A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence
暂无分享,去创建一个
Wing-Kin Sung | William C. Nierman | Christina Nilsson | Yijun Ruan | Paul Keim | Talima Pearson | Richard W. Titball | Donald Woods | Liliana Losada | Jason F. Kreisberg | Catherine Ong | W. Sung | Y. Ruan | P. Ariyaratne | W. Nierman | C. Nilsson | I. Beacham | P. Keim | J. Kreisberg | C. Ronning | P. Tan | T. Nandi | R. Titball | T. Pearson | D. Woods | Patrick Tan | Mitali Sarkar-Tyson | J. Boddey | L. Losada | Timothy Atkins | Tannistha Nandi | C. Ong | Arvind P Singh | T. Atkins | M. Sarkar-Tyson | Angela E. Essex-Lopresti | H. Chua | I. Peak | Arvind Pratap Singh | Justin Boddey | Hui Hoon Chua | Pramila Ariyaratne | Catherine Ronning | Ifor Beacham | Ian Peak | A. Singh | Talima R. Pearson | Christina Nilsson | Mitali Sarkar-Tyson
[1] C. Hart,et al. Evidence for the presence in Burkholderia pseudomallei of a type III secretion system-associated gene cluster. , 1999, Journal of medical microbiology.
[2] Nick Goldman,et al. Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites , 2004, Genetics.
[3] Jin Wang,et al. MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes , 2007, BMC Bioinformatics.
[4] Thomas E. Royce,et al. Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.
[5] Xavier Messeguer,et al. Analyzing patterns of microbial evolution using the mauve genome alignment system. , 2007, Methods in molecular biology.
[6] Mark Gerstein,et al. New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. , 2007, Genes & development.
[7] J. Anné,et al. The importance of the twin-arginine translocation pathway for bacterial virulence. , 2008, Trends in microbiology.
[8] Z. Yang,et al. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. , 2001, Molecular biology and evolution.
[9] Ploeg,et al. Identification of sulfate starvation-regulated genes in Escherichia coli: a gene cluster involved in the utilization of taurine as a sulfur source , 1996, Journal of bacteriology.
[10] Jaideep P. Sundaram,et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[11] M. Gouy,et al. WWW-query: an on-line retrieval system for biological sequence banks. , 1996, Biochimie.
[12] R. Doolittle,et al. A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.
[13] Jon R. Armstrong,et al. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[14] A. Salamov,et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods , 2007, Nature Methods.
[15] John A. Tainer,et al. Type IV pilus structure and bacterial pathogenicity , 2004, Nature Reviews Microbiology.
[16] Bernard B. Suh,et al. The genome of the protist parasite Entamoeba histolytica , 2005, Nature.
[17] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[18] O. White,et al. Structural flexibility in the Burkholderia mallei genome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[19] Monica Riley,et al. A functional update of the Escherichia coli K-12 genome , 2001, Genome Biology.
[20] P. Keim,et al. Fine-Scale Genetic Diversity among Burkholderia pseudomallei Soil Isolates in Northeast Thailand , 2007, Applied and Environmental Microbiology.
[21] Donald Woods,et al. The Core and Accessory Genomes of Burkholderia pseudomallei: Implications for Human Melioidosis , 2008, PLoS pathogens.
[22] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[23] Richard A. Moore,et al. Genome-wide expression analysis of iron regulation in Burkholderia pseudomallei and Burkholderia mallei using DNA microarrays. , 2005, FEMS microbiology letters.
[24] M. Stanhope,et al. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition , 2007, Genome Biology.
[25] Raymond K. Auerbach,et al. A Horizontal Gene Transfer Event Defines Two Distinct Groups within Burkholderia pseudomallei That Have Dissimilar Geographic Distributions , 2007, Journal of bacteriology.
[26] M. Whiteley,et al. Revisiting the host as a growth medium , 2008, Nature Reviews Microbiology.
[27] David DeShazer,et al. Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis , 2006, BMC Microbiology.
[28] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[29] Theresa L. Smith,et al. Management of Accidental Laboratory Exposure to Burkholderia pseudomallei and B. mallei , 2008, Emerging infectious diseases.
[30] P. Brown,et al. A Burkholderia pseudomallei Type III Secreted Protein, BopE, Facilitates Bacterial Invasion of Epithelial Cells and Exhibits Guanine Nucleotide Exchange Factor Activity , 2003, Journal of bacteriology.
[31] I. Beacham,et al. Temperature-Regulated Microcolony Formation by Burkholderia pseudomallei Requires pilA and Enhances Association with Cultured Human Cells , 2006, Infection and Immunity.
[32] Direk Limmathurotsakul,et al. Burkholderia pseudomallei genome plasticity associated with genomic island variation , 2008, BMC Genomics.
[33] R J Huxtable,et al. Physiological actions of taurine. , 1992, Physiological reviews.
[34] Rodrigo Lopez,et al. Clustal W and Clustal X version 2.0 , 2007, Bioinform..
[35] Arturo Casadevall,et al. Accidental Virulence, Cryptic Pathogenesis, Martians, Lost Hosts, and the Pathogenicity of Environmental Microbes , 2007, Eukaryotic Cell.
[36] Patricia Siguier,et al. ISfinder: the reference centre for bacterial insertion sequences , 2005, Nucleic Acids Res..
[37] S. Sawyer. Statistical tests for detecting gene conversion. , 1989, Molecular biology and evolution.
[38] Folker Meyer,et al. GISMO—gene identification using a support vector machine for ORF classification , 2006, Nucleic acids research.
[39] Peer Bork,et al. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..
[40] Y. Gan,et al. Model of Differential Susceptibility to Mucosal Burkholderia pseudomallei Infection , 2002, Infection and Immunity.
[41] N. Ketheesan,et al. Burkholderia pseudomallei virulence: definition, stability and association with clonality. , 2001, Microbes and infection.
[42] W. Nierman,et al. Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species of different survival strategies , 2005, BMC Genomics.
[43] K. Yuen,et al. Cloning and characterisation of malE in Burkholderia pseudomallei. , 2001, Journal of medical microbiology.
[44] D. Bryant,et al. A Simple and Robust Statistical Test for Detecting the Presence of Recombination , 2006, Genetics.
[45] Zhenbiao Yang,et al. RHO Gtpases and the Actin Cytoskeleton , 2000 .
[46] Feng Chen,et al. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups , 2005, Nucleic Acids Res..
[47] D. Woods,et al. Flagellum-Mediated Adhesion by Burkholderia pseudomallei Precedes Invasion of Acanthamoeba astronyxis , 2003, Infection and Immunity.
[48] L. Sprague,et al. Melioidosis in animals: a review on epizootiology, diagnosis and clinical presentation. , 2004, Journal of veterinary medicine. B, Infectious diseases and veterinary public health.
[49] Klaus Aktories,et al. Bacterial cytotoxins: targeting eukaryotic switches , 2005, Nature Reviews Microbiology.
[50] Kim Rutherford,et al. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[51] Ronald W. Davis,et al. Comparative genomes of Chlamydia pneumoniae and C. trachomatis , 1999, Nature Genetics.
[52] D. Falush,et al. Inference of Bacterial Microevolution Using Multilocus Sequence Data , 2007, Genetics.
[53] B. Currie. Advances and remaining uncertainties in the epidemiology of Burkholderia pseudomallei and melioidosis. , 2008, Transactions of the Royal Society of Tropical Medicine and Hygiene.
[54] Y. Gan,et al. Flagella Are Virulence Determinants of Burkholderia pseudomallei , 2003, Infection and Immunity.
[55] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[56] Nicholas J. White,et al. Melioidosis: insights into the pathogenicity of Burkholderia pseudomallei , 2006, Nature Reviews Microbiology.
[57] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[58] Robert D. Finn,et al. Rfam: updates to the RNA families database , 2008, Nucleic Acids Res..
[59] Steven Salzberg,et al. A probabilistic method for identifying start codons in bacterial genomes , 2001, Bioinform..
[60] E. Delong,et al. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea , 2006, Nature.
[61] Steven Salzberg,et al. Identifying bacterial genes and endosymbiont DNA with Glimmer , 2007, Bioinform..
[62] P. Tan,et al. Characterization of Burkholderia pseudomallei infection and identification of novel virulence factors using a Caenorhabditis elegans host system , 2002, Molecular microbiology.
[63] I. Beacham,et al. A Type IV Pilin, PilA, Contributes to Adherence of Burkholderia pseudomallei and Virulence In Vivo , 2005, Infection and Immunity.
[64] T. Leisinger,et al. Characterization of α-Ketoglutarate-dependent Taurine Dioxygenase from Escherichia coli * , 1997, The Journal of Biological Chemistry.