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Dr. Leslie Cope


Instructor in Oncology


Ph.D., The Johns Hopkins University School of Engineering, Department of Mathematical Sciences

Journal Citations

Eberhart, C.G.; Copeland, J.; Abel, T.W. Brief Report: S6 Ribosomal Protein Phosphorylation in Autistic Frontal Cortex and Cerebellum: a Tissue Array Analysis. J Autism Dev Disord. 2006 Jul 15;36(1131-1135).

Glintborg, B.; Weimann, A.; Kensler, T.W.; Poulsen, H.E. Oltipraz chemoprevention trial in Qidong, People's Republic of China: unaltered oxidative biomarkers. Free Radic Biol Med. 2006 Sep 15;41(6):1010-1014.

Liu, H.; Jensen, K.G.; Tran, L.M.; Chen, M.; Zhai, L.; Olsen, C.E.; Sohoel, H.; Denmeade, S.R.; Isaacs, J.T.; Brogger Christensen, S. Cytotoxic phenylpropanoids and an additional thapsigargin analogue isolated from Thapsia garganica. Phytochemistry. 2006 Dec;67(24):2651-2658.

Maggio, M.; Blackford, A.; Taub, D.; Carducci, M.; Ble, A.; Metter, E.J.; Braga-Basaria, M.; Dobs, A.; Basaria, S. Circulating inflammatory cytokine expression in men with prostate cancer undergoing androgen deprivation therapy. J Androl. 2006 Nov-Dec;27(6):725-728.

Mao, T.L.; Hsu, C.Y.; Yen, M.J.; Gilks, B.; Sheu, J.J.; Gabrielson, E.; Vang, R.; Cope, L.; Kurman, R.J.; Wang, T.L.; Shih Ie, M. Expression of Rsf-1, a chromatin-remodeling gene, in ovarian and breast carcinoma. Hum Pathol. 2006 Sep;37(9):1169-1175.

Nakayama, K.; Nakayama, N.; Kurman, R.J.; Cope, L.; Pohl, G.; Samuels, Y.; Velculescu, V.E.; Wang, T.L.; Shih Ie, M. Sequence mutations and amplification of PIK3CA and AKT2 genes in purified ovarian serous neoplasms. Cancer Biol Ther. 2006 Jul;5(7):779-785.

Raman, V.; Artemov, D.; Pathak, A.P.; Winnard, P.T., Jr.; McNutt, S.; Yudina, A.; Bogdanov, A., Jr.; Bhujwalla, Z.M. Characterizing vascular parameters in hypoxic regions: a combined magnetic resonance and optical imaging study of a human prostate cancer model. Cancer Res. 2006 Oct 15;66(20):9929-9936.

Sinibaldi, V.J.; Elza-Brown, K.; Schmidt, J.; Eisenberger, M.A.; Rosenbaum, E.; Denmeade, S.R.; Pili, R.; Walczak, J.; Baker, S.D.; Zahurak, M.; Carducci, M.A. Phase II evaluation of docetaxel plus exisulind in patients with androgen independent prostate carcinoma. American journal of clinical oncology. 2006 Aug;29(4):395-398.

Sohoel, H.; Jensen, A.M.; Moller, J.V.; Nissen, P.; Denmeade, S.R.; Isaacs, J.T.; Olsen, C.E.; Christensen, S.B. Natural products as starting materials for development of second-generation SERCA inhibitors targeted towards prostate cancer cells. Bioorganic & medicinal chemistry. 2006 Apr 15;14(8):2810-2815.

Wolpoe, M.E.; Goldenberg, D.; Koch, W.M. Squamous cell carcinoma of the sinonasal cavity arising as a second primary in individuals with head and neck cancer. Laryngoscope. 2006 May;116(5):696-699.

Basch, E.M.; Somerfield, M.R.; Beer, T.M.; Carducci, M.A.; Higano, C.S.; Hussain, M.H.; Scher, H.I. American Society of Clinical Oncology endorsement of the Cancer Care Ontario Practice Guideline on nonhormonal therapy for men with metastatic hormone-refractory (castration-resistant) prostate cancer. J Clin Oncol. 2007 Nov 20;25(33):5313-5318.

Farrag, T.Y.; Koch, W.M.; Cummings, C.W.; Goldenberg, D.; Abou-Jaoude, P.M.; Califano, J.A.; Flint, P.W.; Webster, K.; Tufano, R.P. Supracricoid laryngectomy outcomes: The Johns Hopkins experience. Laryngoscope. 2007 Jan;117(1):129-132.

Giovannucci, E.; Liu, Y.; Platz, E.A.; Stampfer, M.J.; Willett, W.C. Risk factors for prostate cancer incidence and progression in the health professionals follow-up study. Int J Cancer. 2007 Oct 1;121(7):1571-1578.

Leman, E.S.; Getzenberg, R.H. Nuclear structure as a source of cancer specific biomarkers. J Cell Biochem. 2007 Apr 23.

Nayak, C.S.; Carvalho, A.L.; Jeronimo, C.; Henrique, R.; Kim, M.M.; Hoque, M.O.; Chang, S.; Jiang, W.W.; Koch, W.; Westra, W.; Sidransky, D.; Califano, J. Positive correlation of tissue inhibitor of metalloproteinase-3 and death-associated protein kinase hypermethylation in head and neck squamous cell carcinoma. Laryngoscope. 2007 Aug;117(8):1376-1380.

Schuebel, K.E.; Chen, W.; Cope, L.; Glockner, S.C.; Suzuki, H.; Yi, J.M.; Chan, T.A.; Van Neste, L.; Van Criekinge, W.; van den Bosch, S.; van Engeland, M.; Ting, A.H.; Jair, K.; Yu, W.; Toyota, M.; Imai, K.; Ahuja, N.; Herman, J.G.; Baylin, S.B. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet. 2007 Sep;3(9):1709-1723.

Szewczuk, L.M.; Culhane, J.C.; Yang, M.; Majumdar, A.; Yu, H.; Cole, P.A. Mechanistic analysis of a suicide inactivator of histone demethylase LSD1. Biochemistry. 2007 Jun 12;46(23):6892-6902.

Veltri, R.W.; Marlow, C.; Khan, M.A.; Miller, M.C.; Epstein, J.I.; Partin, A.W. Significant variations in nuclear structure occur between and within Gleason grading patterns 3, 4, and 5 determined by digital image analysis. Prostate. 2007 Aug 1;67(11):1202-1210.

Zahurak, M.; Parmigiani, G.; Yu, W.; Scharpf, R.B.; Berman, D.; Schaeffer, E.; Shabbeer, S.; Cope, L. Pre-processing Agilent microarray data. BMC Bioinformatics. 2007;8:142.

Amanchy, R.; Zhong, J.; Molina, H.; Chaerkady, R.; Iwahori, A.; Kalume, D.E.; Gronborg, M.; Joore, J.; Cope, L.; Pandey, A. Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. J Proteome Res. 2008 Sep;7(9):3900-3910.

Braun, R.; Cope, L.; Parmigiani, G. Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics. 2008;9:488.

Chan, T.A.; Glockner, S.; Yi, J.M.; Chen, W.; Van Neste, L.; Cope, L.; Herman, J.G.; Velculescu, V.; Schuebel, K.E.; Ahuja, N.; Baylin, S.B. Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis. PLoS Med. 2008 May 27;5(5):e114.

Emens, L.A. Cancer vaccines: on the threshold of success. Expert opinion on emerging drugs. 2008 Jun;13(2):295-308.

Garrett-Mayer, E.; Parmigiani, G.; Zhong, X.; Cope, L.; Gabrielson, E. Cross-study validation and combined analysis of gene expression microarray data. Biostatistics. 2008 Apr;9(2):333-354.

Hann, C.L.; Daniel, V.C.; Sugar, E.A.; Dobromilskaya, I.; Murphy, S.C.; Cope, L.; Lin, X.; Hierman, J.S.; Wilburn, D.L.; Watkins, D.N.; Rudin, C.M. Therapeutic efficacy of ABT-737, a selective inhibitor of BCL-2, in small cell lung cancer. Cancer Res. 2008 Apr 1;68(7):2321-2328.

Jimeno, A.; Rudek, M.A.; Kulesza, P.; Ma, W.W.; Wheelhouse, J.; Howard, A.; Khan, Y.; Zhao, M.; Jacene, H.; Messersmith, W.A.; Laheru, D.; Donehower, R.C.; Garrett-Mayer, E.; Baker, S.D.; Hidalgo, M. Pharmacodynamic-guided modified continuous reassessment method-based, dose-finding study of rapamycin in adult patients with solid tumors. J Clin Oncol. 2008 Sep 1;26(25):4172-4179.

Leman, E.S.; Getzenberg, R.H. Nuclear structure as a source of cancer specific biomarkers. J Cell Biochem. 2008 Aug 15;104(6):1988-1993.

McGarvey, K.M.; Van Neste, L.; Cope, L.; Ohm, J.E.; Herman, J.G.; Van Criekinge, W.; Schuebel, K.E.; Baylin, S.B. Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells. Cancer Res. 2008 Jul 15;68(14):5753-5759.
Mikhak, B.; Hunter, D.J.; Spiegelman, D.; Platz, E.A.; Wu, K.; Erdman, J.W., Jr.; Giovannucci, E. Manganese superoxide dismutase (MnSOD) gene polymorphism, interactions with carotenoid levels and prostate cancer risk. Carcinogenesis. 2008 Dec;29(12):2335-2340.

Singla, A.; Denmeade, S.R. Left posterior fascicular block due to high-dose interleukin-2. The Annals of pharmacotherapy. 2008 Sep;42(9):1340-1343.

Tiwari, V.K.; Cope, L.; McGarvey, K.M.; Ohm, J.E.; Baylin, S.B. A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res. 2008 Jul;18(7):1171-1179.

Yung, R.C. Diagnosis and Management of Pleural Metastases in Breast Cancer. In: Bland, K.I.; Copeland, E.M., editors, Bland & Copeland The Breast: Comprehensive Management of Benign and Malignant Disorders, 4th Ed: Elsevier; 2008.

An, S.S.; Kim, J.; Ahn, K.; Trepat, X.; Drake, K.J.; Kumar, S.; Ling, G.; Purington, C.; Rangasamy, T.; Kensler, T.W.; Mitzner, W.; Fredberg, J.J.; Biswal, S. Cell stiffness, contractile stress and the role of extracellular matrix. Biochem Biophys Res Commun. 2009 May 15;382(4):697-703.

Christensen, S.B.; Skytte, D.M.; Denmeade, S.R.; Dionne, C.; Moller, J.V.; Nissen, P.; Isaacs, J.T. A Trojan horse in drug development: targeting of thapsigargins towards prostate cancer cells. Anticancer Agents Med Chem. 2009 Mar;9(3):276-294.

Hristov, A.C.; Cope, L.; Reyes, M.D.; Singh, M.; Iacobuzio-Donahue, C.; Maitra, A.; Resar, L.M. HMGA2 protein expression correlates with lymph node metastasis and increased tumor grade in pancreatic ductal adenocarcinoma. Mod Pathol. 2009 Jan;22(1):43-49.
Kortenhorst, M.S.; Isharwal, S.; van Diest, P.J.; Chowdhury, W.H.; Marlow, C.; Carducci, M.A.; Rodriguez, R.; Veltri, R.W. Valproic acid causes dose- and time-dependent changes in nuclear structure in prostate cancer cells in vitro and in vivo. Mol Cancer Ther. 2009 Apr;8(4):802-808.

Scheibner, K.A.; Boodoo, S.; Collins, S.; Black, K.E.; Chan-Li, Y.; Zarek, P.; Powell, J.D.; Horton, M.R. The adenosine a2a receptor inhibits matrix-induced inflammation in a novel fashion. Am J Respir Cell Mol Biol. 2009 Mar;40(3):251-259.

Seow, H.; Snyder, C.F.; Mularski, R.A.; Shugarman, L.R.; Kutner, J.S.; Lorenz, K.A.; Wu, A.W.; Dy, S.M. A framework for assessing quality indicators for cancer care at the end of life. J Pain Symptom Manage. 2009 Dec;38(6):903-912.

Vander Griend, D.J.; Antony, L.; Dalrymple, S.L.; Xu, Y.; Christensen, S.B.; Denmeade, S.R.; Isaacs, J.T. Amino acid containing thapsigargin analogues deplete androgen receptor protein via synthesis inhibition and induce the death of prostate cancer cells. Mol Cancer Ther. 2009 May 5;8(5):1340-1349.

Venugopal, A.; Chaerkady, R.; Pandey, A. Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Ann Indian Acad Neurol. 2009 Jan;12(1):3-11.

Wuthrich, C.; Dang, X.; Westmoreland, S.; McKay, J.; Maheshwari, A.; Anderson, M.P.; Ropper, A.H.; Viscidi, R.P.; Koralnik, I.J. Fulminant JC virus encephalopathy with productive infection of cortical pyramidal neurons. Ann Neurol. 2009 Jun;65(6):742-748.
Daniels, B.R.; Dobrowsky, T.M.; Perkins, E.M.; Sun, S.X.; Wirtz, D. MEX-5 enrichment in the C. elegans early embryo mediated by differential diffusion. Development. 2010 Aug 1;137(15):2579-2585.

Easwaran, H.P.; Van Neste, L.; Cope, L.; Sen, S.; Mohammad, H.P.; Pageau, G.J.; Lawrence, J.B.; Herman, J.G.; Schuebel, K.E.; Baylin, S.B. Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus. Cancer Res. 2010 Oct 15;70(20):8015-8024 NIHMSID # 263537 PMCID Journal: In process.

Hristov, A.C.; Cope, L.; Di Cello, F.; Reyes, M.D.; Singh, M.; Hillion, J.A.; Belton, A.; Joseph, B.; Schuldenfrei, A.; Iacobuzio-Donahue, C.A.; Maitra, A.; Resar, L.M. HMGA1 correlates with advanced tumor grade and decreased survival in pancreatic ductal adenocarcinoma. Mod Pathol. 2010 Jan;23(1):98-104.

Kristal, A.R.; Arnold, K.B.; Neuhouser, M.L.; Goodman, P.; Platz, E.A.; Albanes, D.; Thompson, I.M. Diet, supplement use, and prostate cancer risk: results from the prostate cancer prevention trial. Am J Epidemiol. 2010 Sep 1;172(5):566-577.

Licchesi, J.D.; Van Neste, L.; Tiwari, V.K.; Cope, L.; Lin, X.; Baylin, S.B.; Herman, J.G. Transcriptional regulation of Wnt inhibitory factor-1 by Miz-1/c-Myc. Oncogene. 2010 Nov 4;29(44):5923-5934

Lotan, T.L.; Epstein, J.I. Clinical implications of changing definitions within the Gleason grading system. Nat Rev Urol. 2010 Mar;7(3):136-142.

Noushmehr, H.; Weisenberger, D.J.; Diefes, K.; Phillips, H.S.; Pujara, K.; Berman, B.P.; Pan, F.; Pelloski, C.E.; Sulman, E.P.; Bhat, K.P.; Verhaak, R.G.; Hoadley, K.A.; Hayes, D.N.; Perou, C.M.; Schmidt, H.K.; Ding, L.; Wilson, R.K.; Van Den Berg, D.; Shen, H.; Bengtsson, H.; Neuvial, P.; Cope, L.M.; Buckley, J.; Herman, J.G.; Baylin, S.B.; Laird, P.W.; Aldape, K. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010 May 18;17(5):510-522.

Ohm, J.E.; Mali, P.; Van Neste, L.; Berman, D.M.; Liang, L.; Pandiyan, K.; Briggs, K.J.; Zhang, W.; Argani, P.; Simons, B.; Yu, W.; Matsui, W.; Van Criekinge, W.; Rassool, F.V.; Zambidis, E.; Schuebel, K.E.; Cope, L.; Yen, J.; Mohammad, H.P.; Cheng, L.; Baylin, S.B. Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells. Cancer Res. 2010 Oct 1;70(19):7662-7673.

Peng, S.; Best, S.R.; Hung, C.F.; Loyo, M.; Lyford-Pike, S.; Flint, P.W.; Tunkel, D.E.; Saunders, J.R.; Wu, T.C.; Pai, S.I. Characterization of human papillomavirus type 11-specific immune responses in a preclinical model. Laryngoscope. 2010 Mar;120(3):504-510.

Scharpf, R.B.; Iacobuzio-Donahue, C.A.; Cope, L.; Ruczinski, I.; Garrett-Mayer, E.; Lakkur, S.; Campagna, D.; Parmigiani, G. Cross-platform Comparison of Two Pancreatic Cancer Phenotypes. Cancer Inform. 2010;9:257-264.

Shaha, M.; Pandian, V.; Choti, M.A.; Stotsky, E.; Herman, J.M.; Khan, Y.; Libonati, C.; Pawlik, T.M.; Schulick, R.D.; Belcher, A.E. Transitoriness in cancer patients: a cross-sectional survey of lung and gastrointestinal cancer patients. Support Care Cancer. 2010 Feb;19(2):271-279.

Shih Ie, M.; Chen, L.; Wang, C.C.; Gu, J.; Davidson, B.; Cope, L.; Kurman, R.J.; Xuan, J.; Wang, T.L. Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis. Am J Obstet Gynecol. 2010 Dec;203(6):584 e581-522.

Tirado, Y.; Lewin, J.S.; Hutcheson, K.A.; Kupferman, M.E. Office-based injection laryngoplasty in the irradiated larynx. Laryngoscope. 2010 Apr;120(4):703-706.

Brandy, Y.; Ononiwu, I.; Adedeji, D.; Williams, V.; Mouamba, C.; Kanaan, Y.; Copeland, R.L., Jr.; Wright, D.A.; Butcher, R.J.; Denmeade, S.R.; Bakare, O. Synthesis and cytotoxic activities of some 2-Arylnaphtho[2,3-d]oxazole-4,9-dione derivatives on androgen-dependent (LNCaP) and androgen-independent (PC3) human prostate cancer cell lines. Invest New Drugs. 2011 Jan 18;Epub 1/19/11.

Li, Y.; Tian, Y.; Rezai, T.; Prakash, A.; Lopez, M.F.; Chan, D.W.; Zhang, H. Simultaneous analysis of glycosylated and sialylated prostate-specific antigen revealing differential distribution of glycosylated prostate-specific antigen isoforms in prostate cancer tissues. Anal Chem. 2011 Jan 1;83(1):240-245.

Cappola, T. P., Cope, L. M., Cernetich, A., Barouch, L. A., Minhas, K., Irizarry, R. A., Parmigiani, G., et al. 2003. Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy. Physiol. Genomics. 14:25-34.

Cope, L. M., Irizarry, R. A., Jaffee, H., Wu, Z., & Speed, T. P. 2004. A benchmark for affymetrix genechip expression measures. Bioinformatics. 20:323-331.

Cope, L. M., Zhong, X., Garrett, E., & Parmigiani, G. 2004. MergeMaid: R tools for merging and cross-study validation of gene expression data. Stat. Appl. Genet. Mol. Biol. 3:Article29.

Gautier, L., Cope, L. M., Bolstad, B. M., & Irizarry, R. A. 2004. Affy - a package for the analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 20:323-331.

Irizarry, R. A., Gautier, L., & Cope L. M. 2003. Affymetrix oligonucleotide arrays. In G. Parmigiani, E. S. Garrett, R. A. Irizarry, & S. L. Zeger (Eds.), The analysis of gene expression data: methods and software. NY: Springer-Verlag.

Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B. & Speed, T. P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e15.


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