I King Jordan

Summary

Affiliation: Georgia Institute of Technology
Country: USA

Publications

  1. ncbi Transcription factor binding sites are highly enriched within microRNA precursor sequences
    Jittima Piriyapongsa
    Genome Institute, National Center for Genetic Engineering and Biotechnology, Klong1, Klong Luang, Pathumthani 12120, Thailand
    Biol Direct 6:61. 2011
  2. ncbi Evaluating the protein coding potential of exonized transposable element sequences
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Biol Direct 2:31. 2007
  3. ncbi Global similarity and local divergence in human and mouse gene co-expression networks
    Panayiotis Tsaparas
    Basic Research Unit, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
    BMC Evol Biol 6:70. 2006
  4. ncbi Epigenetic histone modifications of human transposable elements: genome defense versus exaptation
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
    Mob DNA 1:2. 2010
  5. ncbi Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans
    I King Jordan
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    BMC Syst Biol 2:96. 2008
  6. ncbi Repetitive DNA elements, nucleosome binding and human gene expression
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Gene 436:12-22. 2009
  7. ncbi Neisseria Base: a comparative genomics database for Neisseria meningitidis
    Lee S Katz
    School of Biology, Georgia Institute of Technology, USA
    Database (Oxford) 2011:bar035. 2011
  8. ncbi Endogenous retroviruses of the chicken genome
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Biol Direct 3:9. 2008
  9. ncbi Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
    Nalini Polavarapu
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    BMC Genomics 9:226. 2008
  10. ncbi Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq
    Andrew B Conley
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Methods Mol Biol 674:225-40. 2010

Detail Information

Publications30

  1. ncbi Transcription factor binding sites are highly enriched within microRNA precursor sequences
    Jittima Piriyapongsa
    Genome Institute, National Center for Genetic Engineering and Biotechnology, Klong1, Klong Luang, Pathumthani 12120, Thailand
    Biol Direct 6:61. 2011
    ..However, in the course of analyzing the genomics of human microRNA genes, we noticed that annotated transcription factor binding sites commonly lie within 70- to 110-nt long microRNA small hairpin precursor sequences...
  2. ncbi Evaluating the protein coding potential of exonized transposable element sequences
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Biol Direct 2:31. 2007
    ....
  3. ncbi Global similarity and local divergence in human and mouse gene co-expression networks
    Panayiotis Tsaparas
    Basic Research Unit, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
    BMC Evol Biol 6:70. 2006
    ..Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species...
  4. ncbi Epigenetic histone modifications of human transposable elements: genome defense versus exaptation
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
    Mob DNA 1:2. 2010
    ..To date, all available evidence points to the genome defense hypothesis as the best explanation for the biological role of TE epigenetic modifications...
  5. ncbi Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans
    I King Jordan
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    BMC Syst Biol 2:96. 2008
    ..elegans mutation accumulation (MA) lines evolve essentially free from the effects of natural selection, whereas natural isolate (NI) populations are subject to selective constraints...
  6. ncbi Repetitive DNA elements, nucleosome binding and human gene expression
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Gene 436:12-22. 2009
    ..These observations indicate that repetitive DNA elements mediate chromatin accessibility in proximal promoter regions and the repeat content of promoters is relevant to both gene expression and function...
  7. ncbi Neisseria Base: a comparative genomics database for Neisseria meningitidis
    Lee S Katz
    School of Biology, Georgia Institute of Technology, USA
    Database (Oxford) 2011:bar035. 2011
    ..Using the virulent ST-11 lineage as an example, we demonstrate how this comparative genomics utility can be used to identify novel genomic markers for molecular profiling of N. meningitidis...
  8. ncbi Endogenous retroviruses of the chicken genome
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Biol Direct 3:9. 2008
    ..The abundance and diversity of chicken ERVs we discovered underscore the utility of an approach that combines multiple methods for the identification of interspersed repeats in vertebrate genomes...
  9. ncbi Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
    Nalini Polavarapu
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    BMC Genomics 9:226. 2008
    ..We also evaluated the position-specific patterns of variation among TFBS to look for signs of functional constraint on TFBS derived from repetitive and non-repetitive DNA...
  10. ncbi Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq
    Andrew B Conley
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Methods Mol Biol 674:225-40. 2010
    ..Many of these TE-derived TFBS show poor conservation and would go unnoticed using conservation screens. Here, we describe a simple pipeline method for using data generated through ChIP-seq to identify TE-derived TFBS...
  11. ncbi A c-Myc regulatory subnetwork from human transposable element sequences
    Jianrong Wang
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Mol Biosyst 5:1831-9. 2009
    ..These data point to a substantial contribution of TEs to the regulation of human genes by c-Myc. Genes that are regulated by TE-derived c-Myc binding sites appear to form a distinct c-Myc regulatory subnetwork...
  12. ncbi Effect of the transposable element environment of human genes on gene length and expression
    Daudi Jjingo
    School of Biology, Georgia Institute of Technology, GA, USA
    Genome Biol Evol 3:259-71. 2011
    ..Our results confirm the overall relevance of the TE environment to gene expression and point to distinct mechanisms by which different TE families may contribute to gene regulation...
  13. ncbi A family of human microRNA genes from miniature inverted-repeat transposable elements
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS ONE 2:e203. 2007
    ..Finally, we propose that MITEs may represent an evolutionary link between siRNAs and miRNAs...
  14. ncbi A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags
    Jianrong Wang
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Bioinformatics 26:2501-8. 2010
    ..Such ambiguous tags are typically eliminated from consideration resulting in a potential loss of important biological information...
  15. ncbi Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis
    Lee S Katz
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    J Bacteriol 193:3633-41. 2011
    ..A number of overrepresented functional categories related to virulence were uncovered among SNP-associated genes, including genes related to the category "symbiosis, encompassing mutualism through parasitism."..
  16. ncbi Retroviral promoters in the human genome
    Andrew B Conley
    School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA
    Bioinformatics 24:1563-7. 2008
    ..These data illustrate the potential of retroviral sequences to regulate human transcription on a large scale consistent with a substantial effect of ERVs on the function and evolution of the human genome...
  17. ncbi A computational genomics pipeline for prokaryotic sequencing projects
    Andrey O Kislyuk
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Bioinformatics 26:1819-26. 2010
    ..biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems...
  18. ncbi Genome-wide prediction and analysis of human chromatin boundary elements
    Jianrong Wang
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Nucleic Acids Res 40:511-29. 2012
    ....
  19. ncbi Origin and evolution of human microRNAs from transposable elements
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    Genetics 176:1323-37. 2007
    ..Our results indicate that TEs provide a natural mechanism for the origination miRNAs that can contribute to regulatory divergence between species as well as a rich source for the discovery of as yet unknown miRNA genes...
  20. ncbi Dual coding of siRNAs and miRNAs by plant transposable elements
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 0230, USA
    RNA 14:814-21. 2008
    ..The siRNA-to-miRNA evolutionary transition is representative of a number of other regulatory mechanisms that evolved to silence TEs and were later co-opted to serve as regulators of host gene expression...
  21. ncbi Prediction of transposable element derived enhancers using chromatin modification profiles
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS ONE 6:e27513. 2011
    ....
  22. ncbi Epigenetic regulation of Mammalian genomes by transposable elements
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30306, USA
    Ann N Y Acad Sci 1178:276-84. 2009
    ..It is hoped that these proposed scenarios may help to serve as a roadmap for future investigations into the epigenetic regulatory effects of mammalian TEs...
  23. ncbi Analysis of transposable element sequences using CENSOR and RepeatMasker
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Methods Mol Biol 537:323-36. 2009
    ..We briefly consider the strengths and weaknesses of these different classes of methods with an emphasis on their complementary utility for the analysis of repetitive DNA in eukaryotes...
  24. ncbi Epigenetic regulation of transposable element derived human gene promoters
    Ahsan Huda
    School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
    Gene 475:39-48. 2011
    ....
  25. ncbi Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data
    Lee S Katz
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Nucleic Acids Res 37:W606-11. 2009
    ....
  26. ncbi A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences
    Amin A Momin
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    J Lipid Res 52:1073-83. 2011
    ....
  27. ncbi Human cis natural antisense transcripts initiated by transposable elements
    Andrew B Conley
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30306, USA
    Trends Genet 24:53-6. 2008
    ..The TE sequences that promote antisense transcription within human genes are relatively ancient, suggesting that selection has acted to conserve their function...
  28. ncbi Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal
    Jianrong Wang
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
    Cell Cycle 10:3016-30. 2011
    ..Stable suppression of Alu transcription can reverse the senescent phenotype, reinstating the cells' self-renewing properties and increasing their plasticity by altering so-called "master" pluripotency regulators...
  29. ncbi Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters
    I King Jordan
    School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
    Proc Natl Acad Sci U S A 105:18865-70. 2008
    ..This analysis sets the stage for understanding the evolutionary and functional relationships that make CFTR a unique ABC transporter protein...
  30. ncbi Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus
    I King Jordan
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia30333, USA
    J Bacteriol 193:5879-80. 2011
    ..Preliminary analyses indicate that these genome sequences encode markers that distinguish H. haemolyticus from its closest Haemophilus relatives and provide clues to the identity of its virulence factors...