Eugene V. Koonin Ph.D.

    Adjunct Professor
    Office: Multi-Purpose Building, Room 149 | Phone: 972-4-8240-447 | Fax: 972-4-8288-235
    Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
    Subject: Evolutionary systems biology: emergence and evolution of genomics, comparison of prokaryotic and eukaryotic genomes
    Website | Publications | CV

    Research Interests

    • Comparative and evolutionary genomics with a focus on predicting gene functions
    • Horizontal gene transfer between diverse organisms, in particular, from prokaryotes to eukaryotes and vice versa
    • Development of comprehensive approaches to the representation of genome evolution, combining tree-like and net-like trends
    • Adaptation and selection in different categories of genes and different organismal lineages
    • Evolutionary analysis of protein domains and domain architectures
    • Origin and evolution of viruses

    Selected publications

    1. Books

    Koonin EV (2011) The logic of chance: the nature and origin of biological evolution. Upper Saddle River (NJ): FT Press.

    Koonin EV, Karev GP, Wolf YI  (Eds). Power laws, scalefree networks and genome biology, in press, Landes Biosciences and Springer Verlag (2006)

    Koonin EV, Galperin MY. (2002 )SEQUENCE - EVOLUTION - FUNCTION. Computational Approaches in Comparative Genomics. Kluwer Academic Publishers.

    Galperin MY, Koonin EV (Eds). (2002) Computational genomics: from sequence to function. Horizon Press.

    2. Invited articles and book chapters

    Galperin MY, Koonin EV. From complete genome sequence to 'complete' understanding? Trends Biotechnol. 2010 Aug;28(8):398-406

    Koonin EV, Wolf YI. Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet. 2010 Jun 15;11(7):487-498

    Koonin EV, Yutin N. Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology. 2010 Jun;53(5):284-92

    Koonin EV. The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol. 2010 May 5;11(5):209

    Koonin EV, Moss B. Viruses know more than one way to don a cap. Proc Natl Acad. Sci U S A. 2010 Feb 23;107(8):3283-4

    Koonin EV. Preview. The incredible expanding ancestor of eukaryotes. Cell. 2010 Mar 5;140(5):606-8

    Koonin EV. Taming of the shrewd: novel eukaryotic genes from RNA viruses. BMC Biol. 2010 Jan 12;8:2

    Koonin EV, Makarova KS. CRISPR-Cas: an adaptive immunity system in prokaryotes. F1000 Biol Rep. 2009 Dec 1;1:95

    Koonin EV. On the origin of cells and viruses: primordial virus world scenario. Ann N Y Acad Sci. 2009 Oct;1178:47-64. PubMed PMID: 19845627.

    Koonin EV. The Origin at 150: is a new evolutionary synthesis in sight? Trends Genet. 2009 Nov;25(11):473-5. Epub 2009 Oct 14. PubMed PMID: 19836100; PubMed Central PMCID: PMC2784144.

    Koonin EV, Wolf YI, Puigbò P. The Phylogenetic Forest and the Quest for the Elusive Tree of Life. Cold Spring Harb Symp Quant Biol. 2009 Aug 17. [Epub ahead of print] PubMed PMID: 19687142.

    Koonin EV, Aravind L. Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle. 2009 Jul 1;8(13):1984-5.

    Shabalina, S. A., and E. V. Koonin. 2008. Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol.

    Koonin, E. V. 2007a. Metagenomic sorcery and the expanding protein universe. Nat Biotechnol 25:540-542.

    Koonin, E. V. 2007b. Chance and necessity in cellular response to challenge. Mol Syst Biol 3:107.

    Koonin, E. V. 2007c. An RNA-making reactor for the origin of life. Proc Natl Acad Sci U S A 104:9105-9106.

    Makarova, K. S., and E. V. Koonin. 2007. Evolutionary genomics of lactic acid bacteria. J Bacteriol 189:1199-1208.

    Aravind, L., L. M. Iyer, and E. V. Koonin. 2006. Comparative genomics and structural biology of the molecular innovations of eukaryotes. Curr Opin Struct Biol 16:409-419

    Prangishvili, D., R. A. Garrett, and E. V. Koonin. 2006. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res 117:52-67

    Iyer, L. M., S. Balaji, E. V. Koonin, and L. Aravind. 2006. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 117:156-184.

    Koonin, E. V., and V. V. Dolja. 2006. Evolution of complexity in the viral world: the dawn of a new vision. Virus Res 117:1-4.

    Koonin, E. V., L. F. Landweber, and D. J. Lipman. 2006. A community experiment with fully open and published peer review. Biol Direct 1:1.

    Makarova, K. S., and E. V. Koonin. 2005. Evolutionary and functional genomics of the Archaea. Curr Opin Microbiol 8:586-594.

    Novozhilov, A. S., G. P. Karev, and E. V. Koonin. 2006. Biological applications of the theory of birth-and-death processes. Brief Bioinform 7:70-85.

    Koonin, E. V., and Y. I. Wolf. 2006. Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotechnol 17:481-487.

    Koonin, E. V. 2005a. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39:309-338.

    Koonin, E. V. 2005b. Paralogs and mutational robustness linked through transcriptional reprogramming. Bioessays 27:865-868.

    Koonin, E. V. 2005c. Virology: Gulliver among the Lilliputians. Curr Biol 15:R167-169.

    Koonin, E. V. 2005d. Systemic determinants of gene evolution and function. Mol Syst Biol 1:2005 0021.

    Rogozin, I. B., A. V. Sverdlov, V. N. Babenko, and E. V. Koonin. 2005b. Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform 6:118-134.

    Rogozin, I. B., K. S. Makarova, Y. I. Wolf, and E. V. Koonin. 2004. Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief Bioinform 5:131-149.

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