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Genetic flux over time in the Salmonella lineage
Georgios S Vernikos, Nicholas R Thomson, Julian Parkhill
Genome Biol. 2007; 8(6): R100. Published online 2007 June 4. doi: 10.1186/gb-2007-8-6-r100
PMCID:
PMC2394748
Abstract Full Text PDF–484K Supplementary Material
 Is Cited by the Following 22 Articles in this Archive:
An Integrative Method for Identifying the Over-Annotated Protein-Coding Genes in Microbial Genomes
Jia-Feng Yu, Ke Xiao, Dong-Ke Jiang, Jing Guo, Ji-Hua Wang, Xiao Sun
DNA Res. 2011 December; 18(6): 435–449. Published online 2011 September 8. doi: 10.1093/dnares/dsr030
PMCID:
PMC3223076
Abstract Full Text PDF–396K Supplementary Material
Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella
Jason E. McDermott, Hyunjin Yoon, Ernesto S. Nakayasu, Thomas O. Metz, Daniel R. Hyduke, Afshan S. Kidwai, Bernhard O. Palsson, Joshua N. Adkins, Fred Heffron
Front Microbiol. 2011; 2: 121. Published online 2011 June 2. doi: 10.3389/fmicb.2011.00121
PMCID:
PMC3108385
Abstract Full Text PDF–885K
Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes
Todd J. Treangen, Eduardo P. C. Rocha
PLoS Genet. 2011 January; 7(1): e1001284. Published online 2011 January 27. doi: 10.1371/journal.pgen.1001284
PMCID:
PMC3029252
Abstract Full Text PDF–713K Supplementary Material
Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes
Todd J. Treangen, Eduardo P. C. Rocha
PLoS Genet. 2011 January; 7(1): e1001284. Published online 2011 January 27. doi: 10.1371/journal.pgen.1001284
PMCID:
PMC3029252
Abstract Full Text PDF–713K Supplementary Material
Classification of genomic islands using decision trees and their ensemble algorithms
Dongsheng Che, Cory Hockenbury, Robert Marmelstein, Khaled Rasheed
BMC Genomics. 2010; 11(Suppl 2): S1. Published online 2010 November 2. doi: 10.1186/1471-2164-11-S2-S1
PMCID:
PMC2975412
Abstract Full Text PDF–495K Supplementary Material
The Extinction Dynamics of Bacterial Pseudogenes
Chih-Horng Kuo, Howard Ochman
PLoS Genet. 2010 August; 6(8): e1001050. Published online 2010 August 5. doi: 10.1371/journal.pgen.1001050
PMCID:
PMC2916853
Abstract Full Text PDF–451K Supplementary Material
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Aaron E. Darling, Bob Mau, Nicole T. Perna
PLoS One. 2010; 5(6): e11147. Published online 2010 June 25. doi: 10.1371/journal.pone.0011147
PMCID:
PMC2892488
Abstract Full Text PDF–1.3M Supplementary Material
Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish
Rike B Stelkens, Corinne Schmid, Oliver Selz, Ole Seehausen
BMC Evol Biol. 2009; 9: 283. Published online 2009 December 4. doi: 10.1186/1471-2148-9-283
PMCID:
PMC2796671
Abstract Full Text PDF–1.2M Supplementary Material
DsbL and DsbI contribute to periplasmic disulfide bond formation in Salmonella enterica serovar Typhimurium
Dongxia Lin, Byoungkwan Kim, James M. Slauch
Microbiology. 2009 December; 155(Pt 12): 4014–4024. doi: 10.1099/mic.0.032904-0
PMCID:
PMC2889420
Abstract Full Text PDF–298K
Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome
Tyler Jarvik, Chris Smillie, Eduardo A. Groisman, Howard Ochman
J Bacteriol. 2010 January; 192(2): 560–567. Published online 2009 November 6. doi: 10.1128/JB.01233-09
PMCID:
PMC2805332
Abstract Full Text PDF–211K Supplementary Material
Life in the inflamed intestine, Salmonella style
Renato L. Santos, Manuela Raffatellu, Charles L. Bevins, L. Garry Adams, Çagla Tükel, Renée M. Tsolis, Andreas J. Bäumler
Trends Microbiol. Author manuscript; available in PMC 2011 December 11.
Published in final edited form as: Trends Microbiol. 2009 November; 17(11): 498–506. Published online 2009 October 12. doi: 10.1016/j.tim.2009.08.008
PMCID:
PMC3235402
Abstract Full Text PDF–920K
Detection of genomic islands via segmental genome heterogeneity
Aaron J. Arvey, Rajeev K. Azad, Alpan Raval, Jeffrey G. Lawrence
Nucleic Acids Res. 2009 September; 37(16): 5255–5266. Published online 2009 September. doi: 10.1093/nar/gkp576
PMCID:
PMC2760805
Abstract Full Text PDF–4.6M Supplementary Material
Association of virulence plasmid and antibiotic resistance determinants with chromosomal multilocus genotypes in Mexican Salmonella enterica serovar Typhimurium strains
Magdalena Wiesner, Mussaret B Zaidi, Edmundo Calva, Marcos Fernández-Mora, Juan J Calva, Claudia Silva
BMC Microbiol. 2009; 9: 131. Published online 2009 July 3. doi: 10.1186/1471-2180-9-131
PMCID:
PMC2715408
Abstract Full Text PDF–1.5M Supplementary Material
Genome-Derived Criteria for Assigning Environmental narG and nosZ Sequences to Operational Taxonomic Units of Nitrate Reducers
Katharina Palmer, Harold L. Drake, Marcus A. Horn
Appl Environ Microbiol. 2009 August; 75(15): 5170–5174. Published online 2009 June 5. doi: 10.1128/AEM.00254-09
PMCID:
PMC2725509
Abstract Full Text PDF–3.2M Supplementary Material
Biogeography of the Sulfolobus islandicus pan-genome
Michael L. Reno, Nicole L. Held, Christopher J. Fields, Patricia V. Burke, Rachel J. Whitaker
Proc Natl Acad Sci U S A. 2009 May 26; 106(21): 8605–8610. Published online 2009 May 12. doi: 10.1073/pnas.0808945106
Correction in:
Proc Natl Acad Sci U S A. 2009 November 3; 106(44): 18873.
PMCID:
PMC2689034
Abstract Full Text PDF–512K Supplementary Material Correction
Bioinformatic detection of horizontally transferred DNA in bacterial genomes
Morgan GI Langille, Fiona SL Brinkman
F1000 Biol Rep. 2009; 1: 25. Published online 2009 March 24. doi: 10.3410/B1-25
PMCID:
PMC2920674
Abstract Full Text PDF–103K
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
Genomic islands: tools of bacterial horizontal gene transfer and evolution
Mario Juhas, Jan Roelof van der Meer, Muriel Gaillard, Rosalind M Harding, Derek W Hood, Derrick W Crook
FEMS Microbiol Rev. 2009 March; 33(2): 376–393. Published online 2008 October 30. doi: 10.1111/j.1574-6976.2008.00136.x
PMCID:
PMC2704930
Abstract Full Text PDF–296K
Evaluation of genomic island predictors using a comparative genomics approach
Morgan GI Langille, William WL Hsiao, Fiona SL Brinkman
BMC Bioinformatics. 2008; 9: 329. Published online 2008 August 5. doi: 10.1186/1471-2105-9-329
PMCID:
PMC2518932
Abstract Full Text PDF–507K 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
Resolving the structural features of genomic islands: A machine learning approach
Georgios S. Vernikos, Julian Parkhill
Genome Res. 2008 February; 18(2): 331–342. doi: 10.1101/gr.7004508
PMCID:
PMC2203631
Abstract Full Text PDF–809K
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