB), Shanghai, China
C. Peer-reviewed publications or manuscript in press (in chronological order).
(Publications selected from 66 peer-reviewed publications)
1. Zhang B, Kirov S. Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological
contexts. Nucleic Acids Res, 33:W741-748, 2005 [PMCID: 1160236]
2. Zhang B, VerBerkmoes NC, Langston MA, Uberbacher E, Hettich RL, Samatova NF. Detecting differential
and correlated protein expression in label-free shotgun proteomics. J Proteome Res, 5:2909-2918, 2006
[PMID: 17081042]
3. Zhang B, Chambers M, Tabb D. Proteomic Parsimony through bipartite graph analysis improves accuracy
and transparency. J Proteome Res, 6:3549-3557, 2007 [PMCID: 2810678]
4. Zhang B, Park B, Karpinets T, Samatova NF. From pull-down data to protein interaction networks and
complexes with biological relevance. Bioinformatics, 24:979-986, 2008 [PMID: 18304937]
5. Li J, Zimmerman LJ, Park BH, Tabb DL, Liebler DC, Zhang B. Network-assisted protein identification and
data interpretation in shotgun proteomics. Mol Syst Biol, 5:303, 2009 [PMCID: 2736651]
6. Li J, Su Z, Ma ZQ, Slebos RJ, Halvey P, Tabb DL, Liebler DC, Pao W, Zhang B. A bioinformatics workflow
for variant peptide detection in shotgun proteomics. Mol Cell Proteomics, 10:M110.006536, 2011 [PMCID:
7. Zhang B, Shi Z, Duncan DT, Prodduturi N, Marnett LJ, Liebler DC. Relating protein adduction to gene
expression changes: a systems approach. Mol Biosyst, 7:2118-2127, 2011 [PMID: 21594272]
8. Shi M, Zhang B. Semi-supervised learning improves gene expression-based prediction of cancer
recurrence. Bioinformatics, 27:3017-3023, 2011 [PMCID: 3198572]
9. Wang X, Slebos RJC, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B. Protein identification using
customized protein sequence databases derived from RNA-Seq data. J Proteome Res. 11:1009-1017,
2012. [PMCID: 3727138]
10. Shi M, Beauchamp RD, Zhang B. A network-based gene expression signature informs prognosis and
treatment for colorectal cancer patients. PLoS One, 7:e41292, 2012. [PMCID: 3402487]
11. Liu Q, Ullery J, Zhu J, Liebler DC, Marnett LJ, Zhang B. RNA-seq data analysis at the gene and CDS levels
provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal. Mol Biosyst,
9:3036-3046, 2013. [PMCID: 3864034]
12. Wang X, Zhang B. customProDB: an R package for generating customized protein databases from next
generation sequencing data. Bioinformatics, 29:3235-3237, 2013. [PMCID: 3842753]
13. Liu Q, Halvey PJ, Shyr Y, Slebos RJC, Liebler DC, Zhang B. Integrative omics analysis reveals the
importance and scope of translational repression in microRNA-mediated regulation. Mol Cell Proteomics,
12:1900-1911, 2013. [PMCID: 3708174]
14. Wang J, Duncan D, Shi Z, Zhang B. Web-based gene set analysis toolkit (WebGestalt): update 2013.
Nucleic Acids Res, 41:W77-83, 2013. [PMCID: 3692109]
15. Shi Z, Wang J, Zhang B. NetGestalt: integrating multidimensional omics data over biological networks.
Nature Methods, 10:597-598, 2013. [PMID: 23807191]
D. Research Support
Active Research Support
5 R01 GM088822-04 (Zhang/Beauchamp)
08/20/2009 – 06/30/2014
$1,535,603 total
Systems Approach to the Biological Basis of Colon Cancer Metastases
Role: Principal Investigator
The long-term goal of this project is to use integrative systems biology approaches to investigate the molecular
mechanisms that underlie colorectal cancer (CRC) metastasis in order to develop new strategies for the
prognosis and treatment of CRC patients.
SAIC 13XS029 (Zhang)
SAIC Frederick, Inc.
$967,875 total
Network-based integration, visualization and analysis of TCGA/CPTAC data
Role: Principal Investigator
This project will support the continuous development of NetGestalt, a web application for integrating
multidimensional omic data over biological networks. NetGestalt will be used to build a cancer omics data
browser for data generated from the NCI TCGA and CPTAC projects.
1 U19 CA179514 (Coffey)
Secreted RNA during CRC progression biogenesis function and clinical markers
Role: Bioinformatics and biotechnology core director
This grant proposal includes two projects as well as one core and will focus on understanding the biogenesis of
exosome-associated, secreted RNAs during CRC progression.
1 P50 MH096972-01 (Blakely)
07/01/2012 – 06/30/2017
Enduring Effects of Early-Life Serotonin Signaling
Role: Bioinformatics and biostatistics core director
Autism Spectrum Disorder (ASD) is increasingly realized to be much more prevalent than previously believed.
Our research focuses on a newly developed animal model carrying an ASD-associated gene variant in the
serotonin transporter (SERT). SERT is responsibility for inactivating serotonin in the brain and periphery and
we suspect that altered availability of serotonin contributes to multiple components of ASD.
1 U24 CA159988-01 (Liebler)
08/26/2011 – 07/31/2016
Vanderbilt Proteome Characterization Center
Role: Co-Investigator, co-director of the discovery unit
This application proposes the Vanderbilt Proteome Characterization Center (Vanderbilt PCC) built on the
expertise and infrastructure of the Ayers Institute. The overall goal of the Vanderbilt PCC is to integrate
genomic information with proteomic technologies to discover and verify protein biomarkers for cancer.
5 P50 CA095103-10 (Coffey)
09/07/2012 – 04/30/2017
SPORE in GI Cancer
Role: Co-Investigator
This SPORE continues to focus on colorectal cancer, the second leading cause of cancer deaths in the US,
where it affects more men and women than all other gastrointestinal malignancies combined.
2 R01 CA069457-16A1 (Beauchamp)
08/01/2012 – 05/31/2017
EMT Regulation in Gastrointestinal Epithelial Cells
Role: Co-Investigator
The long-term goal of our laboratory is to delineate the mechanisms that drive colorectal carcinogenesis and
tumor progression and to identify improved prognostic biomarkers and novel therapeutic targets in colon
cancer to improve care of cancer patients.
1 R01 CA158472-01A1 (Chen/Beauchamp) 08/01/2012 – 05/31/2017
Integrative Prediction Models for Metastasis Risk in Colon Cancer
Role: Co-Investigator
The long-term goal for this proposal is to develop a clinically useful metastasis score from diverse type of data
that can be applied to stage II and III colon cancer patients for the purpose of reducing mortality, morbidity, and
the cost associated with colon cancer and colon cancer treatment.
Completed Research Support
5 P01 ES013125-08 (Porter)
09/15/2008 – 06/30/2013
Lipid Peroxidation and Antioxidant Mechanisms
Role: Co-Investigator
The studies proposed in this competitive renewal application will test the hypothesis that the balance of
competing oxidation pathways for different lipid substrates governs adaptation to oxidative stress and oxidative
5 P50 MH078028-02 (Blakely)
09/15/2007 - 06/30/2012
Genes Controlling Assembly and Function of Serotonin Systems
Role: Bioinformatics and Biostatistics Core Director
This proposal seeks the creation of an NIMH Silvio O. Conte Center for Neuroscience Research at Vanderbilt
University to investigate "Genes Controlling Assembly and Function of Serotonin Systems".
DOE-ORNL subcontract (Zhang)
12/22/2008 – 03/31/2010
Comparative analysis of proteomics datasets
Role: Principal Investigator
In this project, we will use statistical methods established in our group to analyze microbial proteome datasets,
in particular for the bacterium Pseudomonas putida investigated under a DOE-ERSP project at ORNL. We will
extend the computational/statistical methods for the analysis of metaproteome datasets, in particular for
microbial community proteome research under a DOE-GTL project at ORNL.
5P50CA095103-10 (Coffey)
07/25/2007 - 04/30/2012
SPORE in GI cancer
Role: Co-investigator
The major goal of this project is to investigate the molecular features of gastrointestinal tumors.
5 R01 CA126218-03 ( Tabb)
09/27/2006 - 07/31/2011
New Proteomic Algorithms to Identify Mutant or Modified Proteins
Role: Co-investigator
This project focuses upon the development of an automated infrastructure for sequence tag identification of
proteins bearing mutations and post-translational modifications. New tools to assemble these peptide
identifications into proteins in light of sequence homology are also proposed.
5 U54 CA113007-04 (Quaranta)
09/30/2005 - 03/31/2010
Multiscale Mathematical Modeling of Cancer Invasion
Role: Co-investigator
This project will produce mathematical models and simulation software that describe quantitatively the process
of cancer invasion and encapsulate the knowledge derived from a wide range of experimental observations
into a correlative and predictive tool.