Yongchao Dou

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)

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)

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.

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.

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.

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.

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 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)

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)

Proteogenomics unveils mechanistic insights to precision oncology.

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

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

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.

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

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)

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)

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.

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)

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 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)

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

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

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