Research Topics
Genomes and Genes | James C MullikinSummaryAffiliation: National Institutes of Health Country: USA Publications
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Detail Information
Publications
Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus OryzaHyeran Kim
Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Genome Biol 9:R45. 2008..sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date...- The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensisJoseph F Ryan
Bioinformatics Program, Boston University, Cummington Street, Boston, MA 02215, USA
Genome Biol 7:R64. 2006..The origin of particular homeobox genes may, therefore, be associated with the evolution of particular animal traits. Here we report the first near-complete set of homeodomains from a basal (diploblastic) animal... - Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily?Adam M Reitzel
Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Evodevo 2:3. 2011..In addition, to gain insight into conserved or novel functions, we examined NR expression during ctenophore development... - Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore Mnemiopsis leidyiKevin Pang
Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, USA
Evodevo 1:10. 2010..Genomic data from ctenophores could be particularly relevant, as ctenophores have been proposed to be one of the earliest branching metazoan phyla... - The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoaJoseph F Ryan
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Evodevo 1:9. 2010..The homeobox superfamily of genes is particularly suited for these kinds of gene content comparisons, since it is large, diverse, and features a highly conserved domain... - Light whole genome sequence for SNP discovery across domestic cat breedsJames C Mullikin
Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
BMC Genomics 11:406. 2010..However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery... - Exome sequencing as a diagnostic tool in a case of undiagnosed juvenile-onset GM1-gangliosidosisTyler Mark Pierson
NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research, Neurogenetics Branch, Bethesda, MD, USA
Neurology 79:123-6. 2012..To utilize high-throughput sequencing to determine the etiology of juvenile-onset neurodegeneration in a 19-year-old woman with progressive motor and cognitive decline... - Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genesJennifer J Johnston
Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Am J Hum Genet 91:97-108. 2012.... - An intermediate grade of finished genomic sequence suitable for comparative analysesRobert W Blakesley
NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Genome Res 14:2235-44. 2004..Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses... - Incidental medical information in whole-exome sequencingBenjamin D Solomon
Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Pediatrics 129:e1605-11. 2012.... - Personalized genomic medicine: lessons from the exomeBenjamin D Solomon
Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Mol Genet Metab 104:189-91. 2011.... - Exome sequencing and SNP analysis detect novel compound heterozygosity in fatty acid hydroxylase-associated neurodegenerationTyler Mark Pierson
NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, 35 Convent Drive, Bethesda, MD 20892
Eur J Hum Genet 20:476-9. 2012..The presence of a sural nerve axonal neuropathy had not been previously associated with this disorder and so may extend the phenotype... - Correlation of rare coding variants in the gene encoding human glucokinase regulatory protein with phenotypic, cellular, and kinetic outcomesMatthew G Rees
National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
J Clin Invest 122:205-17. 2012..In sum, this study utilizes computational, cell biological, and biochemical methods to present a model for interpreting the clinical significance of rare genetic variants in common disease... - 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... - The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicineLeslie G Biesecker
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Genome Res 19:1665-74. 2009..The early experiences with ClinSeq illustrate how large-scale medical sequencing can be a practical, productive, and critical component of research in genomic medicine... - VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computerJamie K Teer
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Bioinformatics 28:599-600. 2012..Availability and Implementation: VarSifter is written in Java, and is freely available in source and binary versions, along with a User Guide, at http://research.nhgri.nih.gov/software/VarSifter/... - Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palateJennifer J Johnston
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 4472, USA
Am J Hum Genet 86:743-8. 2010..We conclude that massively parallel sequencing is useful to characterize large candidate linkage intervals and that it can be used successfully to allow identification of disease-causing gene mutations... 
Analysis of DNA sequence variants detected by high-throughput sequencingDavid R Adams
NIH Undiagnosed Diseases Program, NIH, Bethesda, Maryland, USA
Hum Mutat 33:599-608. 2012..The article is designed to provide an analytic roadmap for variant analysis, thereby enabling a wide range of researchers and clinical genetics practitioners to perform direct analysis of HTS data for their patients and projects...- Genomic features defining exonic variants that modulate splicingAdam Woolfe
Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20892, USA
Genome Biol 11:R20. 2010..In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative... - 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.... - 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... - 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... - A mosaic activating mutation in AKT1 associated with the Proteus syndromeMarjorie J Lindhurst
National Human Genome Research Institute, Bethesda, Maryland, USA
N Engl J Med 365:611-9. 2011..The Proteus syndrome is characterized by the overgrowth of skin, connective tissue, brain, and other tissues. It has been hypothesized that the syndrome is caused by somatic mosaicism for a mutation that is lethal in the nonmosaic state... - 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... - Exome sequencing: the sweet spot before whole genomesJamie K Teer
Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, 5625 Fishers Lane, Bethesda, MD 20892, USA
Hum Mol Genet 19:R145-51. 2010..In this review, we briefly describe some of the methodologies currently used for genomic and exome capture and highlight recent applications of this technology... - Mutations in the lysosomal enzyme-targeting pathway and persistent stutteringChangsoo Kang
National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
N Engl J Med 362:677-85. 2010..Genetic factors have been implicated in this disorder, and previous studies of stuttering have identified linkage to markers on chromosome 12... - Circadian changes in long noncoding RNAs in the pineal glandSteven L Coon
Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 109:13319-24. 2012..Organ culture studies indicate that expression of these lncRNAs is regulated by norepinephrine acting through cAMP. These findings point to a dynamic role of lncRNAs in the circadian system... - 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... - The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseasesWilliam A Gahl
NIH Undiagnosed Diseases Program, NIH, Bethesda, Maryland, USA
Genet Med 14:51-9. 2012..This report describes the National Institutes of Health Undiagnosed Diseases Program, details the Program's application of genomic technology to establish diagnoses, and details the Program's success rate during its first 2 years... - Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sitesGregory E Crawford
Genome Technology Branch and National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 101:992-7. 2004....