Sudhir Varma

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Bias in error estimation when using cross-validation for model selection
    Sudhir Varma
    Biometric Research Branch, National Cancer Institute, Bethesda, MD, USA
    BMC Bioinformatics 7:91. 2006
  2. pmc High recombination rates and hotspots in a Plasmodium falciparum genetic cross
    Hongying Jiang
    Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Genome Biol 12:R33. 2011
  3. pmc Iterative class discovery and feature selection using Minimal Spanning Trees
    Sudhir Varma
    Biometric Research Branch, National Cancer Institute, Rockville, USA
    BMC Bioinformatics 5:126. 2004
  4. pmc Transcription poisoning by Topoisomerase I is controlled by gene length, splice sites, and miR-142-3p
    Stéphanie Solier
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute NIH Center for Advancing Translational Sciences, Bethesda, MD 20892 4255, USA
    Cancer Res 73:4830-9. 2013
  5. pmc Clinical relevance of multidrug resistance gene expression in ovarian serous carcinoma effusions
    Jean Pierre Gillet
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
    Mol Pharm 8:2080-8. 2011
  6. pmc DNA fingerprinting of the NCI-60 cell line panel
    Philip L Lorenzi
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    Mol Cancer Ther 8:713-24. 2009
  7. pmc Multidrug resistance-linked gene signature predicts overall survival of patients with primary ovarian serous carcinoma
    Jean Pierre Gillet
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Clin Cancer Res 18:3197-206. 2012
  8. pmc CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set
    William C Reinhold
    Laboratory of Molecular Pharmacology, CCR, National Cancer Institute, NIH, Bethesda, Maryland, USA
    Cancer Res 72:3499-511. 2012
  9. pmc Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors
    Stéphanie Solier
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 4255, USA
    Cancer Res 70:8055-65. 2010
  10. pmc The clinical relevance of cancer cell lines
    Jean Pierre Gillet
    Laboratory of Cell Biology, National Cancer Institute, 37 Convent Dr, Rm 2108, Bethesda, MD 20892, USA
    J Natl Cancer Inst 105:452-8. 2013

Detail Information

Publications33

  1. pmc Bias in error estimation when using cross-validation for model selection
    Sudhir Varma
    Biometric Research Branch, National Cancer Institute, Bethesda, MD, USA
    BMC Bioinformatics 7:91. 2006
    ..We have evaluated the validity of using the CV error estimate of the optimized classifier as an estimate of the true error expected on independent data...
  2. pmc High recombination rates and hotspots in a Plasmodium falciparum genetic cross
    Hongying Jiang
    Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Genome Biol 12:R33. 2011
    ..A better understanding of these mechanisms may provide important information for studying parasite evolution, immune evasion and drug resistance...
  3. pmc Iterative class discovery and feature selection using Minimal Spanning Trees
    Sudhir Varma
    Biometric Research Branch, National Cancer Institute, Rockville, USA
    BMC Bioinformatics 5:126. 2004
    ..This has the effect of obscuring clustering in samples that may be evident only when looking at a subset of genes, because noise from irrelevant genes dominates the signal from the relevant genes in the distance calculation...
  4. pmc Transcription poisoning by Topoisomerase I is controlled by gene length, splice sites, and miR-142-3p
    Stéphanie Solier
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute NIH Center for Advancing Translational Sciences, Bethesda, MD 20892 4255, USA
    Cancer Res 73:4830-9. 2013
    ..Our study shows the profound impact of Top1cc on transcription elongation, especially at intron-exon junctions and on transcript stability by microRNA miR-142-3p upregulation...
  5. pmc Clinical relevance of multidrug resistance gene expression in ovarian serous carcinoma effusions
    Jean Pierre Gillet
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
    Mol Pharm 8:2080-8. 2011
    ..This pilot study highlights two new gene signatures that may help in optimizing the treatment for ovarian carcinoma patients with effusions...
  6. pmc DNA fingerprinting of the NCI-60 cell line panel
    Philip L Lorenzi
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    Mol Cancer Ther 8:713-24. 2009
    ..As expected, DNA fingerprints were not able to distinguish different tissues-of-origin. The fingerprints serve principally as a barcodes...
  7. pmc Multidrug resistance-linked gene signature predicts overall survival of patients with primary ovarian serous carcinoma
    Jean Pierre Gillet
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Clin Cancer Res 18:3197-206. 2012
    ..The scope of this research differs substantially from that of previous reports, as a very large set of genes was evaluated whose expression has been shown to affect response to chemotherapy...
  8. pmc CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set
    William C Reinhold
    Laboratory of Molecular Pharmacology, CCR, National Cancer Institute, NIH, Bethesda, Maryland, USA
    Cancer Res 72:3499-511. 2012
    ..CellMiner greatly broadens applications of the extensive NCI-60 database for discovery by creating web-based processes that are rapid, flexible, and readily applied by users without bioinformatics expertise...
  9. pmc Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors
    Stéphanie Solier
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 4255, USA
    Cancer Res 70:8055-65. 2010
    ..The preferential effect of CPT on genes encoding splicing factors may explain the abnormal splicing of a large number of genes in response to Top1cc...
  10. pmc The clinical relevance of cancer cell lines
    Jean Pierre Gillet
    Laboratory of Cell Biology, National Cancer Institute, 37 Convent Dr, Rm 2108, Bethesda, MD 20892, USA
    J Natl Cancer Inst 105:452-8. 2013
    ..However, the success stories should not obscure the growing body of data that motivates us to develop new in vitro preclinical models that would substantially increase the success rate of new in vitro-assessed cancer treatments...
  11. pmc Putative DNA/RNA helicase Schlafen-11 (SLFN11) sensitizes cancer cells to DNA-damaging agents
    Gabriele Zoppoli
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 109:15030-5. 2012
    ....
  12. pmc Redefining the relevance of established cancer cell lines to the study of mechanisms of clinical anti-cancer drug resistance
    Jean Pierre Gillet
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 108:18708-13. 2011
    ....
  13. pmc Asparagine synthetase is a predictive biomarker of L-asparaginase activity in ovarian cancer cell lines
    Philip L Lorenzi
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
    Mol Cancer Ther 7:3123-8. 2008
    ..These findings provide rationale for evaluation of ASNS protein expression as a predictive biomarker of clinical L-ASP activity in ovarian cancer...
  14. pmc CellMiner: a relational database and query tool for the NCI-60 cancer cell lines
    Uma T Shankavaram
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Centre for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
    BMC Genomics 10:277. 2009
    ..S. National Cancer Institute to screen compounds for anticancer activity. To our knowledge, CellMiner is the first online database resource for integration of the diverse molecular types of NCI-60 and related meta data...
  15. pmc A Gene Expression Signature Associated with Overall Survival in Patients with Hepatocellular Carcinoma Suggests a New Treatment Strategy
    Jean Pierre Gillet
    Laboratory of Cell Biology J P G, J P M, C P W, A M C, S V A, M M G and Laboratory of Experimental Carcinogenesis J B A, S S T, Center for Cancer Research, National Cancer Institute, and Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases S V, National Institutes of Health, Bethesda, Maryland and the Viral Technologies Group and Molecular Detection Group, Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Marylanld R K B, K P, W E B
    Mol Pharmacol 89:263-72. 2016
    ..This approach also increases sensitization of HCC cells toward conventional chemotherapeutic agents. This work suggests new treatment strategies for a disease for which few therapeutic options exist. ..
  16. pmc Alterations of DNA repair genes in the NCI-60 cell lines and their predictive value for anticancer drug activity
    Fabricio G Sousa
    Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA Centro de Estudos em Células Tronco, Terapia Celular e Genética Toxicológica, Programa de Pós graduação em Farmácia, Universidade Federal de Mato Grosso do Sul, Campo Grande 79070 900, MS, Brazil
    DNA Repair (Amst) 28:107-15. 2015
    ..Therefore, we propose new rational uses for existing anticancer drugs based on a comprehensive analysis of DNAR genomic parameters. ..
  17. pmc NCI-60 whole exome sequencing and pharmacological CellMiner analyses
    William C Reinhold
    Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 9:e101670. 2014
    ..The new tools are implemented as an updated web-based CellMiner version, for which the present publication serves as a compendium. ..
  18. pmc High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner
    Sudhir Varma
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America HiThru Analytics LLC, Laurel, Maryland, United States of America
    PLoS ONE 9:e92047. 2014
    ..Limiting attention to focal DNA gains or losses, we identify and reveal novel candidate tumor suppressors with matching alterations in transcript level. ..
  19. pmc Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database
    Josiah N Orina
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 4256, USA
    Mol Cancer Ther 8:2057-66. 2009
    ..This study also led to an improved database by revealing previously unidentified substrates for ABCB1, ABCC1, and ABCG2, transporters that contribute to MDR...
  20. pmc Microarray-based analysis of differential gene expression between infective and noninfective larvae of Strongyloides stercoralis
    Roshan Ramanathan
    Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Negl Trop Dis 5:e1039. 2011
    ..DNA microarrays were developed and utilized for this purpose...
  21. pmc Multidrug resistance in relapsed acute myeloid leukemia: evidence of biological heterogeneity
    Chirayu Patel
    Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cancer 119:3076-83. 2013
    ..Most clinical trials evaluating the strategy of inhibiting efflux-mediated chemotherapeutic resistance have been unsuccessful, clearly indicating the need for a better approach...
  22. pmc Regulation and expression of the ATP-binding cassette transporter ABCG2 in human embryonic stem cells
    Raji Padmanabhan
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Stem Cells 30:2175-87. 2012
    ..Our findings clarify the controversy regarding the expression of the ABCG2 gene and also provide new insights into translational control of the expression of membrane transporter mRNAs by miRNAs in hESCs...
  23. pmc Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
    Jeff Skinner
    Bioinformatics and Computational Biosciences Branch BCBB, Office of Cyber Infrastructure and Computational Biology OCICB, National Institute of Allergy and Infectious Disease NIAID, National Institutes if Health NIH, Bethesda, Maryland, USA
    BMC Bioinformatics 12:286. 2011
    ..DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes...
  24. pmc Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer
    William C Reinhold
    Developmental Therapeutic Branch, Center for Cancer Research, NCI, NIH, 9000 Rockville Pike, Building 37, room 5041, Bethesda, MD, 20892, USA
    Hum Genet 134:3-11. 2015
    ..The ultimate goal is to provide a paradigm shift in the way that drugs are selected to provide a more targeted and efficacious outcome for the patient. ..
  25. pmc Effectiveness of gene expression profiling for response prediction of rectal adenocarcinomas to preoperative chemoradiotherapy
    B Michael Ghadimi
    Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bldg 50, Rm 1408, 50 South Dr, Bethesda, MD 20892 8010, USA
    J Clin Oncol 23:1826-38. 2005
    ..This study aimed to investigate whether parallel gene expression profiling of the primary tumor can contribute to stratification of patients into groups of responders or nonresponders...
  26. pmc Circulating cortisol-associated signature of glucocorticoid-related gene expression in subcutaneous fat of obese subjects
    Maria G Pavlatou
    Unit on Molecular Hormone Action, Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Obesity (Silver Spring) 21:960-7. 2013
    ..Serum cortisol concentrations fluctuate in a circadian fashion, and glucocorticoids exert strong effects on adipose tissue and induce obesity through the glucocorticoid receptor...
  27. pmc Regulation of global gene expression in human Loa loa infection is a function of chronicity
    Cathy Steel
    Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Negl Trop Dis 6:e1527. 2012
    ....
  28. pmc Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families
    Natalay Kouprina
    Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, MD, USA
    Genes Chromosomes Cancer 51:933-48. 2012
    ..Our results exclude the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy. Adjacent regions appear to be the most likely candidates to identify the elusive HPCX1 locus...
  29. pmc A new whole genome amplification method for studying clonal evolution patterns in malignant colorectal polyps
    Daniela Hirsch
    Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genes Chromosomes Cancer 51:490-500. 2012
    ..In addition to demonstrating the clonal origin of the adenoma and carcinoma part within a malignant polyp, the gain of chromosome arm 20q was an indicator for progression from adenoma to carcinoma...
  30. doi request reprint Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers
    Ellen V Stevens
    National Cancer Institute, Building 37, Room 5068, Bethesda, MD 20892, USA
    Mol Cancer Ther 7:10-8. 2008
    ..The work reported here provides motivation for larger proteomic studies with more cell types focused on potential biomarkers in additional pharmacologically pertinent pathways...
  31. doi request reprint Calculating confidence intervals for prediction error in microarray classification using resampling
    Wenyu Jiang
    Concordia University, Quebec, Canada
    Stat Appl Genet Mol Biol 7:Article8. 2008
    ..The method provides mildly conservative inference under all circumstances studied and outperforms the other methods in microarray applications with small to moderate sample sizes...
  32. pmc Aneuploidy-dependent massive deregulation of the cellular transcriptome and apparent divergence of the Wnt/beta-catenin signaling pathway in human rectal carcinomas
    Marian Grade
    Department of General Surgery, University Medical Center, Gottingen, Germany
    Cancer Res 66:267-82. 2006
    ....
  33. pmc Gene expression profiling reveals a massive, aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas
    Marian Grade
    Department of General Surgery, University Medical Center, Robert Koch Strasse 40, 37075 Gottingen, Germany
    Cancer Res 67:41-56. 2007
    ....