Wenyi Wang, Ph.D.
Department of Bioinformatics and Computational Biology, Division of Division of Discovery Science
About Dr. Wenyi Wang
Dr. Wenyi Wang is a Professor of Bioinformatics and Computational Biology and Biostatistics at the University of Texas MD Anderson Cancer Center. She received her PhD in Biostatistics from Johns Hopkins University and performed postdoctoral training in statistical genomics at UC Berkeley with Terry Speed and genome technology at Stanford with Ron Davis. Wenyi’s research includes contributions to statistical bioinformatics in cancer, including MuSE for subclonal mutation calling, DeMixT for transcriptomic deconvolution. Recently, she co-led a pan-cancer characterization of genetic intra-tumor heterogeneity in subclonal selection, and led a pan-cancer biomarker identification through integrative deconvolution of transcriptomic/genomic data. Her group is focused on the development of computational methods to study the evolution of cancer cells, and further develop risk prediction models to accelerate the translation of biological findings to clinical practice.
Present Title & Affiliation
Primary Appointment
Professor, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Research Interests
The two main research programs in the Wang laboratory are 1) Deconvolution and single-cell modeling for intra- and inter- tumor heterogeneity and 2) Semi-parametric survival modeling for cancer risk prediction.
Education & Training
Degree-Granting Education
| 2007 | Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, US, Biostatistics, Ph.D |
| 2003 | Columbia University College of Physicians and Surgeons, New York City, New York, US, Human Nutrition, MA |
| 2001 | Fudan University, Shanghai, CN, Biology, BS |
Postgraduate Training
| 2007-2010 | Postdoctoral Fellow, Statistics, University of California at Berkeley, Berkeley, California |
| 2007-2010 | Postdoctoral Fellow, Genome Technology, Stanford University, Stanford, California |
Grant & Contract Support
| Date: | 2025 - 2026 |
| Title: | Conformal inference of risk prediction in benefit from immunotherapy |
| Funding Source: | Joint Rice University-MD Anderson Cancer Center Cancer Bioengineering Collaborative Seed Grant Program |
| Role: | PI |
| Date: | 2022 - 2026 |
| Title: | An integrated genomic definition and therapeutic strategy for androgen indifferent prostate cancers |
| Funding Source: | Department of Defense (DOD) |
| Role: | PI |
| ID: | W81XWH2210258 |
| Date: | 2022 - 2027 |
| Title: | Statistical methods for genomic analysis of heterogeneous tumors |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01CA268380 |
Selected Publications
Peer-Reviewed Articles
- Bhinder, B, Friedl, V, Sethuraman, S, Risso, D, Chiotti, K, Mashl, RJ, Ellrott, K, Lee, JA, Wong, C, Gyan, K, Deshpande, A, Imielinski, MB, Bareja, R, Stuart, JM, Peto, M, Hoadley, KA, Lazar, A, Cherniack, AD, Zhu, J, Cao, S, Rubin, MA, Wang, W, Bathe, OF, Robine, N, Ding, L, Laird, PW, Zhou, W, Shen, H, Thorsson, V, Yeh, JJ, Bailey, M, Zhou, DC, Peng, X, Goldman, M, Li, Y, Korkut, A, Sahni, N, Hayes, DN, Mensah, MK, Felau, I, Kemal, A, Caesar-Johnson, SJ, Demchok, JA, Yang, L, Ferguson, ML, Tarnuzzer, R, Wang, Z, Zenklusen, JC, Wang, Z, Chen, K. Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles. Scientific reports 15(1), 2025. e-Pub 2025. PMID: 40615649.
- Lin, C, Pulliam, TL, Han, JJ, Xu, J, Recio, CV, Wilkenfeld, SR, Shi, Y, Kushwaha, M, Bench, S, Ruiz, E, Senthilkumar, S, Dileep, J, Shepherd, P, Navone, NM, Klekers, AR, Whitley, EM, Ittmann, MM, Eberlin, LS, Wang, W, Frigo, DE. Cholesterol metabolism regulated by CAMKK2-CREB signaling promotes castration-resistant prostate cancer. Cell Reports 44(6), 2025. e-Pub 2025. PMID: 40483692.
- Salcedo, A, Tarabichi, M, Buchanan, A, Espiritu, SG, Zhang, H, Zhu, K, Ou Yang, TH, Leshchiner, I, Anastassiou, D, Guan, Y, Jang, GH, Mootor, MF, Haase, K, Deshwar, AG, Zou, W, Umar, I, Dentro, SC, Wintersinger, J, Chiotti, K, Demeulemeester, J, Jolly, C, Sycza, L, Ko, M, Van Loo, P, Wedge, DC, Spellman, PT, Morris, QD, Wang, W, Zhu, H, Yuan, K, Yao, X, Yang, TP, Wheeler, DA, Vembu, S, Vázquez-García, I, Spiro, O, Stein, LD, Shin, SJ, Shi, R, Sengupta, S, Schumacher, SE, Schlesner, M, Sahinalp, SC, Rosebrock, D, Raphael, BJ, Peto, M, Peifer, M, Oesper, L, Fan, Y, Cao, S. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nature Biotechnology 43(4):581-592, 2025. e-Pub 2025. PMID: 38862616.
- Chowdhury, S, Ferri-Borgogno, S, Yang, P, Wang, W, Peng, J, Mok, S, Wang, P. Learning directed acyclic graphs for ligands and receptors based on spatially resolved transcriptomic data of ovarian cancer. Briefings in bioinformatics 26(2), 2025. e-Pub 2025. PMID: 40062614.
- Guo, S, Liu, X, Cheng, X, Jiang, Y, Ji, S, Liang, Q, Koval, A, Li, Y, Owen, L, Kim, IK, Aparicio, A, Lee, S, Sood, AK, Kopetz, S, Shen, JY, Weinstein, JN, DeAngelis, MM, Chen, R, Wang, W. A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples. Genome Research 35(1):147-161, 2025. e-Pub 2025. PMID: 39586714.
- Duan Y, Guo S, Wang W, Mueller P. Immune Profiling among Colorectal Cancer Subtypes using Dependent Mixture Models. JASA 120(550):671–684, 2025. e-Pub 2025. PMID: 40822234.
- Yousef M, Yousef A, Chowdhury S, Fanaeian MM, Knafl M, Peterson J, Zeineddine M, Alfaro K, Zeineddine F, Goldstein D, Hornstein N, Dasari A, Huey R, Johnson B, Higbie V, Bent A, Kee B, Lee M, Morelli MP, Morris VK, Halperin D, Overman MJ, Parseghian C, Vilar E, Wolff R, Raghav KP, White MG, Uppal A, Sun R, Wang W, Kopetz S, Willis J, Shen JP. Molecular, Socioeconomic, and Clinical Factors Affecting Racial and Ethnic Disparities in Colorectal Cancer Survival. JAMA Oncol 10(11), 2024. e-Pub 2024. PMID: 39264607.
- Wang JR, Zafereo ME, Cabanillas ME, Wu CC, Xu L, Dai Y, Wang W, Lai SY, Henderson Y, Erasmus L, Williams MD, Joshu C, Ray D. The association between thyroid differentiation score and survival outcomes in papillary thyroid carcinoma. J Clin Endocrinol Metab 110(2):356-363, 2024. e-Pub 2024. PMID: 39087944.
- Nguyen NH, Dodd-Eaton EB, Peng G, Corredor JL, Jiao W, Woodman-Ross J, Arun BK, Wang W. LFSPROShiny: An Interactive R/Shiny App for Prediction and Visualization of Cancer Risks in Families With Deleterious Germline TP53 Mutations. JCO Clin Cancer Inform 8:e2300167, 2024. e-Pub 2024. PMID: 38346271.
- Cermakova K, Tao L, Dejmek M, Sala M, Montierth MD, Chan YS, Patel I, Chambers C, Loeza Cabrera M, Hoffman D, Parchem RJ, Wang W, Nencka R, Barbieri E, Hodges HC. Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNF. Nucleic Acids Res 52(1):4-21, 2024. e-Pub 2024. PMID: 37993417.
- Yousef, M, Yousef, A, Fanaeian, M, Chowdhury, S, Knafl, M, Alfaro, KD, Uppal, A, Sun, R, Wang, W, Raghav, KS, Willis, JA, Kopetz, S, Shen, JY. Understanding causes of racial/ethnic survival disparity in 47,178 patients with colorectal cancer. Journal of Clinical Oncology 42(3):1, 2024. e-Pub 2024.
- Wang JR, Zafereo ME, Wang W, Joshu C, Ray D. Association of Polygenic Score With Tumor Molecular Subtypes in Papillary Thyroid Carcinoma. J Clin Endocrinol Metab 109(1):e306-e313, 2023. e-Pub 2023. PMID: 37453101.
- Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee HRL, Tang X, He W, Islam N, Jain A, Chiu Y, Cao S, Diao Y, Meyer-Gauen S, Höök M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz S, Chen Y. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nat Struct Mol Biol 30(12):1878-1892, 2023. e-Pub 2023. PMID: 37932451.
- Zheng C, Wei Y, Zhang Q, Sun M, Wang Y, Hou J, Zhang P, Lv X, Su D, Jiang Y, Gumin J, Sahni N, Hu B, Wang W, Chen X, McGrail DJ, Zhang C, Huang S, Xu H, Chen J, Lang FF, Hu J, Chen Y. Multiomics analyses reveal DARS1-AS1/YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Sci Adv 9(31):eadf3984, 2023. e-Pub 2023. PMID: 37540752.
- Shi Y, Ren X, Cao S, Chen X, Yuan B, Brasil da Costa FH, Rodriguez Rosario AE, Corona A, Michikawa C, Veeramachaneni R, Osman AA, Xie T, Wang W, Sikora AG, Myers JN, Rangel R. TP53 gain-of-function mutation modulates the immunosuppressive microenvironment in non-HPV-associated oral squamous cell carcinoma. J Immunother Cancer 11(8), 2023. e-Pub 2023. PMID: 37604640.
- Chachad D, Patel LR, Recio CV, Pourebrahim R, Whitley EM, Wang W, Su X, Xu A, Lee DF, Lozano G. Unique transcriptional profiles underlie osteosarcomagenesis driven by different p53 mutants. Cancer Res 83(14):2297-2311, 2023. e-Pub 2023. PMID: 37205631.
- Nguyen NH, Shin SJ, Dodd-Eaton EB, Ning J, Wang W. Personalized Risk Prediction for Cancer Survivors: A Bayesian Semi-parametric Recurrent Event Model with Competing Outcomes. bioRxiv, 2023. e-Pub 2023. PMID: 36909464.
- Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, Daw NC, Futreal PA, Efstathiou E, Lim B, Viale A, Zhang J, Nykter M, Czerniak BA, Brown PH, Swanton C, Msaouel P, Maitra A, Kopetz S, Campbell P, Speed TP, Boutros PC, Zhu H, Urbanucci A, Demeulemeester J, Van Loo P, Wang W. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol 40(11):1624-1633, 2022. e-Pub 2022. PMID: 35697807.
- Wang JR, Montierth M, Xu L, Goswami M, Zhao X, Cote G, Wang W, Iyer P, Dadu R, Busaidy NL, Lai SY, Gross ND, Ferrarotto R, Lu C, Gunn GB, Williams MD, Routbort M, Zafereo ME, Cabanillas ME. Impact of Somatic Mutations on Survival Outcomes in Patients With Anaplastic Thyroid Carcinoma. JCO Precis Oncol 6:e2100504, 2022. e-Pub 2022. PMID: 35977347.
- Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh KN, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kus P, Chen H, Weinstein JN, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo CC, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. Erratum: The origin of bladder cancer from mucosal field effects. iScience 25(7):104715, 2022. e-Pub 2022. PMID: 35811851.
- Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh KN, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kus P, Chen H, Weinstein JN, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo CC, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. The origin of bladder cancer from mucosal field effects. iScience 25(7):104551, 2022. e-Pub 2022. PMID: 35747385.
- Wang Z, Kaseb AO, Amin HM, Hassan MM, Wang W, Morris JS. Bayesian Edge Regression in Undirected Graphical Models to Characterize Interpatient Heterogeneity in Cancer. J Am Stat Assoc 117(538):533-546, 2022. e-Pub 2022. PMID: 36090952.
- 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, Analysis Consortium CPT. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell 184(19):5031-5052.e26, 2021. e-Pub 2021. PMID: 34534465.
- Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TLJ, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Nat Commun 12(1):5307, 2021. e-Pub 2021. PMID: 34489465.
- Morris JS, Hassan MM, Zohner YE, Wang Z, Xiao L, Rashid A, Haque A, Abdel-Wahab R, Mohamed YI, Ballard KL, Wolff RA, George B, Li L, Allen G, Weylandt M, Li D, Wang W, Raghav K, Yao J, Amin HM, Kaseb AO. HepatoScore-14: Measures of biological heterogeneity significantly improve prediction of hepatocellular carcinoma risk. Hepatology 73(6):2278-2292, 2021. e-Pub 2021. PMID: 32931023.
- Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P, Evolution P, Group HW, Consortium TP. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184(8):2239-2254.e39, 2021. e-Pub 2021. PMID: 33831375.
- Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11(1):4748, 2020. e-Pub 2020. PMID: 32958763.
- Haider S, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W, Demichelis F, Loda M, Boutros PC, Research Network CGA. Systematic Assessment of Tumor Purity and Its Clinical Implications. JCO Precis Oncol 4, 2020. e-Pub 2020. PMID: 33015524.
- Gao F, Pan X, Dodd-Eaton EB, Recio CV, Montierth MD, Bojadzieva J, Mai PL, Zelley K, Johnson VE, Braun D, Nichols KE, Garber JE, Savage SA, Strong LC, Wang W. A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome. Genome Res 30(8):1170-1180, 2020. e-Pub 2020. PMID: 32817165.
- Shin SJ, Li J, Ning J, Bojadzieva J, Strong LC, Wang W. Bayesian estimation of a semipara- metric recurrent event model with applications to the penetrance estimation of multiple primary cancers in Li-Fraumeni Syndrome. Biostatistics 21(3):467-482, 2020. e-Pub 2020. PMID: 30445420.
- Nikooienejad A, Wang W, Johnson VE. Bayesian variable selection for survival data using inverse moment priors. Ann Appl Stat 14(2):809-828, 2020. e-Pub 2020. PMID: 33456641.
- McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R, Consortium H, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes. Nat Methods 17(4):414-421, 2020. e-Pub 2020. PMID: 32203388.
- Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Evolution P, Group HW, Spellman PT, Wedge DC, Van Loo P, Consortium P. The evolutionary history of 2,658 cancers. Nature 578(7793):122-128, 2020. e-Pub 2020. PMID: 32025013.
- Wu CC, Beird HC, Andrew Livingston J, Advani S, Mitra A, Cao S, Reuben A, Ingram D, Wang WL, Ju Z, Hong Leung C, Lin H, Zheng Y, Roszik J, Wang W, Patel S, Benjamin RS, Somaiah N, Conley AP, Mills GB, Hwu P, Gorlick R, Lazar A, Daw NC, Lewis V, Futreal PA. Immuno-genomic landscape of osteosarcoma. Nat Commun 11(1):1008, 2020. e-Pub 2020. PMID: 32081846.
- Shin SJ, Dodd-Eaton EB, Gao F, Bojadzieva J, Chen J, Kong X, Amos CI, Ning J, Strong LC, Wang W. Penetrance Estimates Over Time to First and Second Primary Cancer Diagnosis in Families with Li-Fraumeni Syndrome: A Single Institution Perspective. Cancer Res 80(2):347-353, 2020. e-Pub 2020. PMID: 31719099.
- Shin SJ, Dodd-Eaton EB, Peng G, Bojadzieva J, Chen J, Amos CI, Frone MN, Khincha PP, Mai PL, Savage SA, Ballinger ML, Thomas DM, Yuan Y, Strong LC, Wang W. Penetrance of Different Cancer Types in Families with Li-Fraumeni Syndrome: A Validation Study Using Multicenter Cohorts. Cancer Res 80(2):354-360, 2020. e-Pub 2020. PMID: 31719101.
- Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W, Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC. A community effort to create standards for evaluating tumor subclonal reconstruction. Nat Biotechnol 38(1):97-107, 2020. e-Pub 2020. PMID: 31919445.
Review Articles
- Dai, Y, Guo, S, Pan, Y, Castignani, C, Montierth, MD, Van Loo, P, Wang, W. A guide to transcriptomic deconvolution in cancer. Nature Reviews Cancer 26(2):84-103, 2026. e-Pub 2026. PMID: 41331516.
- Fortuno C, Frone MN, Mester J, de la Hoya M, Mai PL, Pesaran T, Achatz MI, Bassett R, Bustamante C, Crowley S, de Andrade KC, Evans DG, Feng B, Fuqua L, Harrell MI, Hatton JN, Huether R, Kesserwan C, Lee K, MacFarland SP, Maciaszek JL, Maxwell K, McGoldrick K, Murphy M, Nehoray B, Penkert J, Pinto EM, Plon SE, Schwartz-Levine A, Thompson AS, Wang W, Zambetti GP, Zelley K, James PA, Savage SA, Kratz CP, Spurdle AB. A quantitative, Bayesian-informed approach to gene-specific variant classification: Updated Expert Panel recommendations improve classification of TP53 germline variants for Li-Fraumeni syndrome. Genome Med 17(1):128, 2025. e-Pub 2025. PMID: 41126324.
Patient Reviews
CV information above last modified July 22, 2026