Kai Li

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)

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.

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)

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 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)

Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.

Wen B, Li K, Zhang Y, Zhang B.

Nat Commun, 11(1):1759, 2020.

DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.

Li K, Jain A, Malovannaya A, Wen B, Zhang B.

Proteomics, 2020.

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.

Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA, Clinical Proteomic Tumor Analysis Consortium.

Cell, 182(1):200-225.e35., 2020.

PDV: an integrative proteomics data viewer.

Li K, Vaudel M, Zhang B, Ren Y, Wen B.

Bioinformatics, 35(7):1249-1251, 2019

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.

Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H.

Cell, 179(4):964-983, 2019

Detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity.

Wang X, Codreanu SG, Wen B, Li K, Chambers M, Liebler DC, Zhang B.

Mol Cell Proteomics, 17(3):422-430, 2018