Karthik Devarajan

Summary

Affiliation: Fox Chase Cancer Center
Country: USA

Publications

  1. doi request reprint A Quasi-Likelihood Approach to Nonnegative Matrix Factorization
    Karthik Devarajan
    Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, U S A
    Neural Comput 28:1663-93. 2016
  2. pmc A supervised approach for predicting patient survival with gene expression data
    Karthik Devarajan
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, PA 19111
    Proc IEEE Int Symp Bioinformatics Bioeng 2010:26-31. 2010
  3. doi request reprint On nonnegative matrix factorization algorithms for signal-dependent noise with application to electromyography data
    Karthik Devarajan
    Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111, U S A
    Neural Comput 26:1128-68. 2014
  4. pmc Nonnegative matrix factorization: an analytical and interpretive tool in computational biology
    Karthik Devarajan
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    PLoS Comput Biol 4:e1000029. 2008
  5. pmc A randomized comparison of print and web communication on colorectal cancer screening
    David S Weinberg
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    JAMA Intern Med 173:122-9. 2013
  6. pmc Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome
    Chuan Gao
    Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    BMC Genomics 13:570. 2012
  7. pmc Estrogen and cytochrome P450 1B1 contribute to both early- and late-stage head and neck carcinogenesis
    Ekaterina G Shatalova
    Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Cancer Prev Res (Phila) 4:107-15. 2011
  8. pmc 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
    Russell J Schilder
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Gynecol Oncol 113:21-7. 2009
  9. doi request reprint 5-aminosalicylic acid inhibits colitis-associated colorectal dysplasias in the mouse model of azoxymethane/dextran sulfate sodium-induced colitis
    Margie L Clapper
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Inflamm Bowel Dis 14:1341-7. 2008
  10. pmc Endoscopic imaging and size estimation of colorectal adenomas in the multiple intestinal neoplasia mouse
    Harvey H Hensley
    Divisions of Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Gastrointest Endosc 69:742-9. 2009

Detail Information

Publications39

  1. doi request reprint A Quasi-Likelihood Approach to Nonnegative Matrix Factorization
    Karthik Devarajan
    Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, U S A
    Neural Comput 28:1663-93. 2016
    ..The proposed methods allow modeling of nonlinear effects using appropriate link functions and are illustrated using an application in biomedical signal processing. ..
  2. pmc A supervised approach for predicting patient survival with gene expression data
    Karthik Devarajan
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, PA 19111
    Proc IEEE Int Symp Bioinformatics Bioeng 2010:26-31. 2010
    ..Finally, we evaluate the performance of our methods using extensive simulation studies...
  3. doi request reprint On nonnegative matrix factorization algorithms for signal-dependent noise with application to electromyography data
    Karthik Devarajan
    Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111, U S A
    Neural Comput 26:1128-68. 2014
    ..Our methods are demonstrated using experimental data from electromyography studies, as well as simulated data in the extraction of muscle synergies, and compared with existing algorithms for signal-dependent noise...
  4. pmc Nonnegative matrix factorization: an analytical and interpretive tool in computational biology
    Karthik Devarajan
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    PLoS Comput Biol 4:e1000029. 2008
    ..In this paper, we review this method as a data analytical and interpretive tool in computational biology with an emphasis on these applications...
  5. pmc A randomized comparison of print and web communication on colorectal cancer screening
    David S Weinberg
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    JAMA Intern Med 173:122-9. 2013
    ..Evidence supports the efficacy of health communications that are targeted and tailored to improve the uptake of recommendations...
  6. pmc Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome
    Chuan Gao
    Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    BMC Genomics 13:570. 2012
    ....
  7. pmc Estrogen and cytochrome P450 1B1 contribute to both early- and late-stage head and neck carcinogenesis
    Ekaterina G Shatalova
    Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Cancer Prev Res (Phila) 4:107-15. 2011
    ..024 and 0.008, respectively). These data provide novel insight into the mechanisms underlying head and neck carcinogenesis and facilitate the identification of new targets for chemopreventive intervention...
  8. pmc 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
    Russell J Schilder
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Gynecol Oncol 113:21-7. 2009
    ..Determine if cetuximab dose escalation to induce grade 2 rash correlates with anti-tumor activity and if sera-based markers could predict likelihood of response...
  9. doi request reprint 5-aminosalicylic acid inhibits colitis-associated colorectal dysplasias in the mouse model of azoxymethane/dextran sulfate sodium-induced colitis
    Margie L Clapper
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Inflamm Bowel Dis 14:1341-7. 2008
    ..The chemopreventive activity of 5-ASA was evaluated in the Swiss Webster model of azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced colitis-associated neoplasia...
  10. pmc Endoscopic imaging and size estimation of colorectal adenomas in the multiple intestinal neoplasia mouse
    Harvey H Hensley
    Divisions of Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Gastrointest Endosc 69:742-9. 2009
    ..The scientific potential of animal models of carcinogenesis has not been fully realized because of our limited ability to monitor tumor growth in vivo...
  11. doi request reprint Haploinsufficiency in tumor predisposition syndromes: altered genomic transcription in morphologically normal cells heterozygous for VHL or TSC mutation
    Suraj Peri
    Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, USA
    Oncotarget . 2016
    ..The gene expression changes identified here are related to the metabolic basis of renal cancer and may constitute suitable targets for early intervention...
  12. pmc Kinase Inhibitor Profiling Reveals Unexpected Opportunities to Inhibit Disease-Associated Mutant Kinases
    Krisna C Duong-Ly
    Program in Cancer Biology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Cell Rep 14:772-81. 2016
    ..This study provides a resource for the development of inhibitors against numerous disease-associated mutant kinases and illustrates the potential of unbiased profiling as an approach to compound-centric inhibitor development...
  13. pmc Meta-analysis identifies NF-κB as a therapeutic target in renal cancer
    Suraj Peri
    Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e76746. 2013
    ..To determine the expression patterns of NF-κB regulators and target genes in clear cell renal cell carcinoma (ccRCC), their correlation with von Hippel Lindau (VHL) mutational status, and their association with survival outcomes...
  14. pmc Identifying a highly-aggressive DCIS subgroup by studying intra-individual DCIS heterogeneity among invasive breast cancer patients
    Dana Pape-Zambito
    Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 9:e100488. 2014
    ....
  15. doi request reprint Neoadjuvant chemoradiation and duration of chemotherapy before surgical resection for pancreatic cancer: does time interval between radiotherapy and surgery matter?
    Kathryn T Chen
    Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
    Ann Surg Oncol 21:662-9. 2014
    ..Using our database, we evaluated these relationships and the effect on overall and progression-free survival...
  16. pmc Early changes in gene expression induced by tobacco smoke: Evidence for the importance of estrogen within lung tissue
    Sibele I Meireles
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cancer Prev Res (Phila) 3:707-17. 2010
    ....
  17. ncbi request reprint The effect of total lymph nodes removed and the lymph node ratio on overall survival in resected pancreatic cancer
    Christina Wai
    Fox Chase Cancer Center, Philadelphia, PA
    J Clin Oncol 30:371. 2012
    ..In our study we sought to see if the total number of nodes removed and lymph node ratio (LNR) would influence overall survival...
  18. ncbi request reprint A pilot study evaluating peripheral blood lymphocyte telomere length in elderly versus young patients with colorectal cancer (CRC)
    Efrat Dotan
    Fox Chase Cancer Center, Philadelphia, PA
    J Clin Oncol 30:512. 2012
    ..512 Background: Telomere length (TL) is associated with aging as well as high cancer incidence. We conducted a pilot study to assess the TL of younger versus older (≥70 years) patients with CRC and its effect on survival...
  19. pmc Combination of Imatinib Mesylate and AKT Inhibitor Provides Synergistic Effects in Preclinical Study of Gastrointestinal Stromal Tumor
    Phillip Zook
    Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
    Clin Cancer Res . 2016
    ..Inhibiting additional molecular targets may provide more substantial disease control. Recent studies have implicated the PI3K/AKT pathway in the survival of imatinib mesylate-resistant GIST cell lines and tumors...
  20. pmc Altered gene expression in morphologically normal epithelial cells from heterozygous carriers of BRCA1 or BRCA2 mutations
    Alfonso Bellacosa
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cancer Prev Res (Phila) 3:48-61. 2010
    ....
  21. pmc Patterns of care and outcomes of older versus younger patients with metastatic pancreatic cancer: A Fox Chase Cancer Center experience
    Namrata Vijayvergia
    Deparment of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA Electronic address
    J Geriatr Oncol 6:454-61. 2015
    ....
  22. pmc Pharmacological profiling of kinase dependency in cell lines across triple-negative breast cancer subtypes
    Lauren S Fink
    Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
    Mol Cancer Ther 14:298-306. 2015
    ..Instead, we find that mutation status can be an effective predictor of sensitivity to inhibition of particular kinase pathways for subsets of TNBC...
  23. pmc Patterns of use and tolerance of anti-epidermal growth factor receptor antibodies in older adults with metastatic colorectal cancer
    Efrat Dotan
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA Electronic address
    Clin Colorectal Cancer 13:192-8. 2014
    ..We retrospectively reviewed our experience of treating elderly patients with mCRC with these agents between 2004 and 2011...
  24. doi request reprint Familiarity and self-reported compliance with American Urological Association best practice recommendations for use of thromboembolic prophylaxis among American Urological Association members
    Steve Sterious
    Division of Urologic Oncology, Department of Surgical Oncology, Fox Chase Cancer Center, Temple University School of Medicine, Philadelphia, Pennsylvania 19111, USA
    J Urol 190:992-8. 2013
    ....
  25. pmc The mTOR pathway affects proliferation and chemosensitivity of urothelial carcinoma cells and is upregulated in a subset of human bladder cancers
    Igor Makhlin
    Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
    BJU Int 108:E84-90. 2011
    ..To investigate whether mammalian target of rapamycin (mTOR) inhibition by rapamycin is therapeutically efficacious in combination with cisplatin for bladder cancer...
  26. pmc A prospective study of quality of life among women undergoing risk-reducing salpingo-oophorectomy versus gynecologic screening for ovarian cancer
    Carolyn Y Fang
    Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Gynecol Oncol 112:594-600. 2009
    ..The primary objective of the study was to prospectively assess quality of life (QOL) among women at increased risk of ovarian cancer who are undergoing risk-reducing salpingo-oophorectomy (RRSO) or serial screening...
  27. ncbi request reprint Revisiting the prognostic significance of positive peritoneal cytology in pancreatic cancer
    Kathryn T Chen
    Fox Chase Cancer Center, Philadelphia, PA Temple University Hospital, Philadelphia, PA
    J Clin Oncol 30:177. 2012
    ..We re-evaluate the role of PPC, with particular attention to outcomes following neoadjuvant therapy...
  28. ncbi request reprint ABO blood group and survival in pancreatic cancer
    Christina Wai
    Fox Chase Cancer Center, Philadelphia, PA
    J Clin Oncol 30:380. 2012
    ..Based on this finding, we were interested in seeing if a particular ABO blood group would have an impact on survival outcomes in pancreatic cancer...
  29. ncbi request reprint Assessment of the American Joint Committee on Cancer (6th and 7th editions) for clinically localized prostate cancer and comparison to the National Comprehensive Cancer Network risk stratification method
    Mark K Buyyounouski
    Fox Chase Cancer Center, Philadelphia, PA
    J Clin Oncol 30:23. 2012
    ..23 Background: The purpose was to compare the prognostic value of the AJCC staging version 6 (v6), version 7 (v7), and the risk-stratification model of the NCCN...
  30. pmc 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
    Theonie Anastassiadis
    From the Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
    J Biol Chem 288:28068-77. 2013
    ..These findings suggest a novel approach to polypharmacology in which two or more unrelated kinases are inhibited by a single compound that targets different conformations of each target kinase. ..
  31. pmc Potential prognostic biomarkers of pancreatic cancer
    Kathryn T Chen
    From the Department of Surgical Oncology, Developmental Therapeutics, and Departments of Biostatistics, Pathology, and Gastroenterology, Fox Chase Cancer Center, Philadelphia, PA
    Pancreas 43:22-7. 2014
    ..We evaluated whether pancreatic main duct fluid can provide protein biomarkers with prognostic value...
  32. pmc Build it, and will they come? Unexpected findings from a study on a Web-based intervention to improve colorectal cancer screening
    Linda Fleisher
    Fox Chase Cancer Center, 510 Township Line Road, Cheltenham, PA 19012, USA
    J Health Commun 17:41-53. 2012
    ..004). Among true users, most (81%) logged on once only. These findings raise questions about how to increase use of important health communication interventions...
  33. pmc Synthetic lethal screen of an EGFR-centered network to improve targeted therapies
    Igor Astsaturov
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Sci Signal 3:ra67. 2010
    ..Such a focused approach can potentially improve the coherent design of combination cancer therapies...
  34. pmc The codon 72 polymorphism of p53 regulates interaction with NF-{kappa}B and transactivation of genes involved in immunity and inflammation
    Amanda K Frank
    Fox Chase Cancer Center, W209, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Mol Cell Biol 31:1201-13. 2011
    ..Consistent with this, we show that P72 mice have a markedly enhanced response to inflammatory challenge compared to that of R72 mice. Our data indicate that the codon 72 polymorphism impacts p53's role in inflammation...
  35. pmc Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair
    Salvatore Cortellino
    Cancer Biology Program and Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cell 146:67-79. 2011
    ....
  36. pmc Elevated expression of stromal palladin predicts poor clinical outcome in renal cell carcinoma
    Vivekanand Gupta
    Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 6:e21494. 2011
    ..The clinical value of assessing RCC stromal activation merits further study...
  37. pmc Detection of colorectal adenomas using a bioactivatable probe specific for matrix metalloproteinase activity
    Margie L Clapper
    Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Neoplasia 13:685-91. 2011
    ..Use of this fluorescent probe in combination with colonoscopy could aid in preventing colorectal neoplasias by providing new opportunities for early detection and therapeutic intervention...
  38. ncbi request reprint A mouse model recapitulating molecular features of human mesothelioma
    Deborah A Altomare
    Human Genetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Cancer Res 65:8090-5. 2005
    ....
  39. ncbi request reprint Comparison of RNA amplification methods and chip platforms for microarray analysis of samples processed by laser capture microdissection
    Elena Caretti
    Human Genetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    J Cell Biochem 103:556-63. 2008
    ..986. The quicker NuGEN procedure, when coupled with X3P arrays, also yielded excellent results (correlation of 0.951). These observations will be useful for planning large-scale analyses of LCM-dissected clinical samples...