Research Topics
| Elliott H MarguliesSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
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Detail Information
Publications
High-resolution mapping and characterization of open chromatin across the genomeAlan 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...- Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencingJamie 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... - SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approachJacob 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... 
Confidence in comparative genomicsElliott 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
Approaches to comparative sequence analysis: towards a functional view of vertebrate genomesElliott 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...- Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genomeElliott 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... - Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisonsElliott H Margulies
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Trends Genet 22:187-93. 2006.... - An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencingElliott 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.... - Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomesStephen 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... - Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sitesAmber 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... - Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiationAndre 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... - Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancerMatthew 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... - A new strategy for genome assembly using short sequence reads and reduced representation librariesAndrew 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... - Accurate and comprehensive sequencing of personal genomesSubramanian 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... - A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing dataRachel 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... - Human NPY promoter variation rs16147:T>C as a moderator of prefrontal NPY gene expression and negative affectWolfgang 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... - Identification and characterization of multi-species conserved sequencesElliott H Margulies
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Genome Res 13:2507-18. 2003.... - Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomesElliott 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... - 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... - An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogsHeidi 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... - Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanomaTodd 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... - Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility lociMichael 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... - Early history of mammals is elucidated with the ENCODE multiple species sequencing dataSergey 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... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Functional constraint and small insertions and deletions in the ENCODE regions of the human genomeTaane 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... - Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elementsSergey 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... - Large-scale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanismsTakashi 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....