I K Jordan

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Origin of a substantial fraction of human regulatory sequences from transposable elements
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A Room N511M, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Trends Genet 19:68-72. 2003
  2. pmc No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 3:1. 2003
  3. pmc Evolutionary tinkering with transposable elements
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 103:7941-2. 2006
  4. pmc Evolutionary significance of gene expression divergence
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health 8600 Rockville Pike, Bldg 38A Room 5N511 M, Bethesda, MD 20894, USA
    Gene 345:119-26. 2005
  5. pmc Duplicated genes evolve slower than singletons despite the initial rate increase
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 4:22. 2004
  6. pmc Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894, USA
    Genome Biol 2:RESEARCH0053. 2001
  7. pmc Lineage-specific gene expansions in bacterial and archaeal genomes
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 11:555-65. 2001
  8. ncbi request reprint Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae
    I K Jordan
    National Center for Biotechnology Information, National Institutes of Health, Building 38A Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Trends Genet 17:7-10. 2001
  9. ncbi request reprint Sequence and structural aspects of functional diversification in class I alpha-mannosidase evolution
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 17:965-76. 2001
  10. ncbi request reprint Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genetica 107:3-13. 1999

Detail Information

Publications31

  1. ncbi request reprint Origin of a substantial fraction of human regulatory sequences from transposable elements
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A Room N511M, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Trends Genet 19:68-72. 2003
    ..Thus, TEs have probably contributed substantially to the evolution of both gene-specific and global patterns of human gene regulation...
  2. pmc No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 3:1. 2003
    ..However, the extent to which the number of protein-protein interactions influences evolutionary rates remains unclear. Here, we address this question at several different levels of evolutionary relatedness...
  3. pmc Evolutionary tinkering with transposable elements
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 103:7941-2. 2006
  4. pmc Evolutionary significance of gene expression divergence
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health 8600 Rockville Pike, Bldg 38A Room 5N511 M, Bethesda, MD 20894, USA
    Gene 345:119-26. 2005
    ..Taken together, these results indicate that gene expression divergence is subject to the effects of purifying selective constraint and suggest that it might also be substantially influenced by positive Darwinian selection...
  5. pmc Duplicated genes evolve slower than singletons despite the initial rate increase
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 4:22. 2004
    ..It has been shown that, shortly after the duplication, genes seem to experience a considerable relaxation of purifying selection...
  6. pmc Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894, USA
    Genome Biol 2:RESEARCH0053. 2001
    ..muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat)...
  7. pmc Lineage-specific gene expansions in bacterial and archaeal genomes
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 11:555-65. 2001
    ..The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss...
  8. ncbi request reprint Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae
    I K Jordan
    National Center for Biotechnology Information, National Institutes of Health, Building 38A Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Trends Genet 17:7-10. 2001
    ..pylori strains and two C. pneumoniae strains, we identify multiple independent conversions among these genes. Such recombination events might provide a selective advantage for these bacterial pathogens...
  9. ncbi request reprint Sequence and structural aspects of functional diversification in class I alpha-mannosidase evolution
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 17:965-76. 2001
    ..Thus diversifying selection between the two groups may have acted in a gradual manner consistent with the Darwinian model of natural selection. CONTACT: bishogr@millsaps.edu...
  10. ncbi request reprint Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genetica 107:3-13. 1999
    ..The evolutionary dynamics of S. cerevisae Ty elements uncovered by our analyses are discussed with respect to selection among elements and the interaction between the elements and their host genome...
  11. ncbi request reprint Purifying and directional selection in overlapping prokaryotic genes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 18:228-32. 2002
    ..This could be a general evolutionary mode for genes emerging from noncoding sequences, in which the protein sequence has not been subject to selection...
  12. ncbi request reprint Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Evol 53:622-33. 2001
    ..Copper chaperone-Cu-ATPase operons appear to have evolved independently in different prokaryotic lineages, probably due to a strong selective pressure for coexpression of these genes...
  13. pmc Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe
    Nathan J Bowen
    Section on Eukaryotic Transposable Elements, Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development NICHD, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    Genome Res 13:1984-97. 2003
    ..Finally we describe a novel repetitive sequence, wtf, which was also preferentially located on chromosome III, and was often located near solo LTRs of Tf elements...
  14. ncbi request reprint Conservation and coevolution in the scale-free human gene coexpression network
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health Bethesda, Maryland, USA
    Mol Biol Evol 21:2058-70. 2004
    ....
  15. pmc Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Res 12:962-8. 2002
    ..In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales...
  16. ncbi request reprint Transposable elements and the evolution of eukaryotic complexity
    Nathan J Bowen
    Section on Eukaryotic Transposable Elements, Laboratory of Eukaryotic Gene Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Curr Issues Mol Biol 4:65-76. 2002
    ..A number of specific scenarios are presented that implicate transposable elements in the evolution of the complex molecular and cellular machinery that are characteristic of the eukaryotic domain of life...
  17. ncbi request reprint A universal trend of amino acid gain and loss in protein evolution
    I King Jordan
    National Center for Biotechnology Information, NIH, Bethesda, Maryland 20894, USA
    Nature 433:633-8. 2005
    ..Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day...
  18. pmc Multiple independent evolutionary solutions to core histone gene regulation
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 6075, USA
    Genome Biol 7:R122. 2006
    ..Core histone genes are periodically expressed along the cell cycle and peak during S phase. Core histone gene expression is deeply evolutionarily conserved from the yeast Saccharomyces cerevisiae to human...
  19. ncbi request reprint Computational analysis of transposable element sequences
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 260:59-71. 2004
    ..The emphasis is placed on the identification, retrieval and manipulation of TE sequences. Information is also provided on the evolutionary study of TE sequences including the use phylogenetics programs...
  20. pmc Transposable elements donate lineage-specific regulatory sequences to host genomes
    L Mariño-Ramírez
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Cytogenet Genome Res 110:333-41. 2005
    ..This suggests a particular mechanism by which TEs may drive the diversification of gene regulation between evolutionary lineages...
  21. ncbi request reprint APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis
    Igor B Rogozin
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 4:1281-5. 2005
    ..In mammals, APOBEC4 is expressed primarily in testis which suggests the possibility that it is an editing enzyme for mRNAs involved in spermatogenesis...
  22. ncbi request reprint Microevolutionary genomics of bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Theor Popul Biol 61:435-47. 2002
    ..This suggests the possibility that nonessential genes are responsible for driving the evolutionary diversification between strains...
  23. ncbi request reprint Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Microbiol Biotechnol 5:172-89. 2003
    ....
  24. pmc Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Plant Physiol 130:1697-705. 2002
    ..Consistent with this hypothesis, transcripts from both elements were found in the same expressed sequence tag library...
  25. pmc 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...
  26. pmc 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...
  27. doi request reprint 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. pmc 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...
  29. pmc 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...
  30. doi request reprint 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
    ..We analyzed genome sequence and high-throughput expression data to systematically evaluate the presence of retroviral promoters in the human genome...
  31. pmc Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes
    Marcos A Antezana
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 3:e2145. 2008
    ..Therefore, the non-coding DNA of vertebrates may have been shaped by NBDM only epiphenomenally, with non-genic DNA being affected mainly when found in the proximity of genes...