1: Yutin N, Wolf MY, Wolf YI, Koonin EV.
 The origins of phagocytosis and eukaryogenesis.
Biol Direct. 2009 Feb 26;4(1):9. [Epub ahead of print]
PMID: 19245710 [PubMed - as supplied by publisher]

2: Koonin EV, Wolf YI, Nagasaki K, Dolja VV.
 The complexity of the virus world.
Nat Rev Microbiol. 2009 Feb 9. [Epub ahead of print] No abstract available.
PMID: 19234475 [PubMed - as supplied by publisher]

3: Koonin EV.
 Darwinian evolution in the light of genomics.
Nucleic Acids Res. 2009 Feb 12. [Epub ahead of print]
PMID: 19213802 [PubMed - as supplied by publisher]

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

5: 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.
PMID: 19014707 [PubMed - indexed for MEDLINE]

6: Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A,
Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson
A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH Jr, Richardson PM,
Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO.
 A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum
equitans.
Genome Biol. 2008;9(11):R158. Epub 2008 Nov 10.
PMID: 19000309 [PubMed - indexed for MEDLINE]

7: Koonin EV, Wolf YI, Nagasaki K, Dolja VV.
 The Big Bang of picorna-like virus evolution antedates the radiation of
eukaryotic supergroups.
Nat Rev Microbiol. 2008 Dec;6(12):925-39. Epub 2008 Nov 10. Review.
PMID: 18997823 [PubMed - indexed for MEDLINE]

8: Novichkov PS, Wolf YI, Dubchak I, Koonin EV.
 Trends in prokaryotic evolution revealed by comparison of closely related
bacterial and archaeal genomes.
J Bacteriol. 2009 Jan;191(1):65-73. Epub 2008 Oct 31.
PMID: 18978059 [PubMed - indexed for MEDLINE]

9: 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.
PMID: 18948295 [PubMed - indexed for MEDLINE]

10: Koonin EV.
 Evolution of genome architecture.
Int J Biochem Cell Biol. 2009 Feb;41(2):298-306. Epub 2008 Sep 26.
PMID: 18929678 [PubMed - in process]

11: Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I.
 ATGC: a database of orthologous genes from closely related prokaryotic genomes
and a research platform for microevolution of prokaryotes.
Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54. Epub 2008 Oct 9.
PMID: 18845571 [PubMed - in process]

12: 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.
PMID: 18840284 [PubMed - in process]

13: 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.
PMID: 18824272 [PubMed - indexed for MEDLINE]

14: 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.
PMID: 18818516 [PubMed - indexed for MEDLINE]

15: 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.
PMID: 18774620 [PubMed - indexed for MEDLINE]

16: 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.
PMID: 18718927 [PubMed - indexed for MEDLINE]

17: Shabalina SA, Koonin EV.
 Origins and evolution of eukaryotic RNA interference.
Trends Ecol Evol. 2008 Oct;23(10):578-87. Epub 2008 Aug 18. Review.
PMID: 18715673 [PubMed - indexed for MEDLINE]

18: 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.
PMID: 18703739 [PubMed - indexed for MEDLINE]

19: 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.
PMID: 18684330 [PubMed - in process]

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

21: 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.
PMID: 18593465 [PubMed - in process]

22: 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.
PMID: 18535141 [PubMed - indexed for MEDLINE]

23: 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.
PMID: 18482976 [PubMed - indexed for MEDLINE]

24: 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.
PMID: 18479526 [PubMed - in process]

25: 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.
PMID: 18463089 [PubMed - indexed for MEDLINE]

26: Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV.
 Evolutionary primacy of sodium bioenergetics.
Biol Direct. 2008 Apr 1;3:13.
PMID: 18380897 [PubMed - in process]

27: 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.
PMID: 18346278 [PubMed - in process]

28: 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.
PMID: 18296415 [PubMed - indexed for MEDLINE]

29: 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.
PMID: 18281072 [PubMed - indexed for MEDLINE]

30: 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.
PMID: 18242152 [PubMed - indexed for MEDLINE]

31: 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.
PMID: 18230802 [PubMed - indexed for MEDLINE]

32: 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.
PMID: 18221539 [PubMed - in process]

33: 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.
PMID: 18178670 [PubMed - indexed for MEDLINE]

34: Koonin EV, Makarova KS, Elkins JG.
 Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are
conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".
Biol Direct. 2007 Dec 14;2:38.
PMID: 18081935 [PubMed - indexed for MEDLINE]

35: Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.
 Clusters of orthologous genes for 41 archaeal genomes and implications for
evolutionary genomics of archaea.
Biol Direct. 2007 Nov 27;2:33.
PMID: 18042280 [PubMed - indexed for MEDLINE]

36: De Silva FS, Lewis W, Berglund P, Koonin EV, Moss B.
 Poxvirus DNA primase.
Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18724-9. Epub 2007 Nov 13.
PMID: 18000036 [PubMed - indexed for MEDLINE]

37: Basu MK, Rogozin IB, Deusch O, Dagan T, Martin W, Koonin EV.
 Evolutionary dynamics of introns in plastid-derived genes in plants: saturation
nearly reached but slow intron gain continues.
Mol Biol Evol. 2008 Jan;25(1):111-9. Epub 2007 Oct 31.
PMID: 17974547 [PubMed - indexed for MEDLINE]

38: Novozhilov AS, Wolf YI, Koonin EV.
 Evolution of the genetic code: partial optimization of a random code for
robustness to translation error in a rugged fitness landscape.
Biol Direct. 2007 Oct 23;2:24.
PMID: 17956616 [PubMed - indexed for MEDLINE]

39: Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV.
 Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.
Nat Rev Microbiol. 2007 Nov;5(11):892-9.
PMID: 17938630 [PubMed - indexed for MEDLINE]

40: Carmel L, Rogozin IB, Wolf YI, Koonin EV.
 Patterns of intron gain and conservation in eukaryotic genes.
BMC Evol Biol. 2007 Oct 12;7:192.
PMID: 17935625 [PubMed - in process]

41: Rogozin IB, Wolf YI, Carmel L, Koonin EV.
 Analysis of rare amino acid replacements supports the Coelomata clade.
Mol Biol Evol. 2007 Dec;24(12):2594-7. Epub 2007 Oct 5.
PMID: 17921482 [PubMed - indexed for MEDLINE]

42: Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai
M, Lapidus A, Copeland A, Kim E, Land M, Mavrommatis K, Pitluck S, Richardson PM,
Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A,
Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV, Daly MJ.
 Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
PLoS ONE. 2007 Sep 26;2(9):e955.
PMID: 17895995 [PubMed - indexed for MEDLINE]

43: Zheng J, Rogozin IB, Koonin EV, Przytycka TM.
 Support for the Coelomata clade of animals from a rigorous analysis of the
pattern of intron conservation.
Mol Biol Evol. 2007 Nov;24(11):2583-92. Epub 2007 Sep 24.
PMID: 17893400 [PubMed - indexed for MEDLINE]

44: Koonin EV.
 The Biological Big Bang model for the major transitions in evolution.
Biol Direct. 2007 Aug 20;2:21.
PMID: 17708768 [PubMed - indexed for MEDLINE]

45: Koonin EV.
 The cosmological model of eternal inflation and the transition from chance to
biological evolution in the history of life.
Biol Direct. 2007 May 31;2:15.
PMID: 17540027 [PubMed]

46: Wolf YI, Koonin EV.
 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. 2007 May 31;2:14.
PMID: 17540026 [PubMed]

47: Resch AM, Carmel L, Mariño-Ramírez L, Ogurtsov AY, Shabalina SA, Rogozin IB, 
Koonin EV.
 Widespread positive selection in synonymous sites of mammalian genes.
Mol Biol Evol. 2007 Aug;24(8):1821-31. Epub 2007 May 23.
PMID: 17522087 [PubMed - indexed for MEDLINE]

48: Vitushkina MV, Rogozin IB, Jelkmann W, Koonin EV, Agranovsky AA.
 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. 2007 Sep;128(1-2):153-8. Epub 2007 May 22.
PMID: 17521763 [PubMed - indexed for MEDLINE]

49: Koonin EV.
 An RNA-making reactor for the origin of life.
Proc Natl Acad Sci U S A. 2007 May 29;104(22):9105-6. Epub 2007 May 22. No
abstract available.
PMID: 17519331 [PubMed - indexed for MEDLINE]

50: Carmel L, Rogozin IB, Wolf YI, Koonin EV.
 Evolutionarily conserved genes preferentially accumulate introns.
Genome Res. 2007 Jul;17(7):1045-50. Epub 2007 May 10.
PMID: 17495009 [PubMed - indexed for MEDLINE]

51: Carmel L, Wolf YI, Rogozin IB, Koonin EV.
 Three distinct modes of intron dynamics in the evolution of eukaryotes.
Genome Res. 2007 Jul;17(7):1034-44. Epub 2007 May 10.
PMID: 17495008 [PubMed - indexed for MEDLINE]

52: Koonin EV.
 Metagenomic sorcery and the expanding protein universe.
Nat Biotechnol. 2007 May;25(5):540-2. No abstract available.
PMID: 17483838 [PubMed - indexed for MEDLINE]

53: Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA.
 The evolution of eukaryotes.
Science. 2007 Apr 27;316(5824):542-3; author reply 542-3. No abstract available.
PMID: 17463271 [PubMed - indexed for MEDLINE]

54: Koonin EV.
 Chance and necessity in cellular response to challenge.
Mol Syst Biol. 2007;3:107. Epub 2007 Apr 24. No abstract available.
PMID: 17453048 [PubMed - indexed for MEDLINE]

55: Rogozin IB, Wolf YI, Carmel L, Koonin EV.
 Ecdysozoan clade rejected by genome-wide analysis of rare amino acid
replacements.
Mol Biol Evol. 2007 Apr;24(4):1080-90. Epub 2007 Feb 13.
PMID: 17299026 [PubMed - indexed for MEDLINE]

56: Sverdlov AV, Csuros M, Rogozin IB, Koonin EV.
 A glimpse of a putative pre-intron phase of eukaryotic evolution.
Trends Genet. 2007 Mar;23(3):105-8. Epub 2007 Jan 19.
PMID: 17239982 [PubMed - indexed for MEDLINE]

57: Koonin EV.
 Temporal order of evolution of DNA replication systems inferred by comparison of 
cellular and viral DNA polymerases.
Biol Direct. 2006 Dec 18;1:39.
PMID: 17176463 [PubMed]

58: Dewey CN, Rogozin IB, Koonin EV.
 Compensatory relationship between splice sites and exonic splicing signals
depending on the length of vertebrate introns.
BMC Genomics. 2006 Dec 8;7:311.
PMID: 17156453 [PubMed - indexed for MEDLINE]

59: Makarova KS, Koonin EV.
 Evolutionary genomics of lactic acid bacteria.
J Bacteriol. 2007 Feb;189(4):1199-208. Epub 2006 Nov 3. Review. No abstract
available.
PMID: 17085562 [PubMed - indexed for MEDLINE]

60: Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ.
 Long intervals of stasis punctuated by bursts of positive selection in the
seasonal evolution of influenza A virus.
Biol Direct. 2006 Oct 26;1:34.
PMID: 17067369 [PubMed]

61: Kondrashov FA, Koonin EV, Morgunov IG, Finogenova TV, Kondrashova MN.
 Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal
transfer events and pseudogene formation.
Biol Direct. 2006 Oct 23;1:31.
PMID: 17059607 [PubMed]

62: Shakhnovich BE, Koonin EV.
 Origins and impact of constraints in evolution of gene families.
Genome Res. 2006 Dec;16(12):1529-36. Epub 2006 Oct 19.
PMID: 17053091 [PubMed - indexed for MEDLINE]

63: Correia FF, D'Onofrio A, Rejtar T, Li L, Karger BL, Makarova K, Koonin EV,
Lewis K.
 Kinase activity of overexpressed HipA is required for growth arrest and multidrug
tolerance in Escherichia coli.
J Bacteriol. 2006 Dec;188(24):8360-7. Epub 2006 Oct 13.
PMID: 17041039 [PubMed - indexed for MEDLINE]

64: Karev GP, Novozhilov AS, Koonin EV.
 Mathematical modeling of tumor therapy with oncolytic viruses: effects of
parametric heterogeneity on cell dynamics.
Biol Direct. 2006 Oct 3;1:30.
PMID: 17018145 [PubMed]

65: Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I,
Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM,
Yakunin AF.
 Genome-wide analysis of substrate specificities of the Escherichia coli haloacid 
dehalogenase-like phosphatase family.
J Biol Chem. 2006 Nov 24;281(47):36149-61. Epub 2006 Sep 21.
PMID: 16990279 [PubMed - indexed for MEDLINE]

66: Koonin EV, Senkevich TG, Dolja VV.
 The ancient Virus World and evolution of cells.
Biol Direct. 2006 Sep 19;1:29.
PMID: 16984643 [PubMed]

67: Tsaparas P, Mariño-Ramírez L, Bodenreider O, Koonin EV, Jordan IK.
 Global similarity and local divergence in human and mouse gene co-expression
networks.
BMC Evol Biol. 2006 Sep 12;6:70.
PMID: 16968540 [PubMed - indexed for MEDLINE]

68: Koonin EV, Wolf YI.
 Evolutionary systems biology: links between gene evolution and function.
Curr Opin Biotechnol. 2006 Oct;17(5):481-7. Epub 2006 Sep 8. Review.
PMID: 16962765 [PubMed - indexed for MEDLINE]

69: Martin W, Koonin EV.
 A positive definition of prokaryotes.
Nature. 2006 Aug 24;442(7105):868. No abstract available.
PMID: 16929275 [PubMed - indexed for MEDLINE]

70: Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI,
Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY.
 The cyanobacterial genome core and the origin of photosynthesis.
Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13126-31. Epub 2006 Aug 21.
PMID: 16924101 [PubMed - indexed for MEDLINE]

71: Koonin EV.
 The origin of introns and their role in eukaryogenesis: a compromise solution to 
the introns-early versus introns-late debate?
Biol Direct. 2006 Aug 14;1:22.
PMID: 16907971 [PubMed]

72: Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ,
Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J,
Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee 
SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C.
 Taking the first steps towards a standard for reporting on phylogenies: Minimum
Information About a Phylogenetic Analysis (MIAPA).
OMICS. 2006 Summer;10(2):231-7. Review.
PMID: 16901231 [PubMed - indexed for MEDLINE]

73: Makarova KS, Grishin NV, Koonin EV.
 The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in
archaea and bacteria.
Bioinformatics. 2006 Nov 1;22(21):2581-4. Epub 2006 Aug 8.
PMID: 16895922 [PubMed - indexed for MEDLINE]

74: Wolf YI, Carmel L, Koonin EV.
 Unifying measures of gene function and evolution.
Proc Biol Sci. 2006 Jun 22;273(1593):1507-15.
PMID: 16777745 [PubMed - indexed for MEDLINE]

75: Aravind L, Iyer LM, Koonin EV.
 Comparative genomics and structural biology of the molecular innovations of
eukaryotes.
Curr Opin Struct Biol. 2006 Jun;16(3):409-19. Epub 2006 May 5. Review.
PMID: 16679012 [PubMed - indexed for MEDLINE]

76: Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV.
 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. 2006 Mar 16;1:7.
PMID: 16545108 [PubMed]

77: Makarova KS, Koonin EV, Haselkorn R, Galperin MY.
 Cyanobacterial response regulator PatA contains a conserved N-terminal domain
(PATAN) with an alpha-helical insertion.
Bioinformatics. 2006 Jun 1;22(11):1297-301. Epub 2006 Mar 16.
PMID: 16543275 [PubMed - indexed for MEDLINE]

78: Prangishvili D, Garrett RA, Koonin EV.
 Evolutionary genomics of archaeal viruses: unique viral genomes in the third
domain of life.
Virus Res. 2006 Apr;117(1):52-67. Epub 2006 Feb 28. Review.
PMID: 16503363 [PubMed - indexed for MEDLINE]

79: Koonin EV, Dolja VV.
 Evolution of complexity in the viral world: the dawn of a new vision.
Virus Res. 2006 Apr;117(1):1-4. Epub 2006 Feb 23.
PMID: 16497406 [PubMed - indexed for MEDLINE]

80: Iyer LM, Balaji S, Koonin EV, Aravind L.
 Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.
Virus Res. 2006 Apr;117(1):156-84. Epub 2006 Feb 21. Review.
PMID: 16494962 [PubMed - indexed for MEDLINE]

81: Marinsek N, Barry ER, Makarova KS, Dionne I, Koonin EV, Bell SD.
 GINS, a central nexus in the archaeal DNA replication fork.
EMBO Rep. 2006 May;7(5):539-45. Epub 2006 Feb 17.
PMID: 16485022 [PubMed - in process]