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Items: 20

1.

CDD: a Conserved Domain Database for the functional annotation of proteins.

Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH.

Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9. doi: 10.1093/nar/gkq1189. Epub 2010 Nov 24.

2.

Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus.

Pavlicek J, Sauzet S, Besseau L, Coon SL, Weller JL, Boeuf G, Gaildrat P, Omelchenko MV, Koonin EV, Falcón J, Klein DC.

BMC Evol Biol. 2010 May 25;10:154. doi: 10.1186/1471-2148-10-154.

3.

Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

Omelchenko MV, Galperin MY, Wolf YI, Koonin EV.

Biol Direct. 2010 Apr 30;5:31. doi: 10.1186/1745-6150-5-31.

4.

Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria.

van den Born E, Bekkelund A, Moen MN, Omelchenko MV, Klungland A, Falnes PØ.

Nucleic Acids Res. 2009 Nov;37(21):7124-36. doi: 10.1093/nar/gkp774.

5.

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1.

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.

Genome Biol. 2008;9(11):R161. doi: 10.1186/gb-2008-9-11-r161. Epub 2008 Nov 17.

6.

Viral AlkB proteins repair RNA damage by oxidative demethylation.

van den Born E, Omelchenko MV, Bekkelund A, Leihne V, Koonin EV, Dolja VV, Falnes PØ.

Nucleic Acids Res. 2008 Oct;36(17):5451-61. doi: 10.1093/nar/gkn519. Epub 2008 Aug 21.

7.

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.

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.

Biol Direct. 2008 Jul 1;3:26. doi: 10.1186/1745-6150-3-26.

8.

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.

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.

PLoS One. 2007 Sep 26;2(9):e955.

9.

Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family.

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.

J Biol Chem. 2006 Nov 24;281(47):36149-61. Epub 2006 Sep 21.

10.

Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.

Vasilyeva LV, Omelchenko MV, Berestovskaya YY, Lysenko AM, Abraham WR, Dedysh SN, Zavarzin GA.

Int J Syst Evol Microbiol. 2006 Sep;56(Pt 9):2083-8.

PMID:
16957103
11.

Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation.

Qiu X, Daly MJ, Vasilenko A, Omelchenko MV, Gaidamakova EK, Wu L, Zhou J, Sundin GW, Tiedje JM.

J Bacteriol. 2006 Feb;188(3):1199-204.

12.

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.

Omelchenko MV, Wolf YI, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Daly MJ, Koonin EV, Makarova KS.

BMC Evol Biol. 2005 Oct 20;5:57.

13.

How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress.

Ghosal D, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Venkateswaran A, Zhai M, Kostandarithes HM, Brim H, Makarova KS, Wackett LP, Fredrickson JK, Daly MJ.

FEMS Microbiol Rev. 2005 Apr;29(2):361-75. Review.

14.

Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.

Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin MY, Koonin EV, Makarova KS, Omelchenko MV, Sorokin A, Wolf YI, Li QX, Keum YS, Campbell S, Denery J, Aizawa S, Shibata S, Malahoff A, Alam M.

Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18036-41. Epub 2004 Dec 13.

15.

Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance.

Daly MJ, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Venkateswaran A, Hess M, Omelchenko MV, Kostandarithes HM, Makarova KS, Wackett LP, Fredrickson JK, Ghosal D.

Science. 2004 Nov 5;306(5698):1025-8. Epub 2004 Sep 30.

16.

Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.

Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV.

J Bacteriol. 2004 Oct;186(19):6575-85.

17.

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.

Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV.

Genome Biol. 2003;4(9):R55. Epub 2003 Aug 29.

18.

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation.

Liu Y, Zhou J, Omelchenko MV, Beliaev AS, Venkateswaran A, Stair J, Wu L, Thompson DK, Xu D, Rogozin IB, Gaidamakova EK, Zhai M, Makarova KS, Koonin EV, Daly MJ.

Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4191-6. Epub 2003 Mar 21.

19.

Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain.

Omelchenko MV, Makarova KS, Koonin EV.

FEMS Microbiol Lett. 2002 Apr 9;209(2):255-60.

20.

Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.

Nölling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, Wolf YI, Tatusov RL, Sabathe F, Doucette-Stamm L, Soucaille P, Daly MJ, Bennett GN, Koonin EV, Smith DR.

J Bacteriol. 2001 Aug;183(16):4823-38.

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