Stastical Bioinformatics Lab





Publications

Articles

  • 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. submitted

  • Shin SJ, Peng G, Wang W✉, Yuan Y✉. Bayesian Semiparametric Estimation of Cancer-specic Age-at-onset Penetrance with Application to Li-Fraumeni Syndrome. under revision. Download preprint on arXiv

  • Ahn J, Morita S, Wang W✉ and Yuan Y✉. Bayesian shared-parameter models for longitudinal dyadic data with informative missing data. Statistical Methods in Medical Research under revision

  • 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. Link to the R package LFSPRO

  • 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 [Abstract][TEXT] Link to 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][PDF]

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

  • 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] [PDF] Link to the software Supplemental materials

  • Shen P*, Wang W*, Chi AK, Fan Y, Davis RW and Scharfe C. Multiplex target capture with long padlock probes. Genome Medicine 2013, 5:50 doi:10.1186/gm454 [Abstract] Highly accessed
    *authors contributed equally

  • 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] Link to the software

  • 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 Link to the R package

  • 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] Listed among Most-Read Articles during Apr 2011
    *Authors contributed equally

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

  • 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/. [Abstract]

  • Wang W, Niendorf KB, Patel D, Blackford A, Marroni F, Sober AJ, Parmigiani G and Tsao H. Personalized Prediction of Germline CDKN2A Mutations and Cancer Risk in Hereditary Melanoma. Cancer Research Jan 2010 doi:10.1158/0008-5472. [Abstract]

  • 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.[Pubmed]

  • Wang W, Chen S, Brune KA, Hruban RH, Parmigiani G and Klein AP. Development and Validation of a Risk Assessment Tool for Individuals with a Family History of Pancreatic Cancer: PancPRO. Journal of Clinical Oncology. 2007;25:1417-22.[Pubmed]

  • 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. [Pubmed]

  • 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. [Pubmed]

Collaboration papers

  • 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. [Epub ahead of print]

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

  • 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.

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

  • 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. [Abstract]

  • 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. [Epub ahead of print][Abstract]

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

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

  • 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]

  • 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. [Epub ahead of print]

  • 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 [Abstract]

  • Nicodemus KK, Wang W and 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.[Pubmed]

  • 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. [Pubmed]



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Email: wwang7@mdanderson.org | Contact | © 2013 Wenyi Wang and Emily Johnson

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