Jing Wang

Integrative proteogenomics and forward genetics reveals a novel mitotic vulnerability in triple-negative breast cancer.

Neill NJ, Satpathy S, Krug K, Meena JK, Ramesh Babu N, Calderon C, Reed D, Weber MJ, Dobrolecki LE, Lewis A, Sallas C, Anurag M, Holloway KR, Huang C, Vasaikar S, Cardenas MF, Kim BJ, Chan DW, Avanessian SC, Tyagi S, Orellana M, Mao S, Li H, Gong F, Kurley SJ, Meerbrey KL, Olson CM, Nair A, Sun T, Chung HC, Bowling EA, Wang JH, Zhang P, Xiao P, Yang D, Stossi F, Polley MC, Saltzman AB, Mundt F, Mani DR, Gillette MA, Hilsenbeck SG, Miles G, Gutierrez C, Osborne CK, Lin CY, Gray NS, Sun J, Wheeler DA, Perou CM, Malovannaya A, Lewis MT, Zhang B, Ellis MJ, Carr SA, Westbrook TF.

Cancer Discov., in press, 2025.

COOKIE-Pro: covalent inhibitor binding kinetics profiling on the proteome scale.

Lin H, Yang B, Ding L, Yang YY, Holt MV, Jung SY, Zhang B, Wang MC, Wang J.

Nat Commun., 16(1):8373, 2025.

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.

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.

Death-associated protein kinase 3 modulates migration and invasion of triple-negative breast cancer cells.

Wang J, Tran-Huynh AM, Kim BJ, Chan DW, Holt MV, Fandino D, Yu X, Qi X, Wang J, Zhang W, Wu YH, Anurag M, Zhang XHF, Zhang B, Cheng C, Foulds CE, Ellis MJ.

PNAS Nexus, 3(9):pgae401, 2024.

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)

Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors.

Lv X, Lu X, Cao J, Luo Q, Ding Y, Peng F, Pataer A, Lu D, Han D, Malmberg E, Chan DW, Wang X, Savage SR, Mao S, Yu J, Peng F, Yan L, Meng H, Maneix L, Han Y, Chen Y, Yao W, Chang EC, Catic A, Lin X, Miles G, Huang P, Sun Z, Burt B, Wang H, Wang J, Yao QC, Zhang B, Roth JA, O’Malley BW, Ellis MJ, Rimawi MF, Ying H, Chen X.

Science, 381(6662):eabn4180, 2023.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG.

Cell, 186(16):3476-3498, 2023.

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)

Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer.

Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TY, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XH, Westbrook TF.

Cell, 184(2):384-403, 2021.

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.

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.

Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P; Children’s Brain Tumor Network; Clinical Proteomic Tumor Analysis Consortium.

Cell, 183(7):1962-1985.e31., 2020.

A social encounter drives gene expression changes linked to neuronal function, brain development, and related disorders in mice expressing the serotonin transporter Ala56 variant.

O’Reilly KC, Anacker AMJ, Rogers TD, Forsberg CG, Wang J, Zhang B, Blakely RD, Veenstra-VanderWeele J.

Neurosci Lett, 730:135027, 2020.

Immune Checkpoint Profiles in Luminal B Breast Cancer (Alliance).

Anurag M, Zhu M, Huang C, Vasaikar S, Wang J, Hoog J, Burugu S, Gao D, Suman V, Zhang XH, Zhang B, Nielsen T, Ellis MJ.

J Natl Cancer Inst, 112(7):737-746, 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

Genetic Dissection of Femoral and Tibial Microarchitecture.

Lu L, Huang J, Xu F, Xiao Z, Wang J, Zhang B, David NV, Arends D, Gu W, Ackert-Bicknell C, Sabik OL, Farber CR, Quarles LD, Williams RW.

JBMR Plus, 3(12):e10241, 2019

LinkedOmics: analyzing multi-omics data within and across 32 cancer types.

Vasaikar SV, Straub P, Wang J, Zhang B.

Nucleic Acids Res, 46(D1):D956-D963, 2018

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit.

Wang J, Vasaikar S, Shi Z, Greer M, Zhang B.

Nucleic Acids Res, 45(W1):W130-W137, 2017

Proteome profiling outperforms transcriptome profiling for co-expression based gene function prediction.

Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJ, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B.

Mol Cell Proteomics, 16(1):121-134, 2017

Colorectal cancer cell line proteomes are representative of primary tumors and predict drug sensitivity.

Wang J^#, Mouradov D^#, Wang X^#, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B^@, Sieber OM^@.

Gastroenterology, 153(4):1082-1095, 2017 (# first authors; @ corresponding authors)

Methods, tools and current perspectives in proteogenomics.

Ruggles KV^#, Krug K^#, Wang X^#, Clauser KR, Wang J, Payne SH, Fenyö D^@, Zhang B^@, Mani DR^@.

Mol Cell Proteomics, 16(6):959-981, 2017 (# first authors; @ corresponding authors)

APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism.

Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS.

Nat Commun, 8(1):465, 2017

Effects of a social stimulus on gene expression in a mouse model of fragile X syndrome.

Rogers TD, Anacker AMJ, Kerr TM, Forsberg CG, Wang J, Zhang B, Veenstra-VanderWeele J.

Mol Autism, doi: 10.1186/s13229-017-0148-6, 2017

Blockade of the 5-HT transporter contributes to the behavioural, neuronal and molecular effects of cocaine.

Simmler LD, Anacker AMJ, Levin MH, Vaswani NM, Gresch PJ, Nackenoff AG, Anastasio NC, Stutz SJ, Cunningham KA, Wang J, Zhang B, Keith Henry L, Stewart A, Veenstra-VanderWeele J, Blakely RD.

Br J Pharmacol, 174(16):2716-2738, 2017

Proteogenomics connects somatic mutations to signalling in breast cancer.

Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC.

Nature, 534:55-62, 2016

Integrated proteogenomic characterization of human high-grade serous ovarian cancer.

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators.

Cell, 2016

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC.

J Proteome Res, 15:691-706, 2016

Empowering biologists with multi-omics data: colorectal cancer as a paradigm.

Zhu J, Shi Z, Wang J, Zhang B.

Bioinformatics, 31:1436-1443, 2015

Global gene expression profiling reveals a suppressed immune response pathway associated with 3q amplification in squamous carcinoma of the lung.

Qian J, Zou Y, Wang J, Zhang B, Massion PP.

Genom Data, 5:272-274, 2015.

Proteogenomic characterization of human colon and rectal cancer.

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; the National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI CPTAC).

Nature, 513:382-387, 2014

Functional annotation of differentially regulated gene set using WebGestalt: a gene set predictive of response to ipilimumab in tumor biopsies.

Kirov S, Ji R, Wang J, Zhang B.

Methods Mol Biol, 1101:31-42, 2014

An open-source analytical platform for analysis of C. elegans swimming induced paralysis.

Hardaway JA, Wang J, Fleming PA, Fleming KA, Whitaker SM, Nackenoff A, Snarrenberg CL, Hardie SL, Zhang B, Blakely RD.

J Neurosci Methods, 232:58-62, 2014

Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice.

Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD.

Genes Brain Behav, 13:247-260, 2014

Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.

Halvey PJ, Wang X, Wang J, Bhat AA, Dhawan P, Li M, Zhang B, Liebler DC, Slebos RJ.

Cancer Res, 74:387-397, 2014

NetGestalt: integrating multidimensional omics data over biological networks.

Shi Z, Wang J, Zhang B.

Nat Methods, 10:597-598, 2013

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013.

Wang J, Duncan, D, Shi Z, Zhang B.

Nucleic Acids Res, 41:W77-83, 2013

Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis.

Zhu J, Wang J, Shi Z, Franklin JL, Deane NG, Coffey RJ, Beauchamp RD, Zhang B.

PLoS One, 8:e79282, 2013

Integrative genomics analysis identifies candidate drivers at 3q26-29 amplicon in squamous cell carcinoma of the lung.

Wang J, Qian J, Hoeksema MD, Zou Y, Espinosa AV, Rahman JS, Zhang B^@, Massion PP^@. (@ co-corresponding authors)

Clin Cancer Res, 19:5580-5590, 2013