Strategic Partners for the Evaluation of Predictive Signatures of Prostate Cancer (SPECS)
Publications
1. Stuart RO, Wachsman W, Berry CC, Wang-Rodriguez J, Wasserman L, Klacansky I, Masys D, Arden K, Goodison S., McClelland M, Wang Y, Sawyers A, Kalcheva I, Tarin D, Mercola D. In Silico Dissection of Cell-type-associated Patterns of Gene Expression in Prostate Cancer. Proc National Acad Sci. 2004; Jan 13;101(2):615-20. [pdf]
2. Wang Y, Hayakawa J, Long F, Yu Q, Cho A, Rondeau G, Welsh J, Mittal S, De Belle I, Adamson E, McClelland M, Mercola D. "Promoter Array" Studies Identify Cohorts of Genes Directly Regulated by Methlyation, Copy Number Change, or Transcription Factor Binding in Human Cancer Cells. Ann N.Y. Acad. Sci. 2005; 1058: 162-185. [pdf]
3. Krajewska M, Olson AH, Mercola D, Reed JC, Krajewski S. Claudin-1 immunohistochemistry for distinguishing malignant from benign epithelial lesions of prostate. Prostate. 2007; Jun 15;67(9):907-10. [pdf]
4. Jia Z, Tang S, Mercola D, Xu S. Detection of Quantitative Trait Associated Genes Using Cluster Analysis. In Evolutionary Computation, Machine Learning, and Data Mining in Bioinformatics, Proceeding of the 6th European Conference, EvoBIO 2008, Naples, Italy, March 2008, Elena Marchiori & Jason H. Moorte, Eds., Springer-Verlag, Germany. [pdf]
5. Krajewska M , Kitada S, Winter JN, Variakojis D, Lichtenstein A, Zhai D, Cuddy M, Huang X, Luciano F, Baker CH, Kim H, Shin E, Kennedy S, Olson AH, Badzio A, Jassem J, Meinhold-Heerlein I, Duffy MJ, Schimmer AD, Tsao M, Brown E, Sawyers A, Andreeff M, Mercola D, Krajewski S, Reed JC. Bcl-B Expression in Human Epithelial and Nonepithelial Malignancies. Clinical Cancer Research. 2008; 14: 3011-3021. [pdf]
6. Arrach N, Zhao M, Porwollik S, Hoffman RM, McClelland M. Salmonella Promoters Preferentially Activated Inside Tumors. Cancer Research. 2008; 68:(12) 4827-4832. [pdf]
7. Arora S, Wang Y, Jia Z, Vardar-Sengul S, Munawar A, Doctor KS, Birrer M, McClelland M, Adamson E, Mercola D. Egr1 Regulates the Coordinated Expression of Numerous EGF Receptor Target Genes as identified by ChIP-on-chip. Genome Biology. 2008; 9(11):R166. [pdf]
8. Yu J, Zhang SS, Saito K, Ke Y, Arimura Y, Baron V, Mercola D, Adamson E, Feng G-S, Mustelin T. PTEN Regulation by Akt-EGR1-ARF-PTEN Axis. Embo J. 2009; 28(1): 21-33. Epub 2008 Dec. 4. [pdf]
9. Koziol JA, Feng A, Jia Z, Wang Y, McClelland M, Mercola D. The Wisdom of the Commons: Ensemble Tree Classifiers for Prostate Cancer Prognosis. Bioinformatics. 2009; Vol.25, 1: 54-60. [pdf]
10. Tang Y, Simoneau AR, Liao W-X, Yi G, Hope C, Liu F, Li S, Xie J, Holcombe RF, Jurnak FA, Mercola D, Hoang BH, Zi X. WIF1, a Wnt Pathway Inhibitor, Regulates SKP2 and C-Myc Expression Leading to G1 Arrest and Growth Inhibition of Human Invasive Urinary Bladder Cancer Cells. Mol Cancer Ther. 2009; 8(2):458-468. [pdf]
11. Jia Z, Wang Y, Ye K, Li Q, Tang S, Xu S, Mercola D. Association Study Between Gene Expression and Multiple Relevant Phenotypes with Cluster Analysis. Lect Notes Comput Sci. 2009; 5483: 1-12. [pdf]
12. Wang Y, Xia X-Q, Jia Z, Sawyers A, Yao H, Wang-Rodriguez J, Mercola D, McClelland M. In silico Estimates of Tissue Components in Surgical Samples Based on Expression Profiling Data. Cancer Research, 70(16); July 27, 2010. [pdf] PMID: 20663908 "these two authors contributed equally"
13. Jia Z, Wang Y, Sawyers A, Yao H, Rahmatpanah F, Xia X-Q, Xu Q, Pio R, Turan T, Koziol JA, Goodison S, Carpenter P, Wang-Rodriguez J, Simoneau A, Meyskens F, Sutton M, Lernhardt W, Beach T, *McClelland M, *Mercola D. Diagnosis of Prostate Cancer Using Differentially Expressed Genes in Stroma. Cancer Research, 2011; 71(7): 2476-2487. [pdf] supplement [pdf] PMID: 21459804. *Contributed equally.
14. Chen X, Xu S, Wang Y, McClelland M, Jia Z, Mercola D. Identification of Biomarkers for Prostate Cancer Prognosis Using a Novel Two-Step Cluster Analysis. M. Loog et. al. (Eds.): vol. Pattern Recognition in Bioinformatics; series Lecture Notes in Bioinformatics 7036; Springer-Verlag Berlin Heidelber, 2011. [pdf]
15. Chen X, Xu S, Rahmatpanah F, McClelland, Jia Z, Mercola D. An Accurate Prostate Cancer Prognosticator Using a Seven-Gene Signature Plus Gleason Score by Taking Cell Type-Heterogeneity into Account. Plos One. 2012; 7e45178. PMCID: 3460942.
16. Jia Z, Wang Y, Hu Y, McLaren C, Yu Y, Ye K, Xia XQ, Koziol JA, Lernhardt W, McClelland M, Mercola D. A sample selection strategy to boost the statistical power of signature detection in cancer expression profile studies. Anti-Cancer Agents Medicial Chem. 2013;13:203-11. PMID: 22934703.
17. Lee C, Zhang Q, Kozlowski J, Brendler C, Soares MB, Dash A, McClelland M, Mercola D. Natural products and transforming growth factor-beta (TGF-beta) signaling in cancer development and progression. Curr Cancer Drug Targets. 2013. Epub ahead of print. PMID: 23597196.
In press
18. Zhenyu Jia, Farahnaz Rahmatpanah, Xin Chen, Waldemar Lernhardt, Yipeng Wang, Xiao-Qin Xia, Michael McClelland, Dan Mercola. Prognosis of Prostate Cancer Using Gene Expression Changes in Stroma. Plos One (in press June 2012).
Published abstracts of presentations
19. Saynur Vardar-Senguli, Shilpi Arora, Yipeng Wang, H. Baylas, Michael McClelland, Eileen Adamson, and Dan Mercola. cJun/ATF2 bound promoters in THP1-monocytes and macrophage-like-cells following LPS stimulation. Abstract #92552, International Association for Dental Research, New Orleans, March 2007 [selected for oral presentation].
20. Shilpi Arora, Eileen Adamson, Yipeng Wang, Michael McClelland, Dan Mercola. Identification of Egr1 target genes in prostate cancer cells upon UV stimulation using promoter arrays. 98th AACR Annual Meeting. April 15-18, 2007, Los Angeles, CA. In: Proceedings of the American Association of Cancer Research, 2007;48 (Abstract no.l LB-314).
21. Wang, Yipeng; Koziol, James; Goodison, Steve; Lou, Jian-Hua, Mercola, Dan and McClelland, Michael. The challenge of developing predictive signatures for the outcome of newly diagnosed prostate cancer based on expression analysis and genetic changes of tumor and non-tumor cells. April 15-18, 2007, Los Angeles, CA. In: Proceedings of the 98th Annual Meeting of the American Association of Cancer Research, 2007;48 (symposium oral presentation).
22. Shilpi Arora, Eileen Adamson, Yipeng Wang, Michael McClelland, Dan Mercola. Identification of Egr1 target genes in prostate cancer cells upon UV stimulation using promoter arrays. In: Proceedings of the 99th Annual Meeting of the American Association for Cancer Research, 2008 Apr 12-16; San Diego, CA. Philadelphia (PA) (Abstract no. 5279).
23. Yipeng Wang, Zhenyu Jia, Michael McClelland, and Dan Mercola. In silico estimates of tissue percentage improve cross-validation of potential relapse biomarkers in prostate cancer and adjacent stroma. In: Proceedings of the 99th Annual Meeting of the American Association for Cancer Research, 2008 Apr 12-16; San Diego, CA. Abstract no. 999.
24. Darren R. Tyson, Junichi Inokuchi, Julia D. Wulfkuhle, Zhenyu Jia, Alice Lau, Seiji Naito, Emanual F. Petricoin, Dan E. Mercola, David K. Ornstein. Reduced annexin A1 expression contributes to prostate cancer by activation of Akt and induction of IL-6. In: Proceedings of the 99th Annual Meeting of the AACR, 2008 Apr 12-16; San Diego, CA. Abstract no. 2227.
25. Maryla Krajewska, Jane N. Winter, Daina Variakojis, Alan Lichtenstein, Dayong Zhai, Michael Cuddy, Xianshu Huang, Frederic Luciano, Cheryl H. Baker, Hoguen Kim, Eunah Shin, Susan Kennedy, Allen H. Olson, Andrzej Badzio, Jacek Jassem, Ivo Meinhold-Heerlein, Michael J. Duffy, Aaron D. Schimmer, Ming Tsao, Ewan Brown, Dan Mercola, Stan Krajewski, John C. Reed. Bcl-B expression in human epithelial and non-epithelial malignancies. In: Proceedings of the 99th Annual Meeting of the American Association for Cancer Research, 2008 Apr 12-16; San Diego, CA. Abstract no. 2180.
26. Zhenhu Jia, Yipeng Wang, James Kozio, Yipeng Wang, Michael McClelland, and Dan Mercola. A New Bi-Model Classifier for Prediciting Octcome of Prostate Cancer Patients. In Joint Statistical Meeting, Denver, Colorado, August 5-11, poster, session 242, Section on Health Policy Statistics, Section on Statistical Computing, Section on Statistics in Epidemiology, WNAR, Tuesday, August 5, 2008.
27. Yipeng Wang, Zhenyu Jia, Xiao-Qin Xia, Huazhen Yao, Anne Sawyers, Jessica Wang Rodriguez, Steve Goodison, Dan Mercola, Michael McClelland. Improved identification of RNA prognostic biomarkers for prostate cancer using in silico tissue estimates. In: Proceedings of the 100th Annual Meeting of the American Association for Cancer Research, 2009, April 18-22, 2009, Denver, CO. Abstract no. 1627.
28. Farah Rahmatpanah, Zhenyu Jia, Tatsuya Azumi, Eileen Adamson, Ryan Alipio, Rebecca Pio, Frank Jones, Dan Mercola. Chip-on-chip analysis of mechanism of action of HER2 inhibition in breast cancer cell lines In: Proceedings of the 100th Annual Meeting of the American Association for Cancer Research, 2009, April 18-22, 2009; Denver, CO. Abstract no. 1030.
29. Zhenyu Jia, Yipeng Wang, James A. Koziol, Anne Sawyers, Huazhen Yao, Michael McClelland, Dan Mercola. A bi-model classifier that allows RNA expression in mixed tissues to be used in prostate cancer prognosis. In: Proceedings of the 100th Annual Meeting of the American Association for Cancer Research, 2009, April 18-22, 2009; Denver, CO. Abstract no. 1630.
30. Farah B. Rahmatpanah, Zhenyu, Jia, Jessica E. Alspaugh, Tatsuya Azumi, Eileen Adamson, Rebecca Pio, Frank E. Jones and Dan Mercola. Transcription regulation by HER2 in Breast Cancer Cell Lines. Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications AACR, San Diego, October 13-16, 2009.
31. Zhenyu Jia, Yipeng Wang, Anne Sawyers, Huazhen Yao, Steve Goodison, Michael McClelland, and Dan Mercola "The Prostate Cancer Microenvironment Exhibits Numerous Differential Gene Expression Changes that May be Used for Diagnosis in the Absence of Tumor Cells", AACR EROTC meeting on Prostate Cancer Microenvironment, Versailles, France. Mini-symposium oral presentation. October 22, 2009.
32. Zhenyu Jia, Yipeng Wang, Anne Sawyers, Huazhen Yao, Steve Goodison, Michael McClelland, and Dan Mercola. Diagnosis of prostate cancer without tumor cells using differentially expressed genes in the tumor microenvironment. In: Proceedings of the American Association for Cancer Research 101st AACR Annual Meeting, 2010, April 17-21, 2010; Washington, DC. Poster Session Abstract no. 5184.
33. Zhenyu Jia, Yipeng Wang, Anne Sawyers, Huazhen Yao, Farahnaz Rahmatpanah, Xiao-Qin Xia, Qiang Xu, James Koziol, Philip Carpenter, Jessica Wang-Rodriquez, Anne Simoneau, Frank Meyskens, Atreya Dash, Steven Goodison, Waldemar Lernhardt, Joseph Rogers, Thomas Beach, Manuel Sutton, Michael McClelland and Dan Mercola. A multigene profile derived from expression analysis of the tumor adjacent stroma for the diagnosis of prostate cancer. Meeting of the Cambridge Healthtech Institute: Future Diagnostics, April 27, 2010, University of California at Irvine, Irvine CA.
34. Zhenyu Jia, Yipeng Wang, Anne Sawyers, Huazhen Yao, Farahnaz Rahmatpanah, Xiao-Qin Xia, Qiang Xu, James Koziol, Philip Carpenter, Jessica Wang-Rodriquez, Anne Simoneau, Frank Meyskens, Atreya Dash, Waldemar Lernhardt, Joseph Rogers, Thomas Beach, Manuel Sutton, Michael McClelland and Dan Mercola. Diagnosis of prostate cancer without tumor cells using differentially expressed genes in the tumor microenvironment. The Journal of Urology, 2010; 183:e840 (Abstract no. 2160), oral presentation, Annual Meeting of the American Urology Association, June 2, 2010; San Francisco, CA.
35. Zhenyu Jia, Yipeng Wang, Christine McLaren, Kai Ye, Xiao-Qin Xia, Yuanjia Hu, Hui Li, Sha Tang, Waldemar Lernhardt, James A. Koziol, Michael McClelland, Dan Mercola. Adding more expression profiles does not boost power for detecting prognostic markers in cancer when heterogeneity is a factor. In: Proceedings of the American Association for Cancer Research. 102nd AACR Annual Meeting, 2011, April 2-6, 2011, in Orlando, FL, Poster Session 2, board 15, Sunday, April 3, 2011, 1 p.m.-5 p.m.
36. Zhenyu Jia, Farahnaz Rahmatpanah, Xin Chen, Waldemar Lernhardt, Yipeng Wang, Xiao-Qin Xia, Michael McClelland, Dan Mercola. Prognosis of prostate cancer using gene expression changes in stroma. American Association for Cancer Research Special Conference on Advances in Prostate Cancer Research, February 6-9, 2012, at the Hyatt Regency Grand Cypress in Orlando, FL (poster presentation).
37. Farah Rahmatpanah, Zhenyu Jia, Jessica Char, Michael McClelland, Dan Mercola. The expression of HER2 in human breast cancer cells leads to massive alteration of RNA polyermase II binding and gene activation. In: Proceedings of the American Association of Cancer Research 103rd AACR Annual Meeting, 2012 March 31-April 4, 2012, Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl): Abstract nr 3001. doi: 1538-7445. AM2012-3001. Poster PO MCFG11.01, (Bioinformatics Application and Gene Expression Analysis), Tuesday, April 3, 2012.
38. Shuman Liu, Zhenyu Jia, Zheng Sun, Xuesen Li, Yi Guo, Michael Lilly, Dan Mercola, Bang H. Hoang, Xiaolin Zi. Wnt signaling regulation neuropilin-2 (NRP2) expression and contributes to cancer cell invasiveness in castration-resistant prostate cancer (CRPC). In: Proceedings of the American Association for Cancer Research 103rd AACR Annual Meeting, 2012, March 31-April 4, 2012; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl): Abstract nr 440. doi:1538-7445. AM2012-440. Poster Session PO.TB04.o1 (Metastasis Biomarkers), Sunday, April 1, 2012.