Selected Topics/publications:
Workshops and Invited Lectures
| Society for Clinical Trials Annual Meeting, 2011:
Development of multiplex biomarkers: Statistical considerations with high dimensional
data. Herbert Pang and William Barry
Slides and R code |
| EORTC-NCI-ASCO Annual Meeting, 2011:
A genomic-based signature of response to chemotherapy in ovarian cancer
fails to predict clinical outcome in two independent cohorts
W. Barry, W. Chen, G. Sfakianos, P. Isner, M. Datto, N. Kuderer,
G. Lyman, A. Abernethy, G. Ginsburg, A. Berchuck
Slides and Supplemental material |
Microarrays: Pre-processing and QC
| 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 |
| Bioconductor packages:
affy, simpleaffy, affyPLM |
Microarrays: Pathway analysis ( SAFE )
| 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. |
| 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. | | Bioconductor packages:
safe, GOstats, globaltest |
Microarrays: Predictive/prognostic signatures in cancer
Publications
Barry WT, Kernagis DN, Dressman HK, Griffis RJ, Hunter J, Marcom K, Nevins JR, Geradts J, Datto MB (2010)
Intra-tumor Heterogeneity Does Not Preclude Precise Microarray-Based Prediction of Breast Cancer Biology
Journal of Clinical Oncology, 28(13):2198-206. |
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, 27(12):2022-9. |
Friedman DR, Weinberg JB, Barry WT, Goodman BK, Volkheimer AD, Bond KM, Chen Y, Jiang N, Moore JO, Gockerman JP, Diehl LF, Decastro CM, Potti A, Nevins JR (2009)
A Genomic Approach to Improve Prognosis and Predict Therapeutic Response in Chronic Lymphocytic Leukemia
Clinical Cancer Research, 15(22):6947-55.
Gatza ML, Lucas JE, Barry WT, Kim JW, Wang Q, Crawford MD, Datto MB, Kelley M, Mathey-Prevot B, Potti A, Nevins JR (2010)
A pathway-based classification of human breast cancer
Proceedings of the National Academy of Sciences USA, 107(15):6994-9.
Software packages:
BinReg (Binary Probit Regression with SVD)
BinTree (Binary Tree Prediction Model) |