Whole Genome Sequence Comparisons in Taxonomy

[1]  J. Blom,et al.  Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42. , 2011, Journal of biotechnology.

[2]  H. Klenk,et al.  Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. , 2011, International journal of systematic and evolutionary microbiology.

[3]  Hans-Peter Klenk,et al.  Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison , 2010, Standards in genomic sciences.

[4]  Hans-Peter Klenk,et al.  Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs , 2010, Standards in genomic sciences.

[5]  Ikuo Uchiyama,et al.  MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity , 2009, Nucleic Acids Res..

[6]  W. Ludwig,et al.  Notes on the characterization of prokaryote strains for taxonomic purposes. , 2010, International journal of systematic and evolutionary microbiology.

[7]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[8]  A. Rooney,et al.  Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. , 2009, International journal of systematic and evolutionary microbiology.

[9]  P. de Vos,et al.  Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. , 2009, International journal of systematic and evolutionary microbiology.

[10]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[11]  A. Goesmann,et al.  An evaluation framework for statistical tests on microarray data. , 2009, Journal of Biotechnology.

[12]  Z. Ning,et al.  Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes , 2009, Nature Methods.

[13]  Fiona S. L. Brinkman,et al.  IslandViewer: an integrated interface for computational identification and visualization of genomic islands , 2009, Bioinform..

[14]  Meriem El Karoui,et al.  A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera , 2008, Journal of bacteriology.

[15]  Alexander Goesmann,et al.  EDGAR: A software framework for the comparative analysis of prokaryotic genomes , 2009, BMC Bioinformatics.

[16]  Anna Sergeevna Bosman,et al.  The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage , 2008, BMC Bioinformatics.

[17]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[18]  Gipsi Lima-Mendez,et al.  Reticulate representation of evolutionary and functional relationships between phage genomes. , 2008, Molecular biology and evolution.

[19]  Jacques van Helden,et al.  Prophinder: a computational tool for prophage prediction in prokaryotic genomes , 2008, Bioinform..

[20]  B. Morgenstern,et al.  Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42 , 2007, Nature Biotechnology.

[21]  Gerard Talavera,et al.  Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.

[22]  Sung-Hou Kim,et al.  Global extent of horizontal gene transfer , 2007, Proceedings of the National Academy of Sciences.

[23]  Folker Meyer,et al.  GISMO—gene identification using a support vector machine for ORF classification , 2006, Nucleic acids research.

[24]  Roberto Kolter,et al.  Bacillus subtilis Genome Diversity , 2006, Journal of bacteriology.

[25]  C. Dutta,et al.  Horizontal gene transfer and bacterial diversity , 2002, Journal of Biosciences.

[26]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[27]  Kelly P. Nevin,et al.  Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site , 2007, BMC Genomics.

[28]  J. Kalinowski,et al.  Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression. , 2006, Journal of biotechnology.

[29]  K. Konstantinidis,et al.  The bacterial species definition in the genomic era , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[30]  R. Leplae,et al.  A first global analysis of plasmid encoded proteins in the ACLAME database. , 2006, FEMS microbiology reviews.

[31]  K. Venkateswaran,et al.  Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis. , 2006, International journal of systematic and evolutionary microbiology.

[32]  Folker Meyer,et al.  REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. , 2006, Applied bioinformatics.

[33]  Carsten Damm,et al.  Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models , 2006, BMC Bioinformatics.

[34]  H. Tettelin,et al.  The microbial pan-genome. , 2005, Current opinion in genetics & development.

[35]  C. Landry,et al.  Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains , 2005, BMC Genomics.

[36]  Oleg N. Reva,et al.  Differentiation of regions with atypical oligonucleotide composition in bacterial genomes , 2005, BMC Bioinformatics.

[37]  Timothy J. Harlow,et al.  Highways of gene sharing in prokaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  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.

[39]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[40]  Matthew Berriman,et al.  ACT: the Artemis comparison tool , 2005, Bioinform..

[41]  Daniel H. Huson,et al.  Whole-genome prokaryotic phylogeny , 2005, Bioinform..

[42]  Yong Wang,et al.  Genome Sequencing in Open Microfabricated High Density Picoliter Reactors , 2005 .

[43]  M. P. Cummings.  PHYLIP (Phylogeny Inference Package) , 2004 .

[44]  Oleg N. Reva,et al.  Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns , 2004, BMC Bioinformatics.

[45]  Ulrich Dobrindt,et al.  Genomic islands in pathogenic and environmental microorganisms , 2004, Nature Reviews Microbiology.

[46]  S. Tabata,et al.  Expression Islands Clustered on the Symbiosis Island of the Mesorhizobium loti Genome , 2004, Journal of bacteriology.

[47]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[48]  A. Carattoli,et al.  Tetracycline and Streptomycin Resistance Genes, Transposons, and Plasmids in Salmonella enterica Isolates from Animals in Italy , 2004, Antimicrobial Agents and Chemotherapy.

[49]  D. Kahn,et al.  Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. , 2004, Molecular plant-microbe interactions : MPMI.

[50]  M. Melkonian,et al.  Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). , 2003, Molecular biology and evolution.

[51]  Kelly P. Williams,et al.  Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities , 2004, Nucleic Acids Res..

[52]  Shoshana J. Wodak,et al.  ACLAME: A CLAssification of Mobile genetic Elements , 2004, Nucleic Acids Res..

[53]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[54]  Alexander Sczyrba,et al.  EMMA: a platform for consistent storage and efficient analysis of microarray data. , 2003, Journal of biotechnology.

[55]  N. Moran,et al.  From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria , 2003, PLoS biology.

[56]  E. Top,et al.  The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. , 2003, Current opinion in biotechnology.

[57]  R. Giegerich,et al.  GenDB--an open source genome annotation system for prokaryote genomes. , 2003, Nucleic acids research.

[58]  L. Lindler,et al.  Epidemiology of Tetracycline Resistance Determinants in Shigella spp. and Enteroinvasive Escherichia coli: Characterization and Dissemination of tet(A)-1 , 2003, Journal of Clinical Microbiology.

[59]  Steven J. M. Jones,et al.  IslandPath: aiding detection of genomic islands in prokaryotes , 2003, Bioinform..

[60]  D. Haussler,et al.  Human-mouse alignments with BLASTZ. , 2003, Genome research.

[61]  Santiago Garcia-Vallvé,et al.  HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes , 2003, Nucleic Acids Res..

[62]  U. Dobrindt,et al.  Pathogenicity islands of uropathogenic E. coli and the evolution of virulence. , 2002, International journal of antimicrobial agents.

[63]  W. Whitman,et al.  Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. , 2002, International journal of systematic and evolutionary microbiology.

[64]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[65]  C. Desmarais,et al.  Automated finishing with autofinish. , 2001, Genome research.

[66]  Owen White,et al.  The Comprehensive Microbial Resource , 2001, Nucleic Acids Res..

[67]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.

[68]  G. Olsen,et al.  CRITICA: coding region identification tool invoking comparative analysis. , 1999, Molecular biology and evolution.

[69]  Thomas Wetter,et al.  Genome Sequence Assembly Using Trace Signals and Additional Sequence Information , 1999, German Conference on Bioinformatics.

[70]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[71]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[72]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[73]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[74]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[75]  F. Sanger,et al.  A Rapid Method for Determining Sequences in DNA by Primed Synthesis with DNA Polymerase , 1989 .

[76]  O. Kandler,et al.  International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1987, Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology.

[77]  J. Mekalanos,et al.  Staphylococcal enterotoxin A is encoded by phage. , 1985, Science.

[78]  J. Felsenstein.  Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .