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<italic>Legionella pneumophila fur<\/italic> gene.","volume":"143","author":"EK Hickey","year":"1994","journal-title":"Gene"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1126\/science.1099776","article-title":"The genomic sequence of the accidental pathogen <italic>Legionella pneumophila<\/italic>.","volume":"305","author":"M Chien","year":"2004","journal-title":"Science"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1093\/jb\/mvj010","article-title":"Regulation of polar flagellar number by the <italic>flhF<\/italic> and <italic>flhG<\/italic> genes in <italic>Vibrio alginolyticus<\/italic>.","volume":"139","author":"A Kusumoto","year":"2006","journal-title":"J Biochem"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e1002420","DOI":"10.1371\/journal.ppat.1002420","article-title":"Polar flagellar biosynthesis and a regulator of flagellar number influence spatial parameters of cell division in <italic>Campylobacter 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Almahmoud","year":"2009","journal-title":"J Antimicrob Chemother"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"e1000652","DOI":"10.1371\/journal.pgen.1000652","article-title":"Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation.","volume":"5","author":"HH Chou","year":"2009","journal-title":"PLoS Genet"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"e1002444","DOI":"10.1371\/journal.pgen.1002444","article-title":"Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of <italic>Escherichia coli<\/italic>.","volume":"8","author":"S Quan","year":"2012","journal-title":"PLoS Genet"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1126\/science.1214449","article-title":"Repeatability and contingency in the evolution of a key innovation in phage lambda.","volume":"335","author":"JR Meyer","year":"2012","journal-title":"Science"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1126\/science.285.5426.422","article-title":"Different trajectories of parallel evolution during viral adaptation.","volume":"285","author":"HA Wichman","year":"1999","journal-title":"Science"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"9107","DOI":"10.1073\/pnas.0602917103","article-title":"Tests of parallel molecular evolution in a long-term experiment with <italic>Escherichia coli<\/italic>.","volume":"103","author":"R Woods","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1023\/A:1017067816551","article-title":"The fate of competing beneficial mutations in an asexual population.","volume":"102\u2013103","author":"PJ Gerrish","year":"1998","journal-title":"Genetica"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1615","DOI":"10.1126\/science.1122469","article-title":"An equivalence principle for the incorporation of favorable mutations in asexual populations.","volume":"311","author":"M Hegreness","year":"2006","journal-title":"Science"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1534\/genetics.110.121400","article-title":"Mutational effects and population dynamics during viral adaptation challenge current models.","volume":"187","author":"CR Miller","year":"2011","journal-title":"Genetics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1126\/science.1198914","article-title":"Second-order selection for evolvability in a large <italic>Escherichia coli<\/italic> population.","volume":"331","author":"RJ Woods","year":"2011","journal-title":"Science"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1126\/science.282.5393.1432","article-title":"Experimental evolution of parasites.","volume":"282","author":"D Ebert","year":"1998","journal-title":"Science"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"e1002335","DOI":"10.1371\/journal.ppat.1002335","article-title":"West Nile virus experimental evolution <italic>in vivo<\/italic> and the trade-off hypothesis.","volume":"7","author":"ER Deardorff","year":"2011","journal-title":"PLoS Pathog"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1016\/0022-2836(89)90245-3","article-title":"Receptor specificity of the <italic>Escherichia coli<\/italic> T-even type phage Ox2. Mutational alterations in host range mutants.","volume":"207","author":"K Drexler","year":"1989","journal-title":"J Mol Biol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1534\/genetics.105.051136","article-title":"Pleiotropic costs of niche expansion in the RNA bacteriophage phi 6.","volume":"172","author":"S Duffy","year":"2006","journal-title":"Genetics"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2174\/1874357900903010001","article-title":"The evolution of viruses in multi-host fitness landscapes.","volume":"3","author":"SF Elena","year":"2009","journal-title":"Open Virol J"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1093\/genetics\/156.4.1465","article-title":"Cost of host radiation in an RNA virus.","volume":"156","author":"PE Turner","year":"2000","journal-title":"Genetics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"4316","DOI":"10.1128\/JVI.73.5.4316-4326.1999","article-title":"Genetic and fitness changes accompanying adaptation of an arbovirus to vertebrate and invertebrate cells.","volume":"73","author":"SC Weaver","year":"1999","journal-title":"J Virol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1038\/35037572","article-title":"The population genetics of ecological specialization in evolving <italic>Escherichia coli<\/italic> populations.","volume":"407","author":"VS Cooper","year":"2000","journal-title":"Nature"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/hdy.1997.79","article-title":"Experimental evolution in <italic>Chlamydomonas<\/italic>. III. Evolution of specialist and generalist types in environments that vary in space and time.","volume":"78","author":"X Reboud","year":"1997","journal-title":"Heredity"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"3019","DOI":"10.1021\/bi982574a","article-title":"The dual biosynthetic capability of N-acetylornithine aminotransferase in arginine and lysine biosynthesis.","volume":"38","author":"R Ledwidge","year":"1999","journal-title":"Biochemistry"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1128\/MMBR.00024-09","article-title":"Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.","volume":"73","author":"CC Lo","year":"2009","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"60","DOI":"10.3389\/fmicb.2011.00060","article-title":"<italic>Legionella pneumophila<\/italic> Transcriptome during Intracellular Multiplication in Human Macrophages.","volume":"2","author":"SP Faucher","year":"2011","journal-title":"Front Microbiol"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkr988","article-title":"KEGG for integration and interpretation of large-scale molecular data sets.","volume":"40","author":"M Kanehisa","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"9924","DOI":"10.1073\/pnas.0502767102","article-title":"The phagosomal transporter A couples threonine acquisition to differentiation and replication of <italic>Legionella pneumophila<\/italic> in macrophages.","volume":"102","author":"JD Sauer","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"4504","DOI":"10.1128\/JB.00465-10","article-title":"ArgR-regulated genes are derepressed in the <italic>Legionella<\/italic>-containing vacuole.","volume":"192","author":"G Hovel-Miner","year":"2010","journal-title":"J Bacteriol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"5455","DOI":"10.1073\/pnas.0931379100","article-title":"Complete genome sequence of the Q-fever pathogen <italic>Coxiella burnetii<\/italic>.","volume":"100","author":"R Seshadri","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1046\/j.1469-0691.2001.00193.x","article-title":"Survival of <italic>Coxiella burnetii<\/italic> within free-living amoeba Acanthamoeba castellanii.","volume":"7","author":"B La Scola","year":"2001","journal-title":"Clin Microbiol Infect"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1086\/652442","article-title":"A large Q fever outbreak in an urban school in central Israel.","volume":"50","author":"Z Amitai","year":"2010","journal-title":"Clin Infect Dis"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1128\/IAI.56.6.1449-1455.1988","article-title":"Isolation and characterization of auxotrophic mutants of <italic>Legionella pneumophila<\/italic> that fail to multiply in human monocytes.","volume":"56","author":"CS Mintz","year":"1988","journal-title":"Infect Immun"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1128\/IAI.00956-06","article-title":"Environmental mimics and the Lvh type IVA secretion system contribute to virulence-related phenotypes of <italic>Legionella pneumophila<\/italic>.","volume":"75","author":"P Bandyopadhyay","year":"2007","journal-title":"Infect Immun"},{"key":"ref80","first-page":"330","article-title":"The Peculiarities of <italic>Legionella<\/italic>.","volume":"130","author":"DW Fraser","year":"1986","journal-title":"Proc Am Philos Soc"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"2279","DOI":"10.1101\/gr.091017.109","article-title":"Epidemic multiple drug resistant <italic>Salmonella Typhimurium<\/italic> causing invasive disease in sub-Saharan Africa have a distinct genotype.","volume":"19","author":"RA Kingsley","year":"2009","journal-title":"Genome Res"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"e1001078","DOI":"10.1371\/journal.ppat.1001078","article-title":"Host imprints on bacterial genomes\u2013rapid, divergent evolution in individual patients.","volume":"6","author":"J Zdziarski","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1126\/science.1182395","article-title":"Evolution of MRSA during hospital transmission and intercontinental spread.","volume":"327","author":"SR Harris","year":"2011","journal-title":"Science"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1038\/ng.997","article-title":"Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes.","volume":"43","author":"TD Lieberman","year":"2011","journal-title":"Nat Genet"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"7481","DOI":"10.1073\/pnas.1018249108","article-title":"Evolutionary dynamics of bacteria in a human host environment.","volume":"108","author":"L Yang","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"3065","DOI":"10.1073\/pnas.1121491109","article-title":"Genomic epidemiology of the <italic>Escherichia coli<\/italic> O104:H4 outbreaks in Europe, 2011.","volume":"109","author":"YH Grad","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"2585","DOI":"10.1128\/IAI.64.7.2585-2594.1996","article-title":"Identification of <italic>Legionella pneumophila<\/italic> mutants that have aberrant intracellular fates.","volume":"64","author":"MS Swanson","year":"1996","journal-title":"Infect Immun"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"e1000686","DOI":"10.1371\/journal.ppat.1000686","article-title":"Innate immune recognition of <italic>Yersinia pseudotuberculosis<\/italic> type III secretion.","volume":"5","author":"V Auerbuch","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"3905","DOI":"10.1128\/IAI.00344-10","article-title":"E3 ubiquitin ligase activity and targeting of BAT3 by multiple <italic>Legionella pneumophila<\/italic> translocated substrates.","volume":"78","author":"AW Ensminger","year":"2010","journal-title":"Infect Immun"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for <italic>de novo<\/italic> short read assembly using de Bruijn graphs.","volume":"18","author":"DR Zerbino","year":"2008","journal-title":"Genome Res"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"10325","DOI":"10.1073\/pnas.90.21.10325","article-title":"Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: evidence for solvent-induced bends in DNA heteroduplexes.","volume":"90","author":"A Ganguly","year":"1993","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1073\/pnas.95.4.1681","article-title":"Conformation sensitive gel electrophoresis for simple and accurate detection of mutations: comparison with denaturing gradient gel electrophoresis and nucleotide 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