Bing Zhang

DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations.

Wen B^#, Wang C^#, Li K^#, Han P, Holt MV, Savage SR, Lei JT, Dou Y, Shi Z, Li Y, Zhang B.

Nat Methods, 22(9):1857-1867, 2025. (# first authors)

Mapping the functional network of human cancer through machine learning and pan-cancer proteogenomics.

Shi Z^#, Lei JT^#, Elizarraras JM, Zhang B.

Nat Cancer, 6(1):205-222, 2025. (# first authors)

Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites.

Jiang W, Jaehnig EJ, Liao Y, Shi Z, Yaron-Barir TM, Johnson JL, Cantley LC, Zhang B.

Nat Commun., 16(1):2766, 2025.

Comprehensive evaluation of phosphoproteomic-based kinase activity inference.

Müller-Dott S^#, Jaehnig EJ^#, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B^@, Saez-Rodriguez J^@.

Nat Commun., 16(1):4771, 2025. (# first authors; @ corresponding authors)

Toward real clinical utility: leveraging comprehensive proteomic datasets for clinical insight.

Rodland KD, Zhang B.

Expert Rev Proteomics, in press, 2025.

ZP4: A novel target for CAR-T cell therapy in triple negative breast cancer.

Somes LK, Lei JT, Yi X, Chamorro DF, Shafer P, Gad AZ, Dobrolecki LE, Madaras E, Ahmed N, Lewis MT, Zhang B, Hoyos V.

Mol Ther., 33(4):1621-1641, 2025.

Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer.

Holt MV^#, Dou Y^#, Young MN, Saltzman AB, Anurag M, Lei JT, Jain A, Leng M, Kim BJ, Dobrolecki LE, Faucher SF, Savage S, Wang C, Shi Z, Villanueva H, Kremers K, Drinnon KD, Castro PD, Ittmann MM, Khatani MM, Kim SH, Ellis MJ, Zhang B, Malovannaya A, Lerner SP.

Cell Rep Med., 6(8):102255, 2025. (# first authors)

Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures.

Satpathy S, Clark NM, Chen YJ, Hosseini N, Chang YH, Hsiao Y, Lei JT, Petralia F, Chen JS, Geffen Y, Heiman DI, Paul I, Cho H, Hollenberg M, Marino GB, Lin KT, Mannan R, White CJ, Allen J, Avanessian SC, Kane MH, Wolfe A, Kinarivala M, Liu W, Anand S, Lin MW, Haines M, Bergstrom EJ, Hussey G, Li GX, Mani DC, Fang H, Jaehnig EJ, Keshishian H, Miller B, Su KY, Hsiao YJ, Hsu HH, Hsieh MS, Hsu KH, Monovoukas A, Gohsman S, Thorup JR, Deng Y, Akiyama Y, Deng E, Sheng-Wen Chen E, Krek A, Espinoza R, Ma W, Charytonowicz D, Sebra R, Lin JH, Chen YS, Hsu YC, Lin ZS, Chen KC, Yeh CW, Wang YT, Lazar AJ, Mesri M, An E, Zhang X, Clauser KR, Fenyö D, Chinnaiyan AM, Zhang B, Ding L, Ruggles K, Newton C, Zhang H, Wang P, Hostetter G, Omenn GS, Kumar-Sinha C, Thiagarajan M, Govindan R, Paik P, Parolia A, Li QK, Ma’ayan A, Getz GA, Dhanasekaran SM, Robles AI, Chang GC, Yang PC, Yu SL, Chen HY, Nesvizhskii AI, Carr SA, Mani DR, Cieslik MP, Chen YJ, Gillette MA; Taiwan Cancer Moonshot Program; Clinical Proteomic Tumor Analysis Consortium.

Cancer Cell, 43(9):1731-1757, 2025.

Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers.

Jaehnig EJ, Fernandez-Martinez A, Vashist TD, Holt MV, Williams L, Lei JT, Moon CI, Kim BJ, Dou Y, Zhao H, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Perou CM, Carey LA, Robles AI, Hyslop T, Wen Y, McCart L, Krek A, Petralia F, Miles G, Kavuri SM, Gillette MA, Mani DR, Carr SA, Zhang B, Ellis MJ, Satpathy S, Anurag M.

Cell Rep Med., 6(6):102154, 2025.

Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets.

Kołodziejczak-Guglas I, Simões RLS, de Souza Santos E, Demicco EG, Lazcano Segura RN, Ma W, Wang P, Geffen Y, Storrs E, Petralia F, Colaprico A, da Veiga Leprevost F, Pugliese P, Ceccarelli M, Noushmehr H, Nesvizhskii AI, Kamińska B, Priebe W, Lubiński J, Zhang B, Lazar AJ, Kurzawa P, Mesri M, Robles AI; Clinical Proteomic Tumor Analysis Consortium; Ding L, Malta TM, Wiznerowicz M..

Cell Genom., 5(6):100851, 2025.

Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups.

Ji S, Cao L, Gao J, Du Y, Ye Z, Lou X, Liu F, Zhang Y, Xu J, Shi X, Wang H, Li P, Li Y, Chen H, Yang Z, Gao S, Zhang W, Huang D, Ni S, Wei M, Wang F, Wang Y, Ding T, Jing D, Fan G, Gong Z, Lu R, Qin Y, Chen J, Xu X, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Chang DK, Hruban RH, Gao D, Gao D, Jin G, Zhou H, Wu J, Yu X.

Cancer Cell, 43(4):776-796, 2025.

Integrative proteogenomics and forward genetics reveals a novel mitotic vulnerability in triple-negative breast cancer.

Neill NJ, Satpathy S, Krug K, Meena JK, Ramesh Babu N, Calderon C, Reed D, Weber MJ, Dobrolecki LE, Lewis A, Sallas C, Anurag M, Holloway KR, Huang C, Vasaikar S, Cardenas MF, Kim BJ, Chan DW, Avanessian SC, Tyagi S, Orellana M, Mao S, Li H, Gong F, Kurley SJ, Meerbrey KL, Olson CM, Nair A, Sun T, Chung HC, Bowling EA, Wang JH, Zhang P, Xiao P, Yang D, Stossi F, Polley MC, Saltzman AB, Mundt F, Mani DR, Gillette MA, Hilsenbeck SG, Miles G, Gutierrez C, Osborne CK, Lin CY, Gray NS, Sun J, Wheeler DA, Perou CM, Malovannaya A, Lewis MT, Zhang B, Ellis MJ, Carr SA, Westbrook TF.

Cancer Discov., in press, 2025.

NF1-depleted ER+ breast cancers are differentially sensitive to CDK4/6 inhibitors.

Zheng ZY, Chen A, Jaehnig EJ, Anurag M, Lei JT, Feng L, Wang C, Fandino D, Singh P, Kennedy H, Yadav G, Vollert CT, Tsai J, Chen X, Li Y, Lim B, Thompson A, Li S, Foulds CE, Zhang B, Ellis MJ, Chang EC.

Sci Transl Med., 17(813):eadq5492, 2025.

COOKIE-Pro: covalent inhibitor binding kinetics profiling on the proteome scale.

Lin H, Yang B, Ding L, Yang YY, Holt MV, Jung SY, Zhang B, Wang MC, Wang J.

Nat Commun., 16(1):8373, 2025.

Pan-cancer proteogenomics expands the landscape of therapeutic targets.

Savage SR, Yi X, Lei JT, Wen B, Zhao H, Liao Y, Jaehnig EJ, Somes LK, Shafer PW, Lee TD, Fu Z, Dou Y, Shi Z, Gao D, Hoyos V, Gao Q, Zhang B.

Cell, 187(16):4389-4407, 2024.

Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification.

Yi X, Wen B, Ji S, Saltzman A, Jaehnig EJ, Lei JT, Gao Q, Zhang B.

Mol Cell Proteomics, 23(2):100707, 2024.

IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining.

Savage SR, Zhang Y, Jaehnig EJ, Liao Y, Shi Z, Pham HA, Xu H, Zhang B.

Mol Cell Proteomics, 23(1):100682, 2024.

Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm.

Yi X, Zhao H, Hu S, Dong L, Dou Y, Li J, Gao Q, Zhang B.

Cell Rep Methods, 4(11):100906, 2024.

WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics.

Elizarraras JM, Liao Y, Shi Z, Zhu Q, Pico AR, Zhang B.

Nucleic Acids Res., 52(W1):W415-W421, 2024.

ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials.

Moon CI^#, Elizarraras JM^#, Lei JT, Jia B, Zhang B.

Nucleic Acids Res, 52(D1):D1201-D1209, 2024. (# first authors)

Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma.

Savage SR, Wang Y, Chen L, Jewell S, Newton C, Dou Y, Li QK, Bathe OF, Robles AI, Omenn GS, Thiagarajan M, Zhang H, Hostetter G, Zhang B.

Clin Proteomics, 21(1):7, 2024.

Proteomics Meets Dose Response: A New Paradigm for Deciphering Drug Effects.

Wang C, Zhang B.

Cancer Res., 84(16):2572-2574, 2024.

Pan-cancer proteogenomics characterization of tumor immunity.

Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma’ayan A, Lazar AJ, Ceccarelli M, Wang P; Clinical Proteomic Tumor Analysis Consortium

Cell, 187(5):1255-1277, 2024.

Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies.

Liu Q, Zhang J, Guo C, Wang M, Wang C, Yan Y, Sun L, Wang D, Zhang L, Yu H, Hou L, Wu C, Zhu Y, Jiang G, Zhu H, Zhou Y, Fang S, Zhang T, Hu L, Li J, Liu Y, Zhang H, Zhang B, Ding L, Robles AI, Rodriguez H, Gao D, Ji H, Zhou H, Zhang P.

Cell, 187(1):184-203, 2024.

IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer.

Xu L, Peng F, Luo Q, Ding Y, Yuan F, Zheng L, He W, Zhang SS, Fu X, Liu J, Mutlu AS, Wang S, Nehring RB, Li X, Tang Q, Li C, Lv X, Dobrolecki LE, Zhang W, Han D, Zhao N, Jaehnig E, Wang J, Wu W, Graham DA, Li Y, Chen R, Peng W, Chen Y, Catic A, Zhang Z, Zhang B, Mustoe AM, Koong AC, Miles G, Lewis MT, Wang MC, Rosenberg SM, O’Malley BW, Westbrook TF, Xu H, Zhang XH, Osborne CK, Li JB, Ellis MJ, Rimawi MF, Rosen JM, Chen X.

Cell, 187(25):7248-7266, 2024.

π-HuB: the proteomic navigator of the human body.

He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y; π-HuB Consortium.

Nature, 636(8042):322-331, 2024.

Incongruity between T cell receptor recognition of breast cancer hotspot mutations ESR1 Y537S and D538G following exogenous peptide loading versus endogenous antigen processing.

Shafer P, Leung WK, Woods M, Choi JM, Rodriguez-Plata CM, Maknojia A, Mosquera A, Somes LK, Joubert J, Manliguez A, Ranjan R, Burt B, Lee HS, Zhang B, Fuqua S, Rooney C, Leen AM, Hoyos V.

Cytotherapy, 26(3):266-275, 2024.

A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights..

Yu J, Gui X, Zou Y, Liu Q, Yang Z, An J, Guo X, Wang K, Guo J, Huang M, Zhou S, Zuo J, Chen Y, Deng L, Yuan G, Li N, Song Y, Jia J, Zeng J, Zhao Y, Liu X, Du X, Liu Y, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Zhou H, Shao Z, Wu L, Gao D.

Nat Commun., 15(1):10114, 2024.

Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer.

Yue F, Ku AT, Stevens PD, Michalski MN, Jiang W, Tu J, Shi Z, Dou Y, Wang Y, Feng XH, Hostetter G, Wu X, Huang S, Shroyer NF, Zhang B, Williams BO, Liu Q, Lin X, Li Y.

bioRxiv, doi: 10.1101/2024.01.10.574969, 2024.

Death-associated protein kinase 3 modulates migration and invasion of triple-negative breast cancer cells.

Wang J, Tran-Huynh AM, Kim BJ, Chan DW, Holt MV, Fandino D, Yu X, Qi X, Wang J, Zhang W, Wu YH, Anurag M, Zhang XHF, Zhang B, Cheng C, Foulds CE, Ellis MJ.

PNAS Nexus, 3(9):pgae401, 2024.

A proteome-wide association study identifies putative causal proteins for breast cancer risk.

Zhao T, Xu S, Ping J, Jia G, Dou Y, Henry JE, Zhang B, Guo X, Cote ML, Cai Q, Shu XO, Zheng W, Long J.

Br J Cancer., 131(11):1796-1804, 2024.

SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.

Dou Y, Liu Y, Yi X, Olsen LK, Zhu H, Gao Q, Zhou H, Zhang B.

Nat Commun, 14(1):5809, 2023.

A proteogenomics data-driven knowledge base of human cancer.

Liao Y^#, Savage SR^#, Dou Y, Shi Z, Yi X, Jiang W, Lei JT, Zhang B.

Cell Syst, 14(9):777-787, 2023. (# first authors)

PepQuery2 democratizes public MS proteomics data for rapid peptide searching.

Wen B, Zhang B.

Nat Commun, 14(1):2213, 2023.

Proteogenomic insights suggest druggable pathways in endometrial carcinoma.

Dou Y^#, Katsnelson L^#, Gritsenko MA^#, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJ, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekański A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jędryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML^@, Rodland KD^@, Zhang B^@, Liu T^@, Fenyö D^@; Clinical Proteomic Tumor Analysis Consortium.

Cancer Cell, in press. (# first authors; @ corresponding authors)

Proteogenomic data and resources for pan-cancer analysis.

Li Y^#, Dou Y^#, Da Veiga Leprevost F^#, Geffen Y^#, Calinawan AP^#, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI^@, Zhang B^@, Payne SH^@; Clinical Proteomic Tumor Analysis Consortium.

Cancer Cell, 41(8):1397-1406, 2023. (# first authors; @ corresponding authors)

Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery.

Zhang B, Bassani-Sternberg M.

J Immunother Cancer, 11(10):e007073, 2023.

The Breast Cancer Proteome and Precision Oncology.

Lei JT, Jaehnig EJ, Smith H, Holt MV, Li X, Anurag M, Ellis MJ, Mills GB^@, Zhang B^@, Labrie M^@.

Cold Spring Harb Perspect Med. doi: 10.1101/cshperspect.a041323, 2023 (@ corresponding authors)

Proteogenomics unveils mechanistic insights to precision oncology.

Dou Y, Katsnelson L, Zhang B, Fenyö D, Liu T.

Clin Transl Med, 13(11):e1477, 2023.

Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors.

Lv X, Lu X, Cao J, Luo Q, Ding Y, Peng F, Pataer A, Lu D, Han D, Malmberg E, Chan DW, Wang X, Savage SR, Mao S, Yu J, Peng F, Yan L, Meng H, Maneix L, Han Y, Chen Y, Yao W, Chang EC, Catic A, Lin X, Miles G, Huang P, Sun Z, Burt B, Wang H, Wang J, Yao QC, Zhang B, Roth JA, O’Malley BW, Ellis MJ, Rimawi MF, Ying H, Chen X.

Science, 381(6662):eabn4180, 2023.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG.

Cell, 186(16):3476-3498, 2023.

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

Li Y, Lih TM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kołodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyö D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DW, Ricketts CJ, Nesvizhskii AI, Zhang H, Ding L; Clinical Proteomic Tumor Analysis Consortium.

Cancer Cell, 41(1):139-163, 2023.

Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology.

Ji S, Feng L, Fu Z, Wu G, Wu Y, Lin Y, Lu D, Song Y, Cui P, Yang Z, Sang C, Song G, Cai S, Li Y, Lin H, Zhang S, Wang X, Qiu S, Zhang X, Hua G, Li J, Zhou J, Dai Z, Wang X, Ding L, Wang P, Gao D, Zhang B, Rodriguez H, Fan J, Clevers H, Zhou H, Sun Y, Gao Q.

Sci Transl Med. 15(706):eadg3358, 2023.

Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice.

Bu W, Creighton CJ, Heavener KS, Gutierrez C, Dou Y, Ku AT, Zhang Y, Jiang W, Urrutia J, Jiang W, Yue F, Jia L, Ibrahim AA, Zhang B, Huang S, Li Y.

Sci Adv. 9(19):eade0059, 2023.

Targeting EIF4A triggers an interferon response to synergize with chemotherapy and suppress triple-negative breast cancer.

Zhao N, Kabotyanski EB, Saltzman AB, Malovannaya A, Yuan X, Reineke LC, Lieu N, Gao Y, Pedroza DA, Calderon SJ, Smith AJ, Hamor CW, Safari K, Savage SR, Zhang B, Zhou J, Solis Soto LM, Hilsenbeck SG, Fan C, Perou CM, Rosen JM.

J Clin Invest, e172503, 2023.

Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma.

Zhu H, Lin Y, Lu D, Wang S, Liu Y, Dong L, Meng Q, Gao J, Wang Y, Song N, Suo Y, Ding L, Wang P, Zhang B, Gao D, Fan J, Gao Q, Zhou H.

Natl Sci Rev. 10(8):nwad167, 2023.

Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor-positive Breast Cancers for Targeted Treatment.

Kim BJ, Zheng ZY, Lei JT, Holt MV, Chen A, Peng J, Fandino D, Singh P, Kennedy H, Dou Y, Chica-Parrado MDR, Bikorimana E, Ye D, Wang Y, Hanker AB, Mohamed N, Hilsenbeck SG, Lim B, Asirvatham JR, Sreekumar A, Zhang B, Miles G, Anurag M, Ellis MJ, Chang EC.

Cancer Res Commun. 3(7):1366-1377, 2023.

Toward Practical Integration of Omic and Imaging Data in Co-Clinical Trials.

Alkim E, Dowst H, DiCarlo J, Dobrolecki LE, Hernández-Herrera A, Hormuth DA 2nd, Liao Y, McOwiti A, Pautler R, Rimawi M, Roark A, Srinivasan RR, Virostko J, Zhang B, Zheng F, Rubin DL, Yankeelov TE, Lewis MT.

Tomography. 9(2):810-828, 2023.

OmicsEV: a tool for comprehensive quality evaluation of omics data tables.

Wen B, Jaehnig EJ, Zhang B.

Bioinformatics, 38(24):5463-5465, 2022.

Weakly Unpaired Image Translation from Hematoxylin and Eosin Staining Image to Immunohistochemistry Staining Image.

Huang K, Cheng Y, Gao Q, Zhang B.

2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)., Las Vegas, NV, USA, 2022, pp. 1013-1019, 2022

SEPepQuant enables comprehensive protein isoform characterization in shotgun proteomics.

Y Dou, X Yi, LK Olsen, B Zhang.

bioRxiv, doi: 10.1101/2022.11. 03.515027, 2022.

Proteogenomic markers of chemotherapy resistance and response in triple negative breast cancer.

Anurag M, Jaehnig EJ, Krug K, Lei JT, Bergstrom EJ, Kim BJ, Vashist TD, Tran Huynh AM, Dou Y, Gou X, Huang C, Shi Z, Wen B, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Dobrolecki LE, Rodriguez H, Robles AI, Hiltke T, Lewis MT, Nangia JR, Nemati Shafaee M, Li S, Hagemann IS, Hoog J, Lim B, Osborne CK, Mani DR, Gillette MA, Zhang B, Echeverria GV, Miles G, Rimawi MF, Carr SA, Ademuyiwa FO, Satpathy S, Ellis MJ.

Cancer Discov., 12(11):2586-2605, 2022

Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma.

Dong L, Lu D, Chen R, Lin Y, Zhu H, Zhang Z, Cai S, Cui P, Song G, Rao D, Yi X, Wu Y, Song N, Liu F, Zou Y, Zhang S, Zhang X, Wang X, Qiu S, Zhou J, Wang S, Zhang X, Shi Y, Figeys D, Ding L, Wang P, Zhang B, Rodriguez H, Gao Q, Gao D, Zhou H, Fan J.

Cancer Cell., 40(1):70-87, 2022

Cancer proteogenomics: current impact and future prospects.

Mani DR, Krug K, Zhang B, Satpathy S, Clauser KR, Ding L, Ellis M, Gillette MA, Carr SA.

Nat Rev Cancer., 22(5):298-313, 2022

Multimodule characterization of immune subgroups in intrahepatic cholangiocarcinoma reveals distinct therapeutic vulnerabilities.

Lin J, Dai Y, Sang C, Song G, Xiang B, Zhang M, Dong L, Xia X, Ma J, Shen X, Ji S, Zhang S, Wang M, Fang H, Zhang X, Wang X, Zhang B, Zhou J, Fan J, Zhou H, Gao D, Gao Q.

J Immunother Cancer, 10(7):e004892, 2022

NPY1R exerts inhibitory action on estradiol-stimulated growth and predicts endocrine sensitivity and better survival in ER-positive breast cancer

Bhat R, Thangavel H, Abdulkareem NM, Vasaikar S, De Angelis C, Bae L, Cataldo ML, Nanda S, Fu X, Zhang B, Schiff R, Trivedi MV.

Sci Rep., 12(1):1972, 2022

Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness.

Zheng ZY, Elsarraj H, Lei JT, Hong Y, Anurag M, Feng L, Kennedy H, Shen Y, Lo F, Zhao Z, Zhang B, Zhang XH, Tawfik OW, Behbod F, Chang EC.

Breast Cancer Res., 24(1):68, 2022

Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma.

Li QK, Hu Y, Chen L, Schnaubelt M, Cui Zhou D, Li Y, Lu RJ, Thiagarajan M, Hostetter G, Newton CJ, Jewell SD, Omenn G, Robles AI, Mesri M, Bathe OF, Zhang B, Ding L, Hruban RH, Chan DW, Zhang H.

Clin Proteomics, 19(1):36, 2022.

A SMAD4-modulated gene profile predicts disease-free survival in stage II and III colorectal cancer.

Szeglin BC, Wu C, Marco MR, Park HS, Zhang Z, Zhang B, Garcia-Aguilar J, Beauchamp RD, Chen XS, Smith JJ.

Cancer Rep, 5(1):e1423, 2022.

Identifying biomarkers of differential chemotherapy response in TNBC patient-derived xenografts with a CTD/WGCNA approach.

Petrosyan V, Dobrolecki LE, Thistlethwaite L, Lewis AN, Sallas C, Srinivasan RR, Lei JT, Kovacevic V, Obradovic P, Ellis MJ, Osborne CK, Rimawi MF, Pavlick A, Shafaee MN, Dowst H, Jain A, Saltzman AB, Malovannaya A, Marangoni E, Welm AL, Welm BE, Li S, Wulf GM, Sonzogni O, Huang C, Vasaikar S, Hilsenbeck SG, Zhang B, Milosavljevic A, Lewis MT.

iScience, 26(1):105799, 2022.

Deep learning-derived evaluation metrics enable effective benchmarking of computational tools for phosphopeptide identification.

Jiang W, Wen B, Li K, Zeng WF, da Veiga Leprevost F, Moon J, Petyuk VA, Edwards NJ, Liu T, Nesvizhskii AI, Zhang B.

Mol Cell Proteomics, 20:100171, 2021.

caAtlas: An immunopeptidome atlas of human cancer.

Yi X, Liao Y, Wen B, Li K, Dou Y, Savage SR, Zhang B.

iScience, 24(10):103107, 2021.

Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multi-omics Data.

Shi Z, Wen B, Gao Q, Zhang B.

Mol Cell Proteomics, 20:100083, 2021.

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.

Huang C^#, Chen L^#, Savage SR^#, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieślik M, Chang HY, Wyczalkowski MA, Li K, Colaprico A, Li QK, Clark DJ, Hu Y, Cao L, Pan J, Wang Y, Cho KC, Shi Z, Liao Y, Jiang W, Anurag M, Ji J, Yoo S, Zhou DC, Liang WW, Wendl M, Vats P, Carr SA, Mani DR, Zhang Z, Qian J, Chen XS, Pico AR, Wang P, Chinnaiyan AM, Ketchum KA, Kinsinger CR, Robles AI, An E, Hiltke T, Mesri M, Thiagarajan M, Weaver AM, Sikora AG, Lubiński J, Wierzbicka M, Wiznerowicz M, Satpathy S, Gillette MA, Miles G, Ellis MJ, Omenn GS, Rodriguez H, Boja ES, Dhanasekaran SM, Ding L, Nesvizhskii AI, El-Naggar AK, Chan DW^@, Zhang H^@, Zhang B^@; Clinical Proteomic Tumor Analysis Consortium.

Cancer Cell, 39(3):361-379, 2021. (# first authors; @ corresponding authors)

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cao L^#, Huang C^#, Cui Zhou D^#, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L^@, Zhang B^@, Zhang H^@; Clinical Proteomic Tumor Analysis Consortium.

Cell, 184(19):5031-5052, 2021. (# first authors; @ corresponding authors)

A proteogenomic portrait of lung squamous cell carcinoma.

Satpathy S^#, Krug K^#, Jean Beltran PM^#, Savage SR^#, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA^@, Zhang B^@, Mani DR^@, Gillette MA^@; Clinical Proteomic Tumor Analysis Consortium.

Cell, 184(16):4348-4371, 2021. (# first authors; @ corresponding authors)

A community effort to identify and correct mislabeled samples in proteogenomic studies.

Yoo S^#, Shi Z^#, Wen B^#, Kho S^#, Pan R, Feng H, Chen H, Carlsson A, Edén P, Ma W, Raymer M, Maier EJ, Tezak Z, Johanson E, Hinton D, Rodriguez H, Zhu J, Boja E, Wang P^@, Zhang B^@.

Patterns, 100245, 2021. (# first authors; @ corresponding authors)

Proteogenomics drives therapeutic hypothesis generation for precision oncology.

Lei JT, Zhang B.

Br J Cancer, 125(1):1-3, 2021.

Proteogenomic and metabolomic characterization of human glioblastoma.

Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, Rykunov D, Colaprico A, Rothstein JH, Hong R, Stathias V, Cornwell M, Petralia F, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Cui Zhou D, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schürer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyö D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD, Liu T, Ding L; Clinical Proteomic Tumor Analysis Consortium.

Cancer Cell, 39(4):509-528, 2021.

Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer.

Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TY, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XH, Westbrook TF.

Cell, 184(2):384-403, 2021.

Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer.

Huang D, Chowdhury S, Wang H, Savage SR, Ivey RG, Kennedy JJ, Whiteaker JR, Lin C, Hou X, Oberg AL, Larson MC, Eskandari N, Delisi DA, Gentile S, Huntoon CJ, Voytovich UJ, Shire ZJ, Yu Q, Gygi SP, Hoofnagle AN, Herbert ZT, Lorentzen TD, Calinawan A, Karnitz LM, Weroha SJ, Kaufmann SH, Zhang B, Wang P, Birrer MJ, Paulovich AG.

Cell Rep Med. , 2(12):100471, 2021

Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes.

Lehmann BD, Colaprico A, Silva TC, Chen J, An H, Ban Y, Huang H, Wang L, James JL, Balko JM, Gonzalez-Ericsson PI, Sanders ME, Zhang B, Pietenpol JA, Chen XS.

Nat Commun.12(1):6276, 2021

A highly annotated database of genes associated with platinum resistance in cancer.

Huang D, Savage SR, Calinawan AP, Lin C, Zhang B, Wang P, Starr TK, Birrer MJ, Paulovich AG.

Oncogene, 40(46):6395-6405, 2021.

A novel role of ADGRF1 (GPR110) in promoting cellular quiescence and chemoresistance in human epidermal growth factor receptor 2-positive breast cancer.

Abdulkareem NM, Bhat R, Qin L, Vasaikar S, Gopinathan A, Mitchell T, Shea MJ, Nanda S, Thangavel H, Zhang B, De Angelis C, Schiff R, Trivedi MV.

FASEB J, 35(7):e21719, 2021

Proteogenomic Characterization of Endometrial Carcinoma.

Dou Y^#, Kawaler EA^#, Cui Zhou D^#, Gritsenko MA^#, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD^@, Ding L^@, Zhang B^@, Liu T^@, Fenyö D^@; Clinical Proteomic Tumor Analysis Consortium.

Cell, 180(4):729-748, 2020 (# first authors; @ corresponding authors)

Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.

Wen B, Li K, Zhang Y, Zhang B.

Nat Commun, 11(1):1759, 2020.

DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.

Li K, Jain A, Malovannaya A, Wen B, Zhang B.

Proteomics, 2020.

Deep learning in proteomics.

Wen B, Zeng W, Liao Y, Shi Z, Savage SR, Jiang W, Zhang B.

Proteomics, 2020.

Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.

Savage SR, Zhang B.

Clin Proteomics, 17:27, 2020.

Microscaled proteogenomic methods for precision oncology.

Satpathy S^#@, Jaehnig EJ^#, Krug K, Kim BJ, Saltzman AB, Chan DW, Holloway KR, Anurag M, Huang C, Singh P, Gao A, Namai N, Dou Y, Wen B, Vasaikar SV, Mutch D, Watson MA, Ma C, Ademuyiwa FO, Rimawi MF, Schiff R, Hoog J, Jacobs S, Malovannaya A, Hyslop T, Clauser KR, Mani DR, Perou CM, Miles G, Zhang B, Gillette MA, Carr SA^@, Ellis MJ^@.

Nat Commun, 11(1):532, 2020 (# first authors; @ corresponding authors)

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.

Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA, Clinical Proteomic Tumor Analysis Consortium.

Cell, 182(1):200-225.e35., 2020.

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Krug K, Jaehnig EJ, Satpathy S, Blumenberg L, Karpova A, Anurag M, Miles G, Mertins P, Geffen Y, Tang LC, Heiman DI, Cao S, Maruvka YE, Lei JT, Huang C, Kothadia RB, Colaprico A, Birger C, Wang J, Dou Y, Wen B, Shi Z, Liao Y, Wiznerowicz M, Wyczalkowski MA, Chen XS, Kennedy JJ, Paulovich AG, Thiagarajan M, Kinsinger CR, Hiltke T, Boja ES, Mesri M, Robles AI, Rodriguez H, Westbrook TF, Ding L, Getz G, Clauser KR, Fenyö D, Ruggles KV, Zhang B, Mani DR, Carr SA, Ellis MJ, Gillette MA; Clinical Proteomic Tumor Analysis Consortium.

Cell, 183(5):1436-1456.e31., 2020.

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.

Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P; Children’s Brain Tumor Network; Clinical Proteomic Tumor Analysis Consortium.

Cell, 183(7):1962-1985.e31., 2020.

Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer.

Zheng ZY, Anurag M, Lei JT, Cao J, Singh P, Peng J, Kennedy H, Nguyen NC, Chen Y, Lavere P, Li J, Du XH, Cakar B, Song W, Kim BJ, Shi J, Seker S, Chan DW, Zhao GQ, Chen X, Banks KC, Lanman RB, Shafaee MN, Zhang XH, Vasaikar S, Zhang B, Hilsenbeck SG, Li W, Foulds CE, Ellis MJ, Chang EC.

Cancer Cell, 37(3):387-402, 2020.

Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.

McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD; Clinical Tumor Analysis Consortium.

Cell Rep Med, 1(1):100004, 2020.

A social encounter drives gene expression changes linked to neuronal function, brain development, and related disorders in mice expressing the serotonin transporter Ala56 variant.

O’Reilly KC, Anacker AMJ, Rogers TD, Forsberg CG, Wang J, Zhang B, Blakely RD, Veenstra-VanderWeele J.

Neurosci Lett, 730:135027, 2020.

PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data.

Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L, Chen X.

Proteomics, 20:e1900409, 2020.

Immune Checkpoint Profiles in Luminal B Breast Cancer (Alliance).

Anurag M, Zhu M, Huang C, Vasaikar S, Wang J, Hoog J, Burugu S, Gao D, Suman V, Zhang XH, Zhang B, Nielsen T, Ellis MJ.

J Natl Cancer Inst, 112(7):737-746, 2020

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 (# first authors; @ corresponding authors)

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

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma.

Gao Q, Zhu H, Dong L, Shi W, Chen R, Song Z, Huang C, Li J, Dong X, Zhou Y, Liu Q, Ma L, Wang X, Zhou J, Liu Y, Boja E, Robles AI, Ma W, Wang P, Li Y, Ding L, Wen B, Zhang B, Rodriguez H, Gao D, Zhou H, Fan J.

Cell, 179(2):561-577, 2019

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.

Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H.

Cell, 179(4):964-983, 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, 29(4):286-304, 2019

EPHB2 carried on small extracellular vesicles induces tumor angiogenesis via activation of ephrin reverse signaling.

Sato S, Vasaikar S, Eskaros A, Kim Y, Lewis JS, Zhang B, Zijlstra A, Weaver AM.

JCI Insight, doi: 10.1172/jci.insight.132447, 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

A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer.

Thangavel H, Angelis C, Vasaikar S, Bhat R, Jolly MK, Nagi C, Creighton CJ, Chen F, Dobrolecki LE, George JT, Kumar T, Abdulkareem NM, Mao S, Nardone A, Rimawi M, Osborne CK, Lewis MT, Levine H, Zhang B, Schiff R, Giuliano M, Trivedi MV.

J Clin Med, 8(11). pii: E1772, 2019

Genetic Dissection of Femoral and Tibial Microarchitecture.

Lu L, Huang J, Xu F, Xiao Z, Wang J, Zhang B, David NV, Arends D, Gu W, Ackert-Bicknell C, Sabik OL, Farber CR, Quarles LD, Williams RW.

JBMR Plus, 3(12):e10241, 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 toolkit.

Wang 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 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

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 proteogenomics.

Ruggles 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 study.

Zhao 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 cocaine.

Simmler 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 exosomes.

Dou 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 data.

Wang 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 instability.

Liu 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-Seq.

Wen 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 paradigm.

Zhu J, Shi Z, Wang J, Zhang B.

Bioinformatics, 31:1436-1443, 2015

Proteomic analysis of colon and rectal carcinoma using standard and customized databases.

Slebos 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 data.

Sun 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 exosomes.

Cha 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 Excretion.

Qi 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 aggressiveness.

French 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 paralysis.

Hardaway 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 search.

Wang 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-hydroxynonenal.

Liu 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 regulation.

Liu 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 2013.

Wang 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 patients.

Shi 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