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Marina Omelchenko

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Publications

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Aron Marchler-Bauer; Shennan Lu; John B Anderson; Farideh Chitsaz; Myra K Derbyshire; Carol DeWeese-Scott; Jessica H Fong; Lewis Y Geer; Renata C Geer; Noreen R Gonzales; Marc Gwadz; David I Hurwitz; John D Jackson; Zhaoxi Ke; Christopher J Lanczycki; Fu Lu; Gabriele H Marchler; Mikhail Mullokandov; Marina V Omelchenko; Cynthia L Robertson; James S Song; Narmada Thanki; Roxanne A Yamashita; Dachuan Zhang; Naigong Zhang; Chanjuan Zheng; Stephen H Bryant
CDD: a Conserved Domain Database for the functional annotation of proteins.
Marina V Omelchenko; Michael Galperin; Yuri I Wolf; Eugene V Koonin
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.
Jimmy Saw; Bruce W Mountain; Lu Feng; Marina V Omelchenko; Shaobin Hou; Jennifer A Saito; Matthew B Stott; Dan Li; Guang Zhao; Junli Wu; Michael Galperin; Eugene V Koonin; Kira S Makarova; Yuri I Wolf; Daniel J Rigden; Peter F Dunfield; Lei Wang; Maqsudul Alam
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1.

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All Publications

2011: Aron Marchler-Bauer; Shennan Lu; John B Anderson; Farideh Chitsaz; Myra K Derbyshire; Carol DeWeese-Scott; Jessica H Fong; Lewis Y Geer; Renata C Geer; Noreen R Gonzales; Marc Gwadz; David I Hurwitz; John D Jackson; Zhaoxi Ke; Christopher J Lanczycki; Fu Lu; Gabriele H Marchler; Mikhail Mullokandov; Marina V Omelchenko; Cynthia L Robertson; James S Song; Narmada Thanki; Roxanne A Yamashita; Dachuan Zhang; Naigong Zhang; Chanjuan Zheng; Stephen H Bryant
CDD: a Conserved Domain Database for the functional annotation of proteins.
Nucleic acids research 2011;39(Database issue):D225-9.
2010: Marina V Omelchenko; Michael Galperin; Yuri I Wolf; Eugene V Koonin
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.
Biology direct 2010;5():31.
2008: Jimmy Saw; Bruce W Mountain; Lu Feng; Marina V Omelchenko; Shaobin Hou; Jennifer A Saito; Matthew B Stott; Dan Li; Guang Zhao; Junli Wu; Michael Galperin; Eugene V Koonin; Kira S Makarova; Yuri I Wolf; Daniel J Rigden; Peter F Dunfield; Lei Wang; Maqsudul Alam
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1.
Genome biology 2008;9(11):R161.
2008: Shaobin Hou; Kira S Makarova; Jimmy Saw; Pavel Senin; Benjamin V Ly; Zhemin Zhou; Yan Ren; Jianmei Wang; Michael Galperin; Marina V Omelchenko; Yuri I Wolf; Natalya Yutin; Eugene V Koonin; Matthew B Stott; Bruce W Mountain; Michelle A Crowe; Angela Smirnova; Peter F Dunfield; Lu Feng; Lei Wang; Maqsudul Alam
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.
Biology direct 2008;3():26.
2007: Sujuan Jia; Marina V Omelchenko; Donita Garland; Vasilis Vasiliou; Jyotshnabala Kanungo; Michael Spencer; Yuri Wolf; Eugene Koonin; Joram Piatigorsky
Duplicated gelsolin family genes in zebrafish: a novel scinderin-like gene (scinla) encodes the major corneal crystallin.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2007;21(12):3318-28.
2007: Kira S Makarova; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Alla Lapidus; Alex Copeland; Edwin Kim; Miriam Land; Konstantinos Mavrommatis; Samuel Pitluck; Paul M Richardson; Chris Detter; Thomas S Brettin; Elizabeth Saunders; Barry Lai; Bruce Ravel; Kenneth M Kemner; Yuri I Wolf; Alexei Sorokin; Anna V Gerasimova; Mikhail S Gelfand; James K Fredrickson; Eugene V Koonin; Michael J Daly
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
PloS one 2007;2(9):e955.
2006: Ekaterina Kuznetsova; Michael Proudfoot; Claudio F Gonzalez; Greg Brown; Marina V Omelchenko; Ivan Borozan; Liran Carmel; Yuri I Wolf; Hirotada Mori; Alexei V Savchenko; Cheryl H Arrowsmith; Eugene V Koonin; Aled M Edwards; Alexander F Yakunin
Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family.
The Journal of biological chemistry 2006;281(47):36149-61.
2006: Xiaoyun Qiu; Michael J Daly; Alexander Vasilenko; Marina V Omelchenko; Elena K Gaidamakova; Liyou Wu; ali khawwam; George W Sundin; James M Tiedje
Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation.
Journal of bacteriology 2006;188(3):1199-204.
2005: Debabrota Ghosal; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Amudhan Venkateswaran; Min Zhai; Heather M Kostandarithes; Hassan Brim; Kira S Makarova; Lawrence P Wackett; James K Fredrickson; Michael J Daly
How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress.
FEMS microbiology reviews 2005;29(2):361-75.
2005: Jeremy Foster; Mehul Ganatra; Ibrahim H Kamal; Jennifer Ware; Kira Makarova; Natalia Ivanova; Anamitra Bhattacharyya; Vinayak Kapatral; Sanjay Kumar; Janos Posfai; Tamas Vincze; Jessica Ingram; Laurie Moran; Alla Lapidus; Marina V Omelchenko; Nikos Kyrpides; Elodie Ghedin; Shiliang Wang; Eugene Goltsman; Victor Joukov; Olga Ostrovskaya; Kiryl Tsukerman; Mikhail Mazur; Donald Comb; Eugene Koonin; Barton Slatko
The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.
PLoS biology 2005;3(4):e121.
2005: Marina V Omelchenko; Yuri I Wolf; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Michael J Daly; Eugene V Koonin; Kira S Makarova
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.
BMC evolutionary biology 2005;5():57.
2004: Shaobin Hou; Jimmy Saw; Kit Shan Lee; Tracey Allen K Freitas; Claude Belisle; Yutaka Kawarabayasi; Stuart P Donachie; Alla Pikina; Michael Galperin; Eugene V Koonin; Kira S Makarova; Marina V Omelchenko; Alexei Sorokin; Yuri I Wolf; Qing X Li; Young-Soo Keum; Sonia Campbell; Judith Denery; Shin-Ichi Aizawa; Satoshi Shibata; Alexander Malahoff; Maqsudul Alam
Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(52):18036-41.
2004: Michael J Daly; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Amudhan Venkateswaran; M Hess; Marina V Omelchenko; Heather M Kostandarithes; Kira S Makarova; Lawrence P Wackett; James K Fredrickson; Debabrota Ghosal
Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance.
Science (New York, N.Y.) 2004;306(5698):1025-8.
2004: Pavel Novichkov; Marina V Omelchenko; Mikhail S Gelfand; Andrey A Mironov; Yuri I Wolf; Eugene V Koonin
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.
Journal of bacteriology 2004;186(19):6575-85.
2003: Yongqing Liu; ali khawwam; Marina V Omelchenko; Alex S Beliaev; Amudhan Venkateswaran; Julia Stair; Liyou Wu; Dorothea K Thompson; Dong Xu; Igor Rogozin; Elena K Gaidamakova; Min Zhai; Kira S Makarova; Eugene V Koonin; Michael J Daly
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(7):4191-6.
2003: Marina V Omelchenko; Kira S Makarova; Yuri I Wolf; Igor Rogozin; Eugene V Koonin
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.
Genome biology 2003;4(9):R55.
2002: Marina V Omelchenko; Kira S Makarova; Eugene V Koonin
Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain.
FEMS microbiology letters 2002;209(2):255-60.
2001: J Nölling; G Breton; Marina V Omelchenko; Kira S Makarova; Qiandong Zeng; R Gibson; H M Lee; J Dubois; D Qiu; J Hitti; Yuri I Wolf; Roman L Tatusov; F Sabathe; Lynn Doucette-Stamm; P Soucaille; Michael J Daly; george bennett; Eugene V Koonin; D R Smith
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.
Journal of bacteriology 2001;183(16):4823-38.