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

Original Articles

    1. Cheung, V.C.K., Devarajan, K., Severini, G., Turolla, A., Bonato, P. Decomposing time series data by a non-negative matrix factorization algorithm with temporally constrained coefficients. Proceedings (IEEE Int Conference in Engineering in Medicine and Biology) 2015.
    2. Zibelman M, Wong YN, Devarajan K, Malizzia L, Corrigan A, Olszanski AJ, Denlinger CS, Roethke SK, Tetzlaff CH, Plimack ER. Phase I study of the mTOR inhibitor ridaforolimus and the HDAC inhibitor vorinostat in advanced renal cell carcinoma and other solid tumors. Invest New Drugs. 2015 Jun 20. [Epub ahead of print] PMID: 26091915.
    3. Devarajan K, Wang G, Ebrahimi N. A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing. Mach Learn. 2015 Apr 1;99(1):137-163. PMID: 25821345; PMCID: PMC4371760. COBRA pre-print series, Article 80. (July 2011). http://biostats.bepress.com/cobra/art80.
    4. Chen KT, Devarajan K, Hoffman JP. Morbidity among long-term survivors after pancreatoduodenectomy for pancreatic adenocarcinoma. Ann Surg Oncol. 2015 Apr;22(4):1185-9. doi: 10.1245/s10434-014-3969-y. Epub 2014 Nov 11. PMID: 25384699.
    5. Fink LS, Beatty A, Devarajan K, Peri S, Peterson JR. Pharmacological profiling of kinase dependency in cell lines across triple-negative breast cancer subtypes. Mol Cancer Ther. 2015 Jan;14(1):298-306. doi: 10.1158/1535-7163.MCT-14-0529. Epub 2014 Oct 24. PMID: 25344583; PMCID: PMC4297247.
    6. Dotan E, Devarajan K, D'Silva AJ, Beck A, Kloth DD, Cohen SJ, Denlinger C. Patterns of use and tolerance of anti-epidermal growth factor receptor antibodies in older adults with metastatic colorectal cancer. Clin Colorectal Cancer. 2014 Sep;13(3):192-8. doi: 0.1016/j.clcc.2014.05.003. Epub 2014 Jun 26. PMID: 25074246; PMCID: PMC4162747.
    7. Pape-Zambito D, Jiang Z, Wu H, Devarajan K, Slater CM, Cai KQ, Patchefsky A, Daly MB, Chen X. Identifying a highly-aggressive DCIS subgroup by studying intra-individual DCIS heterogeneity among invasive breast cancer patients. PLoS One. 2014 Jun 30;9(6):e100488. doi: 10.1371/journal.pone.0100488. eCollection 2014. PMID: 24978026; PMCID: PMC4076240.
    8. Toto JM, Chang EI, Agag R, Devarajan K, Patel SA, Topham NS. Improved operative efficiency of free fibula flap mandible reconstruction with patient-specific, computer-guided preoperative planning. Head Neck. 2014 Jun 21. doi: 10.1002/hed.23815. [Epub ahead of print] PMID: 24954814.
    9. Freedman GM, Fowble BL, Li T, Hwang ES, Schechter N, Devarajan K, Anderson PR, Sigurdson ER, Goldstein LJ, Bleicher RJ. Risk of positive nonsentinel nodes in women with 1-2 positive sentinel nodes related to age and molecular subtype approximated by receptor status. Breast J. 2014 Jul-Aug;20(4):358-63. doi: 10.1111/tbj.12276. Epub 2014 May 26. PMID: 24861613; PMCID: PMC4472437.
    10. Devarajan K, Ebrahimi N. On penalized likelihood estimation for a non-proportional hazards regression model. Stat Probab Lett. 2013 Jul;83(7):1703-1710. PMID: 24791034; PMCID: PMC4001813.
    11. Hensley H, Devarajan K, Johnson JR, Piwnica-Worms D, Godwin AK, von Mehren M, Rink L. Evaluating new therapies in gastrointestinal stromal tumor using in vivo molecular optical imaging. Cancer Biol Ther. 2014 Jul;15(7):911-8. doi: 10.4161/cbt.28880. Epub 2014 Apr 22. PMID: 24755645; PMCID: PMC4100992.
    12. Devarajan K, Cheung VC. On nonnegative matrix factorization algorithms for signal-dependent noise with application to electromyography data. Neural Comput. 2014 Jun;26(6):1128-68. doi: 10.1162/NECO_a_00576. Epub 2014 Mar 31. PMID: 24684448.
    13. Wang M, 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 Med Genomics. 2013;6 Suppl 3:S9. doi: 10.1186/1755-8794-6-S3-S9. Epub 2013 Nov 11. Erratum in: BMC Med Genomics. 2013;6 Suppl 3:S11. PMID: 24564861; PMCID: PMC3980825.
    14. Dames DN, Blackman E, Butler R, Taioli E, Eckstein S, Devarajan K, Griffith-Bowe A, Gomez P, Ragin C; African Caribbean Cancer Consortium. High-risk cervical human papillomavirus infections among human immunodeficiency virus-positive women in the Bahamas. PLoS One. 2014 Jan 23;9(1):e85429. doi: 10.1371/journal.pone.0085429. eCollection 2014. PMID: 24465558; Central PMCID: PMC3900425.
    15. 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 Biol Ther. 2014 Mar 1;15(3):329-41. doi: 10.4161/cbt.27314. Epub 2013 Dec 18. PMID: 24351440; PMCID: PMC3974834.
    16. 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. 2014 Jan;43(1):22-7. doi: 10.1097/MPA.0b013e3182a6867e. PMID: 24326364; PMCID: PMC3859961.
    17. 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 Int Conf Bioinformatics Biomed). 2012 Dec;2012. doi: 10.1109/BIBM.2012.6392612. PMID: 24307972; PMCID: PMC3845221.
    18. 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? Ann Surg Oncol. 2014 Feb;21(2):662-9. doi: 10.1245/s10434-013-3396-5. Epub 2013 Nov 26. PMID: 24276638.
    19. Peri S, Devarajan K, Yang DH, Knudson AG, Balachandran S. Meta-analysis identifies NF-κB as a therapeutic target in renal cancer. PLoS One. 2013 Oct 7;8(10):e76746. doi: 10.1371/journal.pone.0076746. eCollection 2013. PMID: 24116146; PMCID: PMC3792024.
    20. 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. J Biol Chem. 2013 Sep 27;288(39):28068-77. doi: 10.1074/jbc.M113.505032. Epub 2013 Aug 9. PMID: 23935097; PMCID: PMC3784719.
    21. 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 Clin Appl. 2013 Oct;7(9-10):690-700. doi: 10.1002/prca.201200125. Epub 2013 Sep 13. PMID: 23857719.
    22. 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 Res Treat. 2013 Jul;140(1):23-33. doi: 10.1007/s10549-013-2600-4. Epub 2013 Jun 21. PMID: 23784380; Central PMCID: PMC4273486.
    23. 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. J Urol. 2013 Sep;190(3):992-8. doi: 10.1016/j.juro.2013.03.076. Epub 2013 Mar 26. PMID: 23538239.
    24. 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. Front Genet. 2012 Dec 21;3:299. doi: 10.3389/fgene.2012.00299. eCollection 2012. PMID: 23267367; PMCID: PMC3528021.
    25. 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. Ann Plast Surg. 2014 Jul;73(1):62-7. doi: 10.1097/SAP.0b013e31826c42a9. PMID: 23241806.
    26. 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. Psychooncology. 2013 Mar;22(3):481-9. doi: 10.1002/pon.3043. Epub 2012 Feb 14. PMID: 22331643; PMCID: PMC3374030.
    27. 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 Intern Med. 2013 Jan 28;173(2):122-9. doi: 10.1001/2013.jamainternmed.1017. PMID: 23128366; PMCID: PMC3615476.
    28. 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. 2012 Oct 30;13:570. doi: 10.1186/1471-2164-13-570. PMID: 23107584; PMCID: PMC3532379.
    29. 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. 2012 Nov 15;118(22):5535-43. doi: 10.1002/cncr.27597. Epub 2012 Apr 27. PMID: 22544661; PMCID: PMC3410044.
    30. 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. J Health Commun. 2012;17(1):41-53. doi: 10.1080/10810730.2011.571338. Epub 2011 Jun 22. PMID: 22217118; PMCID: PMC3257821.
    31. Anastassiadis T, Deacon SW, Devarajan K, Ma H, Peterson JR. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nat Biotechnol. 2011 Oct 30;29(11):1039-45. doi: 10.1038/nbt.2017. PMID: 22037377; PMCID: PMC3230241.
    32. 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. 2011 Aug;13(8):685-91. PMID: 21847360; PMCID: PMC3156659.
    33. 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. 2011;6(6):e21494. doi: 10.1371/journal.pone.0021494. Epub 2011 Jun 28. PMID: 21738681; PMCID: PMC3125241.
    34. 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. 2011 Jul 8;146(1):67-79. doi: 10.1016/j.cell.2011.06.020. Epub 2011 Jun 30. PMID: 21722948; PMCID: PMC3230223.
    35. 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 Biol Ther. 2011 Aug 1;12(3):169-80. Epub 2011 Aug 1. PMID: 21617380; PMCID: PMC3230481.
    36. 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. Mol Cell Biol. 2011 Mar;31(6):1201-13. doi: 10.1128/MCB.01136-10. Epub 2011 Jan 18. PMID: 21245379; PMCID: PMC3067895.
    37. 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 Prev Res (Phila). 2011 Jan;4(1):107-15. doi: 10.1158/1940-6207.CAPR-10-0133. Epub 2012 Dec 31. PMID: 21205741; Central PMCID: PMC3043603.
    38. Devarajan K, Ebrahimi N. A semi-parametric generalization of the Cox proportional hazards regression model: Inference and Applications. Comput Stat Data Anal. 2011 Jan 1;55(1):667-676. PMID: 21076652; PMCID: PMC2976538.
    39. 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 Int. 2011 Jul;108(2 Pt 2):E84-90. doi: 10.1111/j.1464-410X.2010.09844.x. Epub 2010 Nov 2. PMID: 21050361; Central PMCID: PMC3116980.
    40. Devarajan K, Zhou Y, Chachra N, Ebrahimi N. A supervised approach for predicting patient survival with gene expression data. Proc IEEE Int Symp Bioinformatics Bioeng. 2010;2010(5521718):26-31. PMID: 20865131; PMCID: PMC2941901.
    41. 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. Sci Signal. 2010 Sep 21;3(140):ra67. doi: 10.1126/scisignal.2001083. PMID: 20858866; PMCID: PMC2950064.
    42. 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 Prev Res (Phila). 2010 Jun;3(6):707-17. doi: 10.1158/1940-6207.CAPR-09-0162. Epub 2010 Jun 1. PMID: 20515954; PMCID: PMC2896420.
    43. Devarajan K, Ebrahimi N. Testing for Covariate Effect in the Cox Proportional Hazards Regression Model. Commun Stat Theory Methods. 2009 Jan 1;38(14):2333-2347. PMID: 20054448; PMCID: PMC2802211.
    44. 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 Prev Res (Phila). 2010 Jan;3(1):48-61. doi: 10.1158/1940-6207.CAPR-09-0078. PMID: 20051372; PMCID: PMC2804937.
    45. 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. Gastrointest Endosc. 2009 Mar;69(3 Pt 2):742-9. doi: 10.1016/j.gie.2008.09.054. PMID: 19251020; PMCID: PMC2821747.
    46. 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. Gynecol Oncol. 2009 Apr;113(1):21-7. doi: 10.1016/j.ygyno.2008.12.003. Epub 2009 Jan 21. PMID: 19162309; PMCID: PMC2741166.
    47. 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. Gynecol Oncol. 2009 Mar;112(3):594-600. doi: 10.1016/j.ygyno.2008.11.039. Epub 2009 Jan 13. PMID: 19141360; PMCID: PMC2697574.
    48. Devarajan K. Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. PLoS Comput Biol. 2008 Jul 25;4(7):e1000029. doi: 10.1371/journal.pcbi.1000029. Review. PMID: 18654623; PMCID: PMC2447881.
    49. 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. Inflamm Bowel Dis. 2008 Oct;14(10):1341-7. doi: 10.1002/ibd.20489. PMID: 18452197.
    50. Shimizu I, Jellinek NJ, Dufresne RG, Li T, Devarajan K, Perlis C. Multiple antithrombotic agents increase the risk of postoperative hemorrhage in dermatologic surgery. J Am Acad Dermatol. 2008 May;58(5):810-6. doi: 10.1016/j.jaad.2008.01.014. PMID: 18423258.
    51. Devarajan K, Ebrahimi N. Class discovery via nonnegative matrix factorization, American Journal of Mathematical and Management Sciences, 28(3&4): 457-467, 2008.
    52. 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. J Cell Biochem. 2008 Feb 1;103(2):556-63. PMID: 17546586.
    53. 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. J Biol Chem. 2007 May 25;282(21):15667-78. Epub 2007 Mar 28. PMID: 17392278.
    54. 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. Gynecol Oncol. 2006 Nov;103(2):719-28. Epub 2006 May 12. PMID: 16698071.
    55. 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 Res. 2005 Sep 15;65(18):8090-5. PMID: 16166281.
    56. 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.
    57. 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.
    58. Devarajan K, Ebrahimi N. A nonparametric approach to accelerated life testing under multiple stresses. Naval Research Logistics, 45(6):629-44, 1998.
    60. 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.
    61. 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).