PUBLISHED ABSTRACTS AND POSTERS

1. Gene expression module biomarkers to stratify multiple clinical and therapeutic endpoints: A comparison with PAM50 and Oncotype DX®
   Seth Sadis, Scott Tomlins, Paul Williams, Peter Wyngaard, Kahuku Oades, Sukla Chattopadhyay, Yipeng Wang, Joseph Monforte, Byung-In Lee, Daniel Rhodes
   San Antonio Breast Cancer Symposium, 6-10 DEC 2011, San Antonio, TX, USA Poster PDF
2. OncoPredictor: High copy number gain of ERBB2 occurs in 1% of lung cancer patients and predicts sensitivity to lapatinib in lung cancer cell lines.
   Sean F. Eddy, Mark Tomilo, Seth Sadis, Paul D. Williams, Peter Wyngaard, Daniel R. Rhodes
   AACR-NCI-EORTC Molecular Targets and Cancer Therapeutics, 12-16 NOV 2011, San Francisco, CA, USA Poster PDF
3. Target discovery with Oncomine: Discovering new targets and positioning old targets by integrative analysis of 10,000’s of tumor genomes and transcriptomes.
   Presented by Daniel R. Rhodes
   AACR-NCI-EORTC Molecular Targets and Cancer Therapeutics, 12-16 NOV 2011, San Francisco, CA, USA
4. Diagnostic Approaches to Identify Predictive Subgroups.
   Presented by Daniel R. Rhodes
   ASCO-NCI-EORTC Annual Meeting on "Molecular Markers in Cancer", 27-29 OCT 2011, Brussels, Belgium
5. Integrated analysis of patient level genetic aberrations in human cancer.
   Chris Gates, Matt Anstett, Supra Gajjala, Peter Wyngaard, Daniel Rhodes.
   AACR Translation of the Cancer Genome, 15-18 OCT 2011, San Francisco, CA, USA Poster PDF
6. Gene expression module biomarkers associate with multiple clinical and therapeutic endpoints and are translatable to a universal companion diagnostic assay.
   Scott Tomlins, Paul Williams, Seth Sadis, Peter Wyngaard, Byung-in Lee, Kahuku Oades, Sukla Chattopadhyay, Yipeng Wang, Joseph Monforte, Daniel Rhodes.
   ASCO Breast Cancer Symposium, 8-10 SEP 2011, San Francisco, CA, USA Poster PDF
7. Focal amplification of existing kinase inhibitor targets identified from TCGA data and integrative analysis.
   Daniel R. Rhodes, Matthew A. Anstett, Paul D. Williams, Peter Wyngaard.
   Keystone Symposia: Changing Landscape of the Cancer Genome, 25 JUN 2011, Boston, MA, USA Poster PDF
8. Tumor Segregation Panels: FFPE RT-PCR Assays for Molecular Sub-Typing and Rapid Companion Diagnostic Development.
   Presented by Daniel R. Rhodes
   Molecular Medicine Tri-Conference, 23-25 JAN 2011, San Francisco, CA, USA
9. OncoPredictor: A System for Identifying Clinically Relevant Biomarkers from Large Scale Cell Line Profiling.
   Presented by Daniel R. Rhodes
   Molecular Medicine Tri-Conference, 23-25 JAN 2011, San Francisco, CA, USA
10. Genomic Biomarkers to Predict Cancer Drug Response Identified from Large-Scale Cell Line Screening and Parallel Preclinical and Clinical Tumor Biomarker Databases.
    Presented by Seth Sadis
    8th Annual Cancer Drugs Research and Development Conference, 27-28 JAN 2011, San Diego, CA, USA
11. DNA amplifications of kinase inhibitor targets in human cancer.
    Presented by Matthew Anstett
    EORTC-NCI-AACR Symposium on Molecular Targets and Cancer Therapeutics, 14-19 NOV 2010, Berlin, Germany
12. Breast cancer gene expression modules: A platform for companion diagnostics development.
    Scott A. Tomlins, Seth Sadis, Daniel R. Rhodes
    ASCO-NCI-EORTC Annual Meeting on Molecular Markers in Cancer, 18-20 OCT 2010, Hollywood, FL, USA Poster PDF
13. OncoPredictor: An integrative genomics platform to systematically predict responsive tumor populations from in vitro drug response data.
    Daniel Rhodes, Gary Daubresse, Peter Wyngaard, Mark Tomilo, Paul Williams, Christine O'Day, Yulia Ovechkina, Usha Warrior, Seth Sadis
    AACR Translational Cancer Medicine USA, 11-14 Jul 2010, San Francisco, CA, USA Poster PDF
14. Somatic mutations in human cancer cell lines predict sorafenib response.
    Daniel R. Rhodes, Scott H. Kaufmann, Xue Wei Meng, Peter Wyngaard, Judith S. Leopold
    AACR Translational Cancer Medicine, 21-24 MAR 2010, Amsterdam, The Netherlands Poster PDF
15. Gene Expression Modules Associated with Cetuximab Response in Metastatic Colorectal Cancer Predict Additional Patient Populations Likely to Respond.
    Daniel R. Rhodes, Wendy Lockwood Banka, Arul M. Chinnaiyan
    AACR Translation of the Cancer Genome, 7-10 FEB 2009, Boston, MA, USA Poster PDF
16. Meta-analysis of outlier expression profiles in breast cancer identifies AGTR1 overexpression as an opportunity for targeted therapy.
    Daniel R. Rhodes, Scott A. Tomlins, Rohit Mehra, Qi Cao, Bharathi Laxman, Shanker Kalyana-Sundaram, Lei Wang, Beth E. Helgeson, Peter C. Lucas, Celina G. Kleer, Daniel F. Hayes, Sooryanarayana Varambally, Arul M. Chinnaiyan
    AACR Annual Meeting, 12-16 APR 2008, San Diego, CA, USA Poster PDF
17. Investigating biological associations of Dasatinib drug sensitivity using Molecular Concepts Analysis.
    Gary Daubresse, Daniel R. Rhodes, Matthew J. Anstett
    Molecular Medicine Tri-Conference, 25-28 MAR 2008, San Francisco, Ca, USA Poster PDF

Publications

1. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.
   Lupien M, Meyer CA, Bailey ST, Eeckhoute J, Cook J, Westerling T, Zhang X, Carroll JS, Rhodes DR, Liu XS, Brown M.
   Genes Dev. 2010 Oct 1;24(19):2219-27. Pubmed
2. A gene expression signature associated with "K-Ras addiction" reveals regulators of EMT and tumor cell survival.
   Singh A, Greninger P, Rhodes D, Koopman L, Violette S, Bardeesy N, Settleman J.
   Cancer Cell. 2009 Jun 2;15(6):489-500. Pubmed
3. AGTR1 overexpression defines a subset of breast cancer and confers sensitivity to losartan, an AGTR1 antagonist.
   Rhodes DR, Ateeq B, Cao Q, Tomlins SA, Mehra R, Laxman B, Kalyana-Sundaram S, Lonigro RJ, Helgeson BE, Bhojani MS, Rehemtulla A, Kleer CG, Hayes DF, Lucas PC, Varambally S, Chinnaiyan AM.
   Proc Natl Acad Sci U S A. 2009 Jun 1. [Epub ahead of print]. Pubmed
4. Exploring clinical associations using ‘-omics’ based enrichment analyses.
   Hanauer DA, Rhodes DR, Chinnaiyan AM.
   PLoS ONE. 2009;4(4):e5203. Epub 2009 Apr 13. Pubmed
5. Coactivator Function Defines the Active Estrogen Receptor-{alpha} Cistrome.
   Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes DR, Liu XS, Brown M.
   Mol Cell Biol. 2009 Apr 13. [Epub ahead of print] Pubmed
6. The role of SPINK1 in ETS rearrangement-negative prostate cancers.
   Tomlins SA, Rhodes DR, Yu J, Varambally S, Mehra R, Perner S, Demichelis F, Helgeson BE, Laxman B, Morris DS, Cao Q, Cao X, Andrén O, Fall K, Johnson L, Wei JT, Shah RB, Al-Ahmadie H, Eastham JA, Eggener SE, Fine SW, Hotakainen K, Stenman UH, Tsodikov A, Gerald WL, Lilja H, Reuter VE, Kantoff PW, Scardino PT, Rubin MA, Bjartell AS, Chinnaiyan AM.
   Cancer Cell. 2008 Jun;13(6):519-28. Pubmed
   
7. Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer.
   Setlur SR, Mertz KD, Hoshida Y, Demichelis F, Lupien M, Perner S, Sboner A, Pawitan Y, Andrén O, Johnson LA, Tang J, Adami HO, Calza S, Chinnaiyan AM, Rhodes D, Tomlins S, Fall K, Mucci LA, Kantoff PW, Stampfer MJ, Andersson SO, Varenhorst E, Johansson JE, Brown M, Golub TR, Rubin MA.
   J Natl Cancer Inst. 2008 Jun 4;100(11):815-25. Epub 2008 May 27. Pubmed
   
8. A polycomb repression signature in metastatic prostate cancer predicts cancer outcome.
   Yu J, Yu J, Rhodes DR, Tomlins SA, Cao X, Chen G, Mehra R, Wang X, Ghosh D, Shah RB, Varambally S, Pienta KJ, Chinnaiyan AM.
   Cancer Res. 2007 Nov 15;67(22):10657-63. Pubmed
   
9. Identifying significant associations using free text problem summary lists in a clinical data repository.
   Hanauer DA, Rhodes DR, Chinnaiyan AM.
   AMIA Annu Symp Proc. 2007 Oct 11:968.Pubmed
10. Molecular concepts analysis links tumors, pathways, mechanisms, and drugs.
    Rhodes DR, Kalyana-Sundaram S, Tomlins SA, Mahavisno V, Kasper N, Varambally R, Barrette TR, Ghosh D, Varambally S, Chinnaiyan AM.
    Neoplasia. 2007 May;9(5):443-54. Pubmed
11. Integrating biomedical knowledge to model pathways of prostate cancer progression.
    Morris DS, Tomlins SA, Rhodes DR, Mehra R, Shah RB, Chinnaiyan AM.
    Cell Cycle . 2007 May;6(10):1177-87. Pubmed
12. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.
    Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varmbally R, Yu J, Briggs BB, Barrette TR, Anstett MJ, Kincaid-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM.
    Neoplasia. 2007 Feb;9(2):166-80. Pubmed
13. Bioinformatics approaches in the study of cancer.
    Hanauer DA, Rhodes DR, Sinha-Kumar C, Chinnaiyan AM.
    Curr Mol Med. 2007 Feb;7(1):133-41. Review. Pubmed
14. Integrative molecular concept modeling of prostate cancer progression.
    Scott A Tomlins, Rohit Mehra, Daniel R Rhodes, Xuhong Cao, Lei Wang, Saravana M Dhanasekaran, Shanker Kalyana-Sundaram, John T Wei, Mark A Rubin, Kenneth J Pienta, Rajal B Shah & Arul M Chinnaiyan.
    Nature Genetics 2007 Jan.; 39, 41 - 51 Pubmed
15. Delineation, functional validation, and bioinformatic evaluation of gene expression in thyroid follicular carcinomas with the PAX8-PPARG translocation.
    Giordano TJ, Au AYM, Kuick R, Thomas DG, Rhodes DR, Wilhelm KG, Vinco M, Misek DE, Sanders D, Zhu ZW, Ciampi R, Hanash S, Chinnaiyan A, Clifton-Bligh RJ, Robinson BG, Nikiforov YE, Koenig RJ.
    Clinical Cancer Research 2006 Apr 1;12(7 Pt 1):1983-93. Pubmed
16. TMPRSS2:ETV4 gene fusions define a third molecular subtype of prostate cancer.
    Tomlins SA, Mehra R, Rhodes DR, Smith LR, Roulston D, Helgeson BE, Cao X, Wei JT, Rubin MA, Shah RB, Chinnaiyan AM.
    Cancer Res. 2006 Apr 1;66(7):3396-400. Pubmed
17. Whole transcriptome amplification for gene expression profiling and development of molecular archives.
    Tomlins SA, Mehra R, Rhodes DR, Shah RB, Rubin MA, Bruening E, Makarov V, Chinnaiyan AM.
    Neoplasia. 2006 Feb;8(2):153-62. Pubmed
18. Metastasis suppressor gene Raf kinase inhibitor protein (RKIP) is a novel prognostic marker in prostate cancer.
    Fu Z, Kitagawa Y, Shen R, Shah R, Mehra R, Rhodes D, Keller PJ, Mizokami A, Dunn R, Chinnaiyan AM, Yao Z, Keller ET.
    Prostate. 2006 Feb 15;66(3):248-56. Pubmed
19. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression.
    Varambally S, Yu JJ, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM.
    Cancer Cell. 2005 Nov;8(5):393-406. Pubmed
20. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.
    Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM.
    Science 2005 Oct 28;310(5748):644-8. Pubmed
21. Probabilistic model of the human protein-protein interaction network.
    Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM.
    Nat Biotechnology. 2005 Aug; 23(8):951-9 Pubmed
22. Integrative analysis of the cancer transcriptome.
    Rhodes DR, Chinnaiyan AM.
    Nat Genet. 2005 Jun;37 Suppl:S31-7. Review. Pubmed
23. Mining for regulatory programs in the cancer transcriptome.
    Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Barrette TR, Ghosh D, Chinnaiyan AM.
    Nat Genet. 2005 Jun; 37(6):579-83. Pubmed
24. Large-Scale Meta-Analysis of Cancer Microarray Data Identifies Common Transcriptional Profiles of Neoplastic Transformation and Progression.
    Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM.
    PNAS 2004 Jun 22;101(25):9309-14. Pubmed
25. Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer.
    Rubin MA, Varambally S, Beroukhim R, Tomlins SA, Rhodes DR, Paris PL, Hofer MD, Storz-Schweizer M, Kuefer R, Fletcher JA, Hsi BL, Byrne JA, Pienta KJ, Collins C, Sellers WR, Chinnaiyan AM.
    Cancer Res. 2004 Jun; 64 (11): 3814-3822. Pubmed
26. Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers.
    Rhodes DR, Chinnaiyan AM.
    Ann N Y Acad Sci. 2004 May;1020:32-40. Review. Pubmed
27. ONCOMINE: A Cancer Microarray Database and Data-Mining Platform.
    Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM.
    Neoplasia 2004 Jan-Feb; 6(1):1-6 Pubmed
28. Humoral immune response to alpha-methylacyl-CoA racemase and prostate cancer.
    Sreekumar A, Laxman B, Rhodes DR, Bhagavathula S, Harwood J, Giacherio D, Ghosh D, Sanda MG, Rubin MA, Chinnaiyan AM.
    J Natl Cancer Inst. 2004 Jun 2;96(11):834-43. Erratum in: J Natl Cancer Inst. 2004 Jul 21;96(14):1112. Pubmed
    
29. Prostate cancer biomarkers: a current perspective.
    Kumar-Sinha C, Rhodes DR, Yu J, Chinnaiyan AM.
    Expert Rev Mol Diagn. 2003 Jul;3(4):459-70. Review. Pubmed
    
30. Multiplex biomarker approach for determining risk of prostate-specific antigen-defined recurrence of prostate cancer.
    Rhodes DR, Sanda MG, Otte AP, Chinnaiyan AM, Rubin MA.
    J Natl Cancer Inst. 2003 May 7;95(9):661-8. Pubmed
    
31. Dysregulation of the annexin family protein family is associated with prostate cancer progression.
    Xin W, Rhodes DR, Ingold C, Chinnaiyan AM, Rubin MA.
    Am J Pathol. 2003 Jan;162(1):255-61. Pubmed
    
32. DNA microarrays: implications for clinical medicine.
    Rhodes DR, Chinnaiyan AM.
    J Invest Surg. 2002 Sep-Oct;15(5):275-9. Review. Pubmed
    
33. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer.
    Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM.
    Cancer Res. 2002 Aug 1;62(15):4427-33. Pubmed
    
34. CIT: identification of differentially expressed clusters of genes from microarray data.
    Rhodes DR, Miller JC, Haab BB, Furge KA.
    Bioinformatics. 2002 Jan;18(1):205-6. Pubmed
    

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