K H Buetow

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Superposition of transcriptional behaviors determines gene state
    Sol Efroni
    Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
    PLoS ONE 3:e2901. 2008
  2. pmc Detecting cancer gene networks characterized by recurrent genomic alterations in a population
    Sol Efroni
    The Mina and Everard Faculty of Life Science, Bar Ilan University, Ramat Gan, Israel
    PLoS ONE 6:e14437. 2011
  3. pmc Gene functional similarity search tool (GFSST)
    Peisen Zhang
    Laboratory of Population Genetics, National Cancer Institute, NIH, Bethesda, USA
    BMC Bioinformatics 7:135. 2006
  4. ncbi request reprint The NCI Center for Bioinformatics (NCICB): building a foundation for in silico biomedical research
    Kenneth H Buetow
    National Cancer Institute, Center for Bioinformatics, 6116 Executive Blvd, Bethesda, MD 20892 9692, USA
    Cancer Invest 22:117-22. 2004
  5. doi request reprint An infrastructure for interconnecting research institutions
    Kenneth H Buetow
    Center for Bioinformatics and Information Technology, National Cancer Institute, Rockville, MD 20852, USA
    Drug Discov Today 14:605-10. 2009
  6. ncbi request reprint Reliable identification of large numbers of candidate SNPs from public EST data
    K H Buetow
    Laboratory of Population Genetics, NCI, NIH, Bethesda, Maryland 20892, USA
    Nat Genet 21:323-5. 1999
  7. ncbi request reprint Cyberinfrastructure: empowering a "third way" in biomedical research
    Kenneth H Buetow
    National Cancer Institute Center for Bioinformatics, National Institutes of Health, Rockville, MD 20892, USA
    Science 308:821-4. 2005
  8. pmc High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
    K H Buetow
    Laboratory of Population Genetics, Division of Cancer Epidemiology and Genetics, and Office of Genomics, National Cancer Institute, Bethesda, MD 20892 5060, USA
    Proc Natl Acad Sci U S A 98:581-4. 2001
  9. ncbi request reprint In silico analysis of cancer through the Cancer Genome Anatomy Project
    R L Strausberg
    National Cancer Institute, Bethesda, MD 20892, USA
    Trends Cell Biol 11:S66-71. 2001
  10. pmc A high-resolution multistrain haplotype analysis of laboratory mouse genome reveals three distinctive genetic variation patterns
    Jinghui Zhang
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 8302, USA
    Genome Res 15:241-9. 2005

Detail Information

Publications48

  1. pmc Superposition of transcriptional behaviors determines gene state
    Sol Efroni
    Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
    PLoS ONE 3:e2901. 2008
    ..The technique can be applied in almost any multi-sample gene expression experiment, and holds equal promise for protein abundance experiments...
  2. pmc Detecting cancer gene networks characterized by recurrent genomic alterations in a population
    Sol Efroni
    The Mina and Everard Faculty of Life Science, Bar Ilan University, Ramat Gan, Israel
    PLoS ONE 6:e14437. 2011
    ..We demonstrate this method in breast cancer, where the state of a subset of the pathways identified through these regions is shown to be highly associated with disease survival and recurrence...
  3. pmc Gene functional similarity search tool (GFSST)
    Peisen Zhang
    Laboratory of Population Genetics, National Cancer Institute, NIH, Bethesda, USA
    BMC Bioinformatics 7:135. 2006
    ..In recent years, the development of Gene Ontology (GO) has established structured, controlled vocabularies describing gene functions, which makes it possible to develop novel tools to search genes by functional similarity...
  4. ncbi request reprint The NCI Center for Bioinformatics (NCICB): building a foundation for in silico biomedical research
    Kenneth H Buetow
    National Cancer Institute, Center for Bioinformatics, 6116 Executive Blvd, Bethesda, MD 20892 9692, USA
    Cancer Invest 22:117-22. 2004
  5. doi request reprint An infrastructure for interconnecting research institutions
    Kenneth H Buetow
    Center for Bioinformatics and Information Technology, National Cancer Institute, Rockville, MD 20852, USA
    Drug Discov Today 14:605-10. 2009
    ..cancer.gov/) from the National Cancer Institute (NCI) is already enabling many research organizations to implement personalized medicine approaches for their basic and clinical research programs...
  6. ncbi request reprint Reliable identification of large numbers of candidate SNPs from public EST data
    K H Buetow
    Laboratory of Population Genetics, NCI, NIH, Bethesda, Maryland 20892, USA
    Nat Genet 21:323-5. 1999
    ..Our results suggest that existing sequence resources may serve as a valuable source for identifying genetic variation...
  7. ncbi request reprint Cyberinfrastructure: empowering a "third way" in biomedical research
    Kenneth H Buetow
    National Cancer Institute Center for Bioinformatics, National Institutes of Health, Rockville, MD 20892, USA
    Science 308:821-4. 2005
    ..Biomedicine is at the precipice of unlocking the very essence of biologic life and enabling a new generation of medicine. Development and deployment of cyberinfrastructure may prove to be on the critical path to obtaining these goals...
  8. pmc High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
    K H Buetow
    Laboratory of Population Genetics, Division of Cancer Epidemiology and Genetics, and Office of Genomics, National Cancer Institute, Bethesda, MD 20892 5060, USA
    Proc Natl Acad Sci U S A 98:581-4. 2001
    ..These data provide preliminary insights into patterns of polymorphism in a genomewide collection of gene-based polymorphisms...
  9. ncbi request reprint In silico analysis of cancer through the Cancer Genome Anatomy Project
    R L Strausberg
    National Cancer Institute, Bethesda, MD 20892, USA
    Trends Cell Biol 11:S66-71. 2001
    ....
  10. pmc A high-resolution multistrain haplotype analysis of laboratory mouse genome reveals three distinctive genetic variation patterns
    Jinghui Zhang
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 8302, USA
    Genome Res 15:241-9. 2005
    ..The results suggest that the controlled complexity of the laboratory inbred strains may provide a means for uncovering the biological factors that have shaped genetic variation patterns...
  11. ncbi request reprint Genome-wide association study in esophageal cancer using GeneChip mapping 10K array
    Nan Hu
    Cancer Prevention Studies Branch, Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
    Cancer Res 65:2542-6. 2005
    ..In conclusion, we have shown the feasibility of the Affymetrix 10K SNP array in genome-wide association studies of common cancers and identified new candidate loci to study in ESCC...
  12. pmc Allelic variation in gene expression is common in the human genome
    H Shuen Lo
    Laboratory of Population Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
    Genome Res 13:1855-62. 2003
    ..Our studies demonstrate that variation of gene expression between alleles is common, and this variation may contribute to human variability...
  13. ncbi request reprint Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer
    Zhining Wang
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland 20877, USA
    Cancer Res 63:655-7. 2003
    ..Reverse transcription-PCR experiments confirmed association of the alternative splicing isoforms with tumors. These results suggest that alternative splicing may have potential as a diagnostic marker for cancer...
  14. ncbi request reprint Genotypic and phenotypic characterization of a putative tumor susceptibility gene, GNMT, in liver cancer
    Tzu Ling Tseng
    Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cancer Res 63:647-54. 2003
    ..In summary, our results suggest that GNMT alteration may be an early event in HCC development and that GNMT could be a new tumor susceptibility gene for HCC...
  15. ncbi request reprint Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms
    Robert J Clifford
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 20:1006-14. 2004
    ..To efficiently screen SNPs for disease association, it is important to distinguish neutral variants from deleterious ones...
  16. pmc PID: the Pathway Interaction Database
    Carl F Schaefer
    National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
    Nucleic Acids Res 37:D674-9. 2009
    ..The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools...
  17. ncbi request reprint Bioinformatics tools for single nucleotide polymorphism discovery and analysis
    Robert J Clifford
    Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Ann N Y Acad Sci 1020:101-9. 2004
    ..These tools allow researchers to retrieve data about SNPs based on gene of interest, genetic or physical map location, or expression pattern...
  18. ncbi request reprint Hemochromatosis gene mutations and distal adenomatous colorectal polyps
    Katherine A McGlynn
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, EPS 7060, 6120 Executive Boulevard, Rockville, MD 20852 7234, USA
    Cancer Epidemiol Biomarkers Prev 14:158-63. 2005
    ..These results do not support a relationship between HFE heterozygosity and risk of advanced distal adenoma...
  19. ncbi request reprint Cancer Molecular Analysis Project: weaving a rich cancer research tapestry
    Kenneth H Buetow
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cancer Cell 1:315-8. 2002
    ....
  20. ncbi request reprint Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays
    Kevin K Dobbin
    Cancer Diagnosis Program, National Cancer Institute NIH, Bethesda, MD 20894, USA
    Clin Cancer Res 11:565-72. 2005
    ..The findings indicate that under properly controlled conditions it is feasible to perform complete tumor microarray analysis, from tissue processing to hybridization and scanning, at multiple independent laboratories for a single study...
  21. ncbi request reprint Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach
    Jinghui Zhang
    Laboratory of Population Genetics, National Cancer Institute National Institutes of Health, 8424 Helgerman Court, Room 101, MSC 8302, Bethesda, MD 20892 8302, USA
    Genomics 85:297-308. 2005
    ..A Web application was developed to apply our results for improving the accuracy of expression analysis...
  22. doi request reprint Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma
    Robert J Clifford
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Hepatology 52:2034-43. 2010
    ..Conclusion: Combined analysis of CNV, individual SNPs, and pathways suggest that HCC susceptibility is mediated by germline factors affecting the immune response and differences in T-cell receptor processing...
  23. pmc Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
    Michael N Edmonson
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 27:865-6. 2011
    ....
  24. pmc Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array
    Nan Hu
    Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, USA
    BMC Genomics 7:299. 2006
    ..Esophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide. Comprehensive genomic characterization of ESCC will further our understanding of the carcinogenesis process in this disease...
  25. ncbi request reprint A phylogenetic analysis identifies heterogeneity among hepatocellular carcinomas
    Katherine A McGlynn
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
    Hepatology 36:1341-8. 2002
    ..In conclusion, it appears that in HCC, allele loss is not random, but clusters into definable groups that are characterized by distinctive rates of loss...
  26. pmc Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB)
    Jinghui Zhang
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 17:1111-7. 2007
    ....
  27. ncbi request reprint caCORE: a common infrastructure for cancer informatics
    Peter A Covitz
    National Cancer Institute Center for Bioinformatics, National Institutes of Health, U S Department of Health and Human Services, 6116 Executive Boulevard, Suite 403, Rockville MD 20852, USA
    Bioinformatics 19:2404-12. 2003
    ..Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications...
  28. pmc Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations
    Jinghui Zhang
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 8302, USA
    Am J Hum Genet 73:1073-81. 2003
    ....
  29. ncbi request reprint The cancer genome anatomy project: online resources to reveal the molecular signatures of cancer
    Robert L Strausberg
    National Cancer Institute, Bethesda, MD 20892, USA
    Cancer Invest 20:1038-50. 2002
  30. pmc HapScope: a software system for automated and visual analysis of functionally annotated haplotypes
    Jinghui Zhang
    Laboratory of Population Genetics, National Cancer Institute National Institutes of Health, 8424 Helgerman Court, Room 101, MSC 8302, Bethesda, MD 20892 8302, USA
    Nucleic Acids Res 30:5213-21. 2002
    ..We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research...
  31. pmc Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
    Robert L Strausberg
    National Cancer Institute, Bethessda, MD 20892 2580, USA
    Proc Natl Acad Sci U S A 99:16899-903. 2002
    ..All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov)...
  32. ncbi request reprint A genome scan of 18 families with chronic lymphocytic leukaemia
    Lynn R Goldin
    Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute NIH, 6120 Executive Boulevard, Room 7008, MSC 7236, Bethesda, MD 20892 7236, USA
    Br J Haematol 121:866-73. 2003
    ..Four of these six regions (6q, 13q, 12 and 17p) coincide with areas where cytogenetic abnormalities are frequently observed in CLL tumour cells and are, therefore, strong candidate regions for containing germ line changes...
  33. pmc SNPdetector: a software tool for sensitive and accurate SNP detection
    Jinghui Zhang
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 1:e53. 2005
    ..SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov)...
  34. ncbi request reprint A computational approach to measuring coherence of gene expression in pathways
    Howard H Yang
    Laboratory of Population Genetics, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
    Genomics 84:211-7. 2004
    ....
  35. ncbi request reprint An international database and integrated analysis tools for the study of cancer gene expression
    R L Strausberg
    National Cancer Institute, Bethesda, MD 20892, USA
    Pharmacogenomics J 2:156-64. 2002
    ..A suite of informatics tools was designed to facilitate in silico analysis of the gene expression datasets and are available through the NCI Cancer Genome Anatomy Project web site (http://cgap.nci.nih.gov)...
  36. pmc Global transcription in pluripotent embryonic stem cells
    Sol Efroni
    National Cancer Institute Center for Bioinformatics, National Institutes of Health, Rockville, MD 20852, USA
    Cell Stem Cell 2:437-47. 2008
    ..We propose that global transcription is a hallmark of pluripotent ESCs, contributing to their plasticity, and that lineage specification is driven by reduction of the transcribed portion of the genome...
  37. ncbi request reprint Susceptibility to aflatoxin B1-related primary hepatocellular carcinoma in mice and humans
    Katherine A McGlynn
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH DHHS, 6120 Executive Boulevard, Bethesda, MD 20892, USA
    Cancer Res 63:4594-601. 2003
    ..These results indicate that the comparison of results from human studies and the AFB(1)-susceptible mouse model may provide new insights into hepatocarcinogenesis...
  38. pmc Identification of key processes underlying cancer phenotypes using biologic pathway analysis
    Sol Efroni
    National Cancer Institute Center for Bioinformatics, Rockville, Maryland, United States of America
    PLoS ONE 2:e425. 2007
    ..This approach provides a means to use genome-wide characterizations to map key biological processes to important clinical features in disease...
  39. pmc Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome
    Mitsutaka Kadota
    Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Genet 3:e81. 2007
    ..To our knowledge, this is the first demonstration in humans that genetics may be an important factor that influences global chromatin state mediated by histone modification, the hallmark of the epigenetic phenomena...
  40. ncbi request reprint AACR-FDA-NCI Cancer Biomarkers Collaborative consensus report: advancing the use of biomarkers in cancer drug development
    Samir N Khleif
    National Cancer Institute, Raritan, New Jersey, USA
    Clin Cancer Res 16:3299-318. 2010
    ....
  41. pmc Multiple cross and inbred strain haplotype mapping of complex-trait candidate genes
    Yeong Gwon Park
    Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 13:118-21. 2003
    ....
  42. pmc ATG deserts define a novel core promoter subclass
    Maxwell P Lee
    Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 15:1189-97. 2005
    ..We speculate that ATG deserts may provide a core promoter platform upon which complex upstream regulatory signals can be integrated, targeting multiple TSS whose products encode a single protein...
  43. ncbi request reprint Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures
    Zhining Wang
    Laboratory of Population Genetics, National Cancer Institute, Bethesda, MD 20892, USA
    Genomics 83:395-401. 2004
    ..The motifs identified in this study are novel imprinting signatures, which should improve our understanding of genomic imprinting and the role of genomic imprinting in human diseases...
  44. ncbi request reprint Genetic susceptibility and dietary patterns in lung cancer
    Ya Yu Tsai
    Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
    Lung Cancer 41:269-81. 2003
    ..Adjustments using dietary pattern may be useful in elucidating the effects of polymorphisms in genes responsible for carcinogen metabolism...
  45. pmc An anatomy of normal and malignant gene expression
    Kathy Boon
    Duke University Medical Center, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 99:11287-92. 2002
    ..We report here an easily accessible view of nearly any gene's expression in a wide variety of malignant and normal tissues...
  46. ncbi request reprint Significance of genetic variation at the glutathione S-transferase M1 and NAD(P)H:quinone oxidoreductase 1 detoxification genes in breast cancer development
    Nava Siegelmann-Danieli
    Division of Population Science, Fox Chase Center, Philadelphia, PA, USA
    Oncology 62:39-45. 2002
    ..NQO1 results suggest that different quinones (possibly estrogenic quinone metabolites) might affect the histological development of breast tumors...
  47. pmc Long-range heterogeneity at the 3' ends of human mRNAs
    Christian Iseli
    Office of Information Technology, Ludwig Institute for Cancer Research, Switzerland
    Genome Res 12:1068-74. 2002
    ....