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Select item 68065251.

RNA 3D structure prediction guided by independent folding of homologous sequences

Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki

BMC Bioinformatics. 2019; 20: 512. Published online 2019 Oct 22. doi: 10.1186/s12859-019-3120-y

PMCID:: PMC6806525

Abstract Article PDF–2.3M

Select item 67121712.

N⁴-Cytosine DNA Methylation Is Involved in the Maintenance of Genomic Stability in Deinococcus radiodurans

Shengjie Li, Jianling Cai, Huizhi Lu, Shuyu Mao, Shang Dai, Jing Hu, Liangyan Wang, Xiaoting Hua, Hong Xu, Bing Tian, Ye Zhao, Yuejin Hua

Front Microbiol. 2019; 10: 1905. Published online 2019 Aug 21. doi: 10.3389/fmicb.2019.01905

PMCID:: PMC6712171

Abstract Article PDF–2.9M

Select item 59966883.

DdrI, a cAMP Receptor Protein Family Member, Acts as a Major Regulator for Adaptation of Deinococcus radiodurans to Various Stresses

Laura Meyer, Geneviève Coste, Suzanne Sommer, Jacques Oberto, Fabrice Confalonieri, Pascale Servant, Cécile Pasternak

J Bacteriol. 2018 Jul 1; 200(13): e00129-18. Prepublished online 2018 Apr 23. Published online 2018 Jun 11. doi: 10.1128/JB.00129-18

PMCID:: PMC5996688

Abstract Article PDF–3.3M

Select item 56351684.

Characterization of a Deinococcus radiodurans MazF: A UACA‐specific RNA endoribonuclease

Tatsuki Miyamoto, Yuri Ota, Akiko Yokota, Tetsushi Suyama, Satoshi Tsuneda, Naohiro Noda

Microbiologyopen. 2017 Oct; 6(5): e00501. Published online 2017 Jul 3. doi: 10.1002/mbo3.501

PMCID:: PMC5635168

Abstract Article PDF–995K

Select item 53078755.

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

Carlos Y. Valenzuela

Biol Res. 2017; 50: 3. Published online 2017 Feb 13. doi: 10.1186/s40659-017-0112-0

PMCID:: PMC5307875

Abstract Article PDF–2.3M

Select item 51725476.

A Comprehensive Software Suite for the Analysis of cDNAs

Kazuharu Arakawa, Haruo Suzuki, Kosuke Fujishima, Kenji Fujimoto, Sho Ueda, Motomu Matsui, Masaru Tomita

Genomics Proteomics Bioinformatics. 2005; 3(3): 179–188. Published online 2016 Nov 28. doi: 10.1016/S1672-0229(05)03023-8

PMCID:: PMC5172547

Abstract Article PDF–541K

Select item 50099707.

Improved Complete Genome Sequence of the Extremely Radioresistant Bacterium Deinococcus radiodurans R1 Obtained Using PacBio Single-Molecule Sequencing

Xiaoting Hua, Yuejin Hua

Genome Announc. 2016 Sep-Oct; 4(5): e00886-16. Published online 2016 Sep 1. doi: 10.1128/genomeA.00886-16

PMCID:: PMC5009970

Abstract Article PDF–141K

Select item 50016118.

NCBI prokaryotic genome annotation pipeline

Tatiana Tatusova, Michael DiCuccio, Azat Badretdin, Vyacheslav Chetvernin, Eric P. Nawrocki, Leonid Zaslavsky, Alexandre Lomsadze, Kim D. Pruitt, Mark Borodovsky, James Ostell

Nucleic Acids Res. 2016 Aug 19; 44(14): 6614–6624. Published online 2016 Jun 24. doi: 10.1093/nar/gkw569

PMCID:: PMC5001611

Abstract Article PDF–2.6M

Select item 41477239.

Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1

Owen White, Jonathan A. Eisen, John F. Heidelberg, Erin K. Hickey, Jeremy D. Peterson, Robert J. Dodson, Daniel H. Haft, Michelle L. Gwinn, William C. Nelson, Delwood L. Richardson, Kelly S. Moffat, Haiying Qin, Lingxia Jiang, Wanda Pamphile, Marie Crosby, Mian Shen, Jessica J. Vamathevan, Peter Lam, Lisa McDonald, Terry Utterback, Celeste Zalewski, Kira S. Makarova, L. Aravind, Michael J. Daly, Kenneth W. Minton, Robert D. Fleischmann, Karen A. Ketchum, Karen E. Nelson, Steven Salzberg, Hamilton O. Smith, J. Craig Venter, Claire M. Fraser

Science. Author manuscript; available in PMC 2014 Aug 28.

Published in final edited form as: Science. 1999 Nov 19; 286(5444): 1571–1577. doi: 10.1126/science.286.5444.1571

PMCID:: PMC4147723

Abstract Article PDF–894K

Select item 409624410.

luxS in bacteria isolated from 25 to 40 million year-old amber

Tasha M. Santiago-Rodriguez, Ana R. Patrício, Jessica I. Rivera, Mariel Coradin, Alfredo Gonzalez, Gabriela Tirado, Raúl J. Cano, Gary A. Toranzos

FEMS Microbiol Lett. Author manuscript; available in PMC 2014 Jul 14.

Published in final edited form as: FEMS Microbiol Lett. 2014 Jan; 350(1): 117–124. Published online 2013 Oct 7. doi: 10.1111/1574-6968.12275

PMCID:: PMC4096244

Abstract Article PDF–731K

Select item 358228111.

Growth of Serratia liquefaciens under 7 mbar, 0°C, and CO₂-Enriched Anoxic Atmospheres

Andrew C. Schuerger, Richard Ulrich, Bonnie J. Berry, Wayne L. Nicholson

Astrobiology. 2013 Feb; 13(2): 115–131. doi: 10.1089/ast.2011.0811

PMCID:: PMC3582281

Abstract Article PDF–934K

Select item 315233012.

RNIE: genome-wide prediction of bacterial intrinsic terminators

Paul P. Gardner, Lars Barquist, Alex Bateman, Eric P. Nawrocki, Zasha Weinberg

Nucleic Acids Res. 2011 Aug; 39(14): 5845–5852. Published online 2011 Apr 7. doi: 10.1093/nar/gkr168

PMCID:: PMC3152330

Abstract Article PDF–1.7M

Select item 267217313.

Diversity of 23S rRNA Genes within Individual Prokaryotic Genomes

Anna Pei, Carlos W. Nossa, Pooja Chokshi, Martin J. Blaser, Liying Yang, David M. Rosmarin, Zhiheng Pei

PLoS One. 2009; 4(5): e5437. Published online 2009 May 5. doi: 10.1371/journal.pone.0005437

PMCID:: PMC2672173

Abstract Article PDF–425K

Select item 264816114.

The Unique Branching Patterns of Deinococcus Glycogen Branching Enzymes Are Determined by Their N-Terminal Domains

M. Palomo, S. Kralj, M. J. E. C. van der Maarel, L. Dijkhuizen

Appl Environ Microbiol. 2009 Mar; 75(5): 1355–1362. Published online 2009 Jan 9. doi: 10.1128/AEM.02141-08

PMCID:: PMC2648161

Abstract Article PDF–544K

Select item 241287815.

Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

Michael Dekhtyar, Amelie Morin, Vehary Sakanyan

BMC Bioinformatics. 2008; 9: 233. Published online 2008 May 9. doi: 10.1186/1471-2105-9-233

PMCID:: PMC2412878

Abstract Article PDF–492K

Select item 195184516.

Effect of a recD Mutation on DNA Damage Resistance and Transformation in Deinococcus radiodurans

Matthew D. Servinsky, Douglas A. Julin

J Bacteriol. 2007 Jul; 189(14): 5101–5107. Published online 2007 May 11. doi: 10.1128/JB.00409-07

PMCID:: PMC1951845

Abstract Article PDF–159K

Select item 185564517.

Widespread Occurrence and Genomic Context of Unusually Small Polyketide Synthase Genes in Microbial Consortia Associated with Marine Sponges

Lars Fieseler, Ute Hentschel, Lubomir Grozdanov, Andreas Schirmer, Gaiping Wen, Matthias Platzer, Siniša Hrvatin, Daniel Butzke, Katrin Zimmermann, Jörn Piel

Appl Environ Microbiol. 2007 Apr; 73(7): 2144–2155. Published online 2007 Feb 9. doi: 10.1128/AEM.02260-06

PMCID:: PMC1855645

Abstract Article PDF–541K

Select item 152518918.

Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements

Raquel Tobes, Eduardo Pareja

BMC Genomics. 2006; 7: 62. Published online 2006 Mar 24. doi: 10.1186/1471-2164-7-62

PMCID:: PMC1525189

Abstract Article PDF–552K

Select item 55594219.

Gene fusions and gene duplications: relevance to genomic annotation and functional analysis

Margrethe H Serres, Monica Riley

BMC Genomics. 2005; 6: 33. Published online 2005 Mar 9. doi: 10.1186/1471-2164-6-33

PMCID:: PMC555942

Abstract Article PDF–374K

Select item 54943220.

Variation in the strength of selected codon usage bias among bacteria

Paul M. Sharp, Elizabeth Bailes, Russell J. Grocock, John F. Peden, R. Elizabeth Sockett

Nucleic Acids Res. 2005; 33(4): 1141–1153. Published online 2005 Feb 23. doi: 10.1093/nar/gki242

PMCID:: PMC549432

Abstract Article PDF–284K

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