A complete domain-to-species taxonomy for Bacteria and Archaea
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Donovan H. Parks | D. Parks | Christian Rinke | M. Chuvochina | Pierre-Alain Chaumeil | P. Hugenholtz | Aaron J. Mussig
[1] K. Nealson,et al. A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index , 2020, mBio.
[2] V. Denef,et al. To Dereplicate or Not To Dereplicate? , 2019, mSphere.
[3] Donovan H Parks,et al. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..
[4] J. Banfield,et al. Consistent metagenome-derived metrics verify and define bacterial species boundaries , 2019, bioRxiv.
[5] Francesco Asnicar,et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea , 2019, Nature Communications.
[6] K. Carroll,et al. Practical problems when incorporating rapidly changing microbial taxonomy into clinical practice , 2019, Clinical chemistry and laboratory medicine.
[7] Edoardo Pasolli,et al. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle , 2019, Cell.
[8] Donovan H. Parks,et al. The importance of designating type material for uncultured taxa. , 2019, Systematic and applied microbiology.
[9] I-Min A. Chen,et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes , 2018, Nucleic Acids Res..
[10] Christian Ebeling,et al. BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis , 2018, Nucleic Acids Res..
[11] George M Garrity,et al. International Code of Nomenclature of Prokaryotes. , 2015, International journal of systematic and evolutionary microbiology.
[12] A. Phillippy,et al. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries , 2017, Nature Communications.
[13] Donovan H. Parks,et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life , 2018, Nature Biotechnology.
[14] K. Nealson,et al. A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation , 2018, bioRxiv.
[15] James R. Cole,et al. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level , 2018, Nucleic Acids Res..
[16] Michael DiCuccio,et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI , 2018, International journal of systematic and evolutionary microbiology.
[17] A. Parte. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. , 2018, International journal of systematic and evolutionary microbiology.
[18] Henrik Christensen,et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. , 2018, International journal of systematic and evolutionary microbiology.
[19] M. Hazbón,et al. Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis. , 2018, International journal of systematic and evolutionary microbiology.
[20] Donovan H. Parks,et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life , 2017, Nature Microbiology.
[21] Natalia N. Ivanova,et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea , 2017, Nature Biotechnology.
[22] R. Amann,et al. Uncultivated microbes in need of their own taxonomy , 2017, The ISME Journal.
[23] Natalia N. Ivanova,et al. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life , 2017, Nature Biotechnology.
[24] J. Chun,et al. A large-scale evaluation of algorithms to calculate average nucleotide identity , 2017, Antonie van Leeuwenhoek.
[25] H. Ochman,et al. Biological Species Are Universal across Life’s Domains , 2017, Genome biology and evolution.
[26] G. Garrity. A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet? , 2016, Journal of Clinical Microbiology.
[27] W. Whitman. Modest proposals to expand the type material for naming of prokaryotes. , 2016, International journal of systematic and evolutionary microbiology.
[28] Brian C. Thomas,et al. A new view of the tree of life , 2016, Nature Microbiology.
[29] Heike Sichtig,et al. Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015) , 2016, Standards in Genomic Sciences.
[30] Deanna M. Church,et al. Assembly: a resource for assembled genomes at NCBI , 2015, Nucleic Acids Res..
[31] Wen J. Li,et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..
[32] Brian D. Ondov,et al. Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.
[33] A. Oren. Reclassification of Halomonas caseinilytica Wu et al. 2008 as a later synonym of Halomonas sinaiensis—Comments on the proposal by Hwang et al., Antonie van Leeuwenhoek 109:1345–1352, 2016 , 2016, Antonie van Leeuwenhoek.
[34] R. Beiko. Microbial malaise: how can we classify the microbiome? , 2015, Trends in microbiology.
[35] Natalia N. Ivanova,et al. Microbial species delineation using whole genome sequences , 2015, Nucleic acids research.
[36] Connor T. Skennerton,et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.
[37] William B Whitman,et al. Genome sequences as the type material for taxonomic descriptions of prokaryotes. , 2015, Systematic and applied microbiology.
[38] H. Christensen,et al. International Committee on Systematics of Prokaryotes , 2015 .
[39] Scott Federhen,et al. Type material in the NCBI Taxonomy Database , 2014, Nucleic Acids Res..
[40] Bas E. Dutilh,et al. Microbial taxonomy in the post-genomic era: Rebuilding from scratch? , 2014, Archives of Microbiology.
[41] Rick Stevens,et al. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains , 2014, PLoS biology.
[42] Bernard De Baets,et al. StrainInfo introduces electronic passports for microorganisms. , 2014, Systematic and applied microbiology.
[43] Radhey S. Gupta,et al. Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus. , 2013, International journal of systematic and evolutionary microbiology.
[44] W. Hanage. Fuzzy species revisited , 2013, BMC Biology.
[45] Eric P. Nawrocki,et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.
[46] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[47] Hideaki Sugawara,et al. The Sequence Read Archive , 2010, Nucleic Acids Res..
[48] T. Ficht. Brucella taxonomy and evolution. , 2010, Future microbiology.
[49] 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 .
[50] E. Velázquez,et al. Historical evolution and current status of the taxonomy of genus Pseudomonas. , 2009, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[51] R. Rosselló-Móra,et al. Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.
[52] Adam P. Arkin,et al. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.
[53] C. Fraser,et al. The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity , 2009, Science.
[54] P. Vandamme,et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.
[55] K. Konstantinidis,et al. The bacterial species definition in the genomic era , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.
[56] I. Moriyón,et al. International Committee on Systematics of Prokaryotes; Subcommittee on the taxonomy of Brucella: Minutes of the meeting, 17 September 2003, Pamplona, Spain , 2006 .
[57] Konstantinos T. Konstantinidis,et al. Towards a Genome-Based Taxonomy for Prokaryotes , 2005, Journal of bacteriology.
[58] K. Konstantinidis,et al. Genomic insights that advance the species definition for prokaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[59] Ruiting Lan,et al. Escherichia coli in disguise: molecular origins of Shigella. , 2002, Microbes and infection.
[60] F. Cohan. What are bacterial species? , 2002, Annual review of microbiology.
[61] F. Grimont,et al. Brucella, a monospecific genus as shown by deoxyribonucleic acid hybridization , 1985 .