TY - JOUR AU - Lefebure, T. AU - Stanhope, M. J. PY - 2007 DA - 2007// TI - Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-5-r71 DO - 10.1186/gb-2007-8-5-r71 ID - Lefebure2007 ER - TY - JOUR AU - Didelot, X. AU - Maiden, M. C. J. PY - 2010 DA - 2010// TI - Impact of recombination on bacterial evolution JO - Trends in Microbiology VL - 18 UR - https://doi.org/10.1016/j.tim.2010.04.002 DO - 10.1016/j.tim.2010.04.002 ID - Didelot2010 ER - TY - JOUR AU - Vos, M. PY - 2009 DA - 2009// TI - Why do bacteria engage in homologous recombination? JO - Trends in Microbiology VL - 17 UR - https://doi.org/10.1016/j.tim.2009.03.001 DO - 10.1016/j.tim.2009.03.001 ID - Vos2009 ER - TY - JOUR AU - Narra, H. P. AU - Ochman, H. PY - 2006 DA - 2006// TI - Of what use is sex to Bacteria? JO - Current Biology VL - 5 UR - https://doi.org/10.1016/j.cub.2006.08.024 DO - 10.1016/j.cub.2006.08.024 ID - Narra2006 ER - TY - JOUR AU - Basic-Hammer, N. AU - Vogel, V. AU - Basset, P. AU - Blanc, D. S. PY - 2010 DA - 2010// TI - Impact of recombination on genetic variability within Staphylococcus aureus clonal complexes JO - Infection Genetics and Evolution VL - 10 UR - https://doi.org/10.1016/j.meegid.2010.07.013 DO - 10.1016/j.meegid.2010.07.013 ID - Basic-Hammer2010 ER - TY - JOUR AU - Bruen, T. C. AU - Philippe, H. AU - Bryant, D. PY - 2006 DA - 2006// TI - A simple and robust statistical test for detecting the presence of recombination JO - Genetics VL - 172 UR - https://doi.org/10.1534/genetics.105.048975 DO - 10.1534/genetics.105.048975 ID - Bruen2006 ER - TY - JOUR AU - Orsi, R. H. AU - Sun, Q. AU - Wiedmann, M. PY - 2008 DA - 2008// TI - Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-233 DO - 10.1186/1471-2148-8-233 ID - Orsi2008 ER - TY - JOUR AU - Lefebure, T. AU - Stanhope, M. J. PY - 2009 DA - 2009// TI - Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter JO - Genome Research VL - 19 UR - https://doi.org/10.1101/gr.089250.108 DO - 10.1101/gr.089250.108 ID - Lefebure2009 ER - TY - STD TI - Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, El Karoui M, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguenec C, Lescat M, Mangenot S, Martinez-Jehanne V, Matic I, Nassif X, Oztas S, et al: Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths. Plos Genetics. 2009, 5 (1): ID - ref9 ER - TY - JOUR AU - Jeffrey, B. M. AU - Suchland, R. J. AU - Quinn, K. L. AU - Davidson, J. R. AU - Stamm, W. E. AU - Rockey, D. D. PY - 2010 DA - 2010// TI - Genome Sequencing of Recent Clinical Chlamydia trachomatis Strains Identifies Loci Associated with Tissue Tropism and Regions of Apparent Recombination JO - Infection and Immunity VL - 78 UR - https://doi.org/10.1128/IAI.01324-09 DO - 10.1128/IAI.01324-09 ID - Jeffrey2010 ER - TY - JOUR AU - Soyer, Y. AU - Orsi, R. H. AU - Rodriguez-Rivera, L. D. AU - Sun, Q. AU - Wiedmann, M. PY - 2009 DA - 2009// TI - Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes JO - BMC Evol Biol VL - 9 UR - https://doi.org/10.1186/1471-2148-9-264 DO - 10.1186/1471-2148-9-264 ID - Soyer2009 ER - TY - CHAP AU - den Bakker, H. C. AU - Didelot, X. AU - Fortes, E. D. AU - Nightingale, K. K. AU - Wiedmann, M. PY - 2008 DA - 2008// TI - Lineage specific recombination rates and microevolution in Listeria monocytogenes BT - Bmc Evolutionary Biology ID - den Bakker2008 ER - TY - JOUR AU - Redfield, R. J. PY - 2001 DA - 2001// TI - Do bacteria have sex? JO - Nature Review Genetics VL - 2 UR - https://doi.org/10.1038/35084593 DO - 10.1038/35084593 ID - Redfield2001 ER - TY - JOUR AU - Shapiro, B. J. AU - David, L. A. AU - Friedman, J. AU - Alm, E. J. PY - 2009 DA - 2009// TI - Looking for Darwin's footprints in the microbial world JO - Trends in Microbiology VL - 17 UR - https://doi.org/10.1016/j.tim.2009.02.002 DO - 10.1016/j.tim.2009.02.002 ID - Shapiro2009 ER - TY - JOUR AU - Mes, T. H. M. AU - Doeleman, M. AU - Lodders, N. AU - Nubel, U. AU - Stal, L. J. PY - 2006 DA - 2006// TI - Selection on protein-coding genes of natural cyanobacterial populations JO - Environmental Microbiology VL - 8 UR - https://doi.org/10.1111/j.1462-2920.2006.01044.x DO - 10.1111/j.1462-2920.2006.01044.x ID - Mes2006 ER - TY - JOUR AU - Urwin, R. AU - Holmes, E. C. AU - Fox, A. J. AU - Derrick, J. P. AU - Maiden, M. C. J. PY - 2002 DA - 2002// TI - Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB JO - Molecular Biology and Evolution VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003991 DO - 10.1093/oxfordjournals.molbev.a003991 ID - Urwin2002 ER - TY - JOUR AU - Jolley, K. A. AU - Wilson, D. J. AU - Kriz, P. AU - Mcvean, G. AU - Maiden, M. C. J. PY - 2005 DA - 2005// TI - The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis (vol 22, pg 562, 2005) JO - Molecular Biology and Evolution VL - 22 ID - Jolley2005 ER - TY - JOUR AU - Andrews, T. D. AU - Gojobori, T. PY - 2004 DA - 2004// TI - Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen Neisseria meningitidis JO - Genetics VL - 166 UR - https://doi.org/10.1534/genetics.166.1.25 DO - 10.1534/genetics.166.1.25 ID - Andrews2004 ER - TY - JOUR AU - Guttman, D. S. AU - Gropp, S. J. AU - Morgan, R. L. AU - Wang, P. W. PY - 2006 DA - 2006// TI - Diversifying selection drives the evolution of the type III secretion system pilus of Pseudomonas syringae JO - Molecular Biology and Evolution VL - 23 UR - https://doi.org/10.1093/molbev/msl103 DO - 10.1093/molbev/msl103 ID - Guttman2006 ER - TY - JOUR AU - Peek, A. S. AU - Souza, V. AU - Eguiarte, L. E. AU - Gaut, B. S. PY - 2001 DA - 2001// TI - The interaction of protein structure, selection, and recombination on the evolution of the type-1 fimbrial major subunit (fimA) from Escherichia coli JO - Journal of Molecular Evolution VL - 52 ID - Peek2001 ER - TY - JOUR AU - Orsi, R. H. AU - Ripoll, D. R. AU - Yeung, M. AU - Nightingale, K. K. AU - Wiedmann, M. PY - 2007 DA - 2007// TI - Recombination and positive selection contribute to evolution of Listeria monocytogenes inlA JO - Microbiology VL - 153 UR - https://doi.org/10.1099/mic.0.2007/007310-0 DO - 10.1099/mic.0.2007/007310-0 ID - Orsi2007 ER - TY - JOUR AU - Torres-Morquecho, A. AU - Giono-Cerezo, S. AU - Camorlinga-Ponce, M. AU - Vargas-Mendoza, C. F. AU - Torres, J. PY - 2010 DA - 2010// TI - Evolution of bacterial genes: evidences of positive Darwinian selection and fixation of base substitutions in virulence genes of Helicobacter pylori JO - Infect Genet Evol VL - 10 UR - https://doi.org/10.1016/j.meegid.2010.04.005 DO - 10.1016/j.meegid.2010.04.005 ID - Torres-Morquecho2010 ER - TY - JOUR AU - Chen, S. L. AU - Hung, C. S. AU - Xu, J. AU - Reigstad, C. S. AU - Magrini, V. AU - Sabo, A. AU - Blasiar, D. AU - Bieri, T. AU - Meyer, R. R. AU - Ozersky, P. AU - Armstrong, J. R. AU - Fulton, R. S. AU - Latreille, J. P. AU - Spieth, J. AU - Hooton, T. M. AU - Mardis, E. R. AU - Hultgren, S. J. AU - Gordon, J. I. PY - 2006 DA - 2006// TI - Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0600938103 DO - 10.1073/pnas.0600938103 ID - Chen2006 ER - TY - JOUR AU - Larsson, P. AU - Elfsmark, D. AU - Svensson, K. AU - Wikstrom, P. AU - Forsman, M. AU - Brettin, T. AU - Keim, P. AU - Johansson, A. PY - 2009 DA - 2009// TI - Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen JO - PLoS Pathog VL - 5 UR - https://doi.org/10.1371/journal.ppat.1000472 DO - 10.1371/journal.ppat.1000472 ID - Larsson2009 ER - TY - STD TI - Nandi T, Ong C, Singh AP, Boddey J, Atkins T, Sarkar-Tyson M, Essex-Lopresti AE, Chua HH, Pearson T, Kreisberg JF, Nilsson C, Ariyaratne P, Ronning C, Losada L, Ruan YJ, Sung WK, Woods D, Titball RW, Beacham I, Peak I, Keim P, Nierman WC, Tan P: A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence. Plos Pathogens. 2010, 6 (4): ID - ref25 ER - TY - JOUR AU - Thomson, N. R. AU - Holden, M. T. AU - Carder, C. AU - Lennard, N. AU - Lockey, S. J. AU - Marsh, P. AU - Skipp, P. AU - O'Connor, C. D. AU - Goodhead, I. AU - Norbertzcak, H. AU - Harris, B. AU - Ormond, D. AU - Rance, R. AU - Quail, M. A. AU - Parkhill, J. AU - Stephens, R. S. AU - Clarke, I. N. PY - 2008 DA - 2008// TI - Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.7020108 DO - 10.1101/gr.7020108 ID - Thomson2008 ER - TY - JOUR AU - Tsai, Y. H. AU - Orsi, R. H. AU - Nightingale, K. K. AU - Wiedmann, M. PY - 2006 DA - 2006// TI - Listeria monocytogenes internalins are highly diverse and evolved by recombination and positive selection JO - Infect Genet Evol VL - 6 UR - https://doi.org/10.1016/j.meegid.2006.01.004 DO - 10.1016/j.meegid.2006.01.004 ID - Tsai2006 ER - TY - JOUR AU - Thomson, N. R. AU - Clarke, I. N. PY - 2010 DA - 2010// TI - Chlamydia trachomatis: small genome, big challenges JO - Future Microbiology VL - 5 UR - https://doi.org/10.2217/fmb.10.31 DO - 10.2217/fmb.10.31 ID - Thomson2010 ER - TY - JOUR AU - Stephens, R. S. AU - Kalman, S. AU - Lammel, C. AU - Fan, J. AU - Marathe, R. AU - Aravind, L. AU - Mitchell, W. AU - Olinger, L. AU - Tatusov, R. L. AU - Zhao, Q. X. AU - Koonin, E. V. AU - Davis, R. W. PY - 1998 DA - 1998// TI - Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis JO - Science VL - 282 UR - https://doi.org/10.1126/science.282.5389.754 DO - 10.1126/science.282.5389.754 ID - Stephens1998 ER - TY - JOUR AU - Savage, E. J. AU - van de Laar, M. J. AU - Gallay, A. AU - van der Sande, M. AU - Hamouda, O. AU - Sasse, A. AU - Hoffmann, S. AU - Diez, M. AU - Borrego, M. J. AU - Lowndes, C. M. AU - Ison, C. AU - Network, E. PY - 2009 DA - 2009// TI - Lymphogranuloma Venereum in Europe, 2003-2008 JO - Eurosurveillance VL - 14 ID - Savage2009 ER - TY - JOUR AU - Millman, K. AU - Black, C. M. AU - Johnson, R. E. AU - Stamm, W. E. AU - Jones, R. B. AU - Hook, E. W. AU - Martin, D. H. AU - Bolan, G. AU - Tavare, S. AU - Dean, D. PY - 2004 DA - 2004// TI - Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States JO - Journal of Bacteriology VL - 186 UR - https://doi.org/10.1128/JB.186.8.2457-2465.2004 DO - 10.1128/JB.186.8.2457-2465.2004 ID - Millman2004 ER - TY - JOUR AU - Millman, K. L. AU - Tavaré, S. AU - Dean, D. PY - 2001 DA - 2001// TI - Recombination in the ompA gene but not the omcB gene of Chlamydia contributes to serovar-specific differences in tissue tropism, immune surveillance, and persistence of the organism JO - Journal of Bacteriology VL - 183 UR - https://doi.org/10.1128/JB.183.20.5997-6008.2001 DO - 10.1128/JB.183.20.5997-6008.2001 ID - Millman2001 ER - TY - JOUR AU - Dean, D. AU - Millman, K. PY - 1997 DA - 1997// TI - Molecular and mutation trends analyses of omp1 alleles for serovar E of Chlamydia trachomatis - Implications for the immunopathogenesis of disease JO - Journal of Clinical Investigation VL - 99 UR - https://doi.org/10.1172/JCI119182 DO - 10.1172/JCI119182 ID - Dean1997 ER - TY - JOUR AU - Nunes, A. AU - Borrego, M. J. AU - Nunes, B. AU - Florindo, C. AU - Gomes, J. P. PY - 2009 DA - 2009// TI - Evolutionary dynamics of ompA, the gene encoding the Chlamydia trachomatis key antigen JO - J Bacteriol VL - 191 UR - https://doi.org/10.1128/JB.00895-09 DO - 10.1128/JB.00895-09 ID - Nunes2009 ER - TY - STD TI - Nunes A, Nogueira PJ, Borrego MJ, Gomes JP: Adaptive evolution of the Chlamydia trachomatis dominant antigen reveals distinct evolutionary scenarios for B- and T-cell epitopes: worldwide survey. PLoS One. 2010, 5 (10): ID - ref35 ER - TY - JOUR AU - Gomes, J. P. AU - Bruno, W. J. AU - Borrego, M. J. AU - Dean, D. PY - 2004 DA - 2004// TI - Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer JO - Journal of Bacteriology VL - 186 UR - https://doi.org/10.1128/JB.186.13.4295-4306.2004 DO - 10.1128/JB.186.13.4295-4306.2004 ID - Gomes2004 ER - TY - JOUR AU - Gomes, J. P. AU - Nunes, A. AU - Bruno, W. J. AU - Borrego, M. J. AU - Florindo, C. AU - Dean, D. PY - 2006 DA - 2006// TI - Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: Evidence for serovar Da recombination and correlation with tissue tropism JO - Journal of Bacteriology VL - 188 UR - https://doi.org/10.1128/JB.188.1.275-286.2006 DO - 10.1128/JB.188.1.275-286.2006 ID - Gomes2006 ER - TY - JOUR AU - Gomes, J. P. AU - Bruno, W. J. AU - Nunes, A. AU - Santos, N. AU - Florindo, C. AU - Borrego, M. J. AU - Dean, D. PY - 2007 DA - 2007// TI - Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots JO - Genome Research VL - 17 UR - https://doi.org/10.1101/gr.5674706 DO - 10.1101/gr.5674706 ID - Gomes2007 ER - TY - JOUR AU - DeMars, R. AU - Weinfurter, J. PY - 2008 DA - 2008// TI - Interstrain gene transfer in Chlamydia trachomatis in vitro: Mechanism and significance JO - Journal of Bacteriology VL - 190 UR - https://doi.org/10.1128/JB.01592-07 DO - 10.1128/JB.01592-07 ID - DeMars2008 ER - TY - JOUR AU - DeMars, R. AU - Weinfurter, J. AU - Guex, E. AU - Lin, J. AU - Potucek, Y. PY - 2007 DA - 2007// TI - Lateral gene transfer in vitro in the intracellular pathogen Chlamydia trachomatis JO - Journal of Bacteriology VL - 189 UR - https://doi.org/10.1128/JB.00845-06 DO - 10.1128/JB.00845-06 ID - DeMars2007 ER - TY - JOUR AU - Sandoz, K. M. AU - Rockey, D. D. PY - 2010 DA - 2010// TI - Antibiotic resistance in Chlamydia JO - Future Microbiology VL - 5 UR - https://doi.org/10.2217/fmb.10.96 DO - 10.2217/fmb.10.96 ID - Sandoz2010 ER - TY - JOUR AU - Dean, D. AU - Bruno, W. J. AU - Wan, R. AU - Gomes, J. P. AU - Devignot, S. AU - Mehari, T. AU - de Vries, H. J. C. AU - Morre, S. A. AU - Myers, G. AU - Read, T. D. AU - Spratt, B. G. PY - 2009 DA - 2009// TI - Predicting Phenotype and Emerging Strains among Chlamydia trachomatis Infections JO - Emerging Infectious Diseases VL - 15 UR - https://doi.org/10.3201/eid1509.090272 DO - 10.3201/eid1509.090272 ID - Dean2009 ER - TY - JOUR AU - Somboonna, N. AU - Wan, R. AU - Ojcius, D. M. AU - Pettengill, M. A. AU - Joseph, S. J. AU - Chang, A. AU - Hsu, R. AU - Read, T. D. AU - Dean, D. PY - 2011 DA - 2011// TI - Hypervirulent Chlamydia trachomatis Clinical Strain Is a Recombinant between Lymphogranuloma Venereum (L2) and D Lineages JO - Mbio VL - 2 ID - Somboonna2011 ER - TY - JOUR AU - Joseph, S. J. AU - Read, T. D. PY - 2010 DA - 2010// TI - Bacterial population genomics and infectious disease diagnostics JO - Trends Biotechnol VL - 28 UR - https://doi.org/10.1016/j.tibtech.2010.09.001 DO - 10.1016/j.tibtech.2010.09.001 ID - Joseph2010 ER - TY - JOUR AU - Li, L. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2003 DA - 2003// TI - OrthoMCL: identification of ortholog groups for eukaryotic genomes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1224503 DO - 10.1101/gr.1224503 ID - Li2003 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - CHAP AU - Mikita Suyama, D. T. AU - Peer, B. o. r. k. PY - 2006 DA - 2006// TI - PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments BT - Nucleic Acids Research ID - Mikita Suyama2006 ER - TY - JOUR AU - Castresana, J. PY - 2000 DA - 2000// TI - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis JO - Molecular Biology and Evolution VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026334 DO - 10.1093/oxfordjournals.molbev.a026334 ID - Castresana2000 ER - TY - JOUR AU - Schmidt, H. A. AU - Strimmer, K. AU - Vingron, M. AU - von Haeseler, A. PY - 2002 DA - 2002// TI - TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.502 DO - 10.1093/bioinformatics/18.3.502 ID - Schmidt2002 ER - TY - JOUR AU - Felsenstein, J. PY - 1989 DA - 1989// TI - PHYLIP - phylogeny inference package JO - Cladistics VL - 5 ID - Felsenstein1989 ER - TY - JOUR AU - Yang, Z. H. PY - 2007 DA - 2007// TI - PAML 4: Phylogenetic analysis by maximum likelihood JO - Molecular Biology and Evolution VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - JOUR AU - Wong, W. S. W. AU - Yang, Z. H. AU - Goldman, N. AU - Nielsen, R. PY - 2004 DA - 2004// TI - Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites JO - Genetics VL - 168 UR - https://doi.org/10.1534/genetics.104.031153 DO - 10.1534/genetics.104.031153 ID - Wong2004 ER - TY - JOUR AU - Zhang, J. Z. AU - Nielsen, R. AU - Yang, Z. H. PY - 2005 DA - 2005// TI - Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level JO - Molecular Biology and Evolution VL - 22 UR - https://doi.org/10.1093/molbev/msi237 DO - 10.1093/molbev/msi237 ID - Zhang2005 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing JO - Journal of the Royal Statistical Society Series B-Methodological VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Storey, J. D. PY - 2002 DA - 2002// TI - A direct approach to false discovery rates JO - Journal of the Royal Statistical Society Series B-Statistical Methodology VL - 64 UR - https://doi.org/10.1111/1467-9868.00346 DO - 10.1111/1467-9868.00346 ID - Storey2002 ER - TY - STD TI - GENECONV: A computer package for the statistical detection of gene conversion. [http://www.math.wustl.edu/~sawyer/geneconv/] UR - http://www.math.wustl.edu/~sawyer/geneconv/ ID - ref56 ER - TY - JOUR AU - Sawyer, S. PY - 1989 DA - 1989// TI - Statistical Tests for Detecting Gene Conversion JO - Molecular Biology and Evolution VL - 6 ID - Sawyer1989 ER - TY - JOUR AU - Didelot, X. AU - Falush, D. PY - 2007 DA - 2007// TI - Inference of bacterial microevolution using multilocus sequence data JO - Genetics VL - 175 UR - https://doi.org/10.1534/genetics.106.063305 DO - 10.1534/genetics.106.063305 ID - Didelot2007 ER - TY - JOUR AU - Darling, A. C. AU - Mau, B. AU - Blattner, F. R. AU - Perna, N. T. PY - 2004 DA - 2004// TI - Mauve: multiple alignment of conserved genomic sequence with rearrangements JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2289704 DO - 10.1101/gr.2289704 ID - Darling2004 ER - TY - JOUR AU - Darling, A. E. AU - Mau, B. AU - Perna, N. T. PY - 2010 DA - 2010// TI - progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0011147 DO - 10.1371/journal.pone.0011147 ID - Darling2010 ER - TY - JOUR AU - Kalinowski, S. T. AU - Hedrick, P. W. PY - 2001 DA - 2001// TI - Estimation of linkage disequilibrium for loci with multiple alleles: basic approach and an application using data from bighorn sheep JO - Heredity VL - 87 UR - https://doi.org/10.1046/j.1365-2540.2001.00966.x DO - 10.1046/j.1365-2540.2001.00966.x ID - Kalinowski2001 ER - TY - JOUR AU - Kulick, S. AU - Moccia, C. AU - Didelot, X. AU - Falush, D. AU - Kraft, C. AU - Suerbaum, S. PY - 2008 DA - 2008// TI - Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori JO - PLoS One VL - 3 UR - https://doi.org/10.1371/journal.pone.0003797 DO - 10.1371/journal.pone.0003797 ID - Kulick2008 ER - TY - JOUR AU - Didelot, X. AU - Barker, M. AU - Falush, D. AU - Priest, F. G. PY - 2009 DA - 2009// TI - Evolution of pathogenicity in the Bacillus cereus group JO - Systematic and Applied Microbiology VL - 32 UR - https://doi.org/10.1016/j.syapm.2009.01.001 DO - 10.1016/j.syapm.2009.01.001 ID - Didelot2009 ER - TY - JOUR AU - Smith, J. M. AU - Smith, N. H. AU - O'Rourke a, M. AU - Spratt, B. G. PY - 1993 DA - 1993// TI - How clonal are bacteria? JO - PNAS VL - 90 UR - https://doi.org/10.1073/pnas.90.10.4384 DO - 10.1073/pnas.90.10.4384 ID - Smith1993 ER - TY - JOUR AU - Fearnbead, P. AU - Smith, N. G. C. AU - Barrigas, M. AU - Fox, A. AU - French, N. PY - 2005 DA - 2005// TI - Analysis of recombination in Campylobacter jejuni from MLST population data JO - Journal of Molecular Evolution VL - 61 UR - https://doi.org/10.1007/s00239-004-0316-0 DO - 10.1007/s00239-004-0316-0 ID - Fearnbead2005 ER - TY - JOUR AU - Stephens, R. S. AU - Kalman, S. AU - Lammel, C. AU - Fan, J. AU - Marathe, R. AU - Aravind, L. AU - Mitchell, W. AU - Olinger, L. AU - Tatusov, R. L. AU - Zhao, Q. AU - Koonin, E. V. AU - Davis, R. W. PY - 1998 DA - 1998// TI - Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis JO - Science VL - 282 UR - https://doi.org/10.1126/science.282.5389.754 DO - 10.1126/science.282.5389.754 ID - Stephens1998 ER - TY - JOUR AU - Dean, D. AU - Oudens, E. AU - Bolan, G. AU - Padian, N. AU - Schachter, J. PY - 1995 DA - 1995// TI - Major Outer-Membrane Protein Variants of Chlamydia-Trachomatis Are Associated with Severe Upper Genital-Tract Infections and Histopathology in San-Francisco JO - Journal of Infectious Diseases VL - 172 UR - https://doi.org/10.1093/infdis/172.4.1013 DO - 10.1093/infdis/172.4.1013 ID - Dean1995 ER - TY - JOUR AU - Dean, D. AU - Suchland, R. J. AU - Stamm, W. E. PY - 2000 DA - 2000// TI - Evidence for Long-Term Cervical Persistence of Chlamydia trachomatis by ompl Genotyping JO - The Journal of Infectious Diseases VL - 182 UR - https://doi.org/10.1086/315778 DO - 10.1086/315778 ID - Dean2000 ER - TY - STD TI - Millman KL, Tavaré S, Dean D: Recombination in the ompA Gene but Not the omcB Gene of Chlamydia Contributes to Serovar-Specific Differences in Tissue Tropism, Immune Surveillance, and Persistence of the Organism. Journal of Bacteriology. 183 (20): 5997-6008. ID - ref69 ER - TY - JOUR AU - Gomes, J. P. AU - Hsia, R. c. AU - Mead, S. AU - Borrego, M. J. AU - Dean, D. PY - 2005 DA - 2005// TI - Immunoreactivity and differential developmental expression of known and putative Chlamydia trachomatis membrane proteins for biologically variant serovars representing distinct disease groups JO - Microbes and Infection VL - 7 UR - https://doi.org/10.1016/j.micinf.2004.11.014 DO - 10.1016/j.micinf.2004.11.014 ID - Gomes2005 ER - TY - STD TI - Nunes A, Gomes JP, Mead S, Florindo C, Correia H, Borrego MJ, Dean D: Comparative Expression Profiling of the Chlamydia trachomatis pmp Gene Family for Clinical and Reference Strains. Plos One. 2007, 2 (9): ID - ref71 ER - TY - JOUR AU - Tan, C. AU - Hsia, R. C. AU - Shou, H. Z. AU - Haggerty, C. L. AU - Ness, R. B. AU - Gaydos, C. A. AU - Dean, D. AU - Scurlock, A. M. AU - Wilson, D. P. AU - Bavoil, P. M. PY - 2009 DA - 2009// TI - Chlamydia trachomatis-Infected Patients Display Variable Antibody Profiles against the Nine-Member Polymorphic Membrane Protein Family JO - Infection and Immunity VL - 77 UR - https://doi.org/10.1128/IAI.01566-08 DO - 10.1128/IAI.01566-08 ID - Tan2009 ER - TY - JOUR AU - Carlson, J. H. AU - Porcella, S. F. AU - McClarty, G. AU - Caldwell, H. D. PY - 2005 DA - 2005// TI - Comparative genomic analysis of Chlamydia trachomatis oculotropic and genitotropic strains JO - Infection and Immunity VL - 73 UR - https://doi.org/10.1128/IAI.73.10.6407-6418.2005 DO - 10.1128/IAI.73.10.6407-6418.2005 ID - Carlson2005 ER - TY - STD TI - Jewett TJ, Miller NJ, Dooley CA, Hackstadt T: The Conserved Tarp Actin Binding Domain Is Important for Chlamydial Invasion. Plos Pathogens. 2010, 6 (7): ID - ref74 ER - TY - JOUR AU - Lutter, E. I. AU - Bonner, C. AU - Holland, M. J. AU - Suchland, R. J. AU - Stamm, W. E. AU - Jewett, T. J. AU - McClarty, G. AU - Hackstadt, T. PY - 2010 DA - 2010// TI - Phylogenetic Analysis of Chlamydia trachomatis Tarp and Correlation with Clinical Phenotype JO - Infection and Immunity VL - 78 UR - https://doi.org/10.1128/IAI.00515-10 DO - 10.1128/IAI.00515-10 ID - Lutter2010 ER - TY - JOUR AU - Scidmore-Carlson, M. A. AU - Shaw, E. I. AU - Dooley, C. A. AU - Fischer, E. R. AU - Hackstadt, T. PY - 1999 DA - 1999// TI - Identification and characterization of a Chlamydia trachomatis early operon encoding four novel inclusion membrane proteins JO - Molecular Microbiology VL - 33 UR - https://doi.org/10.1046/j.1365-2958.1999.01523.x DO - 10.1046/j.1365-2958.1999.01523.x ID - Scidmore-Carlson1999 ER - TY - JOUR AU - Jakobsen Ingrid, B. E. S. PY - 1996 DA - 1996// TI - A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences JO - Bioinformatics VL - 12 UR - https://doi.org/10.1093/bioinformatics/12.4.291 DO - 10.1093/bioinformatics/12.4.291 ID - Jakobsen Ingrid1996 ER - TY - CHAP AU - Sawyer, S. A. PY - 1999 DA - 1999// BT - GENECONV: A computer package for the statistical detection of gene conversion. Distributed by the author, Department of Mathematics, Washington University in St. Louis ID - Sawyer1999 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. PY - 2001 DA - 2001// TI - Evaluation of methods for detecting recombination from DNA sequences: computer simulations JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.241370698 DO - 10.1073/pnas.241370698 ID - Posada2001 ER - TY - JOUR AU - Moran, N. A. PY - 1996 DA - 1996// TI - Accelerated evolution and Muller's rachet in endosymbiotic bacteria JO - Proceedings of the National Academy of Sciences of the United States of America VL - 93 UR - https://doi.org/10.1073/pnas.93.7.2873 DO - 10.1073/pnas.93.7.2873 ID - Moran1996 ER - TY - JOUR AU - Gerrish, P. J. AU - Lenski, R. E. PY - 1998 DA - 1998// TI - The fate of competing beneficial mutations in an asexual population JO - Genetica VL - 102-103 UR - https://doi.org/10.1023/A:1017067816551 DO - 10.1023/A:1017067816551 ID - Gerrish1998 ER - TY - JOUR AU - Barton, N. H. PY - 1995 DA - 1995// TI - Linkage and the limits to natural selection JO - Genetics VL - 140 ID - Barton1995 ER - TY - JOUR AU - Horn, M. AU - Collingro, A. AU - Schmitz-Esser, S. AU - Beier, C. L. AU - Purkhold, U. AU - Fartmann, B. AU - Brandt, P. AU - Nyakatura, G. J. AU - Droege, M. AU - Frishman, D. AU - Rattei, T. AU - Mewes, H. W. AU - Wagner, M. PY - 2004 DA - 2004// TI - Illuminating the evolutionary history of chlamydiae JO - Science VL - 304 UR - https://doi.org/10.1126/science.1096330 DO - 10.1126/science.1096330 ID - Horn2004 ER - TY - JOUR AU - Otto, S. P. AU - Lenormand, T. PY - 2002 DA - 2002// TI - Resolving the paradox of sex and recombination JO - Nat Rev Genet VL - 3 UR - https://doi.org/10.1038/nrg761 DO - 10.1038/nrg761 ID - Otto2002 ER - TY - JOUR AU - Smith, J. M. AU - Feil, E. J. AU - Smith, N. H. PY - 2000 DA - 2000// TI - Population structure and evolutionary dynamics of pathogenic bacteria JO - Bioessays VL - 22 UR - https://doi.org/3.0.CO;2-R DO - 3.0.CO;2-R ID - Smith2000 ER - TY - JOUR AU - McCarthy, N. D. AU - Colles, F. M. AU - Dingle, K. E. AU - Bagnall, M. C. AU - Manning, G. AU - Maiden, M. C. AU - Falush, D. PY - 2007 DA - 2007// TI - Host-associated genetic import in Campylobacter jejuni JO - Emerg Infect Dis VL - 13 UR - https://doi.org/10.3201/eid1302.060620 DO - 10.3201/eid1302.060620 ID - McCarthy2007 ER - TY - JOUR AU - Trent, M. AU - Chung, S. E. AU - Forrest, L. AU - Ellen, J. M. PY - 2008 DA - 2008// TI - Subsequent sexually transmitted infection after outpatient treatment of pelvic inflammatory disease JO - Arch Pediatr Adolesc Med VL - 162 UR - https://doi.org/10.1001/archpedi.162.11.1022 DO - 10.1001/archpedi.162.11.1022 ID - Trent2008 ER - TY - JOUR AU - Niccolai, L. M. AU - Hochberg, A. L. AU - Ethier, K. A. AU - Lewis, J. B. AU - Ickovics, J. R. PY - 2007 DA - 2007// TI - Burden of recurrent Chlamydia trachomatis infections in young women: further uncovering the "hidden epidemic" JO - Arch Pediatr Adolesc Med VL - 161 UR - https://doi.org/10.1001/archpedi.161.3.246 DO - 10.1001/archpedi.161.3.246 ID - Niccolai2007 ER - TY - JOUR AU - Molano, M. AU - Meijer, C. J. AU - Weiderpass, E. AU - Arslan, A. AU - Posso, H. AU - Franceschi, S. AU - Ronderos, M. AU - Munoz, N. AU - van den Brule, A. J. PY - 2005 DA - 2005// TI - The natural course of Chlamydia trachomatis infection in asymptomatic Colombian women: a 5-year follow-up study JO - J Infect Dis VL - 191 UR - https://doi.org/10.1086/428287 DO - 10.1086/428287 ID - Molano2005 ER - TY - JOUR AU - Brunham, R. C. AU - Kimani, J. AU - Bwayo, J. AU - Maitha, G. AU - Maclean, I. AU - Yang, C. L. AU - Shen, C. X. AU - Roman, S. AU - Nagelkerke, N. J. D. AU - Cheang, M. AU - Plummer, F. A. PY - 1996 DA - 1996// TI - The epidemiology of Chlamydia trachomatis within a sexually transmitted diseases core group JO - Journal of Infectious Diseases VL - 173 UR - https://doi.org/10.1093/infdis/173.4.950 DO - 10.1093/infdis/173.4.950 ID - Brunham1996 ER - TY - JOUR AU - Barnes, R. C. AU - Rompalo, A. M. AU - Stamm, W. E. PY - 1987 DA - 1987// TI - Comparison of Chlamydia trachomatis serovars causing rectal and cervical infections JO - J Infect Dis VL - 156 UR - https://doi.org/10.1093/infdis/156.6.953 DO - 10.1093/infdis/156.6.953 ID - Barnes1987 ER - TY - JOUR AU - Boisvert, J. F. AU - Koutsky, L. A. AU - Suchland, R. J. AU - Stamm, W. E. PY - 1999 DA - 1999// TI - Clinical features of Chlamydia trachomatis rectal infection by serovar among homosexually active men JO - Sexually Transmitted Diseases VL - 26 UR - https://doi.org/10.1097/00007435-199908000-00006 DO - 10.1097/00007435-199908000-00006 ID - Boisvert1999 ER - TY - JOUR AU - Geisler, W. M. AU - Whittington, W. L. H. AU - Suchland, R. J. AU - Stamm, W. E. PY - 2002 DA - 2002// TI - Epidemiology of anorectal chlamydial and gonococcal infections among men having sex with men in Seattle - Utilizing serovar and auxotype strain typing JO - Sexually Transmitted Diseases VL - 29 UR - https://doi.org/10.1097/00007435-200204000-00001 DO - 10.1097/00007435-200204000-00001 ID - Geisler2002 ER - TY - JOUR AU - Gordo, I. AU - Campos, P. R. A. PY - 2006 DA - 2006// TI - Adaptive evolution in a spatially structured asexual population JO - Genetica VL - 127 UR - https://doi.org/10.1007/s10709-005-4012-9 DO - 10.1007/s10709-005-4012-9 ID - Gordo2006 ER - TY - JOUR AU - Rasko, D. A. AU - Myers, G. S. AU - Ravel, J. PY - 2005 DA - 2005// TI - Visualization of comparative genomic analyses by BLAST score ratio JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-2 DO - 10.1186/1471-2105-6-2 ID - Rasko2005 ER - TY - JOUR AU - Read, T. D. AU - Myers, G. S. AU - Brunham, R. C. AU - Nelson, W. C. AU - Paulsen, I. T. AU - Heidelberg, J. AU - Holtzapple, E. AU - Khouri, H. AU - Federova, N. B. AU - Carty, H. A. AU - Umayam, L. A. AU - Haft, D. H. AU - Peterson, J. AU - Beanan, M. J. AU - White, O. AU - Salzberg, S. L. AU - Hsia, R. C. AU - McClarty, G. AU - Rank, R. G. AU - Bavoil, P. M. AU - Fraser, C. M. PY - 2003 DA - 2003// TI - Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg321 DO - 10.1093/nar/gkg321 ID - Read2003 ER -