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Items: 1 to 20 of 99

1.

Genome sequence-based species delimitation with confidence intervals and improved distance functions.

Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M.

BMC Bioinformatics. 2013 Feb 21;14:60. doi: 10.1186/1471-2105-14-60.

2.

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison.

Auch AF, von Jan M, Klenk HP, Göker M.

Stand Genomic Sci. 2010 Jan 28;2(1):117-34. doi: 10.4056/sigs.531120.

3.

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs.

Auch AF, Klenk HP, Göker M.

Stand Genomic Sci. 2010 Jan 28;2(1):142-8. doi: 10.4056/sigs.541628.

4.

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes.

Kim M, Oh HS, Park SC, Chun J.

Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):346-51. doi: 10.1099/ijs.0.059774-0. Erratum in: Int J Syst Evol Microbiol. 2014 May;64(Pt 5):1825.

PMID:
24505072
5.

The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes.

Li X, Huang Y, Whitman WB.

Antonie Van Leeuwenhoek. 2015 Jan;107(1):241-9. doi: 10.1007/s10482-014-0322-1. Epub 2014 Nov 5.

PMID:
25370015
6.

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.

Auch AF, Henz SR, Holland BR, Göker M.

BMC Bioinformatics. 2006 Jul 19;7:350.

7.

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
8.

A proposed genus boundary for the prokaryotes based on genomic insights.

Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhou J, Oren A, Zhang YZ.

J Bacteriol. 2014 Jun;196(12):2210-5. doi: 10.1128/JB.01688-14. Epub 2014 Apr 4.

9.

Shifting the genomic gold standard for the prokaryotic species definition.

Richter M, Rosselló-Móra R.

Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31. doi: 10.1073/pnas.0906412106. Epub 2009 Oct 23.

10.

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.

Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM.

Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):81-91.

PMID:
17220447
11.

Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.

Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J.

MBio. 2014 Nov 18;5(6):e02136. doi: 10.1128/mBio.02136-14.

12.

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.

13.

Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories.

Rosselló-Móra R.

Environ Microbiol. 2012 Feb;14(2):318-34. doi: 10.1111/j.1462-2920.2011.02599.x. Epub 2011 Sep 29. Review.

PMID:
21958017
14.

Microbial species delineation using whole genome sequences.

Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A.

Nucleic Acids Res. 2015 Aug 18;43(14):6761-71. doi: 10.1093/nar/gkv657. Epub 2015 Jul 6.

15.

Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age.

Meier-Kolthoff JP, Klenk HP, Göker M.

Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):352-6. doi: 10.1099/ijs.0.056994-0.

PMID:
24505073
16.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea.

Chun J, Rainey FA.

Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):316-24. doi: 10.1099/ijs.0.054171-0. Review.

PMID:
24505069
17.

Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods.

Chang HW, Nam YD, Jung MY, Kim KH, Roh SW, Kim MS, Jeon CO, Yoon JH, Bae JW.

J Microbiol Methods. 2008 Dec;75(3):523-30. doi: 10.1016/j.mimet.2008.08.003. Epub 2008 Aug 17.

PMID:
18782592
18.

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.

19.

When should a DDH experiment be mandatory in microbial taxonomy?

Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP.

Arch Microbiol. 2013 Jun;195(6):413-8. doi: 10.1007/s00203-013-0888-4. Epub 2013 Apr 17.

PMID:
23591456
20.

Reclassification of Desulfurococcus mobilis as a synonym of Desulfurococcus mucosus, Desulfurococcus fermentans and Desulfurococcus kamchatkensis as synonyms of Desulfurococcus amylolyticus, and emendation of the D. mucosus and D. amylolyticus species descriptions.

Perevalova AA, Kublanov IV, Bidzhieva SKh, Mukhopadhyay B, Bonch-Osmolovskaya EA, Lebedinsky AV.

Int J Syst Evol Microbiol. 2016 Jan;66(1):514-7. doi: 10.1099/ijsem.0.000747. Epub 2015 Nov 6.

PMID:
26596623

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