Elliott H Margulies

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
  2. pmc Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
    Jamie K Teer
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 20:1420-31. 2010
  3. pmc SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approach
    Jacob L McCauley
    Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
    BMC Genomics 8:266. 2007
  4. doi request reprint Confidence in comparative genomics
    Elliott H Margulies
    Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 18:199-200. 2008
  5. doi request reprint Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
    Elliott H Margulies
    Genome Technology Branch, Genome Informatics Section, National Human Genome Research Institute, National Institutes of Health, 5625 Fishers Lane, Room 5N 01N, MSC9400, Bethesda, Maryland 20892, USA
    Nat Rev Genet 9:303-13. 2008
  6. ncbi request reprint Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Trends Genet 22:187-93. 2006
  7. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
  8. pmc An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:4795-800. 2005
  9. pmc Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes
    Stephen C J Parker
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Genet 8:e1002871. 2012
  10. doi request reprint Somatic Mutations in MAP3K5 Attenuate Its Proapoptotic Function in Melanoma through Increased Binding to Thioredoxin
    Todd D Prickett
    The Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    J Invest Dermatol 134:452-60. 2014

Detail Information

Publications29

  1. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
    ..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
  2. pmc Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
    Jamie K Teer
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 20:1420-31. 2010
    ..We find that these three genomic enrichment methods are highly accurate and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data...
  3. pmc SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approach
    Jacob L McCauley
    Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
    BMC Genomics 8:266. 2007
    ..We chose annotated SNPs in the region based on location within MCSs (termed MCS-SNPs). We then obtained genotypes for 478 MCS-SNPs in 989 individuals from MS families...
  4. doi request reprint Confidence in comparative genomics
    Elliott H Margulies
    Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 18:199-200. 2008
  5. doi request reprint Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
    Elliott H Margulies
    Genome Technology Branch, Genome Informatics Section, National Human Genome Research Institute, National Institutes of Health, 5625 Fishers Lane, Room 5N 01N, MSC9400, Bethesda, Maryland 20892, USA
    Nat Rev Genet 9:303-13. 2008
    ..Approaches to determining the biological significance of constrained sequence are also explored...
  6. ncbi request reprint Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Trends Genet 22:187-93. 2006
    ....
  7. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  8. pmc An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:4795-800. 2005
    ....
  9. pmc Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes
    Stephen C J Parker
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Genet 8:e1002871. 2012
    ..Such information helps establish a broader mechanistic understanding of the linkage between non-coding genomic variations and the cellular evolution of cancer...
  10. doi request reprint Somatic Mutations in MAP3K5 Attenuate Its Proapoptotic Function in Melanoma through Increased Binding to Thioredoxin
    Todd D Prickett
    The Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    J Invest Dermatol 134:452-60. 2014
    ..This mutation represents a potential target for the design of new therapies to treat melanoma. ..
  11. pmc Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites
    Amber Hogart
    Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 22:1407-18. 2012
    ..Our genome-wide survey demonstrates that DNA methylation is markedly altered during myeloid differentiation and identifies critical regions of the genome and transcription factor programs that contribute to hematopoiesis...
  12. pmc Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma
    Jared J Gartner
    National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 110:13481-6. 2013
    ..Our data indicate that silent alterations have a role to play in human cancer, emphasizing the importance of their investigation in future cancer genome studies. ..
  13. pmc Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation
    Andre M Pilon
    National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
    Blood 118:e139-48. 2011
    ..The EKLF interactome shows very little overlap with the interactomes of GATA1, GATA2, or TAL1, leading to a model in which EKLF directs programs that are independent of those regulated by the GATA factors or TAL1...
  14. pmc A new strategy for genome assembly using short sequence reads and reduced representation libraries
    Andrew L Young
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 20:249-56. 2010
    ..melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrificing quality...
  15. ncbi request reprint Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer
    Matthew E Portnoy
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genomics 86:295-305. 2005
    ..Several other MCSs represent candidate GDF6 regulatory elements; many of these are not conserved in fish or frog, but are strongly conserved in mammals...
  16. pmc Accurate and comprehensive sequencing of personal genomes
    Subramanian S Ajay
    Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 21:1498-505. 2011
    ..These results help provide a "sequencing guide" for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported...
  17. pmc A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data
    Rachel L Goldfeder
    Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e23683. 2011
    ..Our results suggest that examining the concordance of detected genotypes from lanes purported to be from the same sample is a relatively simple approach for confirming that combined lanes of data are of the same identity and quality...
  18. pmc Human NPY promoter variation rs16147:T>C as a moderator of prefrontal NPY gene expression and negative affect
    Wolfgang H Sommer
    Laboratory of Clinical and Translational Studies, NIAAA, National Institutes of Health, Bethesda, USA
    Hum Mutat 31:E1594-608. 2010
    ..Our results show the importance of rs16147:T>C for regulation of NPY gene expression and brain function...
  19. pmc Identification and characterization of multi-species conserved sequences
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 13:2507-18. 2003
    ....
  20. pmc Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes
    Elliott H Margulies
    Genome Technology Branch and NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:3354-9. 2005
    ..Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome...
  21. pmc Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
    Gregory E Crawford
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 16:123-31. 2006
    ..This strategy, which can be applied to any cell line or tissue, will enable a better understanding of how chromatin structure dictates cell function and fate...
  22. pmc An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs
    Heidi G Parker
    Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Science 325:995-8. 2009
    ..These results illustrate the important role of a single evolutionary event in constraining and directing phenotypic diversity in the domestic dog...
  23. pmc Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci
    Michael L Stitzel
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cell Metab 12:443-55. 2010
    ..These findings present a global snapshot of the human islet epigenome and should provide functional context for noncoding variants emerging from genetic studies of T2D and other islet disorders...
  24. pmc Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma
    Todd D Prickett
    Cancer Genetics Branch, National Human Genome Research Institute, US National Institutes of Health NIH, Bethesda, Maryland, USA
    Nat Genet 43:1119-26. 2011
    ..Our study yields the most comprehensive map of genetic alterations in the GPCR gene family...
  25. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  26. pmc Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
    Taane G Clark
    Department of Epidemiology and Public Health, Imperial College, Norfolk Place, London, W2 1PG, UK
    Genome Biol 8:R180. 2007
    ..We relate indels to known genomic annotation features and measures of evolutionary constraint...
  27. pmc Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
    Sergey I Nikolaev
    Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel Servet, 1211 Geneva, Switzerland
    Proc Natl Acad Sci U S A 104:20443-8. 2007
    ..This observation may explain why the evolution of CNCs fits the expectations of the nearly neutral theory less well than the evolution of nonsynonymous sites...
  28. pmc Early history of mammals is elucidated with the ENCODE multiple species sequencing data
    Sergey Nikolaev
    Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
    PLoS Genet 3:e2. 2007
    ..Thus, the two datasets support the Afrotheria hypothesis; however, none can reject both of the remaining topological alternatives...
  29. pmc Large-scale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms
    Takashi Angata
    Glycobiology Research and Training Center, University of California at San Diego, La Jolla, CA 92093 0687, USA
    Proc Natl Acad Sci U S A 101:13251-6. 2004
    ....