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Original Articles

• Large-scale kinase inhibitor profiling reveals features of target selectivity, Anastassiadis, T., Deacon, S., Devarajan, K., Ma, H., Peterson, J. (2011). Nature Biotechnology, In Press (to appear in Nov. issue). NIHMS328213.
• A unified approach to non-negative matrix factorization and probabilistic latent semantic indexing" (July 2011). Devarajan, K., Wang, G., Ebrahimi, N. COBRA Preprint Series. Article 80. http://biostats.bepress.com/cobra/ps/art80.
• Detection of colorectal adenomas using a bioactivatable probe specific for matrix metalloproteinase activity. Clapper ML, Hensley HH, Chang WC, Devarajan K, Nguyen MT, Cooper HS. Neoplasia. 2011 Aug;13(8):685-91. PMID: 21847360
• Elevated expression of stromal palladin predicts poor clinical outcome in renal cell carcinoma. Gupta V, Bassi DE, Simons JD, Devarajan K, Al-Saleem T, Uzzo RG, Cukierman E. PLoS One. 2011;6(6):e21494. Epub 2011 Jun 28. PMID: 21738681
• Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cortellino S, Xu J, Sannai M, Moore R, Caretti E, Cigliano A, Le Coz M, Devarajan K, Wessels A, Soprano D, Abramowitz LK, Bartolomei MS, Rambow F, Bassi MR, Bruno T, Fanciulli M, Renner C, Klein-Szanto AJ, Matsumoto Y, Kobi D, Davidson I, Alberti C, Larue L, Bellacosa A. Cell. 2011 Jul 8;146(1):67-79. Epub 2011 Jun 30. PMID: 21722948
• Novel surface targets and serum biomarkers from the ovarian cancer vasculature. Sasaroli D, Gimotty PA, Pathak HB, Hammond R, Kougioumtzidou E, Katsaros D, Buckanovich R, Devarajan K, Sandaltzopoulos R, Godwin AK, Scholler N, Coukos G. Cancer Biol Ther. 2011 Aug 1;12(3):169-80. Epub 2011 Aug 1. PMID: 21617380
• The codon 72 polymorphism of p53 regulates interaction with NF-{kappa}B and transactivation of genes involved in immunity and inflammation. Frank AK, Leu JI, Zhou Y, Devarajan K, Nedelko T, Klein-Szanto A, Hollstein M, Murphy ME. Mol Cell Biol. 2011 Mar;31(6):1201-13. Epub 2011 Jan 18. PMID: 21245379
• Estrogen and cytochrome P450 1B1 contribute to both early- and late-stage head and neck carcinogenesis. Shatalova EG, Klein-Szanto AJ, Devarajan K, Cukierman E, Clapper ML. Cancer Prev Res (Phila). 2011 Jan;4(1):107-15. PMID: 1205741
• A semi-parametric generalization of the Cox proportional hazards regression model: Inference and Applications. Devarajan K, Ebrahimi N. Comput Stat Data Anal. 2011 Jan 1;55(1):667-676. PMID: 21076652
• Matrix and Tensor Decompositions, Devarajan, K., Problem Solving Handbook in Computational Biology and Bioinformatics, 2011, Part 5, 291-318, Springer. DOI: 10.1007/978-0-387-09760-2_14
• Fleisher L, Kandadai V, Keenan E, Miller SM, Devarajan K, Ruth KJ, Rodoletz M, Bieber EJ, Weinberg DS. Build It, and Will They Come? Unexpected Findings From a Study on a Web-Based Intervention to Improve Colorectal Cancer Screening. Journal of Health Communication (0):1-13, 2011.
• The mTOR pathway affects proliferation and chemosensitivity of urothelial carcinoma cells and is upregulated in a subset of human bladder cancers. Makhlin I, Zhang J, Long CJ, Devarajan K, Zhou Y, Klein-Szanto AJ, Huang M, Chernoff J, Boorjian SA. BJU Int. 2011 Jul;108(2 Pt 2):E84-90. doi: 10.1111/j.1464-410X.2010.09844.x. Epub 2010 Nov 2. PMID: 21050361
• Synthetic lethal screen of an EGFR-centered network to improve targeted therapies. Astsaturov I, Ratushny V, Sukhanova A, Einarson MB, Bagnyukova T, Zhou Y, Devarajan K, Silverman JS, Tikhmyanova N, Skobeleva N, Pecherskaya A, Nasto RE, Sharma C, Jablonski SA, Serebriiskii IG, Weiner LM, Golemis EA. Sci Signal. 2010 Sep 21;3(140):ra67. PMID: 20858866
• A supervised approach for predicting patient survival with gene expression data. Devarajan K, Zhou Y, Chachra N, Ebrahimi N. Proc IEEE Int Symp Bioinformatics Bioeng. 2010;2010(5521718):26-31. PMID: 20865131
• Early changes in gene expression induced by tobacco smoke: Evidence for the importance of estrogen within lung tissue. Meireles SI, Esteves GH, Hirata R Jr, Peri S, Devarajan K, Slifker M, Mosier SL, Peng J, Vadhanam MV, Hurst HE, Neves EJ, Reis LF, Gairola CG, Gupta RC, Clapper ML. Cancer Prev Res (Phila). 2010 Jun;3(6):707-17. Epub 2010 Jun 1. PMID: 20515954
• Testing for Covariate Effect in the Cox Proportional Hazards Regression Model. Devarajan K, Ebrahimi N. Commun Stat Theory Methods. 2009 Jan 1;38(14):2333-2347. PMID: 20054448
• Altered gene expression in morphologically normal epithelial cells from heterozygous carriers of BRCA1 or BRCA2 mutations. Bellacosa A, Godwin AK, Peri S, Devarajan K, Caretti E, Vanderveer L, Bove B, Slater C, Zhou Y, Daly M, Howard S, Campbell KS, Nicolas E, Yeung AT, Clapper ML, Crowell JA, Lynch HT, Ross E, Kopelovich L, Knudson AG. Cancer Prev Res (Phila). 2010 Jan;3(1):48-61. PMID: 20051372
• Endoscopic imaging and size estimation of colorectal adenomas in the multiple intestinal neoplasia mouse. Hensley HH, Merkel CE, Chang WC, Devarajan K, Cooper HS, Clapper ML. Gastrointest Endosc. 2009 Mar;69(3 Pt 2):742-9. PMID: 19251020
• Phase II trial of single agent cetuximab in patients with persistent or recurrent epithelial ovarian or primary peritoneal carcinoma with the potential for dose escalation to rash. Schilder RJ, Pathak HB, Lokshin AE, Holloway RW, Alvarez RD, Aghajanian C, Min H, Devarajan K, Ross E, Drescher CW, Godwin AK. Gynecol Oncol. 2009 Apr;113(1):21-7. Epub 2009 Jan 21. PMID: 19162309
• A prospective study of quality of life among women undergoing risk-reducing salpingo-oophorectomy versus gynecologic screening for ovarian cancer. Fang CY, Cherry C, Devarajan K, Li T, Malick J, Daly MB. Gynecol Oncol. 2009 Mar;112(3):594-600. Epub 2009 Jan 13. PMID: 19141360
• Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. Devarajan K. PLoS Comput Biol. 2008 Jul 25;4(7):e1000029. Review. PMID: 18654623
• Class discovery via nonnegative matrix factorization, Devarajan K, Ebrahimi N., American Journal of Mathematical and Management Sciences, 2008;28(3&4):457-67.
• 5-aminosalicylic acid inhibits colitis-associated colorectal dysplasias in the mouse model of azoxymethane/dextran sulfate sodium-induced colitis. Clapper ML, Gary MA, Coudry RA, Litwin S, Chang WC, Devarajan K, Lubet RA, Cooper HS. Inflamm Bowel Dis. 2008 Oct;14(10):1341-7. PMID: 18452197
• Multiple antithrombotic agents increase the risk of postoperative hemorrhage in dermatologic surgery. Shimizu I, Jellinek NJ, Dufresne RG, Li T, Devarajan K, Perlis C. J Am Acad Dermatol. 2008 May;58(5):810-6. PMID: 18423258
• Comparison of RNA amplification methods and chip platforms for microarray analysis of samples processed by laser capture microdissection. Caretti E, Devarajan K, Coudry R, Ross E, Clapper ML, Cooper HS, Bellacosa A. J Cell Biochem. 2008 Feb 1;103(2):556-63. PMID: 17546586
• Specificity profiling of Pak kinases allows identification of novel phosphorylation sites. Rennefahrt UE, Deacon SW, Parker SA, Devarajan K, Beeser A, Chernoff J, Knapp S, Turk BE, Peterson JR. J Biol Chem. 2007 May 25;282(21):15667-78. Epub 2007 Mar 28. PMID: 17392278
• Age-dependent morphological alterations of human ovaries from populations with and without BRCA mutations. Cai KQ, Klein-Szanto A, Karthik D, Edelson M, Daly MB, Ozols RF, Lynch HT, Godwin AK, Xu XX. Gynecol Oncol. 2006 Nov;103(2):719-28. Epub 2006 May 12. PMID: 16698071
• A mouse model recapitulating molecular features of human mesothelioma. Altomare DA, Vaslet CA, Skele KL, De Rienzo A, Devarajan K, Jhanwar SC, McClatchey AI, Kane AB, Testa JR. Cancer Res. 2005 Sep 15;65(18):8090-5. PMID: 16166281
• Goodness of fit testing for the Cox proportional hazards model, Goodness-of-Fit Tests and Model Validity, Devarajan K, Ebrahimi N., Statistics for Industry and Technology, 235-251, Birkhauser Publishers, Boston, 2001.
• The maximum penalized likelihood approach using nonhomogeneous Poisson processes for software reliability and reliability growth models, Devarajan K, Ebrahimi N., Applied Statistical Science V, 63-76, Nova Science Publishers, New York, 2000.
• A nonparametric approach to accelerated life testing under multiple stresses, Devarajan K, Ebrahimi N., Naval Research Logistics, 1998;45:629-644.