Search Results - "Omelchenko, Marina V"

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments by Rangwala, Sanjida H, Rudnev, Dmitry V, Ananiev, Victor V, Oh, Dong-Ha, Asztalos, Andrea, Benica, Barrett, Borodin, Evgeny A, Bouk, Nathan, Evgeniev, Vladislav I, Kodali, Vamsi K, Lotov, Vadim, Mozes, Eyal, Omelchenko, Marina V, Savkina, Sofya, Sukharnikov, Ekaterina, Virothaisakun, Joël, Murphy, Terence D, Pruitt, Kim D, Schneider, Valerie A

“…We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV)…”
Get full text

Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution by Omelchenko, Marina V, Galperin, Michael Y, Wolf, Yuri I, Koonin, Eugene V

“…Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The…”
Get full text

Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family by Kuznetsova, Ekaterina, Proudfoot, Michael, Gonzalez, Claudio F., Brown, Greg, Omelchenko, Marina V., Borozan, Ivan, Carmel, Liran, Wolf, Yuri I., Mori, Hirotada, Savchenko, Alexei V., Arrowsmith, Cheryl H., Koonin, Eugene V., Edwards, Aled M., Yakunin, Alexander F.

“…Haloacid dehalogenase (HAD)-like hydrolases are a vast superfamily of largely uncharacterized enzymes, with a few members shown to possess phosphatase,…”
Get full text

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks by Makarova, Kira S, Omelchenko, Marina V, Gaidamakova, Elena K, Matrosova, Vera Y, Vasilenko, Alexander, Zhai, Min, Lapidus, Alla, Copeland, Alex, Kim, Edwin, Land, Miriam, Mavrommatis, Konstantinos, Pitluck, Samuel, Richardson, Paul M, Detter, Chris, Brettin, Thomas, Saunders, Elizabeth, Lai, Barry, Ravel, Bruce, Kemner, Kenneth M, Wolf, Yuri I, Sorokin, Alexander, Gerasimova, Anna V, Gelfand, Mikhail S, Fredrickson, James K, Koonin, Eugene V, Daly, Michael J

“…Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus…”
Get full text

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance by Omelchenko, Marina V, Wolf, Yuri I, Gaidamakova, Elena K, Matrosova, Vera Y, Vasilenko, Alexander, Zhai, Min, Daly, Michael J, Koonin, Eugene V, Makarova, Kira S

“…Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a…”
Get full text

Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum by Jörk Nölling, Gary Breton, Marina V. Omelchenko, Kira S. Makarova, Qiandong Zeng, Rene Gibson, Hong Mei Lee, JoAnn Dubois, Dayong Qiu, Joseph Hitti, GTC Sequencing Center Production Finishing, and Bioinformatics Teams, Yuri I. Wolf, Roman L. Tatusov, Fabrice Sabathe, Lynn Doucette-Stamm, Philippe Soucaille, Michael J. Daly, George N. Bennett, Eugene V. Koonin, Douglas R. Smith

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
Get full text

Transcriptome Dynamics of Deinococcus radiodurans Recovering from Ionizing Radiation by Liu, Yongqing, Zhou, Jizhong, Omelchenko, Marina V., Beliaev, Alex S., Venkateswaran, Amudhan, Stair, Julia, Wu, Liyou, Thompson, Dorothea K., Xu, Dong, Rogozin, Igor B., Gaidamakova, Elena K., Zhai, Min, Makarova, Kira S., Koonin, Eugene V., Daly, Michael J.

“…Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular…”
Get full text

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia by Hou, Shaobin, Makarova, Kira S, Saw, Jimmy H W, Senin, Pavel, Ly, Benjamin V, Zhou, Zhemin, Ren, Yan, Wang, Jianmei, Galperin, Michael Y, Omelchenko, Marina V, Wolf, Yuri I, Yutin, Natalya, Koonin, Eugene V, Stott, Matthew B, Mountain, Bruce W, Crowe, Michelle A, Smirnova, Angela V, Dunfield, Peter F, Feng, Lu, Wang, Lei, Alam, Maqsudul

“…The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this…”
Get full text

Genome Sequence of the Deep-Sea γ-Proteobacterium Idiomarina loihiensis Reveals Amino Acid Fermentation as a Source of Carbon and Energy by Hou, Shaobin, Saw, Jimmy H, Lee, Kit Shan, Freitas, Tracey A, Belisle, Claude, Kawarabayasi, Yutaka, Donachie, Stuart P, Pikina, Alla, Galperin, Michael Y, Koonin, Eugene V, Makarova, Kira S, Omelchenko, Marina V, Sorokin, Alexander, Wolf, Yuri I, Li, Qing X, Keum, Young Soo, Campbell, Sonia, Denery, Judith, Aizawa, Shin-Ichi, Shibata, Satoshi, Malahoff, Alexander, Alam, Maqsudul

“…We report the complete genome sequence of the deep-sea γ-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on…”
Get full text

Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution by Novichkov, Pavel S, Omelchenko, Marina V, Gelfand, Mikhail S, Mironov, Andrei A, Wolf, Yuri I, Koonin, Eugene V

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
Get full text

Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus by Pavlicek, Jiri, Sauzet, Sandrine, Besseau, Laurence, Coon, Steven L, Weller, Joan L, Boeuf, Gilles, Gaildrat, Pascaline, Omelchenko, Marina V, Koonin, Eugene V, Falcón, Jack, Klein, David C

“…The arylalkylamine N-acetyltransferase (AANAT) family is divided into structurally distinct vertebrate and non-vertebrate groups. Expression of vertebrate…”
Get full text

CDD: a Conserved Domain Database for the functional annotation of proteins by Marchler-Bauer, Aron, Lu, Shennan, Anderson, John B, Chitsaz, Farideh, Derbyshire, Myra K, DeWeese-Scott, Carol, Fong, Jessica H, Geer, Lewis Y, Geer, Renata C, Gonzales, Noreen R, Gwadz, Marc, Hurwitz, David I, Jackson, John D, Ke, Zhaoxi, Lanczycki, Christopher J, Lu, Fu, Marchler, Gabriele H, Mullokandov, Mikhail, Omelchenko, Marina V, Robertson, Cynthia L, Song, James S, Thanki, Narmada, Yamashita, Roxanne A, Zhang, Dachuan, Zhang, Naigong, Zheng, Chanjuan, Bryant, Stephen H

“…NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional…”
Get full text

Transcriptome Analysis Applied to Survival of Shewanella oneidensis MR-1 Exposed to Ionizing Radiation by XIAOYUN QIU, DALY, Michael J, VASILENKO, Alexander, OMELCHENKO, Marina V, GAIDAMAKOVA, Elena K, LIYOU WU, JIZHONG ZHOU, SUNDIN, George W, TIEDJE, James M

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
Get full text

Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil by Vasilyeva, Lina V, Omelchenko, Marina V, Berestovskaya, Yulia Y, Lysenko, Anatolii M, Abraham, Wolf-Rainer, Dedysh, Svetlana N, Zavarzin, George A

“…1 S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, Moscow 117312, Russia 2 German Research Centre for…”
Get full text

Viral AlkB proteins repair RNA damage by oxidative demethylation by van den Born, Erwin, Omelchenko, Marina V, Bekkelund, Anders, Leihne, Vibeke, Koonin, Eugene V, Dolja, Valerian V, Falnes, Pål Ø

“…Bacterial and mammalian AlkB proteins are iron(II)- and 2-oxoglutarate-dependent dioxygenases that reverse methylation damage, such as 1-methyladenine and…”
Get full text

How radiation kills cells: Survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress by Ghosal, Debabrota, Omelchenko, Marina V., Gaidamakova, Elena K., Matrosova, Vera Y., Vasilenko, Alexander, Venkateswaran, Amudhan, Zhai, Min, Kostandarithes, Heather M., Brim, Hassan, Makarova, Kira S., Wackett, Lawrence P., Fredrickson, James K., Daly, Michael J.

“…Abstract We have recently shown that Deinococcus radiodurans and other radiation resistant bacteria accumulate exceptionally high intracellular manganese and…”
Get full text

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1 by Saw, Jimmy H, Mountain, Bruce W, Feng, Lu, Omelchenko, Marina V, Hou, Shaobin, Saito, Jennifer A, Stott, Matthew B, Li, Dan, Zhao, Guang, Wu, Junli, Galperin, Michael Y, Koonin, Eugene V, Makarova, Kira S, Wolf, Yuri I, Rigden, Daniel J, Dunfield, Peter F, Wang, Lei, Alam, Maqsudul

“…Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed…”
Get full text

Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria by van den Born, Erwin, Bekkelund, Anders, Moen, Marivi N., Omelchenko, Marina V., Klungland, Arne, Falnes, Pål Ø.

“…The iron(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from Escherichia coli (EcAlkB) repairs alkylation damage in DNA by direct reversal. EcAlkB…”
Get full text

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ by Omelchenko, Marina V, Makarova, Kira S, Wolf, Yuri I, Rogozin, Igor B, Koonin, Eugene V

“…Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish…”
Get full text

The NCBI Comparative Genome Viewer by Rangwala, Sanjida H, Rudnev, Dmitry V, Ananiev, Victor V, Oh, Dong-Ha, Asztalos, Andrea, Benica, Barrett, Borodin, Evgeny A, Bouk, Nathan, Evgeniev, Vladislav I, Kodali, Vamsi K, Lotov, Vadim, Mozes, Eyal, Omelchenko, Marina V, Savkina, Sofya, Sukharnikov, Ekaterina, Virothaisakun, Joël, Murphy, Terence D, Pruitt, Kim D, Schneider, Valerie A

Get full text