Publications


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2017


Lopez, M.F., Niu, P., Wang, L., Vogelsang, M., Gaur, M., Krastins, B., Zhao, Y., Smagul, A., Nussupbekova, A., Akanov, A.A., Jordan, I.K., and Lunyak, V.V., 2016. Opposing activities of oncogenic MIR17HG and tumor suppressive MIR100HG clusters and their gene targets regulate replicative senescence in human adult stem cells.
NPJ Aging Mech Dis. In Press.

Sepúlveda-Torres L.d.C., Rishishwar L., Rogers M.L., Ríos-Olivares E., Boukli N., Jordan I.K., Cubano L.A. (2017) A decade of viral mutations and associated drug resistance in a population of HIV-1+ Puerto Ricans: 2002–2011
PLoS ONE. E 12(5): e0177452.
[PubMed] [PDF]

Rishishwar, L. and Jordan I.K., 2017. Implications of human evolution and admixture for mitochondrial replacement therapy.
BMC Genomics. 18: 140.
[PubMed] [PDF] [Google Scholar]

Rishishwar, L., Wang, L., Clayton, E.A., Mariño-Ramírez, L., McDonald, J.F. and Jordan I.K., 2017. Population and clinical genetics of human transposable elements in the (post) genomic era.
Mob Genet Elements. 7: 1-20.
[PDF] [Google Scholar]

Gupta, A., Jordan, I.K., Rishishwar, L., 2017. stringMLST: a fast k-mer based tool for multi locus sequence typing.
Bioinformatics. 33: 119-121.
[PubMed] [PDF] [Supplement] [Google Scholar] [GitHub]

2016


Wang, L., Rishishwar, L., Mariño-Ramírez, L. and Jordan I.K., 2016. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.
Nuc. Acids Res. In Press.
[PubMed] [PDF] [Google Scholar]

Rishishwar, L., Mariño-Ramírez, L., and Jordan, I.K., 2016. Benchmarking computational tools for polymorphic transposable element detection.
Brief Bioinform. doi: 10.1093/bib/bbw072
[PubMed] [PDF] [Supplement] [Google Scholar]

Clayton, E.A., Wang, L., Rishishwar, L., Wang, J., McDonald, J.F. and Jordan I.K., 2016. Patterns of transposable element expression and insertion in cancer.
Front. Mol. Biosci. 3: 76.
[PubMed] [PDF] [Supplement] [Google Scholar]

Watve, S., Chande, A.T., Rishishwar, L., Bernardy, E.E., Mariño-Ramírez, L., Jordan, I.K., Hammer, B.K., 2016. Whole genome sequence of 26 environmental Vibrio cholerae isolates.
Genome Announcements. 4: e01396-16
[PubMed] [PDF] [Google Scholar]

Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G.J., Jordan, I.K., Murphy, T.F., Gilsdorf, J.R., Mayer, L.W., and Wang, X., 2016. Comparative genomic analysis of Haemophilus haemolyticus and non-typeable Haemophilus influenzae and a new testing scheme for their discrimination.
J. Clin. Micro. 54: 3010-3017.
[PubMed] [PDF] [Supplement] [Google Scholar]

Orata, F.D., Xu, Y., Gladney, L.M., Rishishwar, L., Case, R.J., Boucher, Y., Jordan, I.K., Tarr, C.L., 2016. Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis.
Int J Syst Evol Microbiol. 66: 4148-4155.
[PubMed] [PDF] [Google Scholar]

Rishishwar, L., Kraft, C.S., Jordan, I.K., 2016. Population genomics of reduced vancomycin susceptibility in Staphylococcus aureus.
mSphere. 1: e00094-16
[PubMed] [PDF] [Google Scholar]

Jordan, I.K., 2016. The Columbian Exchange as a source of adaptive introgression in human populations.
Biol Direct. 11: 17
[PubMed] [PDF] [Google Scholar]

Hemme, C.L., Green, S.J., Rishishwar, L., Prakash, O., Pettenato, A., Chakraborty, R., Deutchbauer, A.M., Van Nostrand, J.D., Wu, L., He, L., Jordan, I.K., Hazen, T.C., Arkin, A.P., Kostka, J.E. and Zhou, J., 2016. Lateral gene transfer in a heavy metal-contaminated groundwater microbial community.
mBio. 7: e02234-15
[PubMed] [PDF] [Google Scholar]

Medina Rivas, M.A., Norris, E.T., Rishishwar, L., Conley, A.B., Medrano Trochez, C., Valderrama-Aguirre, A., Vannberg, F.O., Mariño-Ramírez, L., and Jordan, I.K., 2016. El Chocó Colombia: a hotspot of human biodiversity.
Rev. Biodivers. Neotrop. 6: 45-54
[PubMed] [PDF] [Cover Image] [Google Scholar]

2015


Rishishwar, L., Tellez Villa, C.E. and Jordan, I.K., 2015. Transposable element polymorphisms recapitulate human evolution.
Mob. DNA. 6: 21
[PubMed] [PDF] [Supplement] [Cover Image] [Google Scholar]

Rishishwar, L., Conley, A.B., Vidakovic, B. and Jordan, I.K., 2015. A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.
Gene. 574: 345-351
[PubMed] [PDF] [Supplement] [Google Scholar]

Niu, P., Smagul, A., Wang, L., Sadvakas, A., Sha, Y., Pérez, L.M., Nussupbekova, A., Amirbekov, A., Akanov, A.A., Gálvez, B.G., Jordan, I.K. and Lunyak, V., 2015. Transcriptional profiling of interleukin-2-primed human adipose derived mesenchymal stem cells revealed dramatic changes in stem cells response imposed by replicative senescence.
Oncotarget. 6: 17938-57.
[PubMed] [PDF] [Supplement PDF] [Supplement excel] [Google Scholar]

Wang, J., Vicente-García, C., Seruggia, D., Moltó, E., Fernandez-Miñán, A., Neto, A., Lee, E., Gómez-Skarmeta, J.L., Montoliu, L., Lunyak, V. and Jordan, I.K., 2015. MIR retotransposon sequences provide insulators to the human genome.
Proc. Natl. Acad. Sci. USA. 112: E4428-4437.
[PubMed] [PDF] [Supplement] [Google Scholar]

Rishishwar, L., Conley, A.B., Wigington, C.H., Wang, L., Valderrama-Aguirre, A. and Jordan, I.K., 2015. Ancestry, admixture and fitness in Colombian genomes.
Sci. Rep. 5: 12376
[PubMed] [PDF] [Supplement] [Google Scholar]

2014


Gladney, L.M., Katz, L., Knipe, K.M., Rowe, L., Conley, A.B., Rishishwar, L., Mariño-Ramírez, L., Jordan, I.K., and Tarr, C.L., 2014. Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen.
Genome Announcements. 2: e01188-14
[PubMed] [PDF] [Google Scholar]

Castillo, A., Wang, L., Koriyama, C., Eizuru, Y., Jordan, I.K., and Akiba, S., 2014. A systems biology analysis of the changes in gene expression via silencing of HPV-18 E1 expression in HeLa cells.
Open Biol. 4: 130119
[PubMed] [PDF] [Google Scholar]

Jjingo, D., Conley, A.B., Wang, J., Mariño-Ramírez, L., Lunyak, V.V., and Jordan, I.K., 2014. Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.
Mob DNA. 5: 14
[PubMed] [PDF] [Supplement] [Google Scholar]

Dunn, J., Qiu, H., Kim, S., Jjingo, D., Hoffman, R., Kim, C.W., Jang, I., Son, D.J., Kim, D., Pan, C., Fan, Y., Jordan, I.K., and Jo, H., 2014. Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis.
J Clin Invest. 124: 3187-3199
[PubMed] [PDF] [Supplement] [Google Scholar]

Hu, B., Ying, X., Wang, J., Piriyapongsa, J., Jordan, I.K., Sheng, J., Yu, F., Zhao, P., Li, Y., Wang, H., Ng, W.L., Hu, S., Wang, X., Wang, C., Zheng, X., Li, W., Curran, W.J., and Wang, Y., 2014. Identification of a tumor suppressive human specific microRNA within the FHIT tumor suppressor gene.
Cancer Res. 74: 2283-94
[PubMed] [PDF] [Google Scholar]

Rishishwar, L., Petit, R., Kraft, C.S., and Jordan, I.K., 2014. A genome sequence based discriminator for vancomycin-intermediate Staphylococcus aureus.
J Bacteriol. 196: 940-948
[PubMed] [PDF] [Supplement] [Google Scholar]

2013


Lopes, F.R., Jjingo, D., da Silva, C.R.M., Andrade, A.C., Marraccini, P., Teixeira, J.B., Carazzolle, M.F., Pereira, G.A.G., Pereira, L.P.F., Vanzela, A.L.L., Wang, L., Jordan, I.K., and Carareto, C.M.A., 2013. Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.
PLoS ONE 8: e78931
[PubMed] [PDF] [Google Scholar]

Jjingo, D., Wang, J., Conley, A.B., Lunyak, V.V., and Jordan, I.K, 2013. Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome.
Bioinformatics 29: 3109-3112
[PubMed] [PDF] [Supplement] [Google Scholar]

Zhoa, Y., Jordan, I.K. and Lunyak, V.V., 2013. Epigenetics components of aging in the central nervous system.
Neurotherapeutics 10: 647-663
[PubMed] [PDF] [Google Scholar]

Green, S., Rishishwar, L., Prakash, O., Jordan, I.K. and Kostka, J., 2013. Insights into environmental microbial denitrification from integrated metagenomic, cultivation and genomic analyses.
In: Encyclopedia of Metagenomics, (Nelson, K. ed.) Springer, Berlin.
[PDF]

Sebastian, A., Rishishwar, L., Wang, J., Bernard, K.F., Conley, A.B., McCarty, N.A. and Jordan, I.K., 2013. Origin and evolution of the cystic fibrosis transmembrane regulator protein R domain.
Gene 523: 137-146
[PubMed] [PDF] [Supplement] [Google Scholar]

Wang, J., Lunyak, V.V. and Jordan, I.K., 2013. BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Bioinformatics 29: 492-493
[PubMed] [PDF] [Supplement] [Google Scholar]

2012


Lopez, M.F., Tollervey, J., Krastins, B., Garces, A., Sarracino, D., Prakash, A., Vogelsang, M., Geesman, G., Valderrama, A., Jordan, I.K. and Lunyak, V.V., 2012. Depletion of nuclear histone H2A variants is associated with chronic DNA damage signaling upon drug-evoked senescence of human somatic cells.
Aging 4: 823-842
[PubMed] [PDF] [Google Scholar]

Conley, A.B. and Jordan, I.K., 2012. Cell type-specific termination of transcription by transposable element sequences.
Mob DNA. 3: 15
[PubMed] [PDF] [Supplement] [Google Scholar]

Wang, J., Lunyak, V.V. and Jordan, I.K., 2012. Chromatin signature discovery via histone modification profile alignments.
Nucleic Acids Res. 40: 10642-10656
[PubMed] [PDF] [Supplement] [Google Scholar]

Rishishwar, L., Katz, L.S., Sharma, N.V., Rowe, L., Frace, M., Dolan Thomas,J., Harcourt, B.H., Mayer, L.W. and Jordan, I.K., 2012. Genomic basis of a polyagglutinating isolate of Neisseria meningitidis.
J Bacteriol. 194: 5649-5656
[PubMed] [PDF] [Google Scholar]

Rishishwar, L., Varghese, N., Tyagi, E., Harvey, S.C., Jordan, I.K. and McCarty, N.A., 2012. Relating the disease mutation spectrum to the evolution of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).
PLoS ONE 7: e42336
[PubMed] [PDF] [Google Scholar]

Kostka, J.E., Green, S.J., Rishishwar, L., Prakash, O., Katz, L.S., Marino-Ramirez, L., Jordan, I.K., Watson, D.B., Brown, S.D., Palumbo, A.V. and Brooks, S.C., 2012. Genome sequences for six Rhodanobacter strains isolated from soils and the terrestrial subsurface with variable denitrification capabilities.
J. Bacteriol. 194: 4461
[PubMed] [PDF] [Google Scholar]

Jjingo, D., Conley, A.B., Yi, S.V., Lunyak, V.V. and Jordan, I.K., 2012. On the presence and role of human gene-body DNA methylation.
Oncotarget 3: 462-474
[PubMed] [PDF] [Supplement] [Google Scholar]

Lee, K.J., Conley, A.B., Lunyak, V.V. and Jordan, I.K., 2012. Do human transposable element small RNAs serve primarily as genome defenders or genome regulators?
Mob Genet Elements. 2: 1–7
[PubMed] [PDF] [Google Scholar]

Blackwell, B., Lopez M.F., Wang, J., Krastins, B., Sarracino, D., Tollervey, J.R., Dobke, M.,Jordan, I.K. and Lunyak, V.V., 2012. Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly
Mob Genet Elements. 2: 1–10
[PubMed] [PDF] [Google Scholar]

Conley, A.B. and Jordan, I.K., 2012. Epigenetic regulation of human cis-natural antisense transcripts.
Nucleic Acids Res. 40: 1438–1445
[PubMed] [PDF] [Supplement] [Google Scholar]

Wang, J., Lunyak, V.V., and Jordan, I.K., 2012. Genome-wide prediction and analysis of human chromatin boundary elements.
Nucleic Acids Res. 40: 511-529
[PubMed] [PDF] [Supplement] [Google Scholar]

2011


Piriyapongsa, J., Jordan, I.K., Conley, A.B., Ronan, T. and N.R. Smalheiser, 2011. Transcription factor binding sites are highly enriched within microRNA precursor sequences.
Biol Direct. 6: 61
[PubMed] [PDF] [Supplement] [Google Scholar]

Huda, A., Tyagi, E., Mariño-Ramírez, L., Bowen, N.J., Jjingo, D. and Jordan, I.K., 2011. Prediction of transposable element derived enhancers using chromatin modification profiles.
PLoS ONE 6: e27513
[PubMed] [PDF] [Supplement] [Google Scholar]

Katz, L.S., Humphrey, J.C., Conley, A.B., Nelakuditi, V., Kislyuk, A.O., Agrawal, S., Jayaraman, P., Harcourt, B.H., Olsen- Rasmussen, M.A., Frace, M., Sharma, N.V., Mayer, L.W. and Jordan, I.K., 2011. Neisseria Base: a comparative genomics database for Neisseria meningitidis.
Database 2011: bar 035
[PubMed] [PDF] [Supplement] [Goolge Scholar]

González Pérez, M., Murcia, M., Landsman, D., Jordan, I.K. and Mariño-Ramírez, L., 2011. The genome sequence of Mycobacterium colombiense CECT 3035 type strain.
J Bacteriol. 193: 5866–5867
[PubMed] [PDF] [Google Scholar]

Jordan, I.K., Conley, A., Antonov, I., Arthur, R., Cook, E., Cooper, G., Jones, B., Knipe, K., Lee, K., Liu, X., Mitchell, G., Pande, P., Petit, R., Qin, S., Rajan, V., Sarda, S., Sebastian, A., Tang, S., Thapliyal, R., Varghese, N., Ye, T., Katz, L.S., Wang, X., Rowe, L., Frace, M. and Mayer, L., 2011. Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus.
J Bacteriol. 193: 5879–5880
[PubMed] [PDF] [Google Scholar]

Wang, J., Geesman, G.J., Hostikka, S.L., Atallah, M., Blackwell, B., Lee, E., Cook, P.J., Pasaniuc, B., Shariat, G., Halperin, E., Dobke, M., Rosenfeld, M.G., Jordan, I.K. and Lunyak, V.V., 2011. Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal.
Cell Cycle 10: 3016-3030
[Pubmed] [PDF] [Google Scholar]

Katz, L.S., Sharma, N.V., Harcourt, B.H., Thomas, J.D., Wang, X., Mayer L.W. and Jordan, I.K., 2011. Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis.
J Bacteriol. 193: 3633-3641
[PubMed] [PDF] [Supplement] [Google Scholar]

Jordan, K., 2011. Computational approaches for the transcriptomics, proteomics and epigenetic analysis in adult stem cells.
Cell Cycle. 10: 4187
[PubMed] [PDF] [Google Scholar]

Momin, A.A., Park, H., Portz, B.J., Haynes, C.A., Shaner, R.L., Kelly, S.L., Jordan, I.K. and Merrill Jr., A.H., 2011. A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences.
J Lipid Res. 52: 1073-1083
[PubMed] [PDF] [Supplement] [Google Scholar]

Jjingo, D., Huda, A., Gundapuneni, M., Mariño-Ramírez, L. and Jordan, I.K., 2011. Effect of the transposable element environment of human genes on gene length and expression.
Genome Biol. Evol. 3: 259-271
[PubMed] [PDF] [Supplement] [Google Scholar]

Huda, A., Bowen, N.J., Conley, A.B. and Jordan, I.K., 2011. Epigenetic regulation of transposable element derived human gene promoters.
Gene 475: 39-48
[PubMed] [PDF] [Google Scholar]

2010


Wang, J., Huda, A., Lunyak, V.V. and Jordan, I.K., 2010. A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.
Bioinformatics 26: 2501-2508
[PubMed] [PDF] [Google Scholar]

Conley, A.B. and Jordan, I.K., 2010. Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.
Methods Mol. Biol. 674: 225-240
[PubMed] [PDF] [Google Scholar]

Kislyuk, A.O., Katz, L.S., Agrawal, S., Hagen, M.S., Conley, A.B., Jayaraman, P., Nelakuditi V., Humphrey, J.C., Sammons, S.A., Govil, D., Mair, R.D., Tatti, K.M., Tondella, M.L., Harcourt, B.H., Mayer, L.W. and Jordan, I.K., 2010. A computational genomics pipeline for prokaryotic sequencing projects.
Bioinformatics 26: 1819-1826
[PubMed] [PDF] [Google Scholar]

Huda, A., Mariño-Ramírez, L. and Jordan, I.K., 2010. Epigenetic histone modifications of human transposable elements: genome defense versus exaptation.
Mob DNA. 1: 2
[PubMed] [PDF] [Google Scholar]

2009


Wang, J., Bowen, N.J., Mariño-Ramírez, L. and Jordan, I.K., 2009. A c-Myc regulatory subnetwork from human transposable element sequences.
Mol Biosyst 5: 1831-1839
[PubMed] [PDF] [Google Scholar]

Huda, A. and Jordan, I.K., 2009. Epigenetic regulation of mammalian genomes by transposable elements.
Ann NY Acad. Sci. 1178: 276-284
[PubMed] [PDF] [Google Scholar]

Katz, L.S., Bolen, C.R., Harcourt B.H., Schmink S., Wang X., Kislyuk, A., Taylor, R.T., Mayer, L.W. and Jordan, I.K., 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 Jordan, I.K., 2009. Repetitive DNA elements, nucleosome binding and human gene expression.
Gene 436: 12-22
[PubMed] [PDF] [Google Scholar]

Huda, A. and Jordan, I.K., 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 McCarty, N.A., 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 Syst Biol 2: 96
[PubMed] [PDF] [Google Scholar]

Jordan, I.K. and Miller, W.M., 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 Koonin, E.V., 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 Jordan, I.K., 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 Jordan, I.K., 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 Jordan, I.K., 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 Jordan, I.K., 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 McDonald, J.F., 2008. Endogenous retroviruses of the chicken genome.
Biol Direct. 3: 9
[Abstract] [PDF] [Google Scholar]

Conley, A.B., Miller, W.J. and Jordan, I.K., 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 Jordan, I.K., 2007. Evaluating the protein coding potential of exonized transposable element sequences.
Biol Direct. 2: 31
[Abstract] [PDF] [Google Scholar]

Bowen, N.J. and Jordan, I.K., 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. 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 Jordan, I.K., 2007. Origin and evolution of human microRNAs from transposable elements.
Genetics 176: 1323-1337
[Abstract] [PDF] [Supplement] [Google Scholar]

Piriyapongsa, J. and Jordan, I.K., 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 Landsman, D., 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 Jordan, I.K., 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 Jordan, I.K., 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 Sunyaev, S., 2006. Protein evolution: Causes of trends in amino-acid gain and loss (Reply).
Nature 442: E12
[PDF] [Google Scholar]

Mariño-Ramírez, L. and Jordan, I.K., 2006. Transposable element derived DNaseI-hypersensitive sites in the human genome.
Biol Direct. 1:20
[Abstract] [PDF] [Google Scholar]

Jordan, I.K., 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 Jordan, I.K., 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 Koonin, E.V., 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 Koonin, E.V., 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 Sunyaev, S., 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 Koonin, E.V., 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 Koonin, E.V., 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 Koonin, E.V., 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 Bowen, N.J., 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 Levin, H.L., 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 Koonin, E.V., 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 Galperin, M.Y., 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 Koonin, E.V., 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 Koonin, E.V., 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 Wessler, S.R., 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 Jordan, I.K., 2002. Transposable elements and the evolution of eukaryotic complexity.
Curr. Issues Mol. Biol. 4: 65-76
[Abstract] [PDF] [Google Scholar]

Jordan, I.K. and McDonald, J.F., 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 Koonin, E.V., 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 Koonin, E.V., 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 Koonin, E.V., 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 Koonin, E.V., 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 Galperin, M.Y., 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 Gonzalez, D.S., 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 Koonin, E.V., 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 Koonin, E.V., 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 Galperin, M.Y., 2000. Copper chaperones in bacteria: association with copper-transporting ATPases.
Trends Biochem. Sci. 25: 480-481
[Abstract] [PDF] [Google Scholar]

Gonzalez, D.S. and Jordan, I.K., 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 McClure, M.A., 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 McDonald, J.F., 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 McDonald, J.F., 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 McDonald, J.F., 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 McDonald, J.F., 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 McDonald, J.F., 1999. Tempo and mode of Ty element evolution in Saccharomyces cerevisiae.
Genetics 151: 1341-1351
[Abstract] [PDF] [Google Scholar]

Jordan, I.K. and McDonald, J.F., 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 McDonald, J.F., 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 McDonald, J.F., 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 McDonald, J.F., 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 Miller, W.J., 1997. LTR retrotransposons and the evolution of eukaryotic enhancers.
Genetica 100: 3-13
[Abstract] [PDF] [Google Scholar]

1996


Matyunina, LV., Jordan, I.K. and McDonald, J.F., 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]