Yuxing Liao

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.

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.

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)

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.

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.

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)

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.

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