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Publications E. Koonin

BIBLIOGRAPHY, 2004-2010 (a selection out of a total of approximately 600 peer-reviewed and invited articles, books, and book chapters; h-index=124). 

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.

Peer-reviewed papers

2010

Makarova KS, Yutin N, Bell SD, Koonin EV. Evolution of diverse cell division and vesicle formation systems in Archaea. Nat Rev Microbiol. 2010 Oct;8(10):731-41

Wolf YI, Gopich IV, Lipman DJ, Koonin EV. Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. Genome Biol Evol. 2010 Jul 12;2:190-9

Pavlicek J, Sauzet S, Besseau L, Coon SL, Weller JL, Boeuf G, Gaildrat P, Omelchenko MV, Koonin EV, Falcón J, Klein DC. Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus. BMC Evol Biol. 2010 May 25;10:154

Carmel L, Wolf YI, Rogozin IB, Koonin EV. EREM: Parameter Estimation and

Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution. Adv Bioinformatics. 2010:167408. Epub 2010 May 6. PubMed PMID: 20467467; PubMed Central PMCID:PMC2866244.

Makarova KS, Koonin EV. Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea. Biol Direct. 2010 May 7;5(1):33. [Epub ahead of print] PubMed PMID: 20459678.

Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. A Low-Polynomial Algorithm For Assembling Clusters of Orthologous Groups From Intergenomic Symmetric Best Matches. Bioinformatics. 2010 May 2. [Epub ahead of print] PubMed PMID: 20439257.

Omelchenko MV, Galperin MY, Wolf YI, Koonin EV. Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution. Biol Direct. 2010 Apr 30;5(1):31. [Epub ahead of print] PubMed PMID: 20433725.

Shabalina SA, Ogurtsov AY, Spiridonov AN, Novichkov P, Spiridonov NA, Koonin EV. Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes. Mol Biol Evol. 2010 Apr 1. [Epub ahead of print] PubMed PMID: 20360214.

Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G. Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res. 2010 Feb 15. [Epub ahead of print] PubMed PMID: 20156992.

Lobkovsky AE, Wolf YI, Koonin EV. Universal distribution of protein evolution rates as a consequence of protein folding physics. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2983-8. Epub 2010 Jan 26. PubMed PMID: 20133769; PubMed Central PMCID: PMC2840281.

2009

Yutin N, Koonin EV. Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity. Biol Direct. 2009 Dec 18;4:51. PubMed PMID: 20021668; PubMed Central PMCID: PMC2806865.

Yutin N, Wolf YI, Raoult D, Koonin EV. Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J. 2009 Dec 17;6:223. PubMed PMID: 20017929; PubMed Central PMCID: PMC2806869.

Boyer M, Yutin N, Pagnier I, Barrassi L, Fournous G, Espinosa L, Robert C, Azza S, Sun S, Rossmann MG, Suzan-Monti M, La Scola B, Koonin EV, Raoult D. Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21848-53. Epub 2009 Dec 9. PubMed PMID: 20007369; PubMed Central PMCID: PMC2799887.

Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 2010 Jan;18(1):11-9. Epub 2009 Nov 26. PubMed PMID: 19942437.

Novozhilov AS, Koonin EV. Exceptional error minimization in putative primordial genetic codes. Biol Direct. 2009 Nov 19;4:44. PubMed PMID: 19925661; PubMed Central PMCID: PMC2785773.

Koonin EV, Wolf YI. Is evolution Darwinian or/and Lamarckian? Biol Direct. 2009 Nov 11;4:42. PubMed PMID: 19906303; PubMed Central PMCID: PMC2781790.

Blombach F, Makarova KS, Marrero J, Siebers B, Koonin EV, van der Oost J. Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea. Biol Direct. 2009 Oct 14;4:39. PubMed PMID: 19828044; PubMed Central PMCID: PMC2770514.

Senkevich TG, Koonin EV, Moss B. Predicted poxvirus FEN1-like nuclease required for homologous recombination, double-strand break repair and full-size genome formation. Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17921-6. Epub 2009 Oct 1. PubMed PMID: 19805122; PubMed Central PMCID: PMC2755464.

Koonin EV, Wolf YI. The fundamental units, processes and patterns of evolution, and the tree of life conundrum. Biol Direct. 2009 Sep 29;4:33. PubMed PMID: 19788730; PubMed Central PMCID: PMC2761301.

Irimia M, Roy SW, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV. Complex selection on 5' splice sites in intron-rich organisms. Genome Res. 2009 Nov;19(11):2021-7. Epub 2009 Sep 10. PubMed PMID: 19745111; PubMed Central PMCID: PMC2775602.

Huang Y, Koonin EV, Lipman DJ, Przytycka TM. Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage. Nucleic Acids Res. 2009 Nov;37(20):6799-810. Epub 2009 Sep 10. PubMed PMID:19745054; PubMed Central PMCID: PMC2777431.

Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin EV, Wolf YI, Nelson N, Béjà O. Photosystem I gene cassettes are present in marine virus genomes. Nature. 2009 Sep 10;461(7261):258-62. Epub 2009 Aug 26. PubMed PMID: 19710652.

Makarova KS, Wolf YI, van der Oost J, Koonin EV. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct. 2009 Aug 25;4:29. PubMed PMID: 19706170; PubMed Central PMCID: PMC2743648.

Jeyaraju DV, Cisbani G, De Brito OM, Koonin EV, Pellegrini L. Hax1 lacks BH modules and is peripherally associated to heavy membranes: implications for Omi/HtrA2 and PARL activity in the regulation of mitochondrial stress and apoptosis. Cell Death Differ. 2009 Dec;16(12):1622-9. Epub 2009 Aug 14. PubMed PMID: 19680265.

Koonin EV. Intron-dominated genomes of early ancestors of eukaryotes. J Hered. 2009 Sep-Oct;100(5):618-23. Epub 2009 Jul 17. Review. PubMed PMID: 19617525.

Puigbò P, Wolf YI, Koonin EV. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol. 2009;8(6):59. Epub 2009 Jul 13. PubMed PMID: 19594957; PubMed Central PMCID: PMC2737373.

Koonin EV, Senkevich TG, Dolja VV. Compelling reasons why viruses are relevant for the origin of cells. Nat Rev Microbiol. 2009 Aug;7(8):615; author reply 615. PubMed PMID: 19561624.

Rastgou M, Habibi MK, Izadpanah K, Masenga V, Milne RG, Wolf YI, Koonin EV,Turina M. Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin. J Gen Virol. 2009 Oct;90(Pt 10):2525-35. Epub 2009 Jun 17. PubMed PMID: 19535502.

Makarova KS, Wolf YI, Koonin EV. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct. 2009 Jun 3;4:19. PubMed PMID: 19493340; PubMed Central PMCID: PMC2701414.

Ng CL, Waterman DG, Koonin EV, Walters AD, Chong JP, Isupov MN, Lebedev AA,Bunka DH, Stockley PG, Ortiz-Lombardía M, Antson AA. Conformational flexibility and molecular interactions of an archaeal homologue of the

Shwachman-Bodian-Diamond syndrome protein. BMC Struct Biol. 2009 May 19;9:32. PubMed PMID: 19454024; PubMed Central PMCID: PMC2695463.

Carmel L, Rogozin IB, Wolf YI, Koonin EV. A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure. Methods Mol Biol. 2009;541:357-71. Review. PubMed PMID: 19381540.

Resch AM, Ogurtsov AY, Rogozin IB, Shabalina SA, Koonin EV. Evolution of alternative and constitutive regions of mammalian 5'UTRs. BMC Genomics. 2009 Apr  16;10:162. PubMed PMID: 19371439; PubMed Central PMCID: PMC2674463.

Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ. Inaugural Article: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A. 2009 May 5;106(18):7273-80. Epub 2009 Apr 7. PubMed PMID: 19351897; PubMed Central PMCID: PMC2666616.

Mulkidjanian AY, Galperin MY, Koonin EV. Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci. 2009 Apr;34(4):206-15. Epub 2009 Mar 18. Review. PubMed PMID: 19303305; PubMed Central PMCID: PMC2752816.

Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV. Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol Direct. 2009 Mar 18;4:11. PubMed PMID: 19296856; PubMed Central PMCID: PMC2669801.

Yutin N, Wolf MY, Wolf YI, Koonin EV. The origins of phagocytosis and eukaryogenesis. Biol Direct. 2009 Feb 26;4:9. PubMed PMID: 19245710; PubMed Central PMCID: PMC2651865.

Koonin EV. Towards a postmodern synthesis of evolutionary biology. Cell Cycle. 2009 Mar 15;8(6):799-800. Epub 2009 Mar 17. PubMed PMID: 19242109.

Koonin EV, Wolf YI, Nagasaki K, Dolja VV. The complexity of the virus world.  Nat Rev Microbiol. 2009 Feb 9. [Epub ahead of print] PubMed PMID: 19234475.

Koonin EV. Darwinian evolution in the light of genomics. Nucleic Acids Res. 2009 Mar;37(4):1011-34. Epub 2009 Feb 12. PubMed PMID: 19213802; PubMed Central PMCID: PMC2651812.

Koonin EV, Novozhilov AS. Origin and evolution of the genetic code: the universal enigma. IUBMB Life. 2009 Feb;61(2):99-111. Review. PubMed PMID: 19117371.

Carmel L, Koonin EV. A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes. Genome Biol Evol. 2009 Sep 22;2009:382-90. PubMed PMID: 20333206; PubMed Central PMCID: PMC2817431.

Rogozin IB, Basu MK, Csürös M, Koonin EV. Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. Genome Biol Evol. 2009 May 25;2009:99-113. PubMed PMID: 20333181; PubMed Central PMCID: PMC2817406.

Saw JH, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G, Wu J, Galperin MY, Koonin EV, Makarova KS, Wolf YI, Rigden DJ, Dunfield PF, Wang L, Alam M. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol. 2008;9(11):R161. Epub 2008 Nov 17. PubMed PMID: 19014707; PubMed Central PMCID: PMC2614493.

2008

Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 2008 Dec;36(21):6688-719. Epub 2008 Oct 23. Review. PubMed PMID: 18948295; PubMed Central PMCID: PMC2588523.

Wolf MY, Wolf YI, Koonin EV. Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biol Direct. 2008 Oct 7;3:40. PubMed PMID: 18840284; PubMed Central PMCID: PMC2572155.

Basu MK, Rogozin IB, Koonin EV. Primordial spliceosomal introns were probably U2-type. Trends Genet. 2008 Nov;24(11):525-8. Epub 2008 Sep 27. PubMed PMID: 18824272.

Baranovskiy AG, Babayeva ND, Liston VG, Rogozin IB, Koonin EV, Pavlov YI,Vassylyev DG, Tahirov TH. X-ray structure of the complex of regulatory subunits of human DNA polymerase delta. Cell Cycle. 2008 Oct;7(19):3026-36. Epub 2008 Oct 4. PubMed PMID: 18818516; PubMed Central PMCID: PMC2605013.

Assis R, Kondrashov AS, Koonin EV, Kondrashov FA. Nested genes and increasing organizational complexity of metazoan genomes. Trends Genet. 2008 Oct;24(10):475-8. Epub 2008 Sep 5. PubMed PMID: 18774620.

van den Born E, Omelchenko MV, Bekkelund A, Leihne V, Koonin EV, Dolja VV, Falnes PØ. Viral AlkB proteins repair RNA damage by oxidative demethylation. Nucleic Acids Res. 2008 Oct;36(17):5451-61. Epub 2008 Aug 21. PubMed PMID: 18718927; PubMed Central PMCID: PMC2553587.

Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008 Aug 15;321(5891):960-4. PubMed PMID: 18703739.

La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D. The virophage as a unique parasite of the giant mimivirus. Nature. 2008 Sep 4;455(7209):100-4. PubMed PMID: 18690211.

Rogozin IB, Makarova KS, Pavlov YI, Koonin EV. A highly conserved family of inactivated archaeal B family DNA polymerases. Biol Direct. 2008 Aug 6;3:32. PubMed PMID: 18684330; PubMed Central PMCID: PMC2527604.

Churbanov A, Winters-Hilt S, Koonin EV, Rogozin IB. Accumulation of GC donor  splice signals in mammals. Biol Direct. 2008 Jul 9;3:30. PubMed PMID: 18613975; PubMed Central PMCID: PMC2490688.

Hou S, Makarova KS, Saw JH, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct. 2008 Jul 1;3:26. PubMed PMID: 18593465; PubMed Central PMCID: PMC2474590.

Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):8102-7. Epub 2008 Jun 5. PubMed PMID: 18535141; PubMed Central PMCID: PMC2430366.

Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem. 2008 Jul 18;283(29):20361-71. Epub 2008 May 15. PubMed PMID: 18482976; PubMed Central PMCID: PMC2459268.

Basu MK, Makalowski W, Rogozin IB, Koonin EV. U12 intron positions are more strongly conserved between animals and plants than U2 intron positions. Biol Direct. 2008 May 14;3:19. PubMed PMID: 18479526; PubMed Central PMCID: PMC2426677.

Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV. The deep archaeal roots of eukaryotes. Mol Biol Evol. 2008 Aug;25(8):1619-30. Epub 2008 May 6. PubMed PMID: 18463089; PubMed Central PMCID: PMC2464739.

Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV. Evolutionary primacy of sodium bioenergetics. Biol Direct. 2008 Apr 1;3:13. PubMed PMID: 18380897; PubMed Central PMCID: PMC2359735.

Rogozin IB, Thomson K, Csürös M, Carmel L, Koonin EV. Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. Biol Direct. 2008 Mar 17;3:7. PubMed PMID: 18346278; PubMed Central PMCID: PMC2292158.

Csurös M, Rogozin IB, Koonin EV. Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach. Mol Biol Evol. 2008 May;25(5):903-11. Epub 2008 Feb 21. PubMed PMID: 18296415.

Senkevich TG, Wyatt LS, Weisberg AS, Koonin EV, Moss B. A conserved poxvirus NlpC/P60 superfamily protein contributes to vaccinia virus virulence in mice but not to replication in cell culture. Virology. 2008 May 10;374(2):506-14. Epub 2008 Feb 20. PubMed PMID: 18281072; PubMed Central PMCID: PMC2412903.

Kosarek JN, Woodruff RV, Rivera-Begeman A, Guo C, D'Souza S, Koonin EV, Walker GC, Friedberg EC. Comparative analysis of in vivo interactions between Rev1 protein and other Y-family DNA polymerases in animals and yeasts. DNA Repair (Amst). 2008 Mar 1;7(3):439-51. Epub 2008 Jan 31. PubMed PMID: 18242152; PubMed Central PMCID: PMC2363158.

Basu MK, Carmel L, Rogozin IB, Koonin EV. Evolution of protein domain promiscuity in eukaryotes. Genome Res. 2008 Mar;18(3):449-61. Epub 2008 Jan 29. PubMed PMID: 18230802; PubMed Central PMCID: PMC2259109.

Podar M, Wall MA, Makarova KS, Koonin EV. The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system. Biol Direct. 2008 Jan 25;3:2. Review. PubMed PMID: 18221539; PubMed Central PMCID: PMC2253512.

Avisar D, Prokhnevsky AI, Makarova KS, Koonin EV, Dolja VV. Myosin XI-K is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana. Plant Physiol. 2008 Mar;146(3):1098-108. Epub 2008 Jan 4. PubMed PMID: 18178670; PubMed Central PMCID: PMC2259067.

2007

Carmel, L., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. 2007a. Patterns of intron gain and conservation in eukaryotic genes. BMC Evol Biol 7:192.

Carmel, L., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. 2007b. Evolutionarily conserved genes preferentially accumulate introns. Genome Res 17:1045-1050.

Carmel, L., Y. I. Wolf, I. B. Rogozin, and E. V. Koonin. 2007c. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res 17:1034-1044.

De Silva, F. S., W. Lewis, P. Berglund, E. V. Koonin, and B. Moss. 2007. Poxvirus DNA primase. Proc Natl Acad Sci U S A 104:18724-18729.

Jia, S., M. Omelchenko, D. Garland, V. Vasiliou, J. Kanungo, M. Spencer, Y. Wolf, E. Koonin, and J. Piatigorsky. 2007. Duplicated gelsolin family genes in zebrafish: a novel scinderin-like gene (scinla) encodes the major corneal crystallin. Faseb J 21:3318-3328.

Koonin, E. V. 2007d. The Biological Big Bang model for the major transitions in evolution. Biol Direct 2:21.

Koonin, E. V. 2007e. The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life. Biol Direct 2:15.

Koonin, E. V., K. S. Makarova, and J. G. Elkins. 2007. Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota". Biol Direct 2:38.

Makarova, K. S., M. V. Omelchenko, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, A. Lapidus, A. Copeland, E. Kim, M. Land, K. Mavrommatis, S. Pitluck, P. M. Richardson, C. Detter, T. Brettin, E. Saunders, B. Lai, B. Ravel, K. M. Kemner, Y. I. Wolf, A. Sorokin, A. V. Gerasimova, M. S. Gelfand, J. K. Fredrickson, E. V. Koonin, and M. J. Daly. 2007a. Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS ONE 2:e955.

Makarova, K. S., A. V. Sorokin, P. S. Novichkov, Y. I. Wolf, and E. V. Koonin. 2007b. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2:33.

Martin, W., T. Dagan, E. V. Koonin, J. L. Dipippo, J. P. Gogarten, and J. A. Lake. 2007. The evolution of eukaryotes. Science 316:542-543

Mulkidjanian, A. Y., K. S. Makarova, M. Y. Galperin, and E. V. Koonin. 2007. Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nat Rev Microbiol 5:892-899.

Novozhilov, A. S., Y. I. Wolf, and E. V. Koonin. 2007. Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape. Biol Direct 2:24.

Resch, A. M., L. Carmel, L. Marino-Ramirez, A. Y. Ogurtsov, S. A. Shabalina, I. B. Rogozin, and E. V. Koonin. 2007. Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol 24:1821-1831.

Rogozin, I. B., Y. I. Wolf, L. Carmel, and E. V. Koonin. 2007a. Analysis of rare amino acid replacements supports the Coelomata clade. Mol Biol Evol 24:2594-2597.

Rogozin, I. B., Y. I. Wolf, L. Carmel, and E. V. Koonin. 2007b. Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. Mol Biol Evol 24:1080-1090

Sverdlov, A. V., M. Csuros, I. B. Rogozin, and E. V. Koonin. 2007. A glimpse of a putative pre-intron phase of eukaryotic evolution. Trends Genet 23:105-108.

Vitushkina, M. V., I. B. Rogozin, W. Jelkmann, E. V. Koonin, and A. A. Agranovsky. 2007. Completion of the mapping of transcription start sites for the five-gene block subgenomic RNAs of Beet yellows Closterovirus and identification of putative subgenomic promoters. Virus Res 128:153-158.

Wolf, Y. I., and E. V. Koonin. 2007. On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol Direct 2:14

Zheng, J., I. B. Rogozin, E. V. Koonin, and T. M. Przytycka. 2007. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol 24:2583-2592.

2006

Babenko, V. N., M. K. Basu, F. A. Kondrashov, I. B. Rogozin, and E. V. Koonin. 2006. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer 6:36

Chiba, M., J. C. Reed, A. I. Prokhnevsky, E. J. Chapman, M. Mawassi, E. V. Koonin, J. C. Carrington, and V. V. Dolja. 2006. Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon. Virology 346:7-14

Correia, F. F., A. D'Onofrio, T. Rejtar, L. Li, B. L. Karger, K. Makarova, E. V. Koonin, and K. Lewis. 2006. Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol 188:8360-8367.

Dewey, C. N., I. B. Rogozin, and E. V. Koonin. 2006. Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genomics 7:311.

Glazko, G. V., V. N. Babenko, E. V. Koonin, and I. B. Rogozin. 2006. Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection. Biol Direct 1:4

Karev, G. P., A. S. Novozhilov, and E. V. Koonin. 2006. Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics. Biol Direct 1:30.

Kondrashov, F. A., E. V. Koonin, I. G. Morgunov, T. V. Finogenova, and M. N. Kondrashova. 2006. Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct 1:31.

Koonin, E. V. 2006a. Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol Direct 1:39.

Koonin, E. V. 2006b. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct 1:22

Koonin, E. V., T. G. Senkevich, and V. V. Dolja. 2006. The ancient Virus World and evolution of cells. Biol Direct 1:29.

Koonin, E. V., T. G. Senkevich, and V. V. Dolja. 2006. The ancient Virus World and evolution of cells. Biol Direct 1:29.

Kuznetsova, E., M. Proudfoot, C. F. Gonzalez, G. Brown, M. V. Omelchenko, I. Borozan, L. Carmel, Y. I. Wolf, H. Mori, A. V. Savchenko, C. H. Arrowsmith, E. V. Koonin, A. M. Edwards, and A. F. Yakunin. 2006. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem 281:36149-36161.

Leebens-Mack, J., T. Vision, E. Brenner, J. E. Bowers, S. Cannon, M. J. Clement, C. W. Cunningham, C. dePamphilis, R. deSalle, J. J. Doyle, J. A. Eisen, X. Gu, J. Harshman, R. K. Jansen, E. A. Kellogg, E. V. Koonin, B. D. Mishler, H. Philippe, J. C. Pires, Y. L. Qiu, S. Y. Rhee, K. Sjolander, D. E. Soltis, P. S. Soltis, D. W. Stevenson, K. Wall, T. Warnow, and C. Zmasek. 2006. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). Omics 10:231-237.

Makarova, K., A. Slesarev, Y. Wolf, A. Sorokin, B. Mirkin, E. Koonin, A. Pavlov, N. Pavlova, V. Karamychev, N. Polouchine, V. Shakhova, I. Grigoriev, Y. Lou, D. Rohksar, S. Lucas, K. Huang, D. M. Goodstein, T. Hawkins, V. Plengvidhya, D. Welker, J. Hughes, Y. Goh, A. Benson, K. Baldwin, J. H. Lee, I. Diaz-Muniz, B. Dosti, V. Smeianov, W. Wechter, R. Barabote, G. Lorca, E. Altermann, R. Barrangou, B. Ganesan, Y. Xie, H. Rawsthorne, D. Tamir, C. Parker, F. Breidt, J. Broadbent, R. Hutkins, D. O'Sullivan, J. Steele, G. Unlu, M. Saier, T. Klaenhammer, P. Richardson, S. Kozyavkin, B. Weimer, and D. Mills. 2006a. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103:15611-15616.

Makarova, K. S., N. V. Grishin, and E. V. Koonin. 2006. The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics 22:2581-2584.

Makarova, K. S., N. V. Grishin, S. A. Shabalina, Y. I. Wolf, and E. V. Koonin. 2006b. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1:7.

Makarova, K. S., E. V. Koonin, R. Haselkorn, and M. Y. Galperin. 2006c. Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion. Bioinformatics 22:1297-1301.

Marinsek, N., E. R. Barry, K. S. Makarova, I. Dionne, E. V. Koonin, and S. D. Bell. 2006. GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep 7:539-545.

Martin, W., and E. V. Koonin. 2006a. Introns and the origin of nucleus-cytosol compartmentalization. Nature 440:41-45.

Martin, W., and E. V. Koonin. 2006b. A positive definition of prokaryotes. Nature 442:868.

Novozhilov, A. S., F. S. Berezovskaya, E. V. Koonin, and G. P. Karev. 2006. Mathematical modeling of tumor therapy with oncolytic viruses: regimes with complete tumor elimination within the framework of deterministic models. Biol Direct 1:6.

Shakhnovich, B. E., and E. V. Koonin. 2006. Origins and impact of constraints in evolution of gene families. Genome Res 16:1529-1536.

Tsaparas, P., L. Marino-Ramirez, O. Bodenreider, E. V. Koonin, and I. K. Jordan. 2006. Global similarity and local divergence in human and mouse gene co-expression networks. BMC Evol Biol 6:70

Waterman, D. G., M. Ortiz-Lombardia, M. J. Fogg, E. V. Koonin, and A. A. Antson. 2006. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. J Mol Biol 356:97-110.

Wolf, Y. I., L. Carmel, and E. V. Koonin. 2006. Unifying measures of gene function and evolution. Proc Biol Sci 273:1507-1515

Wolf, Y. I., C. Viboud, E. C. Holmes, E. V. Koonin, and D. J. Lipman. 2006. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct 1:34

2005

Basu, M. K., and E. V. Koonin. 2005. Evolution of eukaryotic cysteine sulfinic acid reductase, sulfiredoxin (Srx), from bacterial chromosome partitioning protein ParB. Cell Cycle 4:947-952.

Churbanov, A., I. B. Rogozin, V. N. Babenko, H. Ali, and E. V. Koonin. 2005. Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes. Nucleic Acids Res 33:5512-5520.

Foster, J., M. Ganatra, I. Kamal, J. Ware, K. Makarova, N. Ivanova, A. Bhattacharyya, V. Kapatral, S. Kumar, J. Posfai, T. Vincze, J. Ingram, L. Moran, A. Lapidus, M. Omelchenko, N. Kyrpides, E. Ghedin, S. Wang, E. Goltsman, V. Joukov, O. Ostrovskaya, K. Tsukerman, M. Mazur, D. Comb, E. Koonin, and B. Slatko. 2005. The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol 3:e121.

Glazko, G. V., E. V. Koonin, and I. B. Rogozin. 2005. Molecular dating: ape bones agree with chicken entrails. Trends Genet 21:89-92.

Iyer, L. M., E. V. Koonin, D. D. Leipe, and L. Aravind. 2005. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res 33:3875-3896.

Jordan, I. K., F. A. Kondrashov, I. A. Adzhubei, Y. I. Wolf, E. V. Koonin, A. S. Kondrashov, and S. Sunyaev. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature 433:633-638.

Jordan, I. K., L. Marino-Ramirez, and E. V. Koonin. 2005. Evolutionary significance of gene expression divergence. Gene 345:119-126.

Karev, G. P., F. S. Berezovskaya, and E. V. Koonin. 2005. Modeling genome evolution with a diffusion approximation of a birth-and-death process. Bioinformatics 21 Suppl 3:iii12-19.

Koonin, E. V., and W. Martin. 2005. On the origin of genomes and cells within inorganic compartments. Trends Genet 21:647-654.

Koonin, E. V., I. B. Rogozin, and G. V. Glazko. 2005. p53 gain-of-function: tumor biology and bioinformatics come together. Cell Cycle 4:686-688.

Kravchenko, J. E., I. B. Rogozin, E. V. Koonin, and P. M. Chumakov. 2005. Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. Nature 436:735-739.

Makarova, K. S., Y. I. Wolf, S. L. Mekhedov, B. G. Mirkin, and E. V. Koonin. 2005. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res 33:4626-4638.

Moroz, O. V., A. G. Murzin, K. S. Makarova, E. V. Koonin, K. S. Wilson, and M. Y. Galperin. 2005. Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. J Mol Biol 347:243-255.

Ng, C. L., D. Waterman, E. V. Koonin, A. A. Antson, and M. Ortiz-Lombardia. 2005. Crystal structure of Mil (Mth680): internal duplication and similarity between the Imp4/Brix domain and the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases. EMBO Rep 6:140-146.

Novozhilov, A. S., G. P. Karev, and E. V. Koonin. 2005. Mathematical modeling of evolution of horizontally transferred genes. Mol Biol Evol 22:1721-1732.

Omelchenko, M. V., Y. I. Wolf, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, M. J. Daly, E. V. Koonin, and K. S. Makarova. 2005. Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol Biol 5:57.

Rogozin, I. B., M. K. Basu, I. K. Jordan, Y. I. Pavlov, and E. V. Koonin. 2005a. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle 4:1281-1285.

Ulrich, L. E., E. V. Koonin, and I. B. Zhulin. 2005. One-component systems dominate signal transduction in prokaryotes. Trends Microbiol 13:52-56.

2004

Aravind, L., L. M. Iyer, D. D. Leipe, and E. V. Koonin. 2004. A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. Genome Biol 5:R30.

Babenko, V. N., I. B. Rogozin, S. L. Mekhedov, and E. V. Koonin. 2004. Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res 32:3724-3733.

Budanov, A. V., A. A. Sablina, E. Feinstein, E. V. Koonin, and P. M. Chumakov. 2004. Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD. Science 304:596-600.

Constantinesco, F., P. Forterre, E. V. Koonin, L. Aravind, and C. Elie. 2004. A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea. Nucleic Acids Res 32:1439-1447.

Ettema, T. J., K. S. Makarova, G. L. Jellema, H. J. Gierman, E. V. Koonin, M. A. Huynen, W. M. de Vos, and J. van der Oost. 2004. Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism. J Bacteriol 186:7754-7762.

Galperin, M. Y., and E. V. Koonin. 2004. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 32:5452-5463.

Hou, S., J. H. Saw, K. S. Lee, T. A. Freitas, C. Belisle, Y. Kawarabayasi, S. P. Donachie, A. Pikina, M. Y. Galperin, E. V. Koonin, K. S. Makarova, M. V. Omelchenko, A. Sorokin, Y. I. Wolf, Q. X. Li, Y. S. Keum, S. Campbell, J. Denery, S. Aizawa, S. Shibata, A. Malahoff, and M. Alam. 2004. Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A 101:18036-18041.

Iyer, L. M., L. Aravind, S. L. Coon, D. C. Klein, and E. V. Koonin. 2004. Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role? Trends Genet 20:292-299.

Iyer, L. M., E. V. Koonin, and L. Aravind. 2004a. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335:73-88.

Iyer, L. M., E. V. Koonin, and L. Aravind. 2004b. Novel predicted peptidases with a potential role in the ubiquitin signaling pathway. Cell Cycle 3:1440-1450.

Iyer, L. M., D. D. Leipe, E. V. Koonin, and L. Aravind. 2004c. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol 146:11-31.

Iyer, L. M., K. S. Makarova, E. V. Koonin, and L. Aravind. 2004d. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res 32:5260-5279.

Jordan, I. K., L. Marino-Ramirez, Y. I. Wolf, and E. V. Koonin. 2004. Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol 21:2058-2070.

Jordan, I. K., Y. I. Wolf, and E. V. Koonin. 2004. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 4:22.

Karev, G. P., Y. I. Wolf, F. S. Berezovskaya, and E. V. Koonin. 2004. Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. BMC Evol Biol 4:32.

Kondrashov, F. A., and E. V. Koonin. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet 20:287-290.

Koonin, E. V. 2004b. A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man. Cell Cycle 3:280-285.

Koonin, E. V., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, D. M. Krylov, K. S. Makarova, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, I. B. Rogozin, S. Smirnov, A. V. Sorokin, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. 2004. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5:R7.

Kouprina, N., M. Mullokandov, I. B. Rogozin, N. K. Collins, G. Solomon, J. Otstot, J. I. Risinger, E. V. Koonin, J. C. Barrett, and V. Larionov. 2004. The SPANX gene family of cancer/testis-specific antigens: rapid evolution and amplification in African great apes and hominids. Proc Natl Acad Sci U S A 101:3077-3082.

Leipe, D. D., E. V. Koonin, and L. Aravind. 2004. STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. J Mol Biol 343:1-28.

Mans, B. J., V. Anantharaman, L. Aravind, and E. V. Koonin. 2004. Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle 3:1612-1637.

Novichkov, P. S., M. V. Omelchenko, M. S. Gelfand, A. A. Mironov, Y. I. Wolf, and E. V. Koonin. 2004. Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 186:6575-6585.

Shabalina, S. A., A. Y. Ogurtsov, I. B. Rogozin, E. V. Koonin, and D. J. Lipman. 2004. Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res 32:1774-1782.

Sik, A., B. J. Passer, E. V. Koonin, and L. Pellegrini. 2004. Self-regulated cleavage of the mitochondrial intramembrane-cleaving protease PARL yields Pbeta, a nuclear-targeted peptide. J Biol Chem 279:15323-15329.

Sverdlov, A. V., V. N. Babenko, I. B. Rogozin, and E. V. Koonin. 2004a. Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion. Gene 338:85-91.

Sverdlov, A. V., I. B. Rogozin, V. N. Babenko, and E. V. Koonin. 2004b. Reconstruction of ancestral protosplice sites. Curr Biol 14:1505-1508.

Wertz, I. E., K. M. O'Rourke, H. Zhou, M. Eby, L. Aravind, S. Seshagiri, P. Wu, C. Wiesmann, R. Baker, D. L. Boone, A. Ma, E. V. Koonin, and V. M. Dixit. 2004. De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature 430:694-699.

Wolf, Y. I., I. B. Rogozin, and E. V. Koonin. 2004. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res 14:29-36.

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