Publications

    Underline = past/current group member , * = authors contributed equally, ✉ = corresponding author

2022 -

  • Yuan, Dongbang; Zhang, Yunfeng; Guo, Shuai; Wang, Wenyi; Gaynanova, Irina. Exponential canonical correlation analysis with orthogonal variation. submitted

  • Nguyen NH, Shin SJ, Dodd-Eaton EB, Ning J, Wang W✉. Bayesian Estimation of a Joint Semiparametric Recurrent Event Model of Multiple Cancer Types with Applications to the Li- Fraumeni Syndrome. ASA Section of Statistics in Genomics and Genetics Student Paper Award 2022.

  • Jiang Y*, Yu K*, Ji S*, Shin SJ, Cao S, Montierth MD, 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. [preprint][Github:CliP] *authors contributed equally. ASA Section of Statistics in Genomics and Genetics Student Paper Award 2021.

  • 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. [preprint]

  • Wang JR, Montierth M, Li X, Goswami M, Zhao X, Cote G, Wang W, Iyer P, Dadu R, Busaidy NL, Lai SY, Grosss 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. JCO Precision Oncology accepted

  • Bondaruk J et al., Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. The origin of bladder cancer from mucosal field effects. iScience 2022 Jun 7; 25(7):104551. doi: 10.1016/j.isci.2022.104551. eCollection 2022 Jul 15 [Full text]

  • Ji S, Montierth M, Wang W. MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling. Methods Molecular Biology. 2022; 2493:21-27. doi: 10.1007/978-1-0716-2293-3_2.[Full text]

  • Cao S, et al., Wang W✉ Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nature Biotechnology Published online June 13 2022. doi 10.1038/s41587-022-01342-x. [Abstract]

  • Wang Z, Baladandayuthapani V, Kaseb AO, Amin HM, Hassan MM, Wang W, Morris JS. Bayesian Edge Regression in Undirected Graphical Models to Characterize Interpatient Heterogeneity in Cancer. Journal of the American Statistical Association. Pages 533-546. Published online Jan 5 2022. [Full text]

  • 2021 -

  • Taavitsainen S et al., Wang W, Nykter M, Urbanucci A. Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer. Nature Communications 2021 Sep 6;12(1):5307. doi: 10.1038/s41467-021-25624-1. [Abstract]

  • Cao L et al. Clinical Proteomic Tumor Analysis Consortium. Proteogenomic Characterization of Pancreatic Ductal Adenocarcinoma. Cell 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023. [Abstract]

  • Dentro S*, Leshchiner I*, Haase K*, Tarabichi M*, Wintersinger J*, Deshwar A*, Yu K*, Rubanova Y*, Mcintyre G*, et al. PCAWG Evolution and Heterogeneity Working Group. Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types. Cell, 2021 Apr 15; 184(8): 2239-2254.e39. [abstract] [Full text] [Github:CSR] Wang is a co-last author. Selected for the MD Anderson Wall of Science and Research Excellence webpage.

  • 2020 -

  • Morris JS, Hassan MM, Zohner YE, Wang Z, Xiao L, Rashid A, Abdel-Wahab R, Ballard KL, Wolff RA, George B, Li L, Allen G, Weylandt M, Li D, Wang W, Raghav K, Yao J, Amin HM, Kaseb AO. Deconvolution-based Circulating Biomarker Aberration Score Enhances Hepatocellular Carcinoma Staging. Hepatology. Published online 2020/9/15. [abstract][Full text]

  • Haider H*, 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*, TCGA Research Network. Systematic assessment of tumour purity and its clinical implications. JCO Precision Oncology. No. 4 (2020) 995-1005. Published online September 4, 2020. [abstract][Full text]. *co-senior author

  • Gao F*, Pan X*, Dodd EB, Vera Recio C, Bojadzieva J, Mai PL, Johnson VE, Zelley K, Kim E. 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 Research. 2020 Aug 18. doi: 10.1101/gr.249599.119. Online ahead of print. [Abstract] [Full Text]
    *authors contributed equally

  • Amir Nikooienejad, Wenyi Wang, Valen Johnson. Bayesian Variable Selection For Survival Data Using Inverse Moment Priors. Annals of Applied Statistics. Volume 14, Number 2 (2020), 809-828. [Abstract][preprint]

  • The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5. [Abstract] [Full Text]

  • 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 Nature Methods 2020 Apr;17(4):414-421. doi: 10.1038/s41592-020-0766-3. Epub 2020 Mar 16. [Abstract] [Full Text]

  • Wu CC, Beird H, Livingston JL, Advani S, Cao S, Reuben A, Ingram D, Ju Z, Wang WL, Leung CH, Zheng Y, Mitra A, Lin H, RoszikJ, Wang W, Patel S, Benjamin R, Gordon M, Hwu P, Gorlick R, Lazar A, Daw N, Lewis V, and Futreal PA. Immuno-genomic landscape of osteosarcoma. Nature Communications 2020 Feb 21;11(1):1008. doi: 10.1038/s41467-020-14646-w. [Abstract] [Full Text]

  • Salcedo A, et al. A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology. 2020 Jan;38(1):97-107. doi: 10.1038/s41587-019-0364-z. Epub 2020 Jan 9.

  • 2019 -

  • Seung Jun Shin, Elissa Dodd, Gang Peng, Jasmina Bojadzieva, Jingxiao Chen, Chris Amos, Phuong L. Mai, Sharon A. Savage, Mandy L. Ballinger, David M. Thomas, Ying Yuan, Louise C. Strong, Wenyi Wang✉. Penetrance of Different Cancer Types in Families with Li-Fraumeni Syndrome: A Validation Study Using Multicenter Cohorts. Cancer Research.
    2020 Jan 15;80(2):354-360. doi: 10.1158/0008-5472.CAN-19-0728. Epub 2019 Nov 12.
    [Abstract] [Software: LFSPRO2.0.0] for risk assessment of specific cancer type.

  • Seung Jun Shin, Elissa B. Dodd, Fan Gao, Jasmina Bojadzieva, Jingxiao Chen, Xianhua Kong, Chris Amos, Jing Ning, Louise C. Strong, Wenyi Wang✉. Penetrance Estimates Over Time to First and Second Primary Cancer Diagnosis in Families with Li-Fraumeni Syndrome: A Single Institution Perspective. Cancer Research. 2020 Jan 15;80(2):347-353. doi: 10.1158/0008-5472.CAN-19-0725. Epub 2019 Nov 12.
    [Preprint] [Software: LFSPRO2.0.0] for risk assessment of multiple primary cancers.

  • Gerstung M, et al. PCAWG Evolution and Heterogeneity Working Group.The evolutionary history of 2,658 cancers. Nature. 2020 Feb;578(7793):122-128. doi: 10.1038/s41586-019-1907-7. Epub 2020 Feb 6. [Abstract] [Full Text]

  • Maura F, Agnelli L, Leongamornlert D, Bolli N, Chan J, Dodero A, Carniti C, Heavican T, Pellegrinelli A, Pruneri G, Butler A, Bhosle S, Chiappella A, Rocco AD, 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 improves the Stratification of Peripheral T-Cell Lymphoma. American Journal of Hematology March 4 2019 doi: 10.1002/ajh.25450.

  • Cao S, Wang Z, Gao F, Chen J, Zhang F, Frigo DE, Efstathiou E, Kopetz S, Wang W✉. An R Implementation of Tumor-Stroma-Immune Transcriptome Deconvolution Pipeline using DeMixT. [Preprint] Software: DeMixT 3-component deconvolution pipeline

  • 2018 -

  • Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F; PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjaerde OC, Wedge DC, Van Loo P. Neutral tumor evolution? Nature Genetics 2018 Dec;50(12):1630-1633. doi: 10.1038/s41588-018-0258-x. [Full text]

  • Shin SJ, Li J, Ning J, Bodjadzieva J, Strong LC and Wang W✉ . A Bayesian estimation of semiparametric recurrent event model with applications to the penetrance estimation of multiple primary cancers in Li-Fraumeni syndrome. Biostatistics [Full text]

  • 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 Nov 30;9:451-460. doi: 10.1016/j.isci.2018.10.028. [Full text][Software:DeMixT]

  • Shin SJ, Ying Yuan✉, Louise C. Strong, Jasmina Bojadzieva, Wang W✉ . Bayesian Semiparametric Estimation of Cancer-specic Age-at-onset Penetrance with Application to Li-Fraumeni Syndrome. Journal of the American Statistical Association [Full text]

  • Li J, Fu C, Speed TP, Wang W✉ , Symmans WF✉. Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High Quality Transcriptome From Frozen Tissue. DOI: 10.1200/PO.17.00091 JCO Precision Oncology Published online January 26, 2018. [Full Text] One of the most accessed articles on JCO PO in 2018

  • 2017 -

  • Peng G, Bojadzieva J, Ballinger ML, Thomas DM, Strong LC, Wang W✉ . Estimating TP53 Mutation Carrier Probability in Families with Li-Fraumeni Syndrome Using LFSPRO. Cancer Epidemiology, Biomarker and Prevention Jan 2017. DOI: 10.1158/1055-9965.EPI-16-0695. [Abstract] [Full Text] [Software:LFSPRO]

  • Ahn J, Morita S, Wang W✉ and Yuan Y✉. Bayesian shared-parameter models for longitudinal dyadic data with informative missing data using a dyadic shared-parameter model. Statistical Methods in Medical Research Published online January 1, 2017. DOI: 10.1177/0962280217715051 [Full Text]

  • 2016 -

  • Fan Y, Xi L, Hughes DST, Zhang J, Zhang J, Futreal PA, Wheeler DA and Wang W✉. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biology. 2016. 17:178 DOI: 10.1186/s13059-016-1029-6 [Full Text] [Software:MuSE]

  • Nikooienejad A, Wang W✉ , Johnson VE✉. Bayesian Variable Selection for Binary Outcomes in High Dimensional Genomic Studies Using Non-Local Priors. Bioinformatics Jan 6, 2016. doi: 10.1093/bioinformatics/btv764. [Abstract] [Full Text]

  • 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. 2016 Nov 29. pii: gkw1063. [Abstract] [Full Text]

  • Palculict TB, Ruteshouser EC, Fan Y, Wang W, Strong LC, Huff V. Identification of germline DICER1 mutations and loss of heterozygosity in familial Wilms tumor. Journal of Medical Genetics, 2016 Jun;53(6):385-8. doi: 10.1136/jmedgenet-2015-103311. [Abstract] [Full Text]

  • 2015 -

  • Lefterova MI*, Shen P*, Odegaard JI*, Fung E, Chiang T, Peng G, Davis RW, Wang W, Schrijver I, Scharfe C. Next-generation molecular testing of newborn dried blood spots for cystic brosis. Journal of Molecular Diagnostics, 2016 Mar;18(2):267-82. doi: 10.1016/j.jmoldx.2015.11.005. [Abstract]

  • The Cancer Genome Atlas Research Network. The molecular taxonomy of primary prostate cancer. Cell, 2015 Nov 5;163(4):1011-25. doi: 10.1016/j.cell.2015.10.025. [Abstract]

  • 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. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18.[Full Text]

  • Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biology. 2015 Sep 17;16(1):197. doi: 10.1186/s13059-015-0758-2. [Full Text]

  • 2014 -

  • Peng G, Fan Y, Wang W✉ . FamSeq: a variant calling program for family-based sequencing data using graphics processing units.   PLOS Computational Biology October 30, 2014 doi: 10.1371/journal.pcbi.1003880 [Full Text] [Software:FamSeq]

  • Davis CF et al., The Cancer Genome Atlas Research Network. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. 2014 Aug 20. pii: S1535-6108(14)00304-3. doi: 10.1016/j.ccr.2014.07.014. [Full Text]

  • The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507(7492):315-22, 2014 [Full Text]

  • 2013 -

  • Ahn J, Liu S, Wang W✉ and Yuan Y✉. Bayesian latent-class mixed-effect hybrid models for dyadic longitudinal data with non-ignorable dropouts. Biometrics 69(4):914-24, 2013 Dec [Abstract]

  • Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, and Wang W✉ . DeMix: Deconvolution for Mixed Cancer Transcriptomes Using Raw Measured Data. Bioinformatics 2013 doi: 10.1093/bioinformatics/btt301. [Abstract] [Full Text] [Software:DeMix]

  • Shen P*, Wang W* , Chi AK, Fan Y, Davis RW and Scharfe C. Multiplex target capture with double-stranded DNA probes. Genome Medicine 2013, 5:50 doi:10.1186/gm454 [Full Text] Highly accessed


  • Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW, Huff V, Scharfe C, Wang W✉ . Rare variant detection using family-based sequencing analysis. Proceedings of the National Academy of Sciences. Feb 2013 [Abstract] [Software:FamSeq]

  • The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics 45: 1113-1120, 2013 [Full Text]

  • Srivastava S, Wang W, Manyem G, Ordonez C and Baladandayuthapani V. Integrating Multi-Platform Genomic Data Using Hierarchical Bayesian Relevance Vector Machines. EURASIP Journal on Bioinformatics and Systems Biology. 2013 [Abstract]

  • 2012 -

  • Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C and Wang W✉ . SRMA: an R package for resequencing array data analysis. Bioinformatics 2012; doi: 10.1093/bioinformatics/bts286[Abstract]

  • Hua Y, Gorshkov K, Yang Y, Wang W, Zhang N, Hughes DPM. Slow down to stay live: HER4 protects against cellular stress and confers chemoresistance in neuroblastoma. Cancer. 2012 Mar 13. doi: 10.1002/cncr.27496. [Abstract]

  • Rubio JP, Wilkins EJ, Kostchet K, Cowie TC, O'Hely M, Burfoot R, Wang W, Speed TP, Stankovich J, Horne M. A DNA Resequencing Array for Genes Involved in Parkinson's Disease. Parkinsonism & Related Disorders. January 2012 [Full Text]

  • 2011 -

  • Shen P*, Wang W*, Krishnakumar S, Chi AK, Palm C, Enns GM, Davis RW, Speed TP, Mindrinos M, Scharfe C. High quality DNA sequence capture of 524 disease candidate genes. Proceedings of the National Academy of Sciences. April 2011, doi: 10.1073/pnas.1018981108. [Abstract] [Full Text] Listed among Most-Read Articles during Apr 2011


  • 2010 -

  • Lin S*, Wang W*, Palm C, Davis RW, Juneau K. A Molecular Inversion Probe Assay for Detecting Alternative Splicing. BMC Genomics 2010, 11:712. [Full Text]

  • Wang W, Shen P, Thyagarajan 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 Resequencing.Nucleic Acids Research 2010 Sep 15 doi:10.1093/nar/gkq750/. [Full Text]

  • Wang W, Niendorf KB, Patel D, Blackford A, Marroni F, Sober AJ, Parmigiani G and Tsao H. Estimating CDKN2A Carrier Probability and Personalizing Cancer Risk Assessments in Hereditary Melanoma Using MelaPRO. Cancer Research Jan 2010 doi:10.1158/0008-5472. [Abstract]

  • 2008 -

  • Wang W, Carvalho B, Miller N, Pevsner J, Chakaravarti A and Irizarry RA. Estimating Genome-wide Copy Number using Allele Specific Mixture Models. Journal of Computational Biology. 2008;15:857-66. [Abstract]

  • 2007 -

  • Wang W, Chen S, Brune KA, Hruban RH, Parmigiani G and Klein AP. PancPRO: risk assessment for individuals with a family history of pancreatic cancer. Journal of Clinical Oncology. 2007;25:1417-22. [Abstract]

  • Nicodemus KK, Wang Wand Shugart YY. Stability of Variable Importance Scores and Rankings using Statistical Learning Tools on Single Nucleotide Polymorphisms (SNPs) and Risk Factors Involved in Gene-Gene and Gene-Environment Interactions.BMC Proceedings. 2007;1 Suppl 1:S58. [Abstract]

  • 2006 -

  • 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 N, Casey G, Ellis N, Giardiello FM, the Colon Cancer Family Registry,Offit K, Parmigiani G. Prediction of Germline Mutations and Cancer Risk in the Lynch Syndrome.Journal of the American Medical Association. September 27, 2006; 296(12): 1479-1487. [Abstract]

  • Gonzalez JR, Wang W, Ballana E and Estivill X. A recessive Mendelian model to predict carrier probabilities of DFNB1 for non-Syndromic deafness. Human Mutation. 2006; DOI 10.1002/humu.20390. [Abstract]

  • 2004 -

  • Chen S, Wang W, Broman K and Parmigiani G. BayesMendel: An R Environment for Mendelian Risk Prediction. Statistical Application in Genetics and Molecular Biology. 3(1): Article 21, 2004. [Abstract]