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Items: 1 to 20 of 137

1.

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.

Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P.

Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27.

PMID:
30148503
2.

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P.

ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.

3.

Using the taxon-specific genes for the taxonomic classification of bacterial genomes.

Gupta A, Sharma VK.

BMC Genomics. 2015 May 20;16:396. doi: 10.1186/s12864-015-1542-0.

4.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

Zuo G, Hao B.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):321-31. doi: 10.1016/j.gpb.2015.08.004. Epub 2015 Nov 10.

5.

A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species.

Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M, Sentausa E, Raoult D, Fournier PE.

Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):384-91. doi: 10.1099/ijs.0.057091-0. Review.

PMID:
24505076
6.

Measuring genome conservation across taxa: divided strains and united kingdoms.

Kunin V, Ahren D, Goldovsky L, Janssen P, Ouzounis CA.

Nucleic Acids Res. 2005 Jan 28;33(2):616-21. Print 2005.

7.

A phylum-level bacterial phylogenetic marker database.

Wang Z, Wu M.

Mol Biol Evol. 2013 Jun;30(6):1258-62. doi: 10.1093/molbev/mst059. Epub 2013 Mar 21.

PMID:
23519313
8.

Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy.

Hayashi Sant'Anna F, Bach E, Porto RZ, Guella F, Hayashi Sant'Anna E, Passaglia LMP.

Crit Rev Microbiol. 2019 Mar;45(2):182-200. doi: 10.1080/1040841X.2019.1569587. Epub 2019 May 31. Review.

PMID:
31148498
9.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques.

Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood U, Hira P, Kohli P, Nayyar N, Puri A, Bajaj A, Kumar R, Negi V, Talwar C, Khurana H, Nagar S, Sharma M, Mishra H, Singh AK, Dhingra G, Negi RK, Shakarad M, Singh Y, Lal R.

Antonie Van Leeuwenhoek. 2017 Oct;110(10):1357-1371. doi: 10.1007/s10482-017-0928-1. Epub 2017 Aug 22. Review.

PMID:
28831610
10.

En route to a genome-based classification of Archaea and Bacteria?

Klenk HP, Göker M.

Syst Appl Microbiol. 2010 Jun;33(4):175-82. doi: 10.1016/j.syapm.2010.03.003. Epub 2010 Apr 20. Review.

PMID:
20409658
11.

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction.

Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J.

J Microbiol. 2018 Apr;56(4):280-285. doi: 10.1007/s12275-018-8014-6. Epub 2018 Feb 28.

PMID:
29492869
12.

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy.

Meier-Kolthoff JP, Göker M.

Nat Commun. 2019 May 16;10(1):2182. doi: 10.1038/s41467-019-10210-3.

13.

Telling the whole story in a 10,000-genome world.

Beiko RG.

Biol Direct. 2011 Jun 30;6:34. doi: 10.1186/1745-6150-6-34.

14.

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.

Rohwer RR, Hamilton JJ, Newton RJ, McMahon KD.

mSphere. 2018 Sep 5;3(5). pii: e00327-18. doi: 10.1128/mSphere.00327-18.

15.

Time to revisit polyphasic taxonomy.

Vandamme P, Peeters C.

Antonie Van Leeuwenhoek. 2014 Jul;106(1):57-65. doi: 10.1007/s10482-014-0148-x. Epub 2014 Mar 15. Review.

PMID:
24633913
16.

PHOG: a database of supergenomes built from proteome complements.

Merkeev IV, Novichkov PS, Mironov AA.

BMC Evol Biol. 2006 Jun 22;6:52.

17.

Advantages and limitations of genomics in prokaryotic taxonomy.

Sentausa E, Fournier PE.

Clin Microbiol Infect. 2013 Sep;19(9):790-5. doi: 10.1111/1469-0691.12181. Epub 2013 Mar 13. Review.

18.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA.

Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

19.

Towards a balanced view of the bacterial tree of life.

Schulz F, Eloe-Fadrosh EA, Bowers RM, Jarett J, Nielsen T, Ivanova NN, Kyrpides NC, Woyke T.

Microbiome. 2017 Oct 17;5(1):140. doi: 10.1186/s40168-017-0360-9. Erratum in: Microbiome. 2017 Nov 15;5(1):149.

20.

SyntTax: a web server linking synteny to prokaryotic taxonomy.

Oberto J.

BMC Bioinformatics. 2013 Jan 16;14:4. doi: 10.1186/1471-2105-14-4.

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