Zhiao Shi

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.

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)

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.

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.

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.

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.

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)

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)

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

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 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)

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)

Deep learning in proteomics.

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

Proteomics, 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.

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)

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

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

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)

Empowering biologists with multi-omics data: colorectal cancer as a paradigm.

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

Bioinformatics, 31:1436-1443, 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

NetGestalt: integrating multidimensional omics data over biological networks.

Shi Z, Wang J, Zhang B.

Nat Methods, 10:597-598, 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

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

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