Selected papers

Cell 2019

Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities.

Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B, Clinical Proteomic Tumor Analysis Consortium. 

Cell, 177(4):1035-1049, 2019


MCP 2017

Proteome profiling outperforms transcriptome profiling for co-expression based gene function prediction.

Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJ, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B. 

Mol Cell Proteomics, 16(1):121-134, 2017



Proteogenomic characterization of human colon and rectal cancer.

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; the National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI CPTAC). 

Nature, 513:382-387, 2014


NetGestalt: integrating multidimensional omics data over biological networks.

Shi Z, Wang J, Zhang B.

Nat Methods, 10:597-598, 2013



Protein identification using customized protein sequence databases derived from RNA-Seq data.

Wang X, Slebos RJ, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B.

J Proteome Res, 11:1009-1017, 2012




By year:  2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2002


Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities. Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B, Clinical Proteomic Tumor Analysis Consortium. Cell, 177(4):1035-1049, 2019

PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations. Wen B, Wang X, Zhang B. Genome Res, 29(3):485-493, 2019

Graph algorithms for condensing and consolidating gene set analysis results. Savage SR, Shi Z, Liao Y, Zhang B. Mol Cell Proteomics, 2019

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Liao Y, Wang J, Jaehnig EJ, Shi Z, Zhang B. Nucleic Acids Res, 2019

Clinical potential of mass spectrometry-based proteogenomics. Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG. Nat Rev Clin Oncol, 16(4):256-268, 2019

PDV: an integrative proteomics data viewer. Li K, Vaudel M, Zhang B, Ren Y, Wen B. Bioinformatics, 35(7):1249-1251, 2019

LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition. Hu Q, Li C, Wang S, Li Y, Wen B, Zhang Y, Liang K, Yao J, Ye Y, Hsiao H, Nguyen TK, Park PK, Egranov SD, Hawke DH, Marks JR, Han L, Hung MC, Zhang B, Lin C, Yang L. Cell Res, doi: 10.1038/s41422-018-0134-3, 2019

Tumor microenvironment modulation enhances immunologic benefit of chemoradiotherapy. Hanoteau A, Newton JM, Krupar R, Huang C, Liu HC, Gaspero A, Gartrell RD, Saenger YM, Hart TD, Santegoets SJ, Laoui D, Spanos C, Parikh F, Jayaraman P, Zhang B, Van der Burg SH, Van Ginderachter JA, Melief CJM, Sikora AG. J Immunother Cancer, 7(1):10, 2019

Anti-tumor immunity induced by ectopic expression of viral antigens is transient and limited by immune escape. Dharmaraj N, Piotrowski SL, Huang C, Newton JM, Golfman LS, Hanoteau A, Koshy ST, Li AW, Pulikkathara MX, Zhang B, Burks JK, Mooney DJ, Lei YL, Sikora AG, Young S. Oncoimmunology, 8(4):e1568809, 2019


Detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity. Wang X, Codreanu SG, Wen B, Li K, Chambers M, Liebler DC, Zhang B. Mol Cell Proteomics, 17(3):422-430, 2018

LinkedOmics: analyzing multi-omics data within and across 32 cancer types. Vasaikar SV, Straub P, Wang J, Zhang B. Nucleic Acids Res, 46(D1):D956-D963, 2018

DLAD4U: deriving and prioritizing disease lists from PubMed literature. Shen J, Vasaikar S, Zhang B. BMC Bioinformatics, 19(Suppl 17):495, 2018

How many human proteoforms are there? Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. Nat Chem Biol, 14(3):206-214, 2018

Right data for right patient-a precisionFDA NCI-CPTAC Multi-omics Mislabeling Challenge. Boja E, Težak Ž, Zhang B, Wang P, Johanson E, Hinton D, Rodriguez H. Nat Med, 24(9):1301-1302, 2018

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA. Genome Biol, 19(1):12, 2018

Combinatorial inhibition of PTPN12-regulated receptors leads to a broadly effective therapeutic strategy in triple-negative breast cancer. Nair A, Chung HC, Sun T, Tyagi S, Dobrolecki LE, Dominguez-Vidana R, Kurley SJ, Orellana M, Renwick A, Henke DM, Katsonis P, Schmitt E, Chan DW, Li H, Mao S, Petrovic I, Creighton CJ, Gutierrez C, Dubrulle J, Stossi F, Tyner JW, Lichtarge O, Lin CY, Zhang B, Scott KL, Hilsenbeck SG, Sun J, Yu X, Osborne CK, Schiff R, Christensen JG, Shields DJ, Rimawi MF, Ellis MJ, Shaw CA, Lewis MT, Westbrook TF. Nat Med, 24(4):505-511, 2018

Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells. Hinger SA, Cha DJ, Franklin JL, Higginbotham JN, Dou Y, Ping J, Shu L, Prasad N, Levy S, Zhang B, Liu Q, Weaver AM, Coffey RJ, Patton JG. Cell Rep, 25(3):715-725.e4, 2018

FGFR1-activated Translation of WNT Pathway Components with Structured 5′ UTRs is Vulnerable to Inhibition of EIF4A-dependent Translation Initiation. Nguyen TM, Kabotyanski EB, Dou Y, Reineke LC, Zhang P, Zhang XH, Malovannaya A, Jung SY, Mo Q, Roarty KP, Chen Y, Zhang B, Neilson JR, Lloyd RE, Perou CM, Ellis MJ, Rosen JM. Cancer Res, 2018


WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkitWang J, Vasaikar S, Shi Z, Greer M, Zhang B. Nucleic Acids Res, 45(W1):W130-W137, 2017

Proteome profiling outperforms transcriptome profiling for co-expression based gene function predictionWang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJ, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B. Mol Cell Proteomics, 16(1):121-134, 2017

Colorectal cancer cell line proteomes are representative of primary tumors and predict drug sensitivity. Wang J#, Mouradov D#, Wang X#, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B@, Sieber OM@. Gastroenterology, 153(4):1082-1095, 2017 (# first authors; @ corresponding authors)

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B@, Li Y@, Li J@. J Proteome Res, 16(2):421-432, 2017 (@ corresponding authors)

Methods, tools and current perspectives in proteogenomicsRuggles KV#, Krug K#, Wang X#, Clauser KR, Wang J, Payne SH, Fenyö D@, Zhang B@, Mani DR@Mol Cell Proteomics, 16(6):959-981, 2017 (# first authors; @ corresponding authors)

APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS. Nat Commun, 8(1):465, 2017

Comprehensive and sensitive proteogenomics data analysis strategy based on complementary multi-stage database search. Madar IH#, Lee W#, Wang X#, Ko SI, Kim H, Mun DG, Zhang B@, Paek E@, Lee SW@. Int J Mass Spectrom, doi: 10.1016/j.ijms.2017.08.015, 2017 (# first authors; @ corresponding authors)

Interactions between calcium intake and polymorphisms in genes essential for calcium reabsorption and risk of colorectal neoplasia in a two-phase studyZhao J, Zhu X, Shrubsole MJ, Ness RM, Hibler EA, Cai Q, Long J, Chen Z, Jiang M, Kabagambe EK, Zhang B, Hou L, Smalley WE, Edwards TL, Giovannucci EL, Zheng W, Dai Q. Mol Carcinog, 56(10):2258-2266, 2017

Effects of a social stimulus on gene expression in a mouse model of fragile X syndrome. Rogers TD, Anacker AMJ, Kerr TM, Forsberg CG, Wang J, Zhang B, Veenstra-VanderWeele J.  Mol Autism, doi: 10.1186/s13229-017-0148-6, 2017

Blockade of the 5-HT transporter contributes to the behavioural, neuronal and molecular effects of cocaineSimmler LD, Anacker AMJ, Levin MH, Vaswani NM, Gresch PJ, Nackenoff AG, Anastasio NC, Stutz SJ, Cunningham KA, Wang J, Zhang B, Keith Henry L, Stewart A, Veenstra-VanderWeele J, Blakely RD. Br J Pharmacol, 174(16):2716-2738, 2017

Protein Modification by Endogenously Generated Lipid Electrophiles: Mitochondria as the Source and Target. Beavers WN, Rose KL, Galligan JJ, Mitchener MM, Rouzer CA, Tallman KA, Lamberson CR, Wang X, Hill S, Ivanova PT, Brown HA, Zhang B, Porter NA, Marnett LJ.  ACS Chem Biol, doi: 10.1021/acschembio.7b00480, 2017


Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomesDou Y, Cha DJ, Franklin JL, Higginbotham JN, Jeppesen DK, Weaver AM, Prasad N, Levy S, Coffey RJ, Patton JG, Zhang B. Sci Rep, 6:37982, 2016

proBAMsuite, a bioinformatics framework for genome-based representation and analysis of proteomics dataWang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B. Mol Cell Proteomics, 15:1164-1175, 2016

Integrative omics analysis reveals post-transcriptionally enhanced protective host response in colorectal cancers with microsatellite instabilityLiu Q, Zhang B. J Proteome Res, 15:766-776, 2016

Proteogenomics connects somatic mutations to signalling in breast cancer. Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC.  Nature, 534:55-62, 2016

Integrated proteogenomic characterization of human high-grade serous ovarian cancer. Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators. Cell, 2016

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC. J Proteome Res, 15:691-706, 2016

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-SeqWen B, Xu S, Zhou R, Zhang B, Wang X, Liu X, Xu X, Liu S. BMC Bioinformatics, 17(1):244, 2016


Empowering biologists with multi-omics data: colorectal cancer as a paradigmZhu J, Shi Z, Wang J, Zhang B. Bioinformatics, 31:1436-1443, 2015

Proteomic analysis of colon and rectal carcinoma using standard and customized databasesSlebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC. Sci Data, 2:150022, 2015

Identification of HPV integration and gene mutation in HeLa cell line by integrated analysis of RNA-Seq and MS/MS dataSun H, Chen C, Lian B, Zhang M, Wang X, Zhang B, Li Y, Yang P, Xie L. J Proteome Res, 14(4):1678-86, 2015

Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics. Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C. Sci Rep, 5:10940, 2015

Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa. Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL. J Proteome Res, 14(12):5318-26, 2015

KRAS-dependent sorting of miRNA to exosomesCha DJ, Franklin JL, Dou Y, Liu Q, Higginbotham JN, Demory Beckler M, Weaver AM, Vickers K, Prasad N, Levy S, Zhang B, Coffey RJ, Patton JG. Elife, 10.7554/eLife.07197, 2015

Activation of the Endogenous Renin-Angiotensin-Aldosterone System or Aldosterone Administration Increases Urinary Exosomal Sodium Channel ExcretionQi Y, Wang X, Rose KL, MacDonald WH, Zhang B, Schey KL, Luther JM. J Am Soc Nephrol, 2015

Global gene expression profiling reveals a suppressed immune response pathway associated with 3q amplification in squamous carcinoma of the lung.
 Qian J, Zou Y, Wang J, Zhang B, Massion PP. Genom Data, 5:272-274, 2015.

Linking patient outcome to high throughput protein expression data identifies novel regulators of colorectal adenocarcinoma aggressivenessFrench CL, Ye F, Revetta F, Zhang B, Coffey RJ, Washington MK, Deane NG, Beauchamp RD, Weaver AM. F1000Res, 2015


Proteogenomic characterization of human colon and rectal cancer. 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; the National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI CPTAC). Nature, 513:382-387, 2014

NFAT transcriptional activity is associated with metastatic capacity in colon cancer. Tripathi MK, Deane NG, Zhu J, An H, Mima S, Wang X, Padmanabhan S, Shi Z, Prodduturi N, Ciombor KK, Chen X, Washington MK, Zhang B@, Beauchamp RD@. (@ co-corresponding authors) Cancer Res, 74:6947-6957, 2014

Integrating genomic, transcriptomic and interactome data to improve peptide and protein identification in shotgun proteomics Wang X, Zhang B. J Proteome Res, 13:2715-2723, 2014

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data. Wang X, Liu Q, Zhang B. Proteomics, 14:2676-2687, 2014

Functional annotation of differentially regulated gene set using WebGestalt: a gene set predictive of response to ipilimumab in tumor biopsies. Kirov S, Ji R, Wang J, Zhang B. Methods Mol Biol, 1101:31-42, 2014

An open-source analytical platform for analysis of C. elegans swimming induced paralysisHardaway JA, Wang J, Fleming PA, Fleming KA, Whitaker SM, Nackenoff A, Snarrenberg CL, Hardie SL, Zhang B, Blakely RD. J Neurosci Methods, 232:58-62, 2014

Alkylation damageby lipid electrophilestargets functional protein systems. Codreanu SG, Ullery JC, Zhu J, TallmanKA, Beavers WN, Porter NA, Marnett LJ, Zhang B, Liebler DC. Mol Cell Proteomics, 13:849-859, 2014

Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice. Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD. Genes Brain Behav, 13:247-260, 2014

Quantitative trait loci mapping and gene network analysis implicate protocadherin-15 as a determinant of brain serotonin transporter expression. Ye R, Carneiro AM, Han Q, Airey D, Sanders-Bush E, Zhang B, Lu L, Williams R, Blakely RD. Genes Brain Behav, 13:261-275, 2014

Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair. Halvey PJ, Wang X, Wang J, Bhat AA, Dhawan P, Li M, Zhang B, Liebler DC, Slebos RJ. Cancer Res, 74:387-397, 2014


customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics searchWang X, Zhang B. Bioinformatics, 29:3235-3237, 2013

RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenalLiu Q, Ullery J, Zhu J, Liebler DC, Marnett LJ, Zhang B.  Mol Biosyst, 9:3036-3046, 2013

NetGestalt: integrating multidimensional omics data over biological networks. Shi Z, Wang J, Zhang B. Nat Methods, 10:597-598, 2013

Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulationLiu Q, Halvey PJ, Shyr Y, Slebos RJ, Liebler DC, Zhang B. Mol Cell Proteomics, 12:1900-1911, 2013

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013Wang J, Duncan, D, Shi Z, Zhang B. Nucleic Acids Res, 41:W77-83, 2013

Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis. Zhu J, Wang J, Shi Z, Franklin JL, Deane NG, Coffey RJ, Beauchamp RD, Zhang B. PLoS One, 8:e79282, 2013

Integrative genomics analysis identifies candidate drivers at 3q26-29 amplicon in squamous cell carcinoma of the lung. Wang J, Qian J, Hoeksema MD, Zou Y, Espinosa AV, Rahman JS, Zhang B@, Massion PP@. (@ co-corresponding authors)  Clin Cancer Res, 19:5580-5590, 2013

IDPQuantify: Combining precursor intensity with spectral counts for protein and peptide quantification.  Chen YY, Chambers MC, Li M, Ham AJ, Turner JL, Zhang B, Tabb DL.  J Proteome Res, 12:4111-4121, 2013

Four jointed box 1 promotes angiogenesis and is associated with poor patient survival in colorectal carcinoma. Al-Greene NT, Means AL, Lu P, Jiang A, Schmidt CR, Chakravarthy AB, Merchant NB, Washington MK, Zhang B, Shyr Y, Deane NG, Beauchamp, RD. Plos One, 8:e69660, 2013

Malignant transformation of colonic epithelial cells by a colon-derived long noncoding RNA. Franklin JL, Rankin CR, Levy S, Snoddy JR, Zhang B, Washington MK, Michael TJ, Whitehead RH, Coffey RJ. Biochem Biophys Res Commun, 44:99-104, 2013


GLAD4U: deriving and prioritizing gene lists from PubMed literature. Jerome Jourquin J, Duncan D, Shi Z, Zhang B. BMC Genomics, 13(Suppl 8):S20, 2012

A network-based gene expression signature informs prognosis and treatment for colorectal cancer patientsShi M, Beauchamp RD, Zhang B. PLoS One, 7(7):e41292, 2012

Protein identification using customized protein sequence databases derived from RNA-Seq data. Wang X, Slebos RJ, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B. J Proteome Res, 11(2):1009-17, 2012

Statistical analysis of patient-specific pathway activities vis mixed models. Wang L, Chen X, Zhang B. J Biom Biostat, Suppl 8(1):7313, 2012

Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data.Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr, Y. BMC Genomics, 13(Suppl 8):S8, 2012

Proteomic consequences of a single gene mutation in a colorectal cancer model.  Halvey PJ, Zhang B, Coffey R, Liebler DC, Slebos RJ. J Proteome Res, 11(2):1184-95, 2012

Network analysis of the focal adhesion to invadopodia transition identifies a PI3K-PKCα invasive signaling axis. 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. Sci Signal, 5(241):ra66, 2012

Proteomic profiling of paraffin-embedded samples identifies metaplasia-specific and early-stage gastric cancer biomarkers. Sousa JF, Ham AJ, Whitwell C, Nam KT, Lee HJ, Yang HK, Kim WH, Zhang B, Li M, Lafleur B, Liebler DC, Goldenring JR.  Am J Pathol, 181(5):1560-72, 2012

Forward genetic analysis to identify determinants of dopamine signaling in Caenorhabditis elegans using swimming-induced paralysis. Hardaway JA, Hardie SL, Whitaker SM, Baas SR, Zhang B, Bermingham DP, Lichtenstein AJ, Blakely RD.  G3 (Bethesda), 2(8):961-75, 2012


Semi-supervised learning improves gene expression-based prediction of cancer recurrence. Shi M, Zhang B. Bioinformatics, 27:3017-3023, 2011

Relating protein adduction to gene expression changes: a systems approach. Zhang B, Shi Z, Duncan DT, Prodduturi N, Marnett LJ, Liebler DC. Mol Biosyst, 7:2118-2127, 2011

Fast network centrality analysis using GPUs. Shi Z, Zhang B. BMC Bioinformatics, 12:149, 2011

A bioinformatics workflow for variant peptide detection in shotgun proteomics. Li J, Su Z, Ma ZQ, Slebos RJ, Halvey P, Tabb DL, Liebler DC, Pao W, Zhang B. Mol Cell Proteomics, 10:M110.006536, 2011

Genetic dissection of the Gpnmb network in the eye. Lu H, Wang X, Pullen M, Guan H, Chen H, Sahu S, Zhang B, Chen H, Williams RW, Gelsert EE, Lu L, Jablonski MM. Invest Ophthalmol Vis Sci, 2011

Networked-based Characterization of Extracellular Matrix Proteins from Adult Mouse Pulmonary and Aortic Valves.   Angel PM, Nusinow D, Brown CB, Violette K, Barnett JV, Zhang B, Baldwin HS, Caprioli RM.   J Proteome Res, 10:812-823, 2011


Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression.   Zhiao Shi, Catherine K Derow, Bing Zhang.  BMC Syst Biol, 4:74, 2010

CanProVar: a human cancer proteome variation database. Jing Li, Dexter T Duncan, Bing Zhang. Hum Mutat, 31(3):219-228, 2010

An experimentally derived metastasis gene expression profile predicts recurrence and death in colon cancer patients. J.Joshua Smith, Natasha G. Deane, Fei Wu, Nipun B. Merchant, Bing Zhang, Aixiang Jiang, Pengcheng Lu, J. Chad Johnson, Carl Schmidt, Christina M. Edwards, Steven Eschrich, Christian Kis, Shawn Levy, M. Kay Washington, Martin J. Heslin, Robert J. Coffey, Timothy J. Yeatman, Yu Shyr, R. Daniel Beauchamp. Gastroenterology, 138:958-968, 2010

High-throughput multiplexed transcript analysis yields enhanced resolution of 5-hydroxytryptamine 2C receptor mRNA editing profiles. Morabito MV, Ulbricht RJ, O’Neil RT, Airey DC, Lu P, Zhang B, Wang L, Emeson RB. Mol Pharmacol, 77(6):895-902, 2010 

Distinct transcriptomes define rostral and caudal serotonin neurons. Christi J Wylie, Timothy J Hendricks, Bing Zhang, Lily Wang, Pengcheng Lu, Patrick Leahy, Stephanie Fox, Hiroshi maeno, Evan S. Deneris. J Neurosci, 30(2):670-684, 2010

Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge. Dorothea K Thompson, Karuna Chourey, Gene S Wickham, Stephanie B Thieman, Nathan C VerBerkmoes, Bing Zhang, Andrea T McCarthy, Matt A Rudisill, Manesh Shah, Robert L Hettich.   BMC Genomics, 11:311, 2010


A unified mixed effects model for gene set analysis of time course microarray experiments. Lily Wang, Xi Chen, Russell D Wolfinger, Jeffrey L Franklin, Robert J Coffey, Bing Zhang.  Stat Appl Genet Mol Biol, 8:Article47, 2009

Network-assisted protein identification and data interpretation in shotgun proteomics. Jing Li, Lisa J Zimmerman, Byung-Hoon Park, David L Tabb, Daniel C Liebler, Bing Zhang. Mol Syst Biol, 5:303, 2009

SBDS is a multi-functional protein implicated in cellular stress responses. Heather L. Ball, Bing Zhang, Jacob Riches, Rikesh Gandhi, Jing Li, Johanna M. Rommens, Jeremy S. Myers. Hum Mol Genet, 18(19):3684-95, 2009

Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms. Philip Gerlee, Docent T. Lundh, Bing Zhang, Alexander R.A. Anderson. J R Soc Interface, 6(41):1233-45, 2009

Impact of Phenolic Substrate and Growth Temperature on the Arthrobacter chlorophenolicus Proteome. Maria Unell, Paul E. Abraham, Manesh Shah, Bing Zhang, Christian Rckert, Nathan C. VerBerkmoes, Janet K. Jansson. J Proteome Res, 8(4):1953-64, 2009

Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal.   Simona G. Codreanu, Bing Zhang, Scott M. Sobecki, Dean D. Billheimer, Daniel C. Liebler. Mol Cell Proteomics, 8(4):670-80, 2009  

Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformation.   Karuna Chourey, Melissa R. Thompson, Manesh Shah, Bing Zhang, Nathan C. VerBerkmoes, Dorothea K. Thompson, Robert L. Hettich, J Proteome Res, 8(1):59-71, 2009  


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

An Integrated Approach for the Analysis of Biological Pathways using Mixed Models.   Lily Wang, Bing Zhang, Russell D. Wolfinger, Xi Chen. PLoS Genet, 4(7): e1000115, 2008  

Supervised Principal Component Analysis for Gene Set Enrichment of Microarray Data with Continuous or Survival Outcomes. Xi Chen, Lily Wang, Jonathan D. Smith, Bing Zhang, Bioinformatics, 24(21):2474-81, 2008

Characterization of anaerobic catabolism of p-coumarate in rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics. Chongle Pan, Yasuhiro Oda, Patricia K. Lankford, Bing Zhang, Nagiza F. Samatova, Dale A. Pelletier, Caroline S. Harwood, Robert L. Hettich. Mol Cell Proteomics, 7(5):938-48, 2008

Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal.   Paul Wilmes, Anders F Andersson, Mark G Lefsrud, Margaret Wexler, Manesh Shah, Bing Zhang, Robert L Hettich, Philip L Bond, Nathan C VerBerkmoes, Jillian F Banfield. ISME J, 2(8):853-64, 2008  


Proteomic Parsimony through Bipartite Graph Analysis Improves Accuracy and Transparency. Bing Zhang, Matthew C. Chambers, David L. Tabb. J Proteome Res, 6(9):3549-57, 2007

Association analysis for large scale gene set data. Stefan Kirov, Bing Zhang, Jay Snoddy. Methods Mol Biol, 408, 19-34, 2007  


Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics. Bing Zhang, Nathan C. VerBerkmoes, Michael A. Langston, Edward Uberbacher, Robert L. Hettich, Nagiza F. Samatova. J Proteome Res, 5(11), 2909-18, 2006


WebGestalt: an integrated system for exploring gene sets in various biological contexts.  Bing Zhang, Stefan A. Kirov, Jay R. Snoddy. Nucleic Acids Res, 33:W741-8, 2005

Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks. Nicole E. Baldwin, Elissa J. Chesler, Stefan A. Kirov, Michael A. Langston, Jay R. Snoddy, Robert W. Williams, Bing Zhang. J Biomed Biotechnol, 2005(2), 172-80, 2005  

GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.   Stefan A. Kirov, Xinxia Peng, Eric Baker, Denise Schmoyer, Bing Zhang, Jay R. Snoddy. BMC Bioinformatics, 6, 72, 2005


GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies.  Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy. BMC Bioinformatics, 5, 16, 2004

A Combinatorial Approach to the Analysis of Differential Gene Expression Data: The Use of Graph Algorithms for Disease Prediction and Screening. Michael A. Langston, Lan Lin, Xinxia Peng, Nicole E. Baldwin, Christopher Symons, Bing Zhang, Jay R. Snoddy. In: Methods of Microarray Data Analysis IV, Kluwer Academic Publishers, Boston, 223-238, 2004

Gene expression profiling in adipose tissue.   Naima Moustaid-Moussa, Sumithra Urs, Brett Campbell, Hyoung Yon Kim, Suyeon Kim, Patrick Wortman, Richard Giannone, Bing Zhang, Jay Snoddy, Brynn Voy. In: Genomics and Proteomics in Nutrition, Marcel Dekker Inc., New York, 257-280, 2004  

Gene expression profiling in human preadipocytes and adipocytes by microarray analysis.  Sumithra Urs, Colton Smith, Brett Campbell, Arnold M. Saxton, James Taylor, Bing Zhang, Jay Snoddy, Brynn Voy, Naima Moustaid-Moussa. J Nutr, 134(4), 762-70, 2004  


Characterization of early, chitin-induced gene expression in Arabidopsis.  Bing Zhang, Katrina M. Ramonell, Shauna Somerville, Gary Stacey. Mol Plant Microbe Interact, 15(9), 963-70, 2002

Microarray analysis of chitin elicitation in Arabidopsis.  Katrina M. Ramonell, Bing Zhang, Yu Chen, Dong Xu, Gary Stacey, Shauna Somerville. Mol Plant Pathol, 3(5), 301-311, 2002