Wen Jiang (Faye)

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)

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 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)

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.

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.

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)

Deep learning in proteomics.

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

Proteomics, 2020.