Thomas Brody

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Cis-regulatory complexity within a large non-coding region in the Drosophila genome
    Mukta Kundu
    Neural Cell Fate Determinants Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 8:e60137. 2013
  2. pmc Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, Maryland 20892, USA
    Dev Dyn 241:169-89. 2012
  3. pmc Horizontal gene transfers link a human MRSA pathogen to contagious bovine mastitis bacteria
    Thomas Brody
    The Neural Cell Fate Determinants Section, National Institutes of Health NIH, Bethesda, Maryland, USA
    PLoS ONE 3:e3074. 2008
  4. pmc Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, Maryland, USA
    BMC Genomics 9:371. 2008
  5. ncbi request reprint Regulation of temporal identities during Drosophila neuroblast lineage development
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, Maryland, USA
    Curr Opin Cell Biol 17:672-5. 2005
  6. pmc cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, MD 20892, USA
    Genome Biol 8:R75. 2007
  7. pmc Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis
    Amarendra S Yavatkar
    1Division of Intramural Research, Information Technology Program, NINDS, NIH, Bethesda, Maryland, USA
    BMC Genomics 9:106. 2008
  8. doi request reprint Conserved sequence block clustering and flanking inter-cluster flexibility delineate enhancers that regulate nerfin-1 expression during Drosophila CNS development
    Alexander Kuzin
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
    Gene Expr Patterns 9:65-72. 2009
  9. pmc Functional analysis of conserved sequences within a temporally restricted neural precursor cell enhancer
    Alexander Kuzin
    Neural Cell Fate Determinants Section, NINDS, NIH Bethesda, MD, USA
    Mech Dev 128:165-77. 2011
  10. pmc EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA
    Ward F Odenwald
    Neural Cell Fate Determinants Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:14700-5. 2005

Detail Information

Publications15

  1. pmc Cis-regulatory complexity within a large non-coding region in the Drosophila genome
    Mukta Kundu
    Neural Cell Fate Determinants Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 8:e60137. 2013
    ..By extending these results to the rest of the Drosophila genome, which contains over 70,000 non-coding CSB clusters, we suggest that most function as enhancers...
  2. pmc Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, Maryland 20892, USA
    Dev Dyn 241:169-89. 2012
    ..Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs...
  3. pmc Horizontal gene transfers link a human MRSA pathogen to contagious bovine mastitis bacteria
    Thomas Brody
    The Neural Cell Fate Determinants Section, National Institutes of Health NIH, Bethesda, Maryland, USA
    PLoS ONE 3:e3074. 2008
    ..We have adapted the multi-genome alignment tool EvoPrinter to facilitate discovery of HGT DNA sequences within bacterial genomes and within their mobile genetic elements...
  4. pmc Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, Maryland, USA
    BMC Genomics 9:371. 2008
    ..We describe the use of EvoPrinter and cis-Decoder, a suite of interrelated phylogenetic footprinting and alignment programs, to characterize highly conserved sequences that are shared among co-regulating enhancers...
  5. ncbi request reprint Regulation of temporal identities during Drosophila neuroblast lineage development
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, Maryland, USA
    Curr Opin Cell Biol 17:672-5. 2005
    ..Recent studies shed light on regulatory inputs and timing mechanisms that generate temporally defined cell identities, and new contributions are beginning to establish a link between the temporal network and cell function...
  6. pmc cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
    Thomas Brody
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, MD 20892, USA
    Genome Biol 8:R75. 2007
    ..Our findings suggest that enhancers employ overlapping repertoires of highly conserved core elements...
  7. pmc Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis
    Amarendra S Yavatkar
    1Division of Intramural Research, Information Technology Program, NINDS, NIH, Bethesda, Maryland, USA
    BMC Genomics 9:106. 2008
    ..An EvoPrint reveals with near base-pair resolution those sequences that are essential for gene function...
  8. doi request reprint Conserved sequence block clustering and flanking inter-cluster flexibility delineate enhancers that regulate nerfin-1 expression during Drosophila CNS development
    Alexander Kuzin
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
    Gene Expr Patterns 9:65-72. 2009
    ..In summary, EvoPrinter facilitates the discovery and analysis of enhancers that control crucial aspects of nerfin-1 expression...
  9. pmc Functional analysis of conserved sequences within a temporally restricted neural precursor cell enhancer
    Alexander Kuzin
    Neural Cell Fate Determinants Section, NINDS, NIH Bethesda, MD, USA
    Mech Dev 128:165-77. 2011
    ..Our work also points to an unexpectedly large number of TFs required for optimal enhancer function - mutant TF analysis has identified at least four that are required for full enhancer regulation...
  10. pmc EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA
    Ward F Odenwald
    Neural Cell Fate Determinants Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:14700-5. 2005
    ..Also, evoprinter allows one to assess the degree of evolutionary divergence between orthologous DNAs by highlighting differences between a selected species and the other test species...
  11. ncbi request reprint Cellular diversity in the developing nervous system: a temporal view from Drosophila
    Thomas Brody
    The Neurogenetics Unit, Laboratory of Neurochemistry, NINDS, NIH, Bethesda, MD, USA
    Development 129:3763-70. 2002
    ..Further investigation of the genetic programs that guide both invertebrate and vertebrate neural precursor cell lineage development will ultimately lead to an understanding of the molecular events that control neuronal diversity...
  12. pmc The cis-regulatory dynamics of the Drosophila CNS determinant castor are controlled by multiple sub-pattern enhancers
    Alexander Kuzin
    Neural Cell Fate Determinants Section, NINDS, NIH 9000 Rockville Pike, Bethesda, MD 20892, USA
    Gene Expr Patterns 12:261-72. 2012
    ..Cas limits the expression of one enhancer while two others require cas function for full expression. These studies represent a starting point for the further analysis of cas gene expression and the TFs that regulate it...
  13. pmc The Drosophila nerfin-1 mRNA requires multiple microRNAs to regulate its spatial and temporal translation dynamics in the developing nervous system
    Alexander Kuzin
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
    Dev Biol 310:35-43. 2007
    ....
  14. ncbi request reprint Nerfin-1 is required for early axon guidance decisions in the developing Drosophila CNS
    Alexander Kuzin
    Neural Cell Fate Determinants Section, NINDS, NIH, Bethesda MD 20892 4160, USA
    Dev Biol 277:347-65. 2005
    ..Our studies also show that Nerfin-1 is essential for the proper expression of robo2, wnt5, derailed, G-oalpha47A, Lar, and futsch, genes whose encoded proteins participate in these early navigational events...
  15. ncbi request reprint Identification of novel Drosophila neural precursor genes using a differential embryonic head cDNA screen
    Thomas Brody
    The Neurogenetics Unit, Laboratory of Neurochemistry, NINDS, NIH, Building 36, Room 4D02, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Mech Dev 113:41-59. 2002
    ..bio.purdue.edu/fly/brain/ahome.htm)...