Bill Barry's academic page


Contact information:

William T. Barry, Ph.D.
Assistant Professor
Department of Biostatistics and Bioinformatics
Institute for Genome Science and Policy

Office address
Hock Plaza, Suite 1102, Rm 11097
2424 Erwin Rd
Durham, NC 27705
Phone:  (919) 681-5047
Fax:    (919) 668-9335
E-mail:   bill <DOT> barry <AT> duke <DOT> edu

Mailing address
DUMC Box 2721
Durham, NC 27710


Selected Topics/publications:

Microarrays: Pre-processing and QC
  1. Owzar K, Barry WT, Jung S, Sohn I, George SL (2008) Statistical Challenges in Pre-Processing in Microarray Experiments in Cancer. Clinical Cancer Research 14:5959-5966
  2. Bioconductor packages: affy, simpleaffy, affyPLM

Microarrays: Pathway analysis (SAFE/GSEA)
  1. Barry WT, Nobel AB, Wright FA. (2005) Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 21(9):1943-9. Supplementary material & software.

  2. Barry WT, Nobel AB, Wright FA. (2008) A statistical framework for testing functional categories in microarray data. Annals of Applied Statistics 2(1):286-315. Software.
  3. Bioconductor packages: safe, GOstats, globaltest

Microarrays: Predictive/prognostic signatures (IGSP)
  1. Chemosensitivity Signatures

    Potti A, Dressman HK, Bild A, Riedel RF, Chan G, Sayer R, Cragun J, Cottrill H, Kelley MJ, Petersen R, Harpole D, Marks J, Berchuck A, Ginsburg GS, Febbo P, Lancaster J, Nevins JR. (2006) Genomic signatures to guide the use of chemotherapeutics. Nature Medicine, 12(11):1294-1300

    Hsu DS, Balakumaran BS, Acharya CR, Vlahovic V, Walters KS, Garman K, Anders C Reidel RF, Lancaster J, Harpole D, Dressman HK, Nevins JR, Febbo P, Potti A (2007) Pharmacogenomic Strategies Provide a Rational Approach to the Treatment of Cisplatin-Resistant Patients With Advanced Cancer Journal of Clinical Oncology, 25(28):4350-4357

  2. Pathway Signatures

    Bild AH, Yao G, Chang JT, Wang QL, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA, Marks JR, Dressman HK, West M, Nevins JR (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 439(7074):353-357 2006

    Acharya CR, Hsu DS, Anders CK, Anguiano A, Salter KH, Walters KS, Redman RC, Tuchman SA, Moylan CA, Mukherjee S, Barry WT, Dressman HK, Ginsburg GS, Marcom KP, Garman KS, Lyman GH, Nevins JR, Potti A (2008) Gene Expression Signatures, Clinicopathological Features, and Individualized Therapy in Breast Cancer. Journal of the American Medical Association, 299(13):1574-1587

  3. Lung prognostic signature

    Potti A, Muhkerjee S, Petersen R, Dressman HK, Bild AH, Koontz J, Kratzke R, Watson MA, Kelley MJ, Ginsburg GS, West M, Harpole D, Nevins JR (2006) Genomic Strategy to Refine Prognosis in Early-Stage Non-Small-Cell Lung Cancer New England Journal of Medicine, 355(6):570-80

  4. AR signature

    Mendiratta P, Mostaghel E, Guinney J, Tewari A, Porrello A, Barry WT, Nelson P, Febbo PG (2009) A Genomic Strategy for Targeting Therapy in Castration-Resistant Prostate Cancer Journal of Clinical Oncology, (In press)

  5. Software packages:
    BinReg (Binary Probit Regression with SVD)
    BinTree (Binary Tree Prediction Model)