BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES. NAME POSITION TITLE Zhang, Bing, Ph.D. eRA COMMONS USER NAME (credential, e.g., agency login) Associate Professor of Biomedical Informatics ZHANGB3 EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) INSTITUTION AND LOCATION DEGREE (if applicable) YEAR(s) 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 B.S. M.S. Ph.D. Postdoctorate Postdoctorate 1989-1993 1993-1996 1996-1999 1999-2002 2003-2004 FIELD OF STUDY Biology Biology Molecular Genetics Functional Genomics Bioinformatics 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 1999-2002 Postdoctoral Research Fellow, Dept. of Microbiology, University of Tennessee, Knoxville, TN 2003-2004 Postdoctoral Research Fellow, Graduate School in Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 2005-2006 Research Scientist, Science Alliance, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 2006-2007 Research Assistant Professor, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 2007-2013 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 1997-1999 Member, Chinese Society of Biotechnology 2000-2002 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 Honors 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 Technology 2010 High Impact Research Award, Vanderbilt-Ingram Cancer Center 2011 Innovative Uses of NLM Information Award, National Library of Medicine (NLM) 2011 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: 3098595] 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 NIH/NIGMS $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) 07/01/2013-06/30/2016 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) 09/01/2013-08/31/2018 NIH/NCI $1,034,382/year 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 NIH/NIGMS $1,861,991/year 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 NIH/NCI $1,902,216/year 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 NIH/NCI $2,300,000/year 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 NIH/NCI $200,000/year 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 NIH/NCI $302,895/year 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 NIH/NIEHS $950,823/year 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 injury. 5 P50 MH078028-02 (Blakely) 09/15/2007 - 06/30/2012 NIH/NIMH 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 DOE 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 NIH/NCI 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 NIH/NCI 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 NIH/NCI 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.