- 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. PMCID: PMC1850797
- 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.
- 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. PMCID: PMC208805
- 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. PMCID: PMC1531653
- 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.
- 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. PMCID: PMC544889
- 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.
- 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.
- 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 Epidemiology Biomarkers and Prevention. 2005 Jun; 14(6):1418-23.
- 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 Epidemiology Biomarkers and Prevention. 2005 Jun; 14(6):1424-32.
- 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.
- 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.
- 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. PMCID: PMC1343596
- 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.
- Shen R, Ghosh D, Chinnaiyan AM, Meng Z. Eigengene based linear discriminant model for gene expression data analysis. Bioinformatics 2006; 22: 2635-2642.
- 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.
- 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.
- 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. PMCID: PMC2246152
- 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.
- 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. PMCID: PMC2753194
- 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. PMCID: PMC2447843
- 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. Epub 2008 Oct 14.
- Varambally S, Laxman B, Mehra R, Cao Q, Dhanasekaran SM, Tomlins SA, Granger J, Vellaichamy A, Sreekumar A, Yu J, Gu W, Shen R, Ghosh D, Wright LM, Kladney RD, Kuefer R, Rubin MA, Fimmel CJ, Chinnaiyan AM. Golgi protein GOLM1 is a tissue and urine biomarker of prostate cancer. Neoplasia. 2008 Nov;10(11):1285-94. PMCID: PMC2570605
- Gong Y, Yao E, Shen R, Goel A, Arcila M, Teruya-Feldstein J, Zakowski MF, Frankel S, Peifer M, Thomas RK, Ladanyi M, Pao W. Expression levels of total IGF-1R and sensitivity of NSCLC cells in vitro to an anti-IGF-1R antibody (R1507). PLos ONE. 2009 Oct 6;4(10):e7273.
- Regales L, Gong Y, Shen R, Stanchina E, Vivanco I, Goel A, Koutcher JA, Spassova M, Ouerfelli O, Mellinghoff IK, Zakowski MF, Politi KA, Pao W. Novel dual targeting of EGFR can overcome a major drug resistance mutation in EGFR-mutant lung cancer. Journal of Clinical Investigation. 2009 Oct;119(10):3000-10. doi: 10.1172/JCI38746. Epub 2009 Sep 14.
- Girard N, Shen R, Guo T, Zakowski MF, Heguy A, Riely GJ, Huang J, Lau C, Lash AE, Ladanyi M, Viale A, Antonescu CR, Travis WD, Rusch VW, Kris MG, Pao W. Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas. Clinical Cancer Research 2009; [Epub ahead of print]
- Shen R, Olshen AB, Ladanyi M. Integrative Clustering of Multiple Genomic Data Types using a Joint Latent Variable Model with Application to Breast and Lung Cancer Subtype Analysis. Bioinformatics. 2009 Sep 16. [Epub ahead of print]
- Politi K, Fan PD, Shen R, Zakowski M, Varmus H. Erlotinib resistance in mouse models of epidermal growth factor receptor-induced lung adenocarcinoma. Dis Model Mech. [Epub ahead of print]
- Janjigian YY, McDonnell K, Kris MG, Shen R, Sima CS, Bach PB, Rizvi NA, Riely GJ. Pack-years of cigarette smoking as a prognostic factor in patients with stage IIIB/IV nonsmall cell lung cancer. Cancer. 2009 Dec 22. [Epub ahead of print]
|
