Publication list (2002-current)
1. Zhang B, Ramonell K, Somerville S, Stacey G. Characterization of early, chitin-induced
gene expression in Arabidopsis. Mol Plant Microbe Interact. 15(9): 963-70, 2002. PMID:
12236603.
2. Ramonell KM, Zhang B, Ewing RM, Chen Y, Xu D, Stacey G, Somerville S. Microarray
analysis of chitin elicitation in Arabidopsis thaliana. Mol Plant Pathol. 3(5): 301-11,
2002. PMID: 20569338.
3. 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. 5:16, 2004. PMID: 14975175; PMCID: PMC373441.
4. 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. 134(4): 762-70, 2004. PMID: 15051823.
5. Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in
various biological contexts. Nucleic Acids Res. 33(Web Server issue): W741-8, 2005.
PMID: 15980575; PMCID: PMC1160236.
6. 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. 6: 72, 2005. PMID: 15790402; PMCID: PMC1274265.
7. 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(2): 172-80, 2005. PMID: 16046823;
PMCID: PMC1184052.
8. 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(11): 2909-18, 2006. PMID: 17081042.
9. Kirov SA, Zhang B, Snoddy JR. Association analysis for large-scale gene set data.
Methods Mol Biol. 408: 19-33, 2006 PMID: 18314575.
10. Zhang B, Chambers MC, Tabb DL. Proteomic parsimony through bipartite graph
analysis improves accuracy and transparency. J Proteome Res. 6(9): 3549-57, 2007.
PMID: 17676885; PMCID: PMC2810678.
11. 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. PMID: 18304937.
12. 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. 7(5): 938-48, 2008. PMID: 18156135.
13. Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL,
VerBerkmoes NC, Banfield JF. Community proteogenomics highlights microbial strainvariant protein expression within activated sludge performing enhanced biological
phosphorus removal. ISME J. 2(8): 853-64, 2008. PMID: 18449217.
14. 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. 24(21): 2474-81, 2008. PMID: 18753155; PMCID: PMC2732277.
15. Wang L, Zhang B, Wolfinger RD, Chen X. An integrated approach for the analysis of
biological pathways using mixed models. PLoS Genet. 4(7): e1000115, 2008. PMID:
18852846; PMCID: PMC2565842.
16. 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. PMID: 19954419; PMCID: PMC2861317.
17. 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.
PMID: 19690572; PMCID: PMC2736651.
18. Chourey K, Thompson MR, Shah M, Zhang B, Verberkmoes NC, Thompson DK, Hettich
RL. Comparative temporal proteomics of a response regulator (SO2426)-deficient strain
and wild-type Shewanella oneidensis MR-1 during chromate transformation. J Proteome
Res. 8(1): 59-71, 2009. PMID: 19118451.
19. Unell M, Abraham P, Shah M, Zhang B, Rückert C, Verberkmoes N, Jansson J. Impact of
Phenolic Substrate and Growth Temperature on the Arthrobacter chlorophenolicus
Proteome. J Proteome Res. 8(4): 1953-64, 2009. PMID: 19216575.
20. 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. 8(4): 67080, 2009. PMID: 19054759; PMCID: PMC2667350.
21. 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. 6(41): 1233-45,
2009. PMID: 19324678; PMCID: PMC2817152.
22. 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. 18(19): 3684-95, 2009. PMID: 19602484; PMCID: PMC2742402.
23. Li J, Duncan DT, Zhang B. CanProVar: a human cancer proteome variation database.
Hum Mutat. 31(3): 219-28, 2010. PMID: 20052754; PMCID: PMC2829365.
24. 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. PMID: 19914252.
25. 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. PMID: 20071532.
26. Morabito MV, Ulbricht RJ, O'Neil RT, Airey DC, Lu P, Zhang B, Wang L, Emeson RB. Highthroughput multiplexed transcript analysis yields enhanced resolution of 5hydroxytryptamine 2C receptor mRNA editing profiles. Mol Pharmacol. 77(6): 895-902,
2010. PMID: 20181818; PMCID: PMC2879922.
27. Thompson DK, Chourey K, Wickham GS, Thieman SB, VerBerkmoes NC, Zhang B,
McCarthy AT, Rudisill MA, Shah M, Hettich RL. Proteomics reveals a core molecular
response of Pseudomonas putida F1 to acute chromate challenge. BMC Genomics.
11:311, 2010. PMID: 20482812; PMCID: PMC2996968.
28. 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. 4:74, 2010. PMID: 20507583; PMCID: PMC2902438.
29. 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):812-823, 2011. PMID:
21133377.
30. Lu H, Wang X, Pullen M, Guan H, Chen H, Sahu S, Zhang B, Chen H, Williams RW, Geisert
EE, Lu L, Jablonski MM. Genetic Dissection of the Gpnmb Network in the Eye. Invest
Ophthalmol Vis Sci. 52(7):4132-42, 2011. PMID: 21398278.
31. 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. PMID: 21389108.
32. Shi Z, Zhang B. Fast network centrality analysis using GPUs. BMC Bioinformatics.
12:149, 2011. PMID: 21569426. PMCID: PMC3115853.
33. 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(7):2118-27,
2011. PMID: 21594272.
34. Shi M, Zhang B. Semi-supervised learning improves gene expression-based prediction
of cancer recurrence. Bioinformatics, 27:3017-3023, 2011. PMID: 21893520. PMCID:
PMC3198572.
35. Halvey PJ, Zhang B, Coffey R, Liebler DC, Slebos RJC. Proteomic consequences of a single
gene mutation in a colorectal cancer model. J Proteome Res. In press. PMID: 22103262.
36. 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. In press. PMID: 22103967.