Xinpei Yi

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.

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.

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.

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.

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)

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 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

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.