Statistical Methods for Computational Molecular Biology/Bioinformatics

• Sreekumar A, Nyati MK, Varambally S, Barrette TR, Ghosh D, Lawrence TS, Chinnaiyan AM. (2001). Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins . Cancer Research, 61: 7585 - 93.
• Ghosh, D. and Chinnaiyan, A. M. (2002). Mixture modelling of gene expression data from microarray experiments. Bioinformatics, 18: 275 - 286.
• Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM. Delineation of prognostic biomarkers in prostate cancer. Nature, 412: 822 - 6.
• Goldstein, D., Ghosh, D. and Conlon, E. (2002). Statistical issues in the clustering of gene expression data . Statistica Sinica, 12: 219 -- 240.
• Ghosh, D. (2002). Singular value decomposition regression modelling for classification of tumors from microarray experiments . In Proceedings of the 2002 Pacific Symposium on Biocomputing, Eds. Altman, R. B. et al. pp. 18 -- 29.
• Ghosh, D. (2002). Resampling methods for variance estimation of singular value decomposition analyses from microarray experiments . Functional and Integrative Genomics 2, 92--97.
• Rubin, M. A., Zhou, M., Dhanasekaran, S. M., Varambally, S., Barrette, T. R., Sanda, M. G., Pienta, K. J., Ghosh, D. and Chinnaiyan, A. M. (2002). alpha-Methylacyl Coenzyme A Racemase as a Tissue Biomarker for Prostate Cancer. JAMA 287, 1662--1670.
• Rhodes, D., Barrette, T. T., Rubin, M. A., Ghosh, D. and Chinnaiyan, A. M (2002). Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Research 62, 4427 -- 4433.
• Varambally, S., Dhanasekaran, S. M., Zhou, M., Barrette, T. R., Kumar-Sinha, C., Sanda, M. G., Ghosh, D., Pienta, K. J., Sewalt, R. G. A. B., Otte, A. P., Rubin, M. A., and Chinnaiyan, A. M. (2002). The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419, 624 -- 629.
• Ghosh, D. (2003). Penalized discriminant methods for the classification of tumors from gene expression data . Biometrics 59, 992 - 1000.
• Smolkin, M. and Ghosh, D. (2003). Cluster stability scores for microarray data in cancer studies . BMC Bioinformatics 4, 36 - 42.
• Ghosh, D., Barrette, T. R., Rhodes, D. and Chinnaiyan, A. M. (2003). Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Functional and Integrative Genomics 3, 180 - 188.
• Ghosh, D. (2004). Mixture models for assessing differential expression in complex tissues using microarray data.
• Ghosh, D. and Chinnaiyan, A. M. (2004). Semiparametric methods for identification of tumor progression genes from microarray data.

Debashis Ghosh   ghoshd@sph.umich.edu
UM Biostatistics