Bioinformatics tools for evaluating microbial relationships
暂无分享,去创建一个
[1] S. Lukinmaa,et al. Application of molecular genetic methods in diagnostics and epidemiology of food‐borne bacterial pathogens , 2004, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.
[2] Ziheng Yang,et al. Maximum-likelihood models for combined analyses of multiple sequence data , 1996, Journal of Molecular Evolution.
[3] H. Hoekstra,et al. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits , 2008, Heredity.
[4] Yu-Hui Lin,et al. Comparison of four molecular typing methods to assess genetic relatedness of Candida albicans clinical isolates in Taiwan. , 2005, Journal of medical microbiology.
[5] R. Reid-Smith,et al. Antimicrobial resistance: its emergence and transmission , 2008, Animal Health Research Reviews.
[6] Zhaohui S. Qin,et al. Clustering microarray gene expression data using weighted Chinese restaurant process , 2006, Bioinform..
[7] Wei Wang,et al. Dissecting the transcription networks of a cell using computational genomics. , 2003, Current opinion in genetics & development.
[8] R. Fleischmann,et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.
[9] D. Call,et al. Selective Discrimination of Listeria monocytogenes Epidemic Strains by a Mixed-Genome DNA Microarray Compared to Discrimination by Pulsed-Field Gel Electrophoresis, Ribotyping, and Multilocus Sequence Typing , 2004, Journal of Clinical Microbiology.
[10] G. Bezanson,et al. Involvement of plasmids in determining bacteriophage sensitivity in Salmonella typhimurium: genetic and physical analysis of phagovar 204. , 1982, Canadian journal of microbiology.
[11] M. Wiedmann,et al. Multilocus Variable-Number Tandem-Repeat Method for Typing Salmonella enterica Serovar Newport , 2009, Journal of Clinical Microbiology.
[12] Ikuo Uchiyama,et al. MBGD: microbial genome database for comparative analysis , 2003, Nucleic Acids Res..
[13] A. Bauer,et al. Antibiotic susceptibility testing by a standardized single disk method. , 1966, American journal of clinical pathology.
[14] M. Maiden,et al. Multi-locus sequence typing: a tool for global epidemiology. , 2003, Trends in microbiology.
[15] H. Harbottle,et al. Comparison of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Typing for Characterization of Salmonella enterica Serotype Newport Isolates , 2006, Journal of Clinical Microbiology.
[16] Ren Zhang,et al. The impact of comparative genomics on infectious disease research. , 2006, Microbes and infection.
[17] J. Mesirov,et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. , 1999, Science.
[18] J. Tiedje,et al. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.
[19] Lisa H. Orfe,et al. Impact of compounding error on strategies for subtyping pathogenic bacteria. , 2008, Foodborne pathogens and disease.
[20] Rekha Seshadri,et al. Bacterial Genomics and Pathogen Evolution , 2006, Cell.
[21] S. Edwards. IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? , 2009, Evolution; international journal of organic evolution.
[22] J. Welsh,et al. Fingerprinting genomes using PCR with arbitrary primers. , 1990, Nucleic acids research.
[23] G. Kapperud,et al. Multiple-locus variable-number tandem-repeats analysis of Salmonella enterica subsp. enterica serovar Typhimurium using PCR multiplexing and multicolor capillary electrophoresis. , 2004, Journal of microbiological methods.
[24] Dechang Chen,et al. Selecting Genes by Test Statistics , 2005, Journal of biomedicine & biotechnology.
[25] N. W. Davis,et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 , 2001, Nature.
[26] Jun Zhu,et al. Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations , 2007, PLoS Comput. Biol..
[27] T. M. Toolan,et al. Detection and estimation in non-stationary environments , 2003, The Thrity-Seventh Asilomar Conference on Signals, Systems & Computers, 2003.
[28] Michael Y. Galperin,et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes , 2001, Nucleic Acids Res..
[29] Martti Juhola,et al. Genome-wide selection of unique and valid oligonucleotides , 2005, Nucleic acids research.
[30] Even Heir,et al. DNA Fingerprinting of Salmonella enterica subsp. enterica Serovar Typhimurium with Emphasis on Phage Type DT104 Based on Variable Number of Tandem Repeat Loci , 2003, Journal of Clinical Microbiology.
[31] Shaohua Zhao,et al. Enhanced Subtyping Scheme for Salmonella Enteritidis , 2007, Emerging infectious diseases.
[32] Doolittle Wf. Phylogenetic Classification and the Universal Tree , 1999 .
[33] Lior Pachter,et al. MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.
[34] Thomas G. Dietterich. Multiple Classifier Systems , 2000, Lecture Notes in Computer Science.
[35] Richard Baumgartner,et al. Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions , 2003, Bioinform..
[36] Bryan D. Kolaczkowski,et al. A mixed branch length model of heterotachy improves phylogenetic accuracy. , 2008, Molecular biology and evolution.
[37] K. Mühlemann,et al. Use of the Agilent 2100 Bioanalyzer for Rapid and Reproducible Molecular Typing of Streptococcus pneumoniae , 2007, Journal of Clinical Microbiology.
[38] James R. Cole,et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..
[39] Paul Keim,et al. Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis. , 2007, Mutation research.
[40] F. Tenover,et al. How to Select and Interpret Molecular Strain Typing Methods for Epidemiological Studies of Bacterial Infections A Review for Healthcare Epidemiologists , 1997, Infection Control & Hospital Epidemiology.
[41] D. Lipman,et al. Rapid and sensitive protein similarity searches. , 1985, Science.
[42] T. Cebula,et al. Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk , 2007, PloS one.
[43] B Walsh,et al. Estimating the time to the most recent common ancestor for the Y chromosome or mitochondrial DNA for a pair of individuals. , 2001, Genetics.
[44] Chuong B. Do,et al. Access the most recent version at doi: 10.1101/gr.926603 References , 2003 .
[45] I. Ross,et al. Use of AFLP and PFGE to discriminate between Salmonella enterica serovar Typhimurium DT126 isolates from separate food-related outbreaks in Australia , 2005, Epidemiology and Infection.
[46] Fillia Makedon,et al. HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data , 2005, Bioinform..
[47] Blaise Hanczar,et al. Improving classification of microarray data using prototype-based feature selection , 2003, SKDD.
[48] C. Logue,et al. Multilocus Sequence Typing Lacks the Discriminatory Ability of Pulsed-Field Gel Electrophoresis for Typing Salmonella enterica Serovar Typhimurium , 2005, Journal of Clinical Microbiology.
[49] Kathleen Marchal,et al. A novel approach to identifying regulatory motifs in distantly related genomes , 2005, Genome Biology.
[50] D. Summers. The Biology of Plasmids , 1996 .
[51] B. Swaminathan,et al. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. , 2006, Foodborne pathogens and disease.
[52] M. Torpdahl,et al. Harmonization of the multiple‐locus variable‐number tandem repeat analysis method between Denmark and Norway for typing Salmonella Typhimurium isolates and closer examination of the VNTR loci , 2007, Journal of applied microbiology.
[53] S. Carroll,et al. Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.
[54] P. Bork,et al. Get the most out of your metagenome: computational analysis of environmental sequence data. , 2007, Current opinion in microbiology.
[55] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[56] R. K. Varshney,et al. Multilocus variable number tandem repeat analysis as a tool to discern genetic relationships among strains of Yersinia enterocolitica biovar 1A , 2009, Journal of applied microbiology.
[57] H. Philippe,et al. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. , 2004, Molecular biology and evolution.
[58] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[59] Arun Jagota. Microarray Data Analysis and Visualization , 2001 .
[60] K. Kubota,et al. Analysis of Salmonella enterica Serotype Typhi Pulsed-Field Gel Electrophoresis Patterns Associated with International Travel , 2005, Journal of Clinical Microbiology.
[61] Liza Gross. Are “Ultraconserved” Genetic Elements Really Indispensable? , 2007, PLoS biology.
[62] F. Blattner,et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.
[63] P. Bork,et al. Bioinformatics in the post-sequence era , 2003, Nature Genetics.
[64] Francesco Falciani,et al. DNA Microarrays: a Powerful Genomic Tool for Biomedical and Clinical Research , 2007, Molecular medicine.
[65] Hervé Philippe,et al. The Root of the Tree of Life in the Light of the Covarion Model , 1999, Journal of Molecular Evolution.
[66] Z. Yang,et al. Among-site rate variation and its impact on phylogenetic analyses. , 1996, Trends in ecology & evolution.
[67] D. Call,et al. Discrimination among Listeria monocytogenes isolates using a mixed genome DNA microarray. , 2003, Veterinary microbiology.
[68] Alex van Belkum,et al. Short-Sequence DNA Repeats in Prokaryotic Genomes , 1998, Microbiology and Molecular Biology Reviews.
[69] S. Porwollik,et al. Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[70] Scott J. Emrich,et al. PROBEmer: a web-based software tool for selecting optimal DNA oligos , 2003, Nucleic Acids Res..
[71] Sergio Storari,et al. Finding biological process modifications in cancer tissues by mining gene expression correlations , 2005, BMC Bioinformatics.
[72] E. Eichler,et al. Structural Dynamics of Eukaryotic Chromosome Evolution , 2003, Science.
[73] Constantin F. Aliferis,et al. A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis , 2004, Bioinform..
[74] M. Achtman,et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[75] Anil K. Jain,et al. Statistical Pattern Recognition: A Review , 2000, IEEE Trans. Pattern Anal. Mach. Intell..
[76] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[77] T. Besser,et al. Assessing genetic diversity in plasmids from Escherichia coli and Salmonella enterica using a mixed‐plasmid microarray , 2006, Journal of applied microbiology.
[78] D. Huson,et al. Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.
[79] Thomas Mailund,et al. Recrafting the Neighbor-joining Method , 2006 .
[80] K. Peck,et al. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. , 2004, Nucleic acids research.
[81] P. Fey,et al. Characterization of Plasmids Carrying CMY-2 from Expanded-Spectrum Cephalosporin-Resistant Salmonella Strains Isolated in the United States between 1996 and 1998 , 2002, Antimicrobial Agents and Chemotherapy.
[82] H. Philippe,et al. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. , 2005, Molecular biology and evolution.