Welcome to Wenyi Wang's home page

Publications

Years

2026
2025
2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2014-2004 ▼
- 2014
- 2013
- 2012
- 2011
- 2010
- 2008
- 2007
- 2006
- 2004

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

2026 -

Multi-omic deconvolution and DNA-RNA dynamics in cancer

Montierth MD*, Yan H*, Xie L*, Nemeth K, Pan X, Li R, Ercan C, Yang P, Sinjab A, Zhou T, Peng F, Singh M, Wang L, Kopetz S, Kadara H, Yuan Y, Calin GA, Wang W✉. Deconvolution of sparse-count RNA sequencing data for tumor cells using embedded negative binomial distributions. under review [Preprint] [Software: DeMixT2.0] *authors contributed equally

Dai Y, Pan X, Guo S, Ji S, Cao S, Montierth MD, Jiang Y, Shi L, Shalapour S, Echeverria GV, Yates L, Staaf J, Chang JT, Lim B, Yuan Y, Wang W✉. Tumor Microenvironment Transcriptional Activity Enables Robust Stratification of Chemotherapy Response in Triple-Negative Breast Cancer. Cell Reports Medicine. accepted.

Jiang Y*, Montierth M*, Yu K* , et al., Wang W✉. Subclonal mutation load predicts survival and response to immunotherapy in cancers with low to moderate tumor mutation burden. under revision [Preprint][Github:CliPP]

Risk prediction with machine learning and Bayesian semi-parametric models

Liu X, Yan, H, Shi H, Montellier E, Chi E, Hainaut P, Wang W✉. Transfer learning for survival-based clustering of predictors with an application to TP53 mutation annotation. Journal of the American Statistics Association, under revision. 2025 [Preprint] [GitHub Repo: TL-SCP] Proceedings of The Inaugural Workshop on Frontiers in Statistical Machine Learning (FSML) travel award

Corredor JL*, Ruonan Li*, Dodd-Eaton EB, Woodman-Ross J, Nguyen NH, Peng G, Green S, Gutierrez AM, Arun BK✉, Wang W✉. Performance of LFSPRO TP53 germline carrier risk predictions compared to standard genetic counseling practice on prospectively collected probands. American Journal of Human Genetics, under revision [Preprint]

Collaboration Papers

Li S et al. PRECISE: A prognostic thyrocyte-derived gene signature for papillary thyroid carcinoma. submitted

Duan Y, Guo S, Yan H, Wang W, Mueller P. Spatially aligned random partition models on spatially resolved transcriptomics data. Bayesian Analysis, under 2nd review. [Preprint]

2025 -

Multi-omic deconvolution and DNA-RNA dynamics in cancer

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. 2025, https://doi.org/10.1038/s41568-025-00886-9. [Full text]

Guo S*, Liu X*, Cheng X*, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Lee S, Sood AK, Kopetz S, Shen JP, 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 Res. Published in Advance January 6, 2025, doi:10.1101/gr.279605.124 [abstract] [GitHub repository: DeMixSC]

Risk prediction with machine learning and Bayesian semi-parametric models

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. Annals of Applied Statistics. 19(4): 3091-3112 (December 2025). Doi: 10.1214/25-AOAS2083 [full text] *author contributed equally

Stats Up AI

Zheng et al. Statistics and AI - A Fireside Conversation. Harvard Data Science Review. 2025 Apr 30;7(2). [Full text]

Collaboration Papers

Foutunno C, Fone MN, Mester J, et al. A quantitative, Bayesian-informed approach to gene-specific variant classification: Updated Expert Panel recommendations improve analyses of TP53 germline variants for Li-Fraumeni syndrome. Genome Medicine. 2025 Oct 22;17(1):128. doi: 10.1186/s13073-025-01536-3. [Full text]

Bhinder B et al. Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles. Scientific Reports. 2025 Jul 4;15(1):23921. doi: 10.1038/s41598-025-09075-y. [Full text]

Lin C et al. Cholesterol metabolism regulated by CAMKK2-CREB signaling promotes castration-resistant prostate cancer. Cell Reports. 2025 Jun 24;44(6):115792. doi: 10.1016/j.celrep.2025.115792. [Full text]

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. Briefings in Bioinformatics. 2025 Mar 4;26(2):bbaf085. doi: 10.1093/bib/bbaf085. [Full text]

Ito I et al. Development and Characterization of orthotopic patient-derived xenograft models of mucinous appendiceal adenocarcinoma. ESMO Gastrointestinal Oncology. 2025 Mar 1;7:100133. [Full text]

Duan, Y, Guo, S, Wang, W, Mueller, P. Immune Profiling among Colorectal Cancer Subtypes using Dependent Mixture Models. JASA Published online: 25 Feb 2025. [Abstract]

2024 -

Multi-omic deconvolution and DNA-RNA dynamics in cancer

Ji S, Zhu T, Sethia A, Wang W. Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples. Genome Res. 2024 May 3;. doi: 10.1101/gr.278456.123. [Epub ahead of print] [Full text]

Risk prediction with machine learning and Bayesian semi-parametric models

Nguyen NH, Dodd-Eaton EB, Corredor JL, Woodman-Ross J, Green S, Gutierrez AM, Arun BK, Wang W. Validating Risk Prediction Models for Multiple Primaries and Competing Cancer Outcomes in Families With Li-Fraumeni Syndrome Using Clinically Ascertained Data. J Clin Oncol. 2024 Apr 3;:JCO2301926. doi: 10.1200/JCO.23.01926. [Epub ahead of print] [Full text]

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 Clinical Cancer Informatics. 2024 Feb 12. Volume 8. doi: 10.1200/CCI.23.00167. [Full text] [Github:LFSPROShiny]

Collaboration Papers

Yuan, Dongbang, Zhang, Yunfeng, Guo, Shuai, Wang, Wenyi, Gaynanova, Irina. Exponential canonical correlation analysis with orthogonal variation. [preprint]

Yousef M, Yousef A, Chowdury S, Fanaeian M, Knafl M, Peterson J, Zeineddine M, Alfaro K, Zeineddine F, Godstein D, Horstein 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, Villar E, Wolff R, Raghav KP, White MG, Uppal A, Sun R, Wang W, Kopetz SK, Willis J, Shen JP. Molecular, Socioeconomic, and Clinical Factors Affecting Racial and Ethnic Disparities in Colorectal Cancer Survival. JAMA Oncol. 2024 Sep 12. doi: 10.1001/jamaoncol.2024.3666. Online ahead of print. [Full text]

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. 2024 Aug 1:dgae532. doi: 10.1210/clinem/dgae532. Online ahead of print. [Full text]

Aparicio AM, Tidwell RSS, Yadav SS, Chen JS, Zhang M, Liu J, Guo S, Pilie PG, Yu Y, Song X, Vundavilli H, Jindal S, Zhu K, Viscuse PV, Lebenthal JM, Hahn AW, Soundararajan R, Corn PG, Zurita AJ, Subudhi SK, Zhang J, Wang W, Huff C, Troncoso P, Allison JP, Sharma P, Logothetis CJ. A Modular Trial of Androgen Signaling Inhibitor Combinations Testing a Risk-Adapted Strategy in Patients with Metastatic Castration-Resistant Prostate Cancer. Clin Cancer Res. 2024 Apr 29;. doi: 10.1158/1078-0432.CCR-23-3740. [Epub ahead of print] [Full text]

Bahrambeigi V, Lee JJ, Branchi V, Rajapakshe KI, Xu Z, Kui N, Henry JT, Wang K, Stephens BM, Dhebat S, Hurd MW, Sun R, Yang P, Ruppin E, Wang W, Kopetz S, Maitra A, Guerrero PA. Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype. Cancer Res. 2024 Mar 7;. doi: 10.1158/0008-5472.CAN-23-4070. [Epub ahead of print][Full text]

2023 -

Rangel R et al. TP53 gain-of-function mutation modulates the immunosuppressive microenvironment in non-HPV associated oral squamous cell carcinoma. Journal for ImmunoTherapy of Cancer, 2023 Aug;11(8):e006666. doi: 10.1136/jitc-2023-006666. [full text]

Wang JR, Zafereo ME, Wang W, Joshu C, Debashree R. Association of polygenic score with tumor molecular subtypes in papillary thyroid carcinoma. Journal of Clinical Endocrinology & Metabolism, 2023 Jul 15;dgad407. doi: 10.1210/clinem/dgad407. [full text]

Cermakova K, Tao L, Dejmek M, Sala M, Montierth MD, Chan YS, Patel I, Chambers C, Cabrera ML, 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 Research. gkad1081, https://doi.org/10.1093/nar/gkad1081 Published: 23 November 2023. Selected by NAR as a "breakthrough article" of the journal issue!

Zheng C et al. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nature Structural & Molecular Biology Nov 2023; 30, 1878–1892. doi:10.1038/s41594-023-01117-1. [full text]

Zheng C et al. Multiomics analyses reveal DARS1-AS1/YBX1-controlled post-transcriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Science Advances, Aug 4;9(31):eadf3984. doi: 10.1126/sciadv.adf3984. Epub 2023 Aug 4. [full text]

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 Research, 2023 May 19:CAN-22-3464. doi: 10.1158/0008-5472.CAN-22-3464. Online ahead of print. [Abstract][Full text]

2022 -

Multi-omic deconvolution and DNA-RNA dynamics in cancer

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]

Collaboration Papers

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 no. 6 (2022) e2100504. Published online August 17, 2022. DOI: 10.1200/PO.21.00504 [abstract][full text]

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]

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. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. 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]