Bing Zhang, Ph.D.

Associate Professor

bing.zhang@vanderbilt.edu

Visit Lab Site


Faculty Appointments
Associate Professor of Biomedical Informatics
Education
Ph.D., Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai, ChinaM.S., Biology, Nanjing University of Technology, Nanjing, ChinaB.S., Biology, Nanjing University of Technology, Nanjing, China
Office Address
Suite 1475, 2525 West End Ave
2525 West End Ave
Nashville, TN 37203
Research Description
see <a href=http://bioinfo.vanderbilt.edu/zhanglab/?q=node/1>Zhang Lab Research page</a>
Research Keywords
Network medicine, proteogenomics, democratization of bioinformatics
Publications
Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, . Proteogenomic characterization of human colon and rectal cancer. Nature [print-electronic]. 2014 Sep 9/18/2014; 513(7518): 382-7. PMID: 25043054, PMCID: PMC4249766, PII: nature13438, DOI: 10.1038/nature13438, ISSN: 1476-4687.

Wang X, Zhang B. Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics. J. Proteome Res [print-electronic]. 2014 Jun 6/6/2014; 13(6): 2715-23. PMID: 24792918, PMCID: PMC4059263, DOI: 10.1021/pr500194t, ISSN: 1535-3907.

Halvey PJ, Wang X, Wang J, Bhat AA, Dhawan P, Li M, Zhang B, Liebler DC, Slebos RJ. Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair. Cancer Res [print-electronic]. 2014 Jan 1/1/2014; 74(1): 387-97. PMID: 24247723, PMCID: PMC3896054, PII: 0008-5472.CAN-13-2488, DOI: 10.1158/0008-5472.CAN-13-2488, ISSN: 1538-7445.

Wang X, Zhang B. CustomProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search. Bioinformatics [print-electronic]. 2013 Dec 12/15/2013; 29(24): 3235-7. PMID: 24058055, PMCID: PMC3842753, PII: btt543, DOI: 10.1093/bioinformatics/btt543, ISSN: 1367-4811.

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 [print-electronic]. 2013 Dec; 9(12): 3036-46. PMID: 24056865, PMCID: PMC3864034, DOI: 10.1039/c3mb70114j, ISSN: 1742-2051.

Wang J, Duncan D, Shi Z, Zhang B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res [print-electronic]. 2013 Jul; 41(Web Server issue): W77-83. PMID: 23703215, PMCID: PMC3692109, PII: gkt439, DOI: 10.1093/nar/gkt439, ISSN: 1362-4962.

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 [print-electronic]. 2013 Jul; 12(7): 1900-11. PMID: 23550052, PMCID: PMC3708174, PII: M112.025783, DOI: 10.1074/mcp.M112.025783, ISSN: 1535-9484.

Shi Z, Wang J, Zhang B. NetGestalt: integrating multidimensional omics data over biological networks [letter]. Nat. Methods. 2013 Jul; 10(7): 597-8. PMID: 23807191, PMCID: PMC3951100, PII: nmeth.2517, DOI: 10.1038/nmeth.2517, ISSN: 1548-7105.

Zhu J, Wang J, Shi Z, Franklin JL, Deane NG, Coffey RJ, Beauchamp RD, Zhang B. Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis. PLoS ONE. 2013; 8(11): e79282. PMID: 24260186, PMCID: PMC3829853, PII: PONE-D-13-34057, DOI: 10.1371/journal.pone.0079282, ISSN: 1932-6203.

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 [print-electronic]. 2012 Nov; 181(5): 1560-72. PMID: 22944598, PMCID: PMC3483808, PII: S0002-9440(12)00597-4, DOI: 10.1016/j.ajpath.2012.07.027, ISSN: 1525-2191.

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) [print-electronic]. 2012 Aug; 2(8): 961-75. PMID: 22908044, PMCID: PMC3411251, PII: GGG_003533, DOI: 10.1534/g3.112.003533, ISSN: 2160-1836.

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 [print-electronic]. 2012 Feb 2/3/2012; 11(2): 1009-17. PMID: 22103967, PMCID: PMC3727138, DOI: 10.1021/pr200766z, ISSN: 1535-3907.

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 [print-electronic]. 2012 Feb 2/3/2012; 11(2): 1184-95. PMID: 22103262, PMCID: PMC3271737, DOI: 10.1021/pr2009109, ISSN: 1535-3907.

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. 2012.

Shi M, Beauchamp RD, Zhang B. A network-based gene expression signature informs prognosis and treatment for colorectal cancer patients. PLoS ONE [print-electronic]. 2012; 7(7): e41292. PMID: 22844451, PMCID: PMC3402487, PII: PONE-D-12-08786, DOI: 10.1371/journal.pone.0041292, ISSN: 1932-6203.

Jourquin J, Duncan D, Shi Z, Zhang B. GLAD4U: deriving and prioritizing gene lists from PubMed literature. BMC Genomics [print-electronic]. 2012; 13 Suppl 8: S20. PMID: 23282288, PMCID: PMC3535723, PII: 1471-2164-13-S8-S20, DOI: 10.1186/1471-2164-13-S8-S20, ISSN: 1471-2164.

Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr Y. Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genomics [print-electronic]. 2012; 13 Suppl 8: S8. PMID: 23281772, PMCID: PMC3535703, PII: 1471-2164-13-S8-S8, DOI: 10.1186/1471-2164-13-S8-S8, ISSN: 1471-2164.

Shi M, Zhang B. Semi-supervised learning improves gene expression-based prediction of cancer recurrence. Bioinformatics [print-electronic]. 2011 Nov 11/1/2011; 27(21): 3017-23. PMID: 21893520, PMCID: PMC3198572, PII: btr502, DOI: 10.1093/bioinformatics/btr502, ISSN: 1367-4811.

Zhang B, Shi Z, Duncan DT, Prodduturi N, Marnett LJ, Liebler DC. Relating protein adduction to gene expression changes: a systems approach. Mol Biosyst [print-electronic]. 2011 Jul; 7(7): 2118-27. PMID: 21594272, PMCID: PMC3659419, DOI: 10.1039/c1mb05014a, ISSN: 1742-2051.

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 [print-electronic]. 2011 May; 10(5): M110.006536. PMID: 21389108, PMCID: PMC3098595, PII: M110.006536, DOI: 10.1074/mcp.M110.006536, ISSN: 1535-9484.

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 [print-electronic]. 2011 Feb 2/4/2011; 10(2): 812-23. PMID: 21133377, PMCID: PMC3139330, DOI: 10.1021/pr1009806, ISSN: 1535-3907.

Shi Z, Zhang B. Fast network centrality analysis using GPUs. BMC Bioinformatics. 2011; 12: 149. PMID: 21569426, PMCID: PMC3115853, PII: 1471-2105-12-149, DOI: 10.1186/1471-2105-12-149, ISSN: 1471-2105.

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 5-hydroxytryptamine 2C receptor mRNA editing profiles. Mol. Pharmacol [print-electronic]. 2010 Jun; 77(6): 895-902. PMID: 20181818, PMCID: PMC2879922, PII: mol.109.061903, DOI: 10.1124/mol.109.061903, ISSN: 1521-0111.

Li J, Duncan DT, Zhang B. CanProVar: a human cancer proteome variation database. Hum. Mutat. 2010 Mar; 31(3): 219-28. PMID: 20052754, PMCID: PMC2829365, DOI: 10.1002/humu.21176, ISSN: 1098-1004.

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 [print-electronic]. 2010 Mar; 138(3): 958-68. PMID: 19914252, PMCID: PMC3388775, PII: S0016-5085(09)01964-7, DOI: 10.1053/j.gastro.2009.11.005, ISSN: 1528-0012.

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. 2010 Jan 1/13/2010; 30(2): 670-84. PMID: 20071532, PMCID: PMC3403750, PII: 30/2/670, DOI: 10.1523/JNEUROSCI.4656-09.2010, ISSN: 1529-2401.

Shi Z, Derow CK, Zhang B. Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Syst Biol. 2010; 4: 74. PMID: 20507583, PMCID: PMC2902438, PII: 1752-0509-4-74, DOI: 10.1186/1752-0509-4-74, ISSN: 1752-0509.

Gerlee P, Lundh T, Zhang B, Anderson AR. Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms. J R Soc Interface [print-electronic]. 2009 Dec 12/6/2009; 6(41): 1233-45. PMID: 19324678, PMCID: PMC2817152, PII: rsif.2008.0514, DOI: 10.1098/rsif.2008.0514, ISSN: 1742-5662.

Ball HL, Zhang B, Riches JJ, Gandhi R, Li J, Rommens JM, Myers JS. Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses. Hum. Mol. Genet [print-electronic]. 2009 Oct 10/1/2009; 18(19): 3684-95. PMID: 19602484, PMCID: PMC2742402, PII: ddp316, DOI: 10.1093/hmg/ddp316, ISSN: 1460-2083.

Codreanu SG, Zhang B, Sobecki SM, Billheimer DD, Liebler DC. Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal. Mol. Cell Proteomics [print-electronic]. 2009 Apr; 8(4): 670-80. PMID: 19054759, PMCID: PMC2667350, PII: M800070-MCP200, DOI: 10.1074/mcp.M800070-MCP200, ISSN: 1535-9484.

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 [print-electronic]. 2009; 5: 303. PMID: 19690572, PMCID: PMC2736651, PII: msb200954, DOI: 10.1038/msb.2009.54, ISSN: 1744-4292.

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 [print-electronic]. 2009; 8: Article 47. PMID: 19954419, PMCID: PMC2861317, DOI: 10.2202/1544-6115.1484, ISSN: 1544-6115.

Chen X, Wang L, Smith JD, Zhang B. Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics [print-electronic]. 2008 Nov 11/1/2008; 24(21): 2474-81. PMID: 18753155, PMCID: PMC2732277, PII: btn458, DOI: 10.1093/bioinformatics/btn458, ISSN: 1367-4811.

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 [print-electronic]. 2008 Aug; 2(8): 853-64. PMID: 18449217, PII: ismej200838, DOI: 10.1038/ismej.2008.38, ISSN: 1751-7370.

Wang L, Zhang B, Wolfinger RD, Chen X. An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet [print-electronic]. 2008 Jul; 4(7): e1000115. PMID: 18852846, PMCID: PMC2565842, DOI: 10.1371/journal.pgen.1000115, ISSN: 1553-7404.

Pan C, Oda Y, Lankford PK, Zhang B, Samatova NF, Pelletier DA, Harwood CS, Hettich RL. Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics. Mol. Cell Proteomics [print-electronic]. 2008 May; 7(5): 938-48. PMID: 18156135, PII: M700147-MCP200, DOI: 10.1074/mcp.M700147-MCP200, ISSN: 1535-9484.

Zhang B, Park BH, Karpinets T, Samatova NF. From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics [print-electronic]. 2008 Apr 4/1/2008; 24(7): 979-86. PMID: 18304937, PII: btn036, DOI: 10.1093/bioinformatics/btn036, ISSN: 1367-4811.

Bing Zhang, Byung-Hoon Park, Tatiana Karpinets, Nagiza F. Samatova. From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics. 2008; 24((7)): 979-86.

Zhang B, Chambers MC, Tabb DL. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J. Proteome Res [print-electronic]. 2007 Sep; 6(9): 3549-57. PMID: 17676885, PMCID: PMC2810678, DOI: 10.1021/pr070230d, ISSN: 1535-3893.

Kirov SA, Zhang B, Snoddy JR. Association analysis for large-scale gene set data. Methods Mol. Biol. 2007; 408: 19-33. PMID: 18314575, DOI: 10.1007/978-1-59745-547-3_2, ISSN: 1064-3745.

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. 2006 Nov; 5(11): 2909-18. PMID: 17081042, DOI: 10.1021/pr0600273, ISSN: 1535-3893.

Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005 Jul 7/1/2005; 33(Web Server issue): W741-8. PMID: 15980575, PMCID: PMC1160236, PII: 33/suppl_2/W741, DOI: 10.1093/nar/gki475, ISSN: 1362-4962.

Baldwin NE, Chesler EJ, Kirov S, Langston MA, Snoddy JR, Williams RW, Zhang B. Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks. J. Biomed. Biotechnol. 2005 Jun 6/30/2005; 2005(2): 172-80. PMID: 16046823, PMCID: PMC1184052, PII: S111072430440610X, DOI: 10.1155/JBB.2005.172, ISSN: 1110-7243.

Kirov SA, Peng X, Baker E, Schmoyer D, Zhang B, Snoddy J. GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments. BMC Bioinformatics. 2005; 6: 72. PMID: 15790402, PMCID: PMC1274265, PII: 1471-2105-6-72, DOI: 10.1186/1471-2105-6-72, ISSN: 1471-2105.

Urs S, Smith C, Campbell B, Saxton AM, Taylor J, Zhang B, Snoddy J, Jones Voy B, Moustaid-Moussa N. Gene expression profiling in human preadipocytes and adipocytes by microarray analysis. J. Nutr. 2004 Apr; 134(4): 762-70. PMID: 15051823, ISSN: 0022-3166.

Zhang B, Schmoyer D, Kirov S, Snoddy J. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics. 2004 Feb 2/18/2004; 5: 16. PMID: 14975175, PMCID: PMC373441, PII: 1471-2105-5-16, DOI: 10.1186/1471-2105-5-16, ISSN: 1471-2105.

Zhang B, Ramonell K, Somerville S, Stacey G. Characterization of early, chitin-induced gene expression in Arabidopsis. Mol. Plant Microbe Interact. 2002 Sep; 15(9): 963-70. PMID: 12236603, DOI: 10.1094/MPMI.2002.15.9.963, ISSN: 0894-0282.

Katrina M. Ramonell, Bing Zhang, Yu Chen, Dong Xu, Gary Stacey, Shauna Somerville. Microarray analysis of chitin elicitation in Arabidopsis. Mol Plant Pathol. 2002; 3((5)): 301-11.

Available Postdoctoral Position Details
Posted: 1/2/2015
Postdoctoral Position in Proteo-genomic data integration

A postdoctoral research scientist position is available to study proteo-genomic data integration in Dr. Bing Zhang||||s group at the Department of Biomedical Informatics, Vanderbilt University. We are involved in several large projects that collect multidimensional omics data at DNA, mRNA and protein levels for the same set of biological samples. Although big data presents big opportunities, integrative analysis of these different types of data is complex and challenging. The postdoctoral research scientist is expected to develop innovative proteo-genomic data integration approaches that help reveal novel biological insights from multidimensional omics data. Some examples can be found in our recent publications: Liu et al. MCP, 2013; Wang et al. JPR, 2012; Li et al. MCP, 2011; and Zhang et al. Mol Biosyst, 2011. We are particularly interested in understanding how genomic alterations affect protein output and activity, and how this information can be used to improve disease management.

The position offers an excellent opportunity to conduct research in a supportive and stimulating environment, and to collaborate with bioinformaticians, biostatisticians, computer scientists, and biologists.

Required Skills:
1. At least 3 years experience in one or more of the following languages: Perl, Python, C, C++
2. Strong programming skills in R
3. Hands-on experience with next generation sequencing and/or shotgun proteomics data analysis
4. Good spoken and written communication skills, with the later supported by peer-reviewed publications

Desired Skills:
1. Knowledge of molecular biology
2. Experience with machine learning algorithms
3. Experience with web application and database development

Education:
Candidates must have a Ph. D. in bioinformatics, computer science, biostatistics, biology, or a related field.

How to Apply:
Please send a cover letter and CV to Bing Zhang at bing.zhang@vanderbilt.edu.