Faculty Summaries
Karthik Devarajan, PhD
Karthik Devarajan, PhD
Associate Member & Assistant Professor
Karthik.Devarajan@fccc.edu
Office Phone: 215-728-2794
Fax: 215-728-2553
Office: R383

Original Articles

    PEER-REVIEWED PUBLICATIONS
    1. Dames DN, Blackman E, Butler R, Taioli E, Eckstein S, Devarajan K, Griffith-Bowe A, Gomez P, Ragin C. High-Risk Cervical Human Papillomavirus Infections among Human Immunodeficiency Virus-Positive Women in the Bahamas. PloS one, 9(1):e85429, 2014. PMC3900425
    2. Devarajan K, Cheung VCK. (2013). On non-negative matrix factorization algorithms for signal-dependent noise with application to electromyography data, Neural Computation, In press. doi: 10.1162/NECO_a_00576.
    3. Chen KT, Kim PD, Jones KA, Devarajan K, Patel BB, Hoffman JP, Ehya H, Huang M, Watson JC, Tokar JL, Yeung AT. Potential prognostic biomarkers of pancreatic cancer. Pancreas, 43(1):22-7, 2014. PMC3859961
    4. Weinberg DS, Keenan E, Ruth K, Devarajan K, Rodoletz M, Bieber EJ. A randomized comparison of print and web communication on colorectal cancer screening. JAMA internal medicine, 173(2):122-9, 2013. PMC3615476
    5. Wang MJ, Mehta A, Block TM, Marrero J, Di Bisceglie AM, Devarajan K. A comparison of statistical methods for the detection of hepatocellular carcinoma based on serum biomarkers and clinical variables. Bmc Medical Genomics, 6(Suppl 3):S9, 2013. http://www.biomedcentral.com/bmcmedgenomics/supplements/6/S3.
    6. Sterious S, Simhan J, Uzzo RG, Gershman B, Li T, Devarajan K, Canter D, Walton J, Fogg R, Ginzburg S, Corcoran A, Smaldone MC, Kutikov A. Familiarity and self-reported compliance with American Urological Association best practice recommendations for use of thromboembolic prophylaxis among American Urological Association members. The Journal of urology, 190(3):992-8, 2013.
    7. Devarajan K, Ebrahimi N. (2013). On penalized likelihood estimation for a non-proportional hazards regression model. Statistics and Probability Letters. 83, 1703-1710. NIHMS 462966. http://www.sciencedirect.com/science/article/pii/S0167715213000801. COBRA Preprint Series. Working Paper 92. http://biostats.bepress.com/cobra/art92
    8. Peri S, Devarajan K, Yang DH, Knudson AG, Balachandran S. Meta-analysis identifies NF-kappaB as a therapeutic target in renal cancer. PloS one, 8(10):e76746, 2013. PMC3792024
    9. Miller SM, Hudson SV, Egleston BL, Manne S, Buzaglo JS, Devarajan K, Fleisher L, Millard J, Solarino N, Trinastic J, Meropol NJ. The relationships among knowledge, self-efficacy, preparedness, decisional conflict, and decisions to participate in a cancer clinical trial. Psycho-oncology, 22(3):481-9, 2013. PMC3374030
    10. Gowrishankar B, Ibragimova I, Zhou Y, Slifker MJ, Devarajan K, Al-Saleem T, Uzzo RG, Cairns P. MicroRNA expression signatures of stage, grade, and progression in clear cell RCC. Cancer biology & therapy, 15(3):2013 Dec 18, 2013.
    11. Fernandez SV, Robertson FM, Pei J, Aburto-Chumpitaz L, Mu Z, Chu K, Alpaugh RK, Huang Y, Cao Y, Ye Z, Cai KQ, Boley KM, Klein-Szanto AJ, Devarajan K, Addya S, Cristofanilli M. Inflammatory breast cancer (IBC): clues for targeted therapies. Breast cancer research and treatment, 140(1):23-33, 2013.
    12. Comunale MA, Wang M, Anbarasan N, Betesh L, Karabudak A, Moritz E, Devarajan K, Marrero J, Block TM, Mehta A. Total serum glycan analysis is superior to lectin-FLISA for the early detection of hepatocellular carcinoma. Proteomics Clinical applications, 2013 Jul 16:[epub ahead of print], 2013.
    13. Chen KT, Devarajan K, Milestone BN, Cooper HS, Denlinger C, Cohen SJ, Meyer JE, Hoffman JP. Neoadjuvant Chemoradiation and Duration of Chemotherapy Before Surgical Resection for Pancreatic Cancer: Does Time Interval Between Radiotherapy and Surgery Matter? Annals of surgical oncology, 2013 Nov 26:[Epub ahead of print], 2013.
    14. Anastassiadis T, Duong-Ly KC, Deacon SW, Lafontant A, Ma H, Devarajan K, Dunbrack RL, Jr., Wu J, Peterson JR. A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an extracellular signal-regulated kinase (ERK) inhibitor. The Journal of biological chemistry, 288(39):28068-77, 2013. PMC3784719
    15. Zaorsky NG, Li T, Devarajan K, Horwitz EM, Buyyounouski MK. Assessment of the American Joint Committee on Cancer staging (sixth and seventh editions) for clinically localized prostate cancer treated with external beam radiotherapy and comparison with the National Comprehensive Cancer Network risk-stratification method. Cancer, 118(22):5535-43, 2012. PMC3410044
    16. Wang M, Block TM, Marrero J, Di Bisceglie AM, Devarajan K, Mehta A. Improved biomarker performance for the detection of hepatocellular carcinoma by inclusion of clinical parameters. Proceedings IEEE International Conference on Bioinformatics and Biomedicine, 2012:doi: 10.1109/BIBM.2012.6392612, 2012. PMC3845221
    17. Patel SA, Sandberg LJ, Ranganath B, Devarajan K, Toto J, Topham NS. Impact of Adjuvant Chemotherapy on Abdominal Wall Hernias and Bulges After Muscle-Sparing Free TRAM Flaps for Breast Reconstruction. Annals of plastic surgery, 2012 Dec 18:[Epub ahead of print], 2012.
    18. Jiang Z, Zhou Y, Devarajan K, Slater CM, Daly MB, Chen X. Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis. Frontiers in genetics, 3:299, 2012. PMC3528021
    19. Gao C, Devarajan K, Zhou Y, Slater CM, Daly MB, Chen X. Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome. BMC genomics, 13:570, 2012. PMC3532379
    20. Devarajan K, Wang G, Ebrahimi N. (2011). A unified approach to non-negative matrix factorization and probabilistic latent semantic indexing, COBRA pre-print series, Working Paper 80. http://biostats.bepress.com/cobra/art80.
    21. 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, 17(1):41-53, 2012. PMC3257821
    22. Shatalova EG, Klein-Szanto AJ, Devarajan K, Cukierman E, Clapper ML. Estrogen and cytochrome P450 1B1 contribute to both early- and late-stage head and neck carcinogenesis. Cancer prevention research (Philadelphia, Pa), 4(1):107-15, 2011. PMC3043603
    23. Sasaroli D, Gimotty PA, Pathak HB, Hammond R, Kougioumtzidou E, Katsaros D, Buckanovich R, Devarajan K, Sandaltzopoulos R, Godwin AK, Scholler N, Coukos G. Novel surface targets and serum biomarkers from the ovarian cancer vasculature. Cancer biology & therapy, 12(3):169-80, 2011. PMC3230481
    24. Makhlin I, Zhang J, Long CJ, Devarajan K, Zhou Y, Klein-Szanto AJ, Huang M, Chernoff J, Boorjian SA. The mTOR pathway affects proliferation and chemosensitivity of urothelial carcinoma cells and is upregulated in a subset of human bladder cancers. BJU international, 108(2 Pt 2):E84-90, 2011. PMC3116980
    25. Gupta V, Bassi DE, Simons JD, Devarajan K, Al-Saleem T, Uzzo RG, Cukierman E. Elevated expression of stromal palladin predicts poor clinical outcome in renal cell carcinoma. PloS one, 6(6):e21494, 2011. PMC3125241
    26. Frank AK, Leu JI, Zhou Y, Devarajan K, Nedelko T, Klein-Szanto A, Hollstein M, Murphy ME. The codon 72 polymorphism of p53 regulates interaction with NF-{kappa}B and transactivation of genes involved in immunity and inflammation. Molecular and cellular biology, 31(6):1201-13, 2011. PMC3067895
    27. Devarajan K, Ebrahimi N. A semi-parametric generalization of the Cox proportional hazards regression model: Inference and Applications. Computational statistics & data analysis, 55(1):667-76, 2011. PMC2976538
    28. 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. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell, 146(1):67-79, 2011. PMC3230223
    29. Clapper ML, Hensley HH, Chang WC, Devarajan K, Nguyen MT, Cooper HS. Detection of colorectal adenomas using a bioactivatable probe specific for matrix metalloproteinase activity. Neoplasia (New York, NY), 13(8):685-91, 2011. PMC3156659
    30. Anastassiadis T, Deacon SW, Devarajan K, Ma H, Peterson JR. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nature biotechnology, 29(11):1039-45, 2011. PMC3230241
    31. 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. Early changes in gene expression induced by tobacco smoke: Evidence for the importance of estrogen within lung tissue. Cancer prevention research (Philadelphia, Pa), 3(6):707-17, 2010. PMC2896420
    32. Devarajan K, Zhou Y, Chachra N, Ebrahimi N. A supervised approach for predicting patient survival with gene expression data. Proceedings / Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE) IEEE International Symposium on Bioinformatics and Bioengineering, 2010(5521718):26-31, 2010. PMC2941901
    33. 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. Altered gene expression in morphologically normal epithelial cells from heterozygous carriers of BRCA1 or BRCA2 mutations. Cancer prevention research (Philadelphia, Pa), 3(1):48-61, 2010. PMC2804937
    34. 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. Synthetic lethal screen of an EGFR-centered network to improve targeted therapies. Science signaling, 3(140):ra67, 2010. PMC2950064
    35. Schilder RJ, Pathak HB, Lokshin AE, Holloway RW, Alvarez RD, Aghajanian C, Min H, Devarajan K, Ross E, Drescher CW, Godwin AK. 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. Gynecologic oncology, 113(1):21-7, 2009. PMC2741166
    36. Hensley HH, Merkel CE, Chang WC, Devarajan K, Cooper HS, Clapper ML. Endoscopic imaging and size estimation of colorectal adenomas in the multiple intestinal neoplasia mouse. Gastrointestinal endoscopy, 69(3 Pt 2):742-9, 2009. PMC2821747
    37. Fang CY, Cherry C, Devarajan K, Li T, Malick J, Daly MB. A prospective study of quality of life among women undergoing risk-reducing salpingo-oophorectomy versus gynecologic screening for ovarian cancer. Gynecologic oncology, 112(3):594-600, 2009. PMC2697574
    38. Devarajan K, Ebrahimi N. Testing for Covariate Effect in the Cox Proportional Hazards Regression Model. Communications in statistics: theory and methods, 38(14):2333-47, 2009. PMC2802211
    39. Shimizu I, Jellinek NJ, Dufresne RG, Li T, Devarajan K, Perlis C. Multiple antithrombotic agents increase the risk of postoperative hemorrhage in dermatologic surgery. Journal of the American Academy of Dermatology, 58(5):810-6, 2008.
    40. Devarajan K. Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. PLoS computational biology, 4(7):e1000029, 2008. PMC2447881
    41. Devarajan K, Ebrahimi N. (2008). Class discovery via nonnegative matrix factorization, American Journal of Mathematical and Management Sciences, 28(3&4): 457-467.
    42. Clapper ML, Gary MA, Coudry RA, Litwin S, Chang WC, Devarajan K, Lubet RA, Cooper HS. 5-aminosalicylic acid inhibits colitis-associated colorectal dysplasias in the mouse model of azoxymethane/dextran sulfate sodium-induced colitis. Inflammatory bowel diseases, 14(10):1341-7, 2008.
    43. Caretti E, Devarajan K, Coudry R, Ross E, Clapper ML, Cooper HS, Bellacosa A. Comparison of RNA amplification methods and chip platforms for microarray analysis of samples processed by laser capture microdissection. Journal of cellular biochemistry, 103(2):556-63, 2008.
    44. Rennefahrt UE, Deacon SW, Parker SA, Devarajan K, Beeser A, Chernoff J, Knapp S, Turk BE, Peterson JR. Specificity profiling of Pak kinases allows identification of novel phosphorylation sites. The Journal of biological chemistry, 282(21):15667-78, 2007.
    45. Cai KQ, Klein-Szanto A, Karthik D, Edelson M, Daly MB, Ozols RF, Lynch HT, Godwin AK, Xu XX. Age-dependent morphological alterations of human ovaries from populations with and without BRCA mutations. Gynecologic oncology, 103(2):719-28, 2006.
    46. Altomare DA, Vaslet CA, Skele KL, De Rienzo A, Devarajan K, Jhanwar SC, McClatchey AI, Kane AB, Testa JR. A mouse model recapitulating molecular features of human mesothelioma. Cancer research, 65(18):8090-5, 2005.
    47. Devarajan K, Ebrahimi N. (2000). The maximum penalized likelihood approach using nonhomogeneous Poisson processes for software reliability and reliability growth models, Applied Statistical Science V, 63-76, Nova Science Publishers, New York. 48. Devarajan K, Ebrahimi N. (2001). Goodness of fit testing for the Cox proportional hazards model, Goodness-of-Fit Tests and Model Validity, Statistics for Industry and Technology, 235-251, Birkhauser Publishers, Boston.
    48. Devarajan K, Ebrahimi N. A nonparametric approach to accelerated life testing under multiple stresses. Naval Research Logistics, 45(6):629-44, 1998.
    49. BOOK CHAPTERS & OTHER PUBLICATIONS
    50. Devarajan K. (2011). Matrix and Tensor Decompositions, Problem Solving Handbook in Computational Biology and Bioinformatics, Part 5, 291-318, DOI: 10.1007/978-0-387-09760-2_14.
    51. Devarajan K. (2006). Nonnegative matrix factorization – A new paradigm in large-scale biological data analysis, Proceedings of the Joint Statistical Meetings, Seattle, Washington (CD-ROM)