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Vol. 12, Issue 7, 1080-1090, July 2002
LETTER
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  T. Shi and P. G. Falkowski Genome evolution in cyanobacteria: The stable core and the variable shell PNAS, February 19, 2008; 105(7): 2510 - 2515. [Abstract] [Full Text] [PDF]
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 N. J. Tourasse and A.-B. Kolsto SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis) Nucleic Acids Res., January 11, 2008; 36(suppl_1): D461 - D468. [Abstract] [Full Text] [PDF]
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 M. Martini, I.-M. Lee, K. D. Bottner, Y. Zhao, S. Botti, A. Bertaccini, N. A. Harrison, L. Carraro, C. Marcone, A. J. Khan, et al. Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas Int J Syst Evol Microbiol, September 1, 2007; 57(9): 2037 - 2051. [Abstract] [Full Text] [PDF]
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 M. Ventura, C. Canchaya, A. Tauch, G. Chandra, G. F. Fitzgerald, K. F. Chater, and D. van Sinderen Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum Microbiol. Mol. Biol. Rev., September 1, 2007; 71(3): 495 - 548. [Abstract] [Full Text] [PDF]
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 X. Bailly, I. Olivieri, B. Brunel, J.-C. Cleyet-Marel, and G. Bena Horizontal Gene Transfer and Homologous Recombination Drive the Evolution of the Nitrogen-Fixing Symbionts of Medicago Species J. Bacteriol., July 15, 2007; 189(14): 5223 - 5236. [Abstract] [Full Text] [PDF]
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R. Liu and H. Ochman Stepwise formation of the bacterial flagellar system PNAS, April 24, 2007; 104(17): 7116 - 7121. [Abstract] [Full Text] [PDF]
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 B. E. Dutilh, V. van Noort, R. T. J. M. van der Heijden, T. Boekhout, B. Snel, and M. A. Huynen Assessment of phylogenomic and orthology approaches for phylogenetic inference Bioinformatics, April 1, 2007; 23(7): 815 - 824. [Abstract] [Full Text] [PDF]
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Y. Xu, B. Labedan, and N. Glansdorff Surprising Arginine Biosynthesis: a Reappraisal of the Enzymology and Evolution of the Pathway in Microorganisms Microbiol. Mol. Biol. Rev., March 1, 2007; 71(1): 36 - 47. [Abstract] [Full Text] [PDF]
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 A. Barkan, L. Klipcan, O. Ostersetzer, T. Kawamura, Y. Asakura, and K. P. Watkins The CRM domain: An RNA binding module derived from an ancient ribosome-associated protein RNA, January 1, 2007; 13(1): 55 - 64. [Abstract] [Full Text] [PDF]
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 G. Jin, L. Nakhleh, S. Snir, and T. Tuller Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study Mol. Biol. Evol., January 1, 2007; 24(1): 324 - 337. [Abstract] [Full Text] [PDF]
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B. Titz, S. V. Rajagopala, C. Ester, R. Hauser, and P. Uetz Novel Conserved Assembly Factor of the Bacterial Flagellum J. Bacteriol., November 1, 2006; 188(21): 7700 - 7706. [Abstract] [Full Text] [PDF]
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K. T. Konstantinidis and J. M. Tiedje Towards a Genome-Based Taxonomy for Prokaryotes J. Bacteriol., September 15, 2005; 187(18): 6258 - 6264. [Abstract] [Full Text] [PDF]
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Y. Zhao, R. E. Davis, and I.-M. Lee Phylogenetic positions of 'Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2131 - 2141. [Abstract] [Full Text] [PDF]
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J.-F. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann, and G. Perriere Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases Bioinformatics, June 1, 2005; 21(11): 2596 - 2603. [Abstract] [Full Text] [PDF]
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E. Belda, A. Moya, and F. J. Silva Genome Rearrangement Distances and Gene Order Phylogeny in {gamma}-Proteobacteria Mol. Biol. Evol., June 1, 2005; 22(6): 1456 - 1467. [Abstract] [Full Text] [PDF]
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A. Carbone, F. Kepes, and A. Zinovyev Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle Mol. Biol. Evol., March 1, 2005; 22(3): 547 - 561. [Abstract] [Full Text] [PDF]
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U. Gophna, W. F. Doolittle, and R. L. Charlebois Weighted Genome Trees: Refinements and Applications J. Bacteriol., February 15, 2005; 187(4): 1305 - 1316. [Abstract] [Full Text] [PDF]
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G. Devulder, M. P. de Montclos, and J. P. Flandrois A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model Int J Syst Evol Microbiol, January 1, 2005; 55(1): 293 - 302. [Abstract] [Full Text] [PDF]
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 R. L. Charlebois and W. F. Doolittle Computing prokaryotic gene ubiquity: Rescuing the core from extinction Genome Res., December 1, 2004; 14(12): 2469 - 2477. [Abstract] [Full Text] [PDF]
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F. Kong and G. L. Gilbert Postgenomic taxonomy of human ureaplasmas - a case study based on multiple gene sequences Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1815 - 1821. [Abstract] [Full Text] [PDF]
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H. Philippe, E. A. Snell, E. Bapteste, P. Lopez, P. W. H. Holland, and D. Casane Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments Mol. Biol. Evol., September 1, 2004; 21(9): 1740 - 1752. [Abstract] [Full Text] [PDF]
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L. C. Edwards-Ingram, M. E. Gent, D. C. Hoyle, A. Hayes, L. I. Stateva, and S. G. Oliver Comparative Genomic Hybridization Provides New Insights Into the Molecular Taxonomy of the Saccharomyces Sensu Stricto Complex Genome Res., June 1, 2004; 14(6): 1043 - 1051. [Abstract] [Full Text] [PDF]
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B. Canback, I. Tamas, and S. G. E. Andersson A Phylogenomic Study of Endosymbiotic Bacteria Mol. Biol. Evol., June 1, 2004; 21(6): 1110 - 1122. [Abstract] [Full Text] [PDF]
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M. Wolf, T. Muller, T. Dandekar, and J. D. Pollack Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data Int J Syst Evol Microbiol, May 1, 2004; 54(3): 871 - 875. [Abstract] [Full Text] [PDF]
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A. D. Putteet-Driver, J. Zhong, and A. G. Barbour Transgenic Expression of RecA of the Spirochetes Borrelia burgdorferi and Borrelia hermsii in Escherichia coli Revealed Differences in DNA Repair and Recombination Phenotypes J. Bacteriol., April 15, 2004; 186(8): 2266 - 2274. [Abstract] [Full Text] [PDF]
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V. Daubin and H. Ochman Quartet Mapping and the Extent of Lateral Transfer in Bacterial Genomes Mol. Biol. Evol., January 1, 2004; 21(1): 86 - 89. [Abstract] [Full Text] [PDF]
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 S. Bury-Mone, S. Skouloubris, C. Dauga, J.-M. Thiberge, D. Dailidiene, D. E. Berg, A. Labigne, and H. De Reuse Presence of Active Aliphatic Amidases in Helicobacter Species Able To Colonize the Stomach Infect. Immun., October 1, 2003; 71(10): 5613 - 5622. [Abstract] [Full Text] [PDF]
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R. J. Kinsella, D. A. Fitzpatrick, C. J. Creevey, and J. O. McInerney Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution, and gene duplication PNAS, September 2, 2003; 100(18): 10320 - 10325. [Abstract] [Full Text] [PDF]
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 J. A. Eisen and C. M. Fraser Phylogenomics: Intersection of Evolution and Genomics Science, June 13, 2003; 300(5626): 1706 - 1707. [Abstract] [Full Text] [PDF]
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