Wenyi Wang, Ph.D.
Department of Bioinformatics and Computational Biology, Division of VP, Research
About Dr. Wang
Dr. Wang is a Professor of Bioinformatics and Computational Biology and Biostatistics at the University of Texas MD Anderson Cancer Center. She received her PhD from Johns Hopkins University and performed postdoctoral training in statistical genomics and genome technology at UC Berkeley with Terry Speed and at Stanford with Ron Davis. Wenyi’s research includes significant contributions to statistical bioinformatics in cancer, including MuSE for subclonal mutation calling, DeMixT for transcriptome deconvolution, Famdenovo for de novo mutation identification, and more recently, a pan-cancer characterization of genetic intra-tumor heterogeneity in subclonal selection. Her group is focused on the development and application of computational methods to study the evolution of the human genome as well as the cancer genome, and further develop risk prediction models to accelerate the translation of biological findings to clinical practice. Her lab website is at: https://odin.mdacc.tmc.edu/~wwang7/.
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Present Title & Affiliation
Primary Appointment
Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment
Professor, Department of Biostatistics, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX
Professor, Department of Statistics, Texas A&M University, College Station, TX
Professor, Department of Statistics, Rice University, Houston, TX
Research Interests
Currently her laboratory is focused on two research topics: 1) Development of deconvolution models in order to build an atlas of gene expression states of tumor and immune cells during cancer evolution; and 2) Statistical models for cancer risk counseling for individuals with deleterious germline mutations.
Education & Training
Degree-Granting Education
| 2007 | Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA, PHD, Biostatistics |
| 2003 | Columbia University College of Physicians and Surgeons, New York City, NY, USA, MA, Human Nutrition |
| 2001 | Fudan University, Shanghai, CHN, BS, Biology |
Experience & Service
Administrative Appointments/Responsibilities
Quantitative Sciences Program Co-director, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, 2014 - 2018
Other Appointments/Responsibilities
Faculty member of the TRIUMPH (Translational Research in Multidisciplinary Programs) training program, The University of Texas MD Anderson Cancer Center, Houston, TX, 2021 - Present
Faculty member, Baylor College of Medicine Graduate Program in Quantitative Computational Biology, Houston, TX, 2017 - Present
Selected Publications
Peer-Reviewed Articles
- 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. JASA, 2022. e-Pub 2022.
- 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, PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184(8):2239-2254.e39, 2021. e-Pub 2021. PMID: 33831375.
- 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, Cancer Genome Atlas Research Network. 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 2018. 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, HipSci Consortium, 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, PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium. 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 2019. 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 2019. PMID: 31719101.
- Maura F, Agnelli L, Leongamornlert D, Bolli N, Chan WC, Dodero A, Carniti C, Heavican TB, Pellegrinelli A, Pruneri G, Butler A, Bhosle SG, Chiappella A, Di Rocco A, Zinzani PL, Zaja F, Piva R, Inghirami G, Wang W, Palomero T, Iqbal J, Neri A, Campbell PJ, Corradini P. Integration of transcriptional and mutational data simplifies the stratification of peripheral T-cell lymphoma. Am J Hematol 94(6):628-634, 2019. e-Pub 2019. PMID: 30829413.
- Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P. Neutral tumor evolution?. Nat Genet 50(12):1630-1633, 2018. e-Pub 2018. PMID: 30374075.
- Wang Z, Morris JS, Cao S, Ahn J, Liu R, Tyekucheva S, Li B, Lu W, Tang X, Wistuba II, Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang W. Transcriptome deconvolution of heterogeneous tumor samples with immune infiltration. iScience, 2018. e-Pub 2018.
- Shin SJ, Yuan Y*, Strong LC, Bojadzieva J, Wang W*. Bayesian semiparametric estimation of cancer-specific age-at-onset penetrance with application to Li-Fraumeni Syndrome. JASA, 2018. e-Pub 2018.
- Li J, Fu C, Speed TP, Wang W*, Symmans F*. Accurate RNA Sequencing From Formalin- Fixed Cancer Tissue to Represent High-Quality Transcriptome From Frozen Tissue. Journal of Clinical Oncology Precision Oncology, 2018. e-Pub 2018. PMID: 29862382.
- Peng G, Bojadzieva J, Ballinger ML, Li J, Blackford AL, Mai PL, Savage SA, Thomas DM, Strong LC, Wang W. Estimating TP53 mutation carrier probability in families with Li-Fraumeni Syndrome using LFSPRO. Cancer Epidemiol Biomarkers Prev 26(6):837-844, 2017. e-Pub 2017. PMID: 28137790.
- Holik AZ, Law CW, Liu R, Wang Z, Wang W, Ahn J, Asselin-Labat ML, Smyth GK, Ritchie ME. RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods. Nucleic Acids Res 45(5):e30, 2017. e-Pub 2016. PMID: 27899618.
- Lefterova MI, Shen P, Odegaard JI, Fung E, Chiang T, Peng G, Davis RW, Wang W, Kharrazi M, Schrijver I, Scharfe C. Next-generation molecular testing of newborn dried blood spots for cystic fibrosis. J Mol Diagn 18(2):267-82, 2016. e-Pub 2016. PMID: 26847993.
- Fan Y, Xi L, Hughes DS, Zhang J, Zhang J, Futreal PA, Wheeler DA, Wang W. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biol 17(1):178, 2016. e-Pub 2016. PMID: 27557938.
- Ahn J, Liu S, Wang W*, Yuan Y*. Bayesian latent-class mixed-effect hybrid models for dyadic longitudinal data with non-ignorable dropouts. Biometrics 69(4):914-24, 2013. e-Pub 2013. PMID: 24328715.
- Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45(10):1113-20, 2013. PMID: 24071849.
- Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W. DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics 29(15):1865-71, 2013. e-Pub 2013. PMID: 23712657.
- Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi AK, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proc Natl Acad Sci U S A 110(10):3985-90, 2013. e-Pub 2013. PMID: 23426633.
- Srivastava S, Wang W, Manyam G, Ordonez C, Baladandayuthapani V. Integrating Multi-Platform Genomic Data Using Hierarchical Bayesian Relevance Vector Machines. EURASIP J Bioinform Syst Biol 2013(1):9, 2013. e-Pub 2013. PMID: 23809014.
- Hua Y, Gorshkov K, Yang Y, Wang W, Zhang N, Hughes DP. Slow down to stay alive: HER4 protects against cellular stress and confers chemoresistance in neuroblastoma. Cancer 118(20):5140-54, 2012. e-Pub 2012. PMID: 22415601.
- Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C, Wang W. SRMA: an R package for resequencing array data analysis. Bioinformatics 28(14):1928-30, 2012. e-Pub 2012. PMID: 22581181.
- Wilkins EJ, Rubio JP, Kotschet KE, Cowie TF, Boon WC, O'Hely M, Burfoot R, Wang W, Sue CM, Speed TP, Stankovitch J, Horne MK. A DNA Resequencing Array for Genes Involved in Parkinson's Disease. Parkinsonism Relat Disord 18(4):386-90, 2012. e-Pub 2012. PMID: 22243833.
- Shen P*, Wang W*, Krishnakumar S, Palm C, Chi AK, Enns GM, Davis RW, Speed TP, Mindrinos MN, Scharfe C. High quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A 108(16):6549-54, 2011. PMID: 21467225.
- Wang W, Shen P, Thiyagarajan S, Lin S, Palm C, Horvath R, Klopstock T, Cutler D, Pique L, Schrijver I, Davis RW, Mindrinos M, Speed TP, Scharfe C. Identification of Rare DNA Variants in Mitochondrial Disorders with Improved Array-based Sequencing. Nucleic Acids Res 39(1):doi: 10.1093/nar/gkq750, 2011. PMID: 20843780.
- Wang W, Niendorf KB, Patel D, Blackford A, Marroni F, Sober AJ, Parmigiani G, Tsao H. Estimating CDKN2A carrier probability and personalizing cancer risk assessments in hereditary melanoma using MelaPRO. Cancer Res 70(2):552-9, 2010. e-Pub 2010. PMID: 20068151.
- Lin S*, Wang W*, Palm C, Davis RW, Juneau K. A Molecular Inversion Probe Assay for Detecting Alternative Splicing. BMC Genomics 11:712, 2010. e-Pub 2010. PMID: 21167051.
- Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA. Estimating genome-wide copy number using allele-specific mixture models. J Comput Biol 15(7):857-66, 2008. PMID: 18707534.
- Wang W, Chen S, Brune KA, Hruban RH, Parmigiani G, Klein AP. PancPRO: risk assessment for individuals with a family history of pancreatic cancer. J Clin Oncol 25(11):1417-22, 2007. PMID: 17416862.
- Nicodemus KK, Wang W, Shugart YY. Stability of variable importance scores and rankings using statistical learning tools on single-nucleotide polymorphisms and risk factors involved in gene x gene and gene x environment interactions. BMC Proc 1 Suppl 1:S58, 2007. e-Pub 2007. PMID: 18466558.
- González JR, Wang W, Ballana E, Estivill X. A recessive Mendelian model to predict carrier probabilities of DFNB1 for nonsyndromic deafness. Hum Mutat 27(11):1135-42, 2006. PMID: 16941638.
- Chen S, Wang W, Lee S, Nafa K, Lee J, Romans K, Watson P, Gruber SB, Euhus D, Kinzler KW, Jass J, Gallinger S, Lindor NM, Casey G, Ellis N, Giardiello FM, Offit K, Parmigiani G, Colon Cancer Family Registry. Prediction of germline mutations and cancer risk in the Lynch syndrome. JAMA 296(12):1479-87, 2006. PMID: 17003396.
- Xu Z, Sproul A, Wang W, Kukekov N, Greene LA. Siah1 interacts with the scaffold protein POSH to promote JNK activation and apoptosis. J Biol Chem 281(1):303-12, 2006. e-Pub 2005. PMID: 16230351.
- Chen S, Wang W, Broman KW, Katki HA, Parmigiani G. BayesMendel: an R environment for Mendelian risk prediction. Stat Appl Genet Mol Biol 3:Article21, 2004. e-Pub 2004. PMID: 16646800.
- Nikooienejad A, Wang W*, Johnson VE*.. Bayesian variable selection for binary outcomes in high dimensional genomic studies using non-local priors. Bioinformatics. e-Pub 2016.
- Palculict TB, Ruteshouser EC, Fan Y, Wang W, Strong L, Huff V. Identification of germline DICER1 mutations and loss of heterozygosity in familial Wilms tumor using whole genome sequenc- ing. Journal of Medical Genetics. e-Pub 2015.
- Fang LT, Afshar PT, Chhibber A,Mohiyuddin M, Fan Y, Mu J, Gibeling G, Barr S, Asadi NB, Gerstein M, Koboldt D, Wang W, Wong WH, Lam H.. An ensemble approach to accurately detect so- matic mutations using SomaticSeq. Genome Biology. e-Pub 2015.
- Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P’ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC.. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide- variant detection. Nature Methods. e-Pub 2015.
- Davis CF et al., The Cancer Genome Atlas Research Network.. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. e-Pub 2014.
- Peng G, Fan Y, Wang W. FamSeq: a variant calling program for family-based sequencing data using graphics processing units. PLOS Comput Biol. e-Pub 2014. PMID: 25357123.
- Shen P*, Wang W*, Chi AK, Fan Y, Davis RW, Scharfe C. Multiplex target capture with double-stranded DNA probes. Genome Med 5(5):50. e-Pub 2013. PMID: 23718862.
- Shen P*, Wang W* , Chi AK, Fan Y, Davis RW and Scharfe C. Multiplex target capture with long padlock probes. Genome Medicine(5):50. e-Pub 2013. PMID: 23718862.
- Bondaruk J et al., Wang W, McConkey D, Wei P, Kimmel M, Czerniak B.. The origin of bladder cancer from mucosal fi eld effects.
- Cao S et al., Wang W. Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer.
- Jiang Y*, Yu K*, Guo S, Montierth MD, Ji S, Shin SJ, Cao S, Huang L, Kopetz S, Msaouel P, Wang JR, Kimmel M, Zhu H, Wang W. CliP: subclonal architecture reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model.
- 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 analysis of ovarian cancer. ISMB/ECCB 2021.
- Wang JR, Montierth M, Li X, 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 Anaplastic Thyroid Carcinoma Patients. Journal of Clinical Oncology Precision Oncology.
- The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. e-Pub 2020.
- Ahn J, Morita S, Wang W*, Yuan Y*. Bayesian analysis of longitudinal dyadic data with informative missing data using a dyadic shared-parameter model. Stat Methods Med Res:962280217715051. e-Pub 2017. PMID: 28629259.
Book Chapters
- Wang W, Fan Y, Speed T. DNA Variant Calling in Targeted Sequencing Data. In: Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput. Cambridge University Press: New York, 2013.
Grant & Contract Support
| Title: | Statistical methods and tools for cancer risk prediction in families with germline mutations in TP53 |
| Funding Source: | NIH/NCI |
| Role: | Principal Investigator |
| Title: | Cell Atlas of the Neural Retina |
| Funding Source: | Chan Zuckerberg Initiative |
| Role: | Co-Principal Investigator |
| Title: | Improving risk prediction for Li-Fraumeni Syndrome: A practical tool for clinical health care providers |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-Principal Investigator |
| Title: | Intratumor Heterogeneity in Anaplastic Thyroid Carcinoma: Implications for Response to Neoadjuvant BRAF- and Immune- Directed Therapies |
| Funding Source: | The Mark Foundation |
| Role: | MPI |
| Title: | Integrative genomic analysis to characterize tumor subclonal expansion and immune environment in primary and metastatic colorectal cancer |
| Funding Source: | MD Anderson SPORE in Gastrointestinal Cancer-Developmental Research Program |
| Role: | Principal Investigator-MDACC |