Eric Jaehnig

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)

Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures.

Satpathy S, Clark NM, Chen YJ, Hosseini N, Chang YH, Hsiao Y, Lei JT, Petralia F, Chen JS, Geffen Y, Heiman DI, Paul I, Cho H, Hollenberg M, Marino GB, Lin KT, Mannan R, White CJ, Allen J, Avanessian SC, Kane MH, Wolfe A, Kinarivala M, Liu W, Anand S, Lin MW, Haines M, Bergstrom EJ, Hussey G, Li GX, Mani DC, Fang H, Jaehnig EJ, Keshishian H, Miller B, Su KY, Hsiao YJ, Hsu HH, Hsieh MS, Hsu KH, Monovoukas A, Gohsman S, Thorup JR, Deng Y, Akiyama Y, Deng E, Sheng-Wen Chen E, Krek A, Espinoza R, Ma W, Charytonowicz D, Sebra R, Lin JH, Chen YS, Hsu YC, Lin ZS, Chen KC, Yeh CW, Wang YT, Lazar AJ, Mesri M, An E, Zhang X, Clauser KR, Fenyö D, Chinnaiyan AM, Zhang B, Ding L, Ruggles K, Newton C, Zhang H, Wang P, Hostetter G, Omenn GS, Kumar-Sinha C, Thiagarajan M, Govindan R, Paik P, Parolia A, Li QK, Ma’ayan A, Getz GA, Dhanasekaran SM, Robles AI, Chang GC, Yang PC, Yu SL, Chen HY, Nesvizhskii AI, Carr SA, Mani DR, Cieslik MP, Chen YJ, Gillette MA; Taiwan Cancer Moonshot Program; Clinical Proteomic Tumor Analysis Consortium.

Cancer Cell, 43(9):1731-1757, 2025.

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.

NF1-depleted ER+ breast cancers are differentially sensitive to CDK4/6 inhibitors.

Zheng ZY, Chen A, Jaehnig EJ, Anurag M, Lei JT, Feng L, Wang C, Fandino D, Singh P, Kennedy H, Yadav G, Vollert CT, Tsai J, Chen X, Li Y, Lim B, Thompson A, Li S, Foulds CE, Zhang B, Ellis MJ, Chang EC.

Sci Transl Med., 17(813):eadq5492, 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.

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.

IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer.

Xu L, Peng F, Luo Q, Ding Y, Yuan F, Zheng L, He W, Zhang SS, Fu X, Liu J, Mutlu AS, Wang S, Nehring RB, Li X, Tang Q, Li C, Lv X, Dobrolecki LE, Zhang W, Han D, Zhao N, Jaehnig E, Wang J, Wu W, Graham DA, Li Y, Chen R, Peng W, Chen Y, Catic A, Zhang Z, Zhang B, Mustoe AM, Koong AC, Miles G, Lewis MT, Wang MC, Rosenberg SM, O’Malley BW, Westbrook TF, Xu H, Zhang XH, Osborne CK, Li JB, Ellis MJ, Rimawi MF, Rosen JM, Chen X.

Cell, 187(25):7248-7266, 2024.

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)

The Breast Cancer Proteome and Precision Oncology.

Lei JT, Jaehnig EJ, Smith H, Holt MV, Li X, Anurag M, Ellis MJ, Mills GB^@, Zhang B^@, Labrie M^@.

Cold Spring Harb Perspect Med. doi: 10.1101/cshperspect.a041323, 2023 (@ corresponding authors)

OmicsEV: a tool for comprehensive quality evaluation of omics data tables.

Wen B, Jaehnig EJ, Zhang B.

Bioinformatics, 38(24):5463-5465, 2022.

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

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)

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.

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