1. Shen R, Taylor JM, Ghosh D. Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model. Bioinformatics. 2008 Dec 15; 24(24):2880-6.
2. Shen R, Chinnaiyan AM, Ghosh D. Pathway analysis reveals functional convergence of gene expression profiles in breast cancer. BMC Medical Genomics. 2008 Jun 27;1:28.
3. Shen R, Ghosh D, Taylor JM. Modeling intra-tumor protein expression heterogeneity in tissue microarray experiments. Statistics in Medicine. 2008 May 20;27(11):1944-59.
4. Yu J, Cao Q, Mehra R, Laxman B, Yu J, Tomlins SA, Creighton CJ, Dhanasekaran SM, Shen R, Chen G, Morris DS, Marquez VE, Shah RB, Ghosh D, Varambally S, Chinnaiyan AM. Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer. Cancer Cell. 2007 Nov;12(5):419-31.
5. Choi H, Shen R, Chinnaiyan Am, Ghosh D. A latent variable approach for meta-analysis of gene expression data from multiple microarray experiements. BMC Bioinformatics 2007: 8: 364.
6. Mehra R, Han B, Tomlins SA, Wang L, Menon A, Wasco MJ, Shen R, Montie JE, Chinnaiyan AM, Shah RB. Heterogeneity of TMPRSS2 gene rearrangements in multifocal prostate adenocarcinoma: molecular evidence for an independent group of diseases. Cancer Research 2007; 67: 7991-7995.
7. Mehra R, Tomlins SA, Shen R, Nadeem O, Wang L, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM, Shah RB. Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Modern Pathology 2007; 20: 538-544.
8. Shen R, Ghosh D, Chinnaiyan AM, Meng Z. Eigengene based linear discriminant model for gene expression data analysis. Bioinformatics 2006; 22: 2635-2642. software download: elda.zip.
9. Fu Z, Kitagawa Y, Shen R, Shah R, Mehra R, Rhodes D, Keller PJ, Mizokami A, Dunn R, Chinnaiyan AM, Yao Z, Keller ET. Metastasis suppressor gene raf kinase inhibitor protein (RKIP) is a novel prognostic marker in prostate cancer. Prostate 2006; 66:248-256.
10. Kim R, Demichelis F, Tang J, Riva A, Shen R, Gibbs DF, Mahavishno V, Chinnaiyan AM, Rubin MA. Internet-based profiler system as integrative framework to support translational research. BMC Bioinformatics 2005;6:304.
11. Mehra R, Varambally S, Ding L, Shen R, Sabel MS, Ghosh D, Chinnaiyan AM, Kleer CG. Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis. Cancer Research 2005;65:11259-11264.
12. Wang X, Yu J, Sreekumar A, Varambally S, Shen R, Giacherio D, Mehra R, Montie JE, Pienta KJ, Sanda MG, Kantoff PW, Rubin MA, Wei JT, Ghosh D, Chinnaiyan AM. Autoantibody signatures in prostate cancer. New England Journal of Medicine 2005;353:1224-1235.
13. Rubin MA, Bismar TA, Andrén O, Mucci L, Kim R, Shen R, Ghosh D, Wei JT, Chinnaiyan AM, Adami HO, Kantoff PW, Johansson JE. Decreased alpha-methylacyl CoA racemase expression in localized prostate cancer is associated with an increased rate of biochemical recurrence and cancer-specific death. Cancer Epidemiol Biomarkers Prev. 2005 Jun;14(6):1424-32.
14. Witkiewicz AK, Varambally S, Shen R, Mehra R, Sabel MS, Ghosh D, Chinnaiyan AM, Rubin MA, Kleer CG. Alpha-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysis. Cancer Epidemiol Biomarkers Prev. 2005 Jun;14(6):1418-23.
15. Kwak SH, Shen R, Schiefelbein J. Positional signaling mediated by a receptor-like kinase in Arabidopsis. Science. 2005 Feb 18;307(5712):1111-3. Epub 2004 Dec 23.
16. Shah RB, Mehra R, Chinnaiyan AM, Shen R, Ghosh D, Zhou M, Macvicar GR, Varambally S, Harwood J, Bismar TA, Kim R, Rubin MA, Pienta KJ. Androgen-independent prostate cancer is a heterogeneous group of diseases: Lessons from a rapid autopsy program. Cancer Research 2004;64:9209-9216.
17. Shen R, Ghosh D, Chinnaiyan A. Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data. BMC Genomics 2004;5:94.
18. Shah RB, Kunju LP, Shen R, LeBlanc M, Zhou M, Rubin MA. Usefulness of basal cell cocktail (34betaE12 + p63) in the diagnosis of atypical prostate glandular proliferations. Am J Clin Pathol. 2004 Oct;122(4):517-23.
19. Hofer MD, Fecko A, Shen R, Setlur SR, Pienta KG, Tomlins SA, Chinnaiyan AM, Rubin MA. Expression of the platelet-derived growth factor receptor in prostate cancer and treatment implications with tyrosine kinase inhibitors. Neoplasia. 2004 Sep-Oct;6(5):503-12.
20. Kwak S, Shen R, Schiefelbein J. Positional signaling mediated by a receptor-like kinase in arabidopsis. Science 2004;307:1111-1113.
21. Kleer CG, Cao Q, Varambally S, Shen R, Ota I, Tomlins SA, Ghosh D, Sewalt RG, Otte AP, Hayes DF, Sabel MS, Livant D, Weiss SJ, Rubin MA, Chinnaiyan AM. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proceedings of the National Academy of Sciences 2003;100:11606-11611.
22. Zhou M, Shah R, Shen R, Rubin MA. Basal cell cocktail (34betaE12 + p63) improves the detection of prostate basal cells. Am J Surg Pathol. 2003 Mar;27(3):365-71.
23. Dash A, Maine IP, Varambally S, Shen R, Chinnaiyan AM, Rubin MA. Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens. American Journal of Pathology 2002;161:1743-1748.
