Vanderbilt-Ingram Cancer Center

The VICC.ORG Investigator Directory

Bing Zhang, Ph.D.

See also:

• Zhang Lab
• Biomedical Informatics
• BRET: Biomedical Research Education & Training Faculty Listing

Assistant Professor of Biomedical Informatics
VICC Member
Researcher

Contact Information:

Vanderbilt University Medical Center
400 Eskind Biomedical Library
Nashville, TN 37232-8340
615-936-0090

Research Specialty:

Systems biology and its application on human cancer studies; Gene expression and regulation; Knowledge-guided omics data analysis and interpretation

Publications:

• Liu, Q, Halvey, PJ, Shyr, Y, Slebos, RJ, Liebler, DC, Zhang, B Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation. Mol Cell Proteomics, 2013.
• Wang, J, Duncan, D, Shi, Z, Zhang, B WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res, 2013.
• Shi, M, Beauchamp, RD, Zhang, B A network-based gene expression signature informs prognosis and treatment for colorectal cancer patients. PLoS One, 7(7), e41292, 2012.
• Hardaway, JA, Hardie, SL, Whitaker, SM, Baas, SR, Zhang, B, Bermingham, DP, Lichtenstein, AJ, Blakely, RD Forward genetic analysis to identify determinants of dopamine signaling in Caenorhabditis elegans using swimming-induced paralysis. G3 (Bethesda), 2(8), 961-75, 2012.
• Jourquin J, Duncan D, Shi Z, Zhang B GLAD4U: deriving and prioritizing gene lists from PubMed literature. BMC Genomics, 13(Suppl 8), S20, 2012.
• Hoshino D, Jourquin J, Emmons SW, Miller T, Goldgof M, Costello K, Tyson DR, Brown B, Lu Y, Prasad NK, Zhang B, Mills GB, Yarbrough WG, Quaranta V, Seiki M, Weaver AM Network analysis of the focal adhesion to invadopodia transition identifies a PI3K-PKC?? invasive signaling axis. Sci Signal, 5(241), ra66, 2012.
• Wang, X, Slebos, RJ, 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(2), 1009-17, 2012.
• Halvey, PJ, Zhang, B, Coffey, RJ, Liebler, DC, Slebos, RJ Proteomic consequences of a single gene mutation in a colorectal cancer model. J Proteome Res, 11(2), 1184-95, 2012.
• Sousa, JF, Ham, AJ, Whitwell, C, Nam, KT, Lee, HJ, Yang, HK, Kim, WH, Zhang, B, Li, M, LaFleur, B, Liebler, DC, Goldenring, JR Proteomic profiling of paraffin-embedded samples identifies metaplasia-specific and early-stage gastric cancer biomarkers. Am J Pathol, 181(5), 1560-72, 2012.
• 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(5), M110.006536, 2011.
• Shi, Z, Zhang, B Fast network centrality analysis using GPUs. BMC Bioinformatics, 12(1), 149, 2011.
• Angel, PM, Nusinow, D, Brown, CB, Violette, K, Barnett, JV, Zhang, B, Baldwin, HS, Caprioli, RM Networked-based characterization of extracellular matrix proteins from adult mouse pulmonary and aortic valves. J Proteome Res, 10(2), 812-23, 2011.
• Zhang, B, Shi, Z, Duncan, DT, Prodduturi, N, Marnett, LJ, Liebler, DC Relating protein adduction to gene expression changes: a systems approach. Mol Biosyst, 2011.
• Shi, M, Zhang, B Semi-supervised learning improves gene expression-based prediction of cancer recurrence. Bioinformatics, 27(21), 3017-23, 2011.
• Jing Li, Dexter T Duncan, Bing Zhang CanProVar: a human cancer proteome variation database. Hum Mutat, 31(3), 219-228, 2010.
• Zhiao Shi, Catherine K Derow, Bing Zhang Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Syst Biol, 474, 2010.
• Wylie, CJ, Hendricks, TJ, Zhang, B, Wang, L, Lu, P, Leahy, P, Fox, S, Maeno, H, Deneris, ES Distinct transcriptomes define rostral and caudal serotonin neurons. J Neurosci, 30(2), 670-84, 2010.
• Smith, JJ, Deane, NG, Wu, F, Merchant, NB, Zhang, B, Jiang, A, Lu, P, Johnson, JC, Schmidt, C, Bailey, CE, Eschrich, S, Kis, C, Levy, S, Washington, MK, Heslin, MJ, Coffey, RJ, Yeatman, TJ, Shyr, Y, Beauchamp, RD Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology, 138(3), 958-68, 2010.
• Morabito, MV, Ulbricht, RJ, O''Neil, RT, Airey, DC, Lu, P, Zhang, B, Wang, L, Emeson, RB High-throughput multiplexed transcript analysis yields enhanced resolution of 5HT2C receptor mRNA editing profiles. Mol Pharmacol, 2010.
• Wang, L, Chen, X, Wolfinger, RD, Franklin, JL, Coffey, RJ, Zhang, B A unified mixed effects model for gene set analysis of time course microarray experiments. Stat Appl Genet Mol Biol, 8(1), Article 47, 2009.
• Philip Gerlee, Docent T. Lundh, Bing Zhang, Alexander R.A. Anderson Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms. J R Soc Interface, 2009.
• Simona G. Codreanu, Bing Zhang, Scott M. Sobecki, Dean D. Billheimer, Daniel C. Liebler Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal. Mol Cell Proteomics, 8(4), 670-80, 2009.
• Jing Li, Lisa J Zimmerman, Byung-Hoon Park, David L Tabb, Daniel C Liebler, Bing Zhang Network-assisted protein identification and data interpretation in shotgun proteomics. Mol Syst Biol, 5303, 2009.
• Heather L. Ball, Bing Zhang, Jacob Riches, Rikesh Gandhi, Jing Li, Johanna M. Rommens, Jeremy S. Myers SBDS is a multi-functional protein implicated in cellular stress responses. Hum Mol Genet, 2009.
• Lily Wang, Bing Zhang, Russell D. Wolfinger, Xi Chen An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet, 4(7), e1000115, 2008.
• Chongle Pan, Yasuhiro Oda, Patricia K. Lankford, Bing Zhang, Nagiza F. Samatova, Dale A. Pelletier, Caroline S. Harwood, Robert L. Hettich Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics. Mol Cell Proteomics, 7(5), 938-48, 2008.
• Wilmes, P, Andersson, AF, Lefsrud, MG, Wexler, M, Shah, M, Zhang, B, Hettich, RL, Bond, PL, VerBerkmoes, NC, Banfield, JF Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J, 2(8), 853-64, 2008.
• Bing Zhang, Byung-Hoon Park, Tatiana Karpinets, Nagiza F. Samatova From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics, 24(7), 979-86, 2008.
• Zhang, B, Park, BH, Karpinets, T, Samatova, NF From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics, 24(7), 979-86, 2008.
• Xi Chen, Lily Wang, Jonathan D. Smith, Bing Zhang Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics, 24(21), 2474-81, 2008.
• Stefan A. Kirov, Bing Zhang, Jay R. Snoddy Association analysis for large-scale gene set data. Methods Mol Biol, 40819-33, 2007.
• Bing Zhang, Matthew C. Chambers, David L. Tabb Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res, 6(9), 3549-57, 2007.
• Bing Zhang, Nathan C. VerBerkmoes, Michael A. Langston, Edward Uberbacher, Robert L. Hettich, Nagiza F. Samatova Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics. J Proteome Res, 5(11), 2909-2918, 2006.
• Nicole E. Baldwin, Elissa J. Chesler, Stefan A. Kirov, Michael A. Langston, Jay R. Snoddy, Robert W. Williams, Bing Zhang Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks. J Biomed Biotechnol, 2005(2), 172-80, 2005.
• Stefan A. Kirov, Xinxia Peng, Eric Baker, Denise Schmoyer, Bing Zhang, Jay R. Snoddy GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments. BMC Bioinformatics, 672, 2005.
• Bing Zhang, Stefan A. Kirov, Jay R. Snoddy WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res, 33(Web Server issue), W741-8, 2005.
• Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics, 516, 2004.
• Sumithra Urs, Colton Smith, Brett Campbell, Arnold M. Saxton, James Taylor, Bing Zhang, Jay Snoddy, Brynn Voy, Naima Moustaid-Moussa Gene expression profiling in human preadipocytes and adipocytes by microarray analysis. J Nutr, 134(4), 762-70, 2004.
• Bing Zhang, Katrina M. Ramonell, Shauna Somerville, Gary Stacey Characterization of early, chitin-induced gene expression in Arabidopsis. Mol Plant Microbe Interact, 15(9), 963-70, 2002.
• Katrina M. Ramonell, Bing Zhang, Yu Chen, Dong Xu, Gary Stacey, Shauna Somerville Microarray analysis of chitin elicitation in Arabidopsis. Mol Plant Pathol, 3(5), 301-311, 2002.