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Reduced selection leads to accelerated gene loss in Shigella
Ruth Hershberg, Hua Tang, Dmitri A Petrov
Genome Biol. 2007; 8(8): R164. Published online 2007 August 8. doi: 10.1186/gb-2007-8-8-r164
PMCID:
PMC2374995
Abstract Full Text PDF–314K
 Is Cited by the Following 12 Articles in this Archive:
Gene Decay in Shigella as an Incipient Stage of Host-Adaptation
Ye Feng, Zhe Chen, Shu-Lin Liu
PLoS One. 2011; 6(11): e27754. Published online 2011 November 16. doi: 10.1371/journal.pone.0027754
PMCID:
PMC3218036
Abstract Full Text PDF–142K Supplementary Material
Core and Panmetabolism in Escherichia coli
Gilles Vieira, Victor Sabarly, Pierre-Yves Bourguignon, Maxime Durot, François Le Fèvre, Damien Mornico, David Vallenet, Odile Bouvet, Erick Denamur, Vincent Schachter, Claudine Médigue
J Bacteriol. 2011 March; 193(6): 1461–1472. Published online 2011 January 14. doi: 10.1128/JB.01192-10
PMCID:
PMC3067614
Abstract Full Text PDF–1.3M Supplementary Material
N-gram analysis of 970 microbial organisms reveals presence of biological language models
Hatice Ulku Osmanbeyoglu, Madhavi K Ganapathiraju
BMC Bioinformatics. 2011; 12: 12. Published online 2011 January 10. doi: 10.1186/1471-2105-12-12
PMCID:
PMC3027111
Abstract Full Text PDF–2.8M Supplementary Material
The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function
M. Huvet, T. Toni, X. Sheng, T. Thorne, G. Jovanovic, C. Engl, M. Buck, J.W. Pinney, M.P.H. Stumpf
Mol Biol Evol. 2011 March; 28(3): 1141–1155. Published online 2010 November 8. doi: 10.1093/molbev/msq301
PMCID:
PMC3041696
Abstract Full Text PDF–1.1M Supplementary Material
Evidence That Mutation Is Universally Biased towards AT in Bacteria
Ruth Hershberg, Dmitri A. Petrov
PLoS Genet. 2010 September; 6(9): e1001115. Published online 2010 September 9. doi: 10.1371/journal.pgen.1001115
PMCID:
PMC2936535
Abstract Full Text PDF–1.1M Supplementary Material
Cryptic Lineages of the Genus Escherichia
Seth T. Walk, Elizabeth W. Alm, David M. Gordon, Jeffrey L. Ram, Gary A. Toranzos, James M. Tiedje, Thomas S. Whittam
Appl Environ Microbiol. 2009 October; 75(20): 6534–6544. Published online 2009 August 21. doi: 10.1128/AEM.01262-09
PMCID:
PMC2765150
Abstract Full Text PDF–1.1M Supplementary Material
The consequences of genetic drift for bacterial genome complexity
Chih-Horng Kuo, Nancy A. Moran, Howard Ochman
Genome Res. 2009 August; 19(8): 1450–1454. doi: 10.1101/gr.091785.109
PMCID:
PMC2720180
Abstract Full Text PDF–214K
Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model
Miklós Csűrös, István Miklós
Mol Biol Evol. 2009 September; 26(9): 2087–2095. Published online 2009 June 30. doi: 10.1093/molbev/msp123
PMCID:
PMC2726834
Abstract Full Text PDF–745K Supplementary Material
Effective population size and the rate and pattern of nucleotide substitutions
Megan Woolfit
Biol Lett. 2009 June 23; 5(3): 417–420. Published online 2009 April 8. doi: 10.1098/rsbl.2009.0155
PMCID:
PMC2679941
Abstract Full Text PDF–104K
Inferring genomic flux in bacteria
Xavier Didelot, Aaron Darling, Daniel Falush
Genome Res. 2009 February; 19(2): 306–317. doi: 10.1101/gr.082263.108
PMCID:
PMC2652212
Abstract Full Text PDF–1.6M
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
Marie Touchon, Claire Hoede, Olivier Tenaillon, Valérie Barbe, Simon Baeriswyl, Philippe Bidet, Edouard Bingen, Stéphane Bonacorsi, Christiane Bouchier, Odile Bouvet, Alexandra Calteau, Hélène Chiapello, Olivier Clermont, Stéphane Cruveiller, Antoine Danchin, Médéric Diard, Carole Dossat, Meriem El Karoui, Eric Frapy, Louis Garry, Jean Marc Ghigo, Anne Marie Gilles, James Johnson, Chantal Le Bouguénec, Mathilde Lescat, Sophie Mangenot, Vanessa Martinez-Jéhanne, Ivan Matic, Xavier Nassif, Sophie Oztas, Marie Agnès Petit, Christophe Pichon, Zoé Rouy, Claude Saint Ruf, Dominique Schneider, Jérôme Tourret, Benoit Vacherie, David Vallenet, Claudine Médigue, Eduardo P. C. Rocha, Erick Denamur
PLoS Genet. 2009 January; 5(1): e1000344. Published online 2009 January 23. doi: 10.1371/journal.pgen.1000344
PMCID:
PMC2617782
Abstract Full Text PDF–803K Supplementary Material
The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli
Mark W. J. van Passel, Pradeep Reddy Marri, Howard Ochman
PLoS Comput Biol. 2008 April; 4(4): e1000059. Published online 2008 April 11. doi: 10.1371/journal.pcbi.1000059
PMCID:
PMC2275313
Abstract Full Text PDF–149K Supplementary Material
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