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Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
Tristan Lefébure, Michael J Stanhope
Genome Biol. 2007; 8(5): R71. Published online 2007 May 2. doi: 10.1186/gb-2007-8-5-r71
PMCID:
PMC1929146
Abstract Full Text PDF–1.7M Supplementary Material
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 Is Cited by the Following 49 Articles in this Archive:
PGAP: pan-genomes analysis pipeline
Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao, Jun Yu
Bioinformatics. 2012 February 1; 28(3): 416–418. Published online 2011 November 29. doi: 10.1093/bioinformatics/btr655
PMCID:
PMC3268234
Abstract Full Text PDF–68K Supplementary Material
Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes
Anding Zhang, Ming Yang, Pan Hu, Jiayan Wu, Bo Chen, Yafeng Hua, Jun Yu, Huanchun Chen, Jingfa Xiao, Meilin Jin
BMC Genomics. 2011; 12: 523. Published online 2011 October 25. doi: 10.1186/1471-2164-12-523
PMCID:
PMC3227697
Abstract Full Text PDF–2.6M Supplementary Material
Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination
José L Acosta, Luis E Eguiarte, Rosa I Santamaría, Patricia Bustos, Pablo Vinuesa, Esperanza Martínez-Romero, Guillermo Dávila, Víctor González
BMC Evol Biol. 2011; 11: 305. Published online 2011 October 17. doi: 10.1186/1471-2148-11-305
PMCID:
PMC3215678
Abstract Full Text PDF–856K Supplementary Material
Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae
Zhuofei Xu, Huanchun Chen, Rui Zhou
BMC Evol Biol. 2011; 11: 203. Published online 2011 July 13. doi: 10.1186/1471-2148-11-203
PMCID:
PMC3146884
Abstract Full Text PDF–1023K Supplementary Material
Interplay of recombination and selection in the genomes of Chlamydia trachomatis
Sandeep J Joseph, Xavier Didelot, Khanjan Gandhi, Deborah Dean, Timothy D Read
Biol Direct. 2011; 6: 28. Published online 2011 May 26. doi: 10.1186/1745-6150-6-28
PMCID:
PMC3126793
Abstract Full Text PDF–1.1M Supplementary Material
Probing genomic diversity and evolution of Streptococcus suis serotype 2 by NimbleGen tiling arrays
Zuowei Wu, Ming Li, Changjun Wang, Jing Li, Na Lu, Ruifen Zhang, Yongqiang Jiang, Ruifu Yang, Cuihua Liu, Hui Liao, George F Gao, Jiaqi Tang, Baoli Zhu
BMC Genomics. 2011; 12: 219. Published online 2011 May 10. doi: 10.1186/1471-2164-12-219
PMCID:
PMC3118785
Abstract Full Text PDF–3.5M Supplementary Material
Identification of Genes and Genomic Islands Correlated with High Pathogenicity in Streptococcus suis Using Whole Genome Tilling Microarrays
Xiao Zheng, Han Zheng, Ruiting Lan, Changyun Ye, Yiting Wang, Ji Zhang, Huaiqi Jing, Chen Chen, Mariela Segura, Marcelo Gottschalk, Jianguo Xu
PLoS One. 2011; 6(3): e17987. Published online 2011 March 30. doi: 10.1371/journal.pone.0017987
PMCID:
PMC3068143
Abstract Full Text PDF–1.4M Supplementary Material
Distribution of Putative Virulence Genes in Streptococcus mutans Strains Does Not Correlate with Caries Experience
Silvia Argimón, Page W. Caufield
J Clin Microbiol. 2011 March; 49(3): 984–992. doi: 10.1128/JCM.01993-10
PMCID:
PMC3067729
Abstract Full Text PDF–373K Supplementary Material
Computational Analysis Suggests That Lyssavirus Glycoprotein Gene Plays a Minor Role in Viral Adaptation
Kevin Tang, Xianfu Wu
Int J Evol Biol. 2011; 2011: 143498. Published online 2011 February 6. doi: 10.4061/2011/143498
PMCID:
PMC3039477
Abstract Full Text PDF–1.2M
Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae
Anthony R. Borneman, Brian A. Desany, David Riches, Jason P. Affourtit, Angus H. Forgan, Isak S. Pretorius, Michael Egholm, Paul J. Chambers
PLoS Genet. 2011 February; 7(2): e1001287. Published online 2011 February 3. doi: 10.1371/journal.pgen.1001287
PMCID:
PMC3033381
Abstract Full Text PDF–817K Supplementary Material
Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution
Haruo Suzuki, Tristan Lefébure, Melissa Jane Hubisz, Paulina Pavinski Bitar, Ping Lang, Adam Siepel, Michael J. Stanhope
Genome Biol Evol. 2011; 3: 168–185. Published online 2011 January 31. doi: 10.1093/gbe/evr006
PMCID:
PMC3056289
Abstract Full Text PDF–1.5M
Defining Pathogenic Bacterial Species in the Genomic Era
Kalliopi Georgiades, Didier Raoult
Front Microbiol. 2010; 1: 151. Published online 2011 January 17. doi: 10.3389/fmicb.2010.00151
PMCID:
PMC3109419
Abstract Full Text PDF–2.3M
Genes but Not Genomes Reveal Bacterial Domestication of Lactococcus Lactis
Delphine Passerini, Charlotte Beltramo, Michele Coddeville, Yves Quentin, Paul Ritzenthaler, Marie-Line Daveran-Mingot, Pascal Le Bourgeois
PLoS One. 2010; 5(12): e15306. Published online 2010 December 17. doi: 10.1371/journal.pone.0015306
PMCID:
PMC3003715
Abstract Full Text PDF–504K Supplementary Material
Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences
Xavier Didelot, Daniel Lawson, Aaron Darling, Daniel Falush
Genetics. 2010 December; 186(4): 1435–1449. doi: 10.1534/genetics.110.120121
PMCID:
PMC2998322
Abstract Full Text PDF–3.0M
Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method
Olga K. Kamneva, David A. Liberles, Naomi L. Ward
Genome Biol Evol. 2010; 2: 870–886. Published online 2010 November 3. doi: 10.1093/gbe/evq071
PMCID:
PMC3000692
Abstract Full Text PDF–1.0M
Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie C Dunning Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Morgens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani
Genome Biol. 2010; 11(10): R107. Published online 2010 October 29. doi: 10.1186/gb-2010-11-10-r107
PMCID:
PMC3218663
Abstract Full Text PDF–1.3M Supplementary Material
Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus
Jean-Claude Ogier, Alexandra Calteau, Steve Forst, Heidi Goodrich-Blair, David Roche, Zoé Rouy, Garret Suen, Robert Zumbihl, Alain Givaudan, Patrick Tailliez, Claudine Médigue, Sophie Gaudriault
BMC Genomics. 2010; 11: 568. Published online 2010 October 15. doi: 10.1186/1471-2164-11-568
PMCID:
PMC3091717
Abstract Full Text PDF–1.0M Supplementary Material
The Streptococcus pyogenes proteome: maps, virulence factors and vaccine candidates
Alexander V Dmitriev, Michael S Chaussee
Future Microbiol. Author manuscript; available in PMC 2011 August 1.
Published in final edited form as: Future Microbiol. 2010 October; 5(10): 1539–1551. doi: 10.2217/fmb.10.116
PMCID:
PMC3092638
Abstract Full Text PDF–108K Supplementary Material
Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities
J. Jacob Parnell, Giovanni Rompato, Leigh C. Latta, IV, Michael E. Pfrender, Joy D. Van Nostrand, Zhili He, Jizhong Zhou, Gary Andersen, Patti Champine, Balasubramanian Ganesan, Bart C. Weimer
PLoS One. 2010; 5(9): e12919. Published online 2010 September 23. doi: 10.1371/journal.pone.0012919
PMCID:
PMC2950788
Abstract Full Text PDF–1.7M Supplementary Material
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
Xiangyu Deng, Adam M Phillippy, Zengxin Li, Steven L Salzberg, Wei Zhang
BMC Genomics. 2010; 11: 500. Published online 2010 September 16. doi: 10.1186/1471-2164-11-500
PMCID:
PMC2996996
Abstract Full Text PDF–3.2M Supplementary Material
Inferring Bacterial Genome Flux While Considering Truncated Genes
Weilong Hao, G. Brian Golding
Genetics. 2010 September; 186(1): 411–426. doi: 10.1534/genetics.110.118448
PMCID:
PMC2940306
Abstract Full Text PDF–2.2M
Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins
Timothy G Lilburn, Jianying Gu, Hong Cai, Yufeng Wang
BMC Genomics. 2010; 11: 369. Published online 2010 June 10. doi: 10.1186/1471-2164-11-369
PMCID:
PMC2890568
Abstract Full Text PDF–1.4M Supplementary Material
Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation
Caitriona M. Guinane, Nouri L. Ben Zakour, Maria A. Tormo-Mas, Lucy A. Weinert, Bethan V. Lowder, Robyn A. Cartwright, Davida S. Smyth, Cyril J. Smyth, Jodi A. Lindsay, Katherine A. Gould, Adam Witney, Jason Hinds, Jonathan P. Bollback, Andrew Rambaut, José R. Penadés, J. Ross Fitzgerald
Genome Biol Evol. 2010; 2: 454–466. Published online 2010 June 9. doi: 10.1093/gbe/evq031
PMCID:
PMC2997551
Abstract Full Text PDF–357K
Three Paralogous LysR-Type Transcriptional Regulators Control Sulfur Amino Acid Supply in Streptococcus mutans
Brice Sperandio, Céline Gautier, Nicolas Pons, Dusko S. Ehrlich, Pierre Renault, Eric Guédon
J Bacteriol. 2010 July; 192(13): 3464–3473. Published online 2010 April 23. doi: 10.1128/JB.00119-10
PMCID:
PMC2897675
Abstract Full Text PDF–1.9M Supplementary Material
A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence
Tannistha Nandi, Catherine Ong, Arvind Pratap Singh, Justin Boddey, Timothy Atkins, Mitali Sarkar-Tyson, Angela E. Essex-Lopresti, Hui Hoon Chua, Talima Pearson, Jason F. Kreisberg, Christina Nilsson, Pramila Ariyaratne, Catherine Ronning, Liliana Losada, Yijun Ruan, Wing-Kin Sung, Donald Woods, Richard W. Titball, Ifor Beacham, Ian Peak, Paul Keim, William C. Nierman, Patrick Tan
PLoS Pathog. 2010 April; 6(4): e1000845. Published online 2010 April 1. doi: 10.1371/journal.ppat.1000845
PMCID:
PMC2848565
Abstract Full Text PDF–2.0M Supplementary Material
Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing
Barry G. Hall, Garth D. Ehrlich, Fen Z. Hu
Microbiology. 2010 April; 156(Pt 4): 1060–1068. doi: 10.1099/mic.0.035188-0
PMCID:
PMC2889442
Abstract Full Text PDF–137K Supplementary Material
Legionella pneumophila pangenome reveals strain-specific virulence factors
Giuseppe D'Auria, Nuria Jiménez-Hernández, Francesc Peris-Bondia, Andrés Moya, Amparo Latorre
BMC Genomics. 2010; 11: 181. Published online 2010 March 17. doi: 10.1186/1471-2164-11-181
PMCID:
PMC2859405
Abstract Full Text PDF–2.1M Supplementary Material
OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs
Weilong Hao
BMC Bioinformatics. 2010; 11: 114. Published online 2010 March 2. doi: 10.1186/1471-2105-11-114
PMCID:
PMC2842260
Abstract Full Text PDF–1.1M Supplementary Material
Expanded Multilocus Sequence Typing and Comparative Genomic Hybridization of Campylobacter coli Isolates from Multiple Hosts
Ping Lang, Tristan Lefebure, Wei Wang, Paulina Pavinski Bitar, Richard J. Meinersmann, Katherine Kaya, Michael J. Stanhope
Appl Environ Microbiol. 2010 March; 76(6): 1913–1925. Published online 2010 January 22. doi: 10.1128/AEM.01753-09
PMCID:
PMC2838017
Abstract Full Text PDF–3.9M Supplementary Material
Mapping the Tree of Life: Progress and Prospects
Norman R. Pace
Microbiol Mol Biol Rev. 2009 December; 73(4): 565–576. doi: 10.1128/MMBR.00033-09
PMCID:
PMC2786576
Abstract Full Text PDF–1.4M
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