2009
Huda, A., Mariño-Ramírez, L. and I.K. Jordan, 2009. Epigenetic histone modifications of human transposable elements: genome defense versus exaptation.
Mobile DNA in press
Wang, J., Bowen, N.J., Mariño-Ramírez, L. and I.K. Jordan, 2009. A c-Myc regulatory subnetwork from human transposable element sequences.
Molecular BioSystems in press
Huda, A. and I.K. Jordan, 2009. Epigenetic regulation of mammalian genomes by transposable elements.
Ann. NY. Acad. Sci. 1178: 276-284
[PDF]
Katz, L.S., Bolen, C.R., Harcourt B.H., Schmink S., Wang X., Kislyuk, A., Taylor, R.T., Mayer, L.W. and I.K. Jordan, 2009. Meningococcus Genome Informatics Platform: a system for analyzing multilocus sequence typing data.
Nucleic Acids Res 37: W606-W611
[PubMed] [PDF] [Google Scholar]
Huda, A., Mariño-Ramírez, L., Landsman, D. and I.K. Jordan, 2009. Repetitive DNA elements, nucleosome binding and human gene expression.
Gene 436: 12-22
[PubMed] [PDF] [Google Scholar]
Huda, A. and I.K. Jordan, 2009. Analysis of transposable element sequences using CENSOR and RepeatMasker.
Methods Mol. Biol. 537: 323-336
[PubMed] [PDF] [Google Scholar]
2008
Jordan, I.K., Kota, K.C., Cui, G., Thompson, C.H. and N.A. McCarty, 2008. Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters.
Proc. Natl. Acad. Sci. USA 105: 18865-18870
[PubMed] [PDF] [Supplement] [Google Scholar]
Jordan, I.K., Katz, L.S., Denver, D.R. and J.T. Streelman, 2008. Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans.
BMC Systems Biology 2: 96
[PubMed] [PDF] [Google Scholar]
Jordan, I.K. and W.M. Miller, 2008. Genome defense against transposable elements and the origins of regulatory RNA. in Genome Dynamics and Stability, (Lankenau, D.H. and S. Scharz eds.) Springer, Berlin
[Abstract] [PDF]
Jordan, I.K. and E.V. Koonin, 2008. Comparative human genomics. in Handbook of Human Molecular Evolution, (Cooper, D.N. and H. Kehrer-Sawatzki eds.) John Wiley and Sons, London
Conley, A.B., Piriyapongsa, J. and I.K. Jordan, 2008. Retroviral promoters in the human genome.
Bioinformatics 24: 1563-1567
[Abstract] [PDF] [Supplement] [Google Scholar]
Polavarapu, N., Mariño-Ramírez, L., Landsman, D., McDonald, J.F. and I.K. Jordan, 2008. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.
BMC Genomics 9: 226
[Abstract] [PDF] [Google Scholar]
Antezana, M. and I.K. Jordan, 2008. Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes.
PLoS ONE 3: e2145
[Abstract] [PDF] [Google Scholar]
Piriyapongsa, J. and I.K. Jordan, 2008. Dual coding of siRNAs and miRNAs by plant transposable elements.
RNA 14: 814-821
[Abstract] [PDF] [Supplement] [Google Scholar]
Huda, A., Polavarapu, N., Jordan, I.K. and J.F. McDonald, 2008. Endogenous retroviruses of the chicken genome.
Biol. Direct 3: 9
[Abstract] [PDF] [Google Scholar]
Conley, A.B., Miller, W.J. and I.K. Jordan, 2008. Human cis natural antisense transcripts initiated by transposable elements.
Trends Genet. 24: 53-56
[Abstract] [PDF] [Supplement] [Google Scholar]
2007
Piriyapongsa, J., Rutledge, M.T., Patel, S., Borodovsky, M. and I.K. Jordan, 2007. Evaluating the protein coding potential of exonized transposable element sequences.
Biol. Direct 2: 31
[Abstract] [PDF] [Google Scholar]
Bowen, N.J. and I.K. Jordan, 2007. Exaptation of protein coding sequences from transposable elements.
Genome Dynamics 3: 131-146
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and L. Mariño-Ramírez, 2007. Evolutionary genomics of gene expression. pp.235-252 in Structural approaches to sequence evolution: Molecules, networks, populations, (Bastolla, U., Porto, M., Roman, H.E. and M. Vendruscolo eds.), Springer, New York
[PDF] [Amazon]
Piriyapongsa, J., Mariño-Ramírez, L. and I.K. Jordan, 2007. Origin and evolution of human microRNAs from transposable elements.
Genetics 176: 1323-1337
[Abstract] [PDF] [Supplement] [Google Scholar]
Piriyapongsa, J. and I.K. Jordan, 2007. A family of human microRNA genes from miniature-inverted repeat transposable elements.
PLoS ONE 2: e203
[Abstract] [PDF] [Supplement] [Google Scholar]
2006
Mariño-Ramírez, L., Jordan, I.K. and D. Landsman, 2006. Multiple independent evolutionary solutions to core histone gene regulation.
Genome Biol. 7: R122
[Abstract] [PDF] [Supplement] [Google Scholar]
Mariño-Ramírez, L., Bodenreider, O., Kantz, N. and I.K. Jordan, 2006. Co-evolutionary rates of functionally related yeast genes.
Evol. Bioinform. Online 2: 295-300
[Abstract] [PDF] [Google Scholar]
Tsaparas, P., Mariño-Ramírez, L., Bodenreider, O., Koonin, E.V. and I.K. Jordan, 2006. Global similarity and local divergence in human and mouse gene co-expression networks.
BMC Evol. Biol. 6: 70
[Abstract] [PDF] [Supplement] [Google Scholar]
Jordan I.K., Kondrashov F.A., Adzhubei I.A., Wolf Y.I., Koonin E.V., Kondrashov A.S. and S. Sunyaev, 2006. Protein evolution: Causes of trends in amino-acid gain and loss (Reply).
Nature 442: E12
[PDF] [Google Scholar]
Mariño-Ramírez, L. and I.K. Jordan, 2006. Transposable element derived DNaseI-hypersensitive sites in the human genome.
Biol. Direct 1:20
[Abstract] [PDF] [Google Scholar]
I.K Jordan, 2006. Evolutionary tinkering with transposable elements.
Proc. Natl. Acad. Sci. USA 96: 12621-12625
[Abstract] [PDF] [Google Scholar]
2005
Mariño-Ramírez, L., Lewis, K.C., Landsman, D. and I.K. Jordan, 2005. Transposable elements donate lineage-specific regulatory elements to host genomes.
Cytogenet. Genome Res. 110: 333-341
[Abstract] [PDF] [Google Scholar]
Rogozin, I.B., Basu, M.K., Jordan, I.K., Pavlov, Y.I. and E.V. Koonin, 2005. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis.
Cell Cycle 4: 1281-1285
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Mariño-Ramírez, L. and E.V. Koonin, 2005. Evolutionary significance of gene expression divergence.
Gene 345: 119-126
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Kondrashov F.A., Adzhubei I.A., Wolf Y.I., Koonin E.V., Kondrashov A.S. and S. Sunyaev, 2005. A universal trend of amino acid gain and loss in protein evolution.
Nature 433: 633-638
[Abstract] [PDF] [Supplement] [Google Scholar]
2004
Jordan, I.K., Mariño-Ramírez, L., Wolf, Y.I. and E.V. Koonin, 2004. Conservation and co-evolution in the scale-free human gene co-expression network.
Mol. Biol. Evol. 21: 2058-2070
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Wolf Y.I. and E.V. Koonin, 2004. Duplicated genes evolve slower than singletons despite the initial rate increase.
BMC Evol Biol. 4: 22
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and E.V. Koonin, 2004. Horizontal transfer and prokaryotic genome evolution. Microbial Evolution: Gene Establishment, Survival and Exchange (Day, M. and B. Miller eds.), ASM Press, Washington, DC
[Amazon] [Google Scholar]
Jordan, I.K. and N.J. Bowen, 2004. Computational analysis of transposable element sequences.
Methods Mol. Biol. 260: 59-71
[Abstract] [PDF] [Google Scholar]
2003
Bowen, N.J., Jordan, I.K., Epstein, J.A., Wood, V. and H.L. Levin, 2003. Retrotransposons and their recognition of pol II promoters: A comprehensive survey of the transposable elements derived from the complete genome sequence of Schizosaccharomyces pombe.
Genome Res. 13: 1984-1997
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and E.V. Koonin, 2003. Comparative genomics. Encyclopedia of the Human Genome 1: 897-903 (Cooper, D.N. and M. Calais eds.), Nature Publishing, London, UK
[PDF] [Amazon]
Jordan, I.K., Henze, K., Fedorova, N.D., Koonin, E.V. and M.Y. Galperin, 2003. Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes.
J. Mol. Microbiol. Biotechnol. 5: 172-189
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Rogozin I.B., Glazko G.V. and E.V. Koonin, 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements.
Trends Genet. 19: 68-72
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Wolf, Y.I. and E.V. Koonin, 2003. No simple dependence between protein evolutionary rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly.
BMC Evolutionary Biology 3: 1
[Abstract] [PDF] [Google Scholar]
2002
Jiang N., Jordan I.K. and S.R. Wessler, 2002. Dasheng and RIRE2: a non-autonomous LTR element and its putative autonomous partner in the rice genome.
Plant Physiol. 130: 1697-1705
[Abstract] [PDF] [Google Scholar]
Bowen, N.J. and I.K. Jordan, 2002. Transposable elements and the evolution of eukaryotic complexity.
Curr. Issues Mol. Biol. 4: 65-76
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and J.F. McDonald, 2002. A biologically active family of human endogeneous retroviruses (HERVs) evolved from an ancient inactive lineage.
Genome Lett. 1: 105-109
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Rogozin, I.B., Wolf, Y.I. and E.V. Koonin, 2002. Microevolutionary genomics of bacteria.
Theor. Popul. Biol. 61: 435-447
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Rogozin, I.B., Wolf, Y.I. and E.V. Koonin, 2002. Essential genes are more evolutionarily conserved than non-essential genes in bacteria.
Genome Res. 12: 962-968
[Abstract] [PDF] [Google Scholar]
Rogozin, I.B., Spiridonov, A.N., Sorokin, A.V., Wolf, Y.I., Jordan, I.K., Tatusov, R.L. and E.V. Koonin, 2002. Purifying and directional selection in overlapping prokaryotic genes.
Trends Genet. 18: 228-232
[Abstract] [PDF] [Google Scholar]
2001
Jordan, I.K., Kondrashov, F.A., Rogozin, I.B., Tatusov, R.L., Wolf, Y.I. and E.V. Koonin, 2001. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
Genome Biology 2: 0053.1-0053.9
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Natale, D.A., Koonin, E.V. and M.Y. Galperin, 2001. Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases.
J. Mol. Evol. 53:622-633
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Bishop, G.R. and D.S. Gonzalez, 2001. Sequence and structural aspects of functional diversification in class I alpha-mannosidase evolution.
Bioinformatics 17: 965-976
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Makarova, K.S., Spouge, J.L., Wolf, Y.I. and E.V. Koonin, 2001. Lineage-specific gene expansions in bacterial and archaeal genomes.
Genome Res. 11: 555-565
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Makarova, K.S., Wolf, Y.I. and E.V. Koonin, 2001. Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae.
Trends Genet. 17: 7-10
[Abstract] [PDF] [Google Scholar]
2000
Jordan, I.K., Natale, D.A. and M.Y. Galperin, 2000. Copper chaperones in bacteria: association with copper-transporting ATPases.
Trends Biochem. Sci. 25: 480-481
[Abstract] [PDF] [Google Scholar]
Gonzalez, D.S. and I.K. Jordan, 2000. The alpha-mannosidases: phylogeny and adaptive diversification.
Mol. Biol. Evol. 17: 292-300
[Abstract] [PDF] [Google Scholar]
Jordan, I.K., Sutter, B.A. and M.A. McClure, 2000. Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple protein encoding P gene.
Mol. Biol. Evol. 17: 75-86
[Abstract] [PDF] [Google Scholar]
1999
Jordan, I.K. and J.F. McDonald, 1999. Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements.
Genetica 107: 3-13
[Abstract] [PDF] [Google Scholar]
Promislow, D.E.L., Jordan, I.K. and J.F. McDonald, 1999. Genomic demography: A life history analysis of transposable element evolution.
Proc. Roy. Soc. Lon. B Biol. 266: 1555-1560
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and J.F. McDonald, 1999. Evidence for the recent horizontal transfer of a long terminal repeat retrotransposon.
Proc. Natl. Acad. Sci. USA 96: 12621-12625
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and J.F. McDonald, 1999. The role of interelement selection in Saccharomyces cerevisiae Ty element evolution.
J. Mol. Evol. 49: 352-357
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and J.F. McDonald, 1999. Tempo and mode of Ty element evolution in Saccharomyces cerevisiae.
Genetics 151: 1341-1351
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and J.F. McDonald, 1999. Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome.
Mol. Biol. Evol. 16: 419-422
[Abstract] [PDF] [Google Scholar]
1998
Jordan, I.K. and J.F. McDonald, 1998. Inter-element selection in the regulatory region of the copia retrotransposon.
J. Mol. Evol. 47: 670-676
[Abstract] [PDF] [Google Scholar]
Jordan , I.K. and J.F. McDonald, 1998. Evolution of the copia retrotransposon in the Drosophila melanogaster species subgroup.
Mol. Biol. Evol. 15: 1160-1171
[Abstract] [PDF] [Google Scholar]
Jordan, I.K. and J.F. McDonald, 1998. Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements.
J. Mol. Evol. 47: 14-20
[Abstract] [PDF] [Google Scholar]
1997
McDonald, J.F., Matyunina, L.V., Wilson, S., Jordan, I.K., Bowen, N.J. and W.J. Miller, 1997. LTR retrotransposons and the evolution of eukaryotic enhancers.
Genetica 100: 3-13
[Abstract] [PDF] [Google Scholar]
1996
Matyunina, LV., Jordan, I.K. and J.F. McDonald, 1996. Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation.
Proc. Natl. Acad. Sci. USA 93: 7097-7102
[Abstract] [PDF] [Google Scholar]