Publications

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. Submitted. bioRxiv [Preprint]. 2025 Nov 24:2025.11.21.689822. doi: 10.1101/2025.11.21.689822.

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**. Deciphering transcriptional activity of the tumor microenvironment for robust stratification of chemotherapy response in triple-negative breast cancer. Accepted.

Dai Y, Guo S, Pan Y, Castignani C, Montierth MD, Van Loo P**, Wang W**. A guide to transcriptomic deconvolution in cancer. Nat Rev Cancer. 2025 Dec 2. doi: 10.1038/s41568-025-00886-9.

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. bioRxiv [Preprint]. 2025 Jun 10:2024.07.03.601939. doi: 10.1101/2024.07.03.601939.

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. 2025 Jan 22;35(1):147-161. doi: 10.1101/gr.278822.123.

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. Under review. bioRxiv [Preprint]. 2025 Oct 6:2025.10.06.680732. doi: 10.1101/2025.10.06.680732.
Proceedings of The Inaugural Workshop on Frontiers in Statistical Machine Learning (FSML) travel award

Corredor JL*, Li R*, Dodd-Eaton EB, Woodman-Ross J, Woodson A, 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. Under revision. medRxiv [Preprint]. 2024 Jul 10:2024.07.09.24310095. doi: 10.1101/2024.07.09.24310095.

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.

Stats Up AI

Zheng et al. Statistics and AI: A Fireside Conversation. Harvard Data Science Review. 2025 Apr 30;7(2).

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 second review. bioRxiv [Preprint]. 2025.04.16.649218; doi: 10.1101/2025.04.16.649218.

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.

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.

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.

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.

Ito I et al. Development and Characterization of orthotopic patient-derived xenograft models of mucinous appendiceal adenocarcinoma. ESMO Gastrointest Oncol. 2025 Mar;7:100133. doi: 10.1016/j.esmogo.2025.100133.

Duan Y, Guo S, Wang W, Mueller P. Immune Profiling among Colorectal Cancer Subtypes using Dependent Mixture Models. J Am Stat Assoc. 2025;120(550):671-684. doi: 10.1080/01621459.2024.2427936.

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 15;34(4):633-641. doi: 10.1101/gr.278456.123.

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.

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.

Collaboration Papers

Yuan D, Zhang Y, Guo S, Wang W, Gaynanova I. 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 Nov 1;10(11):1519-1529. doi: 10.1001/jamaoncol.2024.3666.

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.

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.

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.

Rangel R et al. TP53 gain-of-function mutation modulates the immunosuppressive microenvironment in non-HPV associated oral squamous cell carcinoma. J Immunother Cancer. 2023 Aug;11(8):e006666. doi: 10.1136/jitc-2023-006666.

Wang JR, Zafereo ME, Wang W, Joshu C, Debashree R. Association of polygenic score with tumor molecular subtypes in papillary thyroid carcinoma. J Clin Endocrinol Metab. 2023 Dec 21;109(1):e306-e313. doi: 10.1210/clinem/dgad407.

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 Res. 2024 Jan 11;52(1):4-21. doi: 10.1093/nar/gkad1081.
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.

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.

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.

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 Mol Biol. 2022;2493:21-27. doi: 10.1007/978-1-0716-2293-3_2.

Cao S, et al., Wang W**. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol. 2022 Nov;40(11):1624-1633. doi: 10.1038/s41587-022-01342-x. Epub 2022 Jun 13.

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 Precis Oncol. 2022 Aug;6:e2100504. doi: 10.1200/PO.21.00504.

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.

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. J Am Stat Assoc. 2022;117(538):533-546. doi: 10.1080/01621459.2021.2000866. Epub 2022 Jan 5.

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. Nat Commun 2021 Sep 6;12(1):5307. doi: 10.1038/s41467-021-25624-1.

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.

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. doi: 10.1016/j.cell.2021.03.009. Epub 2021 Apr 7.
Wang is a co-last author.
Selected for the MD Anderson Wall of Science and Research Excellence webpage.

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.

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 Precis Oncol. 2020 Sep 4;4:PO.20.00016. doi: 10.1200/PO.20.00016.

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 Res. 2020 Aug;30(8):1170-1180. doi: 10.1101/gr.249599.119. Epub 2020 Aug 18.

Nikooienejad A, Wang W, Johnson V. Bayesian Variable Selection For Survival Data Using Inverse Moment Priors. Ann Appl Stat. 2020 Jun;14(2):809-828. doi: 10.1214/20-AOAS1325. Epub 2020 Jun 29.

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.

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 2020 Apr;17(4):414-421. doi: 10.1038/s41592-020-0766-3. Epub 2020 Mar 16.

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, Futreal PA. Immuno-genomic landscape of osteosarcoma. Nat Commun 2020 Feb 21;11(1):1008. doi: 10.1038/s41467-020-14646-w.

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

Shin SJ, Dodd E, Peng G, Bojadzieva J, Chen J, Amos C, 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. 2020 Jan 15;80(2):354-360. doi: 10.1158/0008-5472.CAN-19-0728. Epub 2019 Nov 12.

Shin SJ, Dodd EB, Gao F, Bojadzieva J, Chen J, Kong X, Amos C, 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. 2020 Jan 15;80(2):347-353. doi: 10.1158/0008-5472.CAN-19-0725. Epub 2019 Nov 12.

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.

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. Am J Hematol. 2019 Jun;94(6):628-634. doi: 10.1002/ajh.25450. Epub 2019 Mar 19.

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. bioRxiv [Preprint]. 566075; doi: 10.1101/566075.

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.

Shin SJ, Li J, Ning J, Bodjadzieva J, Strong LC, 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. 2020 Jul 1;21(3):467-482. doi: 10.1093/biostatistics/kxy066.

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.

Shin SJ, Yuan Y**, Strong LC, Bojadzieva J, Wang W**. Bayesian Semiparametric Estimation of Cancer-specic Age-at-onset Penetrance with Application to Li-Fraumeni Syndrome. J Am Stat Assoc. 2019;114(526):541-552. doi: 10.1080/01621459.2018.1482749.

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. JCO Precis Oncol. 2018;2018:PO.17.00091. doi: 10.1200/PO.17.00091.
One of the most accessed articles on JCO PO in 2018

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 Epidemiol Biomarkers Prev. 2017 Jun;26(6):837-844. doi: 10.1158/1055-9965.EPI-16-0695.

Ahn J, Morita S, Wang W**, Yuan Y**. Bayesian shared-parameter models for longitudinal dyadic data with informative missing data using a dyadic shared-parameter model. Stat Methods Med Res. 2019 Jan;28(1):70-83. doi: 10.1177/0962280217715051.

Fan Y, Xi L, Hughes DST, 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. 2016 Aug 24;17(1):178. doi: 10.1186/s13059-016-1029-6.

Nikooienejad A, Wang W**, Johnson VE**. Bayesian Variable Selection for Binary Outcomes in High Dimensional Genomic Studies Using Non-Local Priors. Bioinformatics. 2016 May 1;32(9):1338-45. doi: 10.1093/bioinformatics/btv764. Epub 2016 Jan 6.

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. 2017 Mar 17;45(5):e30. doi: 10.1093/nar/gkw1063.

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. J Med Genet. 2016 Jun;53(6):385-8. doi: 10.1136/jmedgenet-2015-103311. Epub 2015 Nov 13.

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 fibrosis. J Mol Diagn. 2016 Mar;18(2):267-82. doi: 10.1016/j.jmoldx.2015.11.005. Epub 2016 Feb 1.

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.

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. Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18.

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.

2014

Peng G, Fan Y, Wang W**. FamSeq: a variant calling program for family-based sequencing data using graphics processing units. PLoS Comput Biol. 2014 Oct 30;10(10):e1003880. doi: 10.1371/journal.pcbi.1003880.

Davis CF et al., The Cancer Genome Atlas Research Network. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. 2014 Sep 8;26(3):319-330. doi: 10.1016/j.ccr.2014.07.014.

The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20;507(7492):315-22. doi: 10.1038/nature12965. Epub 2014 Jan 29.

2013

Ahn J, Liu S, Wang W**, Yuan Y**. Bayesian latent-class mixed-effect hybrid models for dyadic longitudinal data with non-ignorable dropouts. Biometrics. 2013 Dec;69(4):914-24. doi: 10.1111/biom.12100. Epub 2013 Nov 6.

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. 2013 Aug 1;29(15):1865-71. doi: 10.1093/bioinformatics/btt301. Epub 2013 May 27.

Shen P*, Wang W* , Chi AK, Fan Y, Davis RW, Scharfe C. Multiplex target capture with double-stranded DNA probes. Genome Med. 2013 May 29;5(5):50. doi: 10.1186/gm454.
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. Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3985-90. doi: 10.1073/pnas.1222158110. Epub 2013 Feb 20.

The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764.

Srivastava S, Wang W, Manyem G, Ordonez C, Baladandayuthapani V. Integrating Multi-Platform Genomic Data Using Hierarchical Bayesian Relevance Vector Machines. EURASIP J Bioinform Syst Biol. 2013 Jun 28;2013(1):9. doi: 10.1186/1687-4153-2013-9.

2012

Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C, Wang W** . SRMA: an R package for resequencing array data analysis. Bioinformatics. 2012 Jul 15;28(14):1928-30. doi: 10.1093/bioinformatics/bts286. Epub 2012 May 10.

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 Oct 15;118(20):5140-54. doi: 10.1002/cncr.27496. Epub 2012 Mar 13.

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 Relat Disord. 2012 May;18(4):386-90. doi: 10.1016/j.parkreldis.2011.12.012. Epub 2012 Jan 12.

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. Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6549-54. doi: 10.1073/pnas.1018981108. Epub 2011 Apr 5.
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 Dec 17;11:712. doi: 10.1186/1471-2164-11-712.

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 Res. 2011 Jan;39(1):44-58. doi: 10.1093/nar/gkq750. Epub 2010 Sep 15.

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 Res. 2010 Jan 15;70(2):552-9. doi: 10.1158/0008-5472.CAN-09-2653. Epub 2010 Jan 12.

2008

Wang W, Carvalho B, Miller N, Pevsner J, Chakaravarti A and Irizarry RA. Estimating Genome-wide Copy Number using Allele Specific Mixture Models. J Comput Biol. 2008 Sep;15(7):857-66. doi: 10.1089/cmb.2007.0148.

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. J Clin Oncol. 2007 Apr 10;25(11):1417-22. doi: 10.1200/JCO.2006.09.2452.

Nicodemus KK, Wang W, 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 Proc. 2007;1 Suppl 1(Suppl 1):S58. doi: 10.1186/1753-6561-1-s1-s58. Epub 2007 Dec 18.

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. JAMA. 2006 Sep 27;296(12):1479-87. doi: 10.1001/jama.296.12.1479.

Gonzalez JR, Wang W, Ballana E, Estivill X. A recessive Mendelian model to predict carrier probabilities of DFNB1 for non-Syndromic deafness. Hum Mutat. 2006 Nov;27(11):1135-42. doi: 10.1002/humu.20390.

2004

Chen S, Wang W, Broman K, Parmigiani G. BayesMendel: An R Environment for Mendelian Risk Prediction. Stat Appl Genet Mol Biol. 2004;3:Article21. doi: 10.2202/1544-6115.1063. Epub 2004 Sep 17.