John N Weinstein

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Transcriptomic analysis of the NCI-60 cancer cell lines
    John N Weinstein
    Laboratory of Molecular Pharmacology, Center for Cancer Research, US National Cancer Institute, NIH, Department of Health and Human Services, 9000 Rockville Pike, Bethesda, MD 20892, USA
    C R Biol 326:909-20. 2003
  2. ncbi request reprint Integromic analysis of the NCI-60 cancer cell lines
    John N Weinstein
    Laboratory of Molecular Pharmacology, Center for Cancer Research, US National Cancer Institute, NIH, Department of Health and Human Services, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Breast Dis 19:11-22. 2004
  3. pmc Three microarray platforms: an analysis of their concordance in profiling gene expression
    David Petersen
    Advanced Technology Center, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD 20877, USA
    BMC Genomics 6:63. 2005
  4. ncbi request reprint 'Omic' and hypothesis-driven research in the molecular pharmacology of cancer
    John N Weinstein
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, US National Cancer Institute, Building 37 Room 5068, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
    Curr Opin Pharmacol 2:361-5. 2002
  5. ncbi request reprint Asparagine synthetase as a causal, predictive biomarker for L-asparaginase activity in ovarian cancer cells
    Philip L Lorenzi
    Genomics and Bioinformatics Group, Room 5056B, 37 Convent Drive, Bethesda, MD 20892, USA
    Mol Cancer Ther 5:2613-23. 2006
  6. 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
  7. ncbi request reprint Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study
    Uma T Shankavaram
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute NIH, Bethesda, MD 20892, USA
    Mol Cancer Ther 6:820-32. 2007
  8. pmc mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities
    Hongfang Liu
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Mol Cancer Ther 9:1080-91. 2010
  9. pmc Multifactorial regulation of E-cadherin expression: an integrative study
    William C Reinhold
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Mol Cancer Ther 9:1-16. 2010
  10. pmc Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel
    Kimberly J Bussey
    Laboratory of Molecular Pharmacology, National Cancer Institute, Building 37, Room 5056, NIH, MSC 4255, 9000 Rockville Pike, Bethesda, MD 20892 4255, USA
    Mol Cancer Ther 5:853-67. 2006

Detail Information

Publications81

  1. ncbi request reprint Transcriptomic analysis of the NCI-60 cancer cell lines
    John N Weinstein
    Laboratory of Molecular Pharmacology, Center for Cancer Research, US National Cancer Institute, NIH, Department of Health and Human Services, 9000 Rockville Pike, Bethesda, MD 20892, USA
    C R Biol 326:909-20. 2003
    ..We discuss conceptual and experimental aspects of the profiling, as well as a number of bioinformatic computer programs that we have developed for biological interpretation of the profiles...
  2. ncbi request reprint Integromic analysis of the NCI-60 cancer cell lines
    John N Weinstein
    Laboratory of Molecular Pharmacology, Center for Cancer Research, US National Cancer Institute, NIH, Department of Health and Human Services, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Breast Dis 19:11-22. 2004
    ..As briefly reviewed here, we have used the combination of NCI-60 data types to identify markers for distinguishing tumor types and to obtain pharmacogenomic clues for possible individualization of a cancer therapy...
  3. pmc Three microarray platforms: an analysis of their concordance in profiling gene expression
    David Petersen
    Advanced Technology Center, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD 20877, USA
    BMC Genomics 6:63. 2005
    ..As part of a validation study for the long oligonucleotide arrays, we compared and contrasted expression profiles from the three formats, testing RNA from six different cell lines against a universal reference standard...
  4. ncbi request reprint 'Omic' and hypothesis-driven research in the molecular pharmacology of cancer
    John N Weinstein
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, US National Cancer Institute, Building 37 Room 5068, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
    Curr Opin Pharmacol 2:361-5. 2002
    ..The two modes of research are complementary and synergistic. The twin complexities of cancer biology and drug discovery demand such synergy as a basis for the next generation of oncopharmacomic research...
  5. ncbi request reprint Asparagine synthetase as a causal, predictive biomarker for L-asparaginase activity in ovarian cancer cells
    Philip L Lorenzi
    Genomics and Bioinformatics Group, Room 5056B, 37 Convent Drive, Bethesda, MD 20892, USA
    Mol Cancer Ther 5:2613-23. 2006
    ..Overall, this pharmacogenomic/pharmacoproteomic study suggests the use of l-ASP for treatment of a subset of ovarian cancers (and perhaps other tumor types), with ASNS as a biomarker for patient selection...
  6. 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...
  7. ncbi request reprint Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study
    Uma T Shankavaram
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute NIH, Bethesda, MD 20892, USA
    Mol Cancer Ther 6:820-32. 2007
    ..71). Because the transcript-based technologies are more mature and are currently able to assess larger numbers of genes at one time, they continue to be useful, even when the ultimate aim is information about proteins...
  8. pmc mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities
    Hongfang Liu
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Mol Cancer Ther 9:1080-91. 2010
    ..The data sets presented here will facilitate the identification of groups of mRNAs, microRNAs, and drugs that potentially affect and interact with one another...
  9. pmc Multifactorial regulation of E-cadherin expression: an integrative study
    William C Reinhold
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Mol Cancer Ther 9:1-16. 2010
    ..Finally, levels of cellular E-cad expression are associated with levels of cell-cell adhesion and response to drug treatment...
  10. pmc Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel
    Kimberly J Bussey
    Laboratory of Molecular Pharmacology, National Cancer Institute, Building 37, Room 5056, NIH, MSC 4255, 9000 Rockville Pike, Bethesda, MD 20892 4255, USA
    Mol Cancer Ther 5:853-67. 2006
    ..The DNA copy number database presented here will enable other investigators to explore DNA transcript-drug relationships in their own domains of research focus...
  11. pmc Chromosomal instability is associated with higher expression of genes implicated in epithelial-mesenchymal transition, cancer invasiveness, and metastasis and with lower expression of genes involved in cell cycle checkpoints, DNA repair, and chromatin mai
    Anna V Roschke
    Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20889 5105, USA
    Neoplasia 10:1222-30. 2008
    ..These same karyotypic features are negatively correlated with the expression of genes involved in cell cycle checkpoints, DNA repair, and chromatin maintenance...
  12. pmc SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies
    Michael C Ryan
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    BMC Bioinformatics 9:313. 2008
    ..In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant...
  13. 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...
  14. 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...
  15. 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...
  16. pmc High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Bioinformatics 6:168. 2005
    ..We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations...
  17. pmc AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies
    Sylvia M Major
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, USA
    BMC Bioinformatics 7:192. 2006
    ....
  18. ncbi request reprint Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells
    Gergely Szakacs
    Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
    Cancer Cell 6:129-37. 2004
    ..Unexpectedly, we also found and validated compounds whose activity is potentiated, rather than antagonized, by the MDR1 multidrug transporter. Such compounds may serve as leads for development...
  19. pmc Selective toxicity of NSC73306 in MDR1-positive cells as a new strategy to circumvent multidrug resistance in cancer
    Joseph A Ludwig
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
    Cancer Res 66:4808-15. 2006
    ..This article shows that NSC73306 kills cells with intrinsic or acquired P-gp-induced MDR and indirectly acts to eliminate resistance to MDR1 substrates...
  20. 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...
  21. ncbi request reprint Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling
    Satoshi Nishizuka
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, NIH, Bethesda, Maryland 20814, USA
    Cancer Res 63:5243-50. 2003
    ..The multistep process introduced here has the potential to produce additional markers for cancer diagnosis, prognosis, and therapy...
  22. ncbi request reprint AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
    Hongfang Liu
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 23:2385-90. 2007
    ..Otherwise, analysis and interpretation of an Affymetrix microarray experiment will be in error...
  23. ncbi request reprint Nonclassic functions of human topoisomerase I: genome-wide and pharmacologic analyses
    Ze Hong Miao
    Laboratories of Molecular Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
    Cancer Res 67:8752-61. 2007
    ..The reported cell lines and approaches described in this article provide new tools to perform detailed functional analyses related to Top1 function...
  24. pmc Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays
    Satoshi Nishizuka
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 100:14229-34. 2003
    ....
  25. ncbi request reprint Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells
    William C Reinhold
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Building 37, Room 5056, Bethesda, MD 20892 4255, USA
    Mol Cancer Ther 6:391-403. 2007
    ..As has been shown in recent years, DNA methylation status can serve as a biomarker for use in choosing therapy...
  26. pmc The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data
    Gabriel S Eichler
    Genomics and Bioinformatics Groups, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Biol 8:R187. 2007
    ..We also compare it with previously published algorithms, including Gene Set Enrichment Analysis. LeFE regularly identifies statistically significant functional themes consistent with known biology...
  27. pmc RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis
    Barry R Zeeberg
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Room 5068, Building 37, 37 Convent Drive, Bethesda, MD 20892, USA
    BMC Bioinformatics 12:52. 2011
    ..The redundancy might typically inflate the report of significant categories by a factor of three-fold, create an illusion of an overly long list of significant categories, and obscure the relevant biological interpretation...
  28. pmc Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intron
    William C Reinhold
    Laboratory of Molecular Pharmacology and Developmental Therapeutics Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20894, USA
    Cancer Res 70:2191-203. 2010
    ..The observations reported here suggest the hypothesis that there is a conserved negative transcription regulator within intron 1 of the TOP1 gene associated with a quadruplex-prone region...
  29. 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...
  30. pmc Profiling SLCO and SLC22 genes in the NCI-60 cancer cell lines to identify drug uptake transporters
    Mitsunori Okabe
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Mol Cancer Ther 7:3081-91. 2008
    ..Our results indicate that the gene expression database can be used to identify SLCO and SLC22 family members that confer sensitivity to cancer cells...
  31. pmc Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells
    Jae K Lee
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 8322, USA
    Genome Biol 4:R82. 2003
    ..Global concordance is parameterized by a 'correlation of correlations' coefficient...
  32. ncbi request reprint Analysis of ATP-binding cassette transporter expression in drug-selected cell lines by a microarray dedicated to multidrug resistance
    Jean Philippe Annereau
    Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 4256, USA
    Mol Pharmacol 66:1397-405. 2004
    ..The custom-designed ABC-Tox microarray presented here will be helpful to elucidate mechanisms leading to anticancer drug resistance...
  33. pmc Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines
    Barry R Zeeberg
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e30317. 2012
    ..The comprehensive and reliable nature of that dataset allows us to study gene co-expression across cancer cell lines...
  34. pmc GoMiner: a resource for biological interpretation of genomic and proteomic data
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 4:R28. 2003
    ..The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources...
  35. pmc Depicting combinatorial complexity with the molecular interaction map notation
    Kurt W Kohn
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
    Mol Syst Biol 2:51. 2006
    ..These comparisons may help cell and systems biologists adopt a graphical language that is unambiguous and generally understood...
  36. pmc Karyotypic "state" as a potential determinant for anticancer drug discovery
    Anna V Roschke
    Genetics Branch and 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 102:2964-9. 2005
    ..Thus, we delineate an approach for the identification of "lead compounds" for anticancer drug discovery complementary to those that are focused at the outset on a given gene or pathway...
  37. pmc MatchMiner: a tool for batch navigation among gene and gene product identifiers
    Kimberly J Bussey
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892 4255, USA
    Genome Biol 4:R27. 2003
    ..The user inputs a list of gene identifiers and then uses the Merge function to find the overlap with a second list of identifiers of either the same or a different type or uses the LookUp function to find corresponding identifiers...
  38. pmc Asparagine synthetase: a new potential biomarker in ovarian cancer
    Philip L Lorenzi
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research CCR, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Drug News Perspect 22:61-4. 2009
    ....
  39. pmc Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research CCR, National Cancer Institute NCI, National Institutes of Health NIH, Bethesda, MD 20892 USA
    BMC Bioinformatics 5:80. 2004
    ..When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names...
  40. pmc Multiplexing siRNAs to compress RNAi-based screen size in human cells
    Scott E Martin
    Gene Silencing Section, Office of Science and Technology Partnership, OD, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    Nucleic Acids Res 35:e57. 2007
    ..This approach is likely to be especially applicable where assay costs or platform limitations are prohibitive...
  41. pmc Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis
    Kurt W Kohn
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Cell Cycle 8:2281-99. 2009
    ..In addition, the network architecture disclosed by the hierarchical map, suggested a speculative model for how molecular crowding and the granular localization of network components in the cell nucleus can facilitate function...
  42. ncbi request reprint Transcriptional regulation of mitotic genes by camptothecin-induced DNA damage: microarray analysis of dose- and time-dependent effects
    Yi Zhou
    Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
    Cancer Res 62:1688-95. 2002
    ....
  43. ncbi request reprint Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping
    William C Reinhold
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cancer Res 63:1000-11. 2003
    ..This model is analogous to one suggested previously for the relationship between oncogene function and apoptosis in carcinogenesis...
  44. pmc Concordance of gene expression and functional correlation patterns across the NCI-60 cell lines and the Cancer Genome Atlas glioblastoma samples
    Barry R Zeeberg
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e40062. 2012
    ..Thus, we are now able to determine which of the processes are robustly shared by both the immortalized cell lines and clinical cancers...
  45. ncbi request reprint A stromal gene signature associated with inflammatory breast cancer
    Brenda J Boersma
    Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4258, USA
    Int J Cancer 122:1324-32. 2008
    ..We identified multiple pathways related to the endoplasmic stress response that could be functionally significant in IBC. Our findings suggest that the gene expression in the tumor stroma may play a role in determining the IBC phenotype...
  46. pmc UPLC-ESI-TOFMS-based metabolomics and gene expression dynamics inspector self-organizing metabolomic maps as tools for understanding the cellular response to ionizing radiation
    Andrew D Patterson
    Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Anal Chem 80:665-74. 2008
    ..Radiation metabolomics," the application of metabolomic analysis to the field of radiobiology, promises to increase our understanding of cellular responses to stressors such as radiation...
  47. pmc The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress
    Frank Staib
    Laboratories of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892 4255, USA
    Cancer Res 65:10255-64. 2005
    ..In summary, the inflammatory stress response is a complex, integrated biological network in which p53 is a key molecular node regulating gene expression...
  48. ncbi request reprint Karyotypic complexity of the NCI-60 drug-screening panel
    Anna V Roschke
    Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20889 5105, USA
    Cancer Res 63:8634-47. 2003
    ....
  49. pmc Chromatin challenges during DNA replication: a systems representation
    Kurt W Kohn
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Biol Cell 19:1-7. 2008
    ..on the complexities of chromatin replication, thereby providing a tool for system-level comprehension of the effects of genetic mutations, altered gene expression, and pharmacologic intervention...
  50. ncbi request reprint Chk2 molecular interaction map and rationale for Chk2 inhibitors
    Yves Pommier
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892 4255, USA
    Clin Cancer Res 12:2657-61. 2006
    ..Visualizing the regulatory circuits underlying cellular signaling may help identify key regulatory reactions and defects that can serve as targets for anticancer drugs...
  51. 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. ..
  52. pmc Metabolomics reveals attenuation of the SLC6A20 kidney transporter in nonhuman primate and mouse models of type 2 diabetes mellitus
    Andrew D Patterson
    Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 286:19511-22. 2011
    ..These observations were validated in the db/db mouse model of T2DM. This study provides convincing evidence of the power of metabolomics for identifying functional changes at many levels in the omics pipeline...
  53. ncbi request reprint Spotlight on molecular profiling: "Integromic" analysis of the NCI-60 cancer cell lines
    John N Weinstein
    Laboratory of Molecular Pharmacology, National Cancer Institute, 37 Convent Drive, Room 5056B, Bethesda, MD 20892, USA
    Mol Cancer Ther 5:2601-5. 2006
  54. ncbi request reprint Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks
    Mirit I Aladjem
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Sci STKE 2004:pe8. 2004
    ....
  55. pmc Molecular interaction maps of bioregulatory networks: a general rubric for systems biology
    Kurt W Kohn
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Biol Cell 17:1-13. 2006
    ..Drawing a MIM diagram, adhering to the rules of notation, imposes a logical discipline that sharpens one's understanding of the structure and function of a network...
  56. ncbi request reprint Biomarkers in cancer staging, prognosis and treatment selection
    Joseph A Ludwig
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Rev Cancer 5:845-56. 2005
    ..Understanding how and when biomarkers can be integrated into clinical care is crucial if we want to translate the promise into reality...
  57. pmc In vitro differential sensitivity of melanomas to phenothiazines is based on the presence of codon 600 BRAF mutation
    Ogechi N Ikediobi
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, USA
    Mol Cancer Ther 7:1337-46. 2008
    ..The findings reported here have potential implications for the use of phenothiazines in the treatment of V600E BRAF mutant melanoma...
  58. pmc SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis
    Ari B Kahn
    Department of Bioinformatics, George Mason University, Fairfax, Virginia, USA
    BMC Bioinformatics 8:75. 2007
    ..Accurate analysis of microarray expression data and design of new arrays for alternative splicing require assessment of probes at the sequence and exon levels...
  59. pmc Properties of switch-like bioregulatory networks studied by simulation of the hypoxia response control system
    Kurt W Kohn
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
    Mol Biol Cell 15:3042-52. 2004
    ..The studies disclosed the mechanism responsible for the sharp transitions. We show how parameter sets giving switch-like behavior can be found and how this type of behavior provides a foundation for quantitative studies in cells...
  60. ncbi request reprint The bioinformatics of microarray gene expression profiling
    John N Weinstein
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, USA
    Cytometry 47:46-9. 2002
  61. pmc Quality assessment of microarrays: visualization of spatial artifacts and quantitation of regional biases
    Mark Reimers
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
    BMC Bioinformatics 6:166. 2005
    ..Current practice in quality assessment for microarrays does not address regional biases...
  62. ncbi request reprint Cancers as wounds that do not heal: differences and similarities between renal regeneration/repair and renal cell carcinoma
    Joseph Riss
    Laboratory of Biosystems and Cancer, Comparative Oncology Program, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
    Cancer Res 66:7216-24. 2006
    ..The observations reported here provide a conceptual framework for further efforts to understand the biology and to develop more effective diagnostic biomarkers and therapeutic strategies for renal tumors and renal ischemia...
  63. ncbi request reprint Human apurinic/apyrimidinic endonuclease (Ape1) and its N-terminal truncated form (AN34) are involved in DNA fragmentation during apoptosis
    Akira Yoshida
    Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892 4255, USA
    J Biol Chem 278:37768-76. 2003
    ..Thus, we propose that AN34 and Ape1 participate in the process of chromatin fragmentation during apoptosis...
  64. pmc VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays
    Hans A Kestler
    Neural Information Processing, University of Ulm, Germany
    BMC Bioinformatics 9:67. 2008
    ..Additional graphical methods are therefore needed to augment the GO graphical representation...
  65. ncbi request reprint Workshop on cancer biometrics: identifying biomarkers and surrogates of cancer in patients: a meeting held at the Masur Auditorium, National Institutes of Health
    Michael T Lotze
    Translational Research, University of Pittsburgh Molecular Medicine Institute, Pittsburgh, Pennsylvania, USA
    J Immunother 28:79-119. 2005
    ..Concrete recommendations for current application and enabling further development in cancer biometrics are summarized. This will allow a more informed, rapid, and accurate assessment of novel cancer therapies...
  66. ncbi request reprint Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance
    Ying Huang
    Program of Pharmacogenomics, Department of Pharmacology, College of Medicine and Public Health, The Ohio State University, Columbus, 43210, USA
    Cancer Res 64:4294-301. 2004
    ..Measurement of transporter gene expression may prove useful in predicting anticancer drug response...
  67. pmc A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
    Jae K Lee
    Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
    Proc Natl Acad Sci U S A 104:13086-91. 2007
    ..Furthermore, we used COXEN for in silico screening of 45,545 compounds and identify an agent with activity against human bladder cancer...
  68. ncbi request reprint MicroRNA expression profiles for the NCI-60 cancer cell panel
    Paul E Blower
    Program of Pharmacogenomics, Department of Pharmacology and the Comprehensive Cancer Center, College of Medicine, The Ohio State University, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, USA
    Mol Cancer Ther 6:1483-91. 2007
    ..Combined with gene expression and other biological data using multivariate analysis, microRNA expression profiles may provide a critical link for understanding mechanisms involved in chemosensitivity and chemoresistance...
  69. ncbi request reprint Impact of p53 knockout and topotecan treatment on gene expression profiles in human colon carcinoma cells: a pharmacogenomic study
    Sayed S Daoud
    Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington 99164, USA
    Cancer Res 63:2782-93. 2003
    ..The new experimental design and gene expression map analysis introduced here are applicable to a wide range of studies that encompass both treatment effects and genotypic or phenotypic differences...
  70. doi request reprint MicroRNAs modulate the chemosensitivity of tumor cells
    Paul E Blower
    Program of Pharmacogenomics, Department of Pharmacology, Ohio State University, 333 West Tenth Street, Columbus, OH 43210, USA
    Mol Cancer Ther 7:1-9. 2008
    ..Ten of those microRNAs have already been implicated in cancer biology. Our results support a substantial role for microRNAs in anticancer drug response, suggesting novel potential approaches to the improvement of chemotherapy...
  71. doi request reprint Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen
    Sally A Amundson
    Center for Radiological Research, Columbia University Medical Center, New York, New York 10032, USA
    Cancer Res 68:415-24. 2008
    ..The response of those genes to gamma-rays seems to be unaffected by the myriad of genetic differences across this diverse cell set; it represents the most penetrant gene expression response to ionizing radiation yet observed...
  72. doi request reprint Biochemistry. A postgenomic visual icon
    John N Weinstein
    Department of Bioinformatics and Computational Biology, M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
    Science 319:1772-3. 2008
  73. ncbi request reprint Is the gene expression pattern of lung cancer detected by screening with spiral computed tomography different from that of symptom-detected lung cancer?
    James L Mulshine
    Clin Cancer Res 10:5973-4. 2004
  74. pmc Mutation analysis of 24 known cancer genes in the NCI-60 cell line set
    Ogechi N Ikediobi
    Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
    Mol Cancer Ther 5:2606-12. 2006
    ....
  75. ncbi request reprint Nova regulates brain-specific splicing to shape the synapse
    Jernej Ule
    Howard Hughes Medical Institute and Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York, USA
    Nat Genet 37:844-52. 2005
    ..Validating a large set of Nova RNA targets has led us to identify a multi-tiered network in which Nova regulates the exon content of RNAs encoding proteins that interact in the synapse...
  76. pmc Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
    Ryan D Morin
    British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
    Genome Res 16:796-803. 2006
    ..Approximately 14% of the paralogous pairs analyzed here also show differential expression indicative of subfunctionalization...
  77. pmc The EDGE hypothesis: epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancer
    Douglas M Ruden
    Institute of Environmental Health Sciences, Wayne State University, Room 4000, 2727 2nd Avenue, Detroit, MI 48201, USA
    Front Neuroendocrinol 29:428-44. 2008
    ..In the model, "epigenetic assimilation" of metastable epialleles of RCPs over many generations can lead to mutations directed to those genes, thereby permanently stabilizing the adaptive phenotype...
  78. ncbi request reprint Connecting genes, drugs and diseases
    John N Weinstein
    Nat Biotechnol 24:1365-6. 2006
  79. ncbi request reprint Opportunities and challenges in ovarian cancer research, a perspective from the 11th Ovarian cancer action/HHMT Forum, Lake Como, March 2007
    Alan Ashworth
    Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
    Gynecol Oncol 108:652-7. 2008
    ..As ovarian cancer becomes a chronic disease, greater emphasis will be placed on the challenges facing survivors...
  80. ncbi request reprint Comparison of methods for sequential screening of large compound sets
    Paul E Blower
    Leadscope, Inc, 1393 Dublin Road, Columbus, OH 43215, USA
    Comb Chem High Throughput Screen 9:115-22. 2006
    ....