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Items: 1 to 20 of 106

2.

Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

Alsop EB, Raymond J.

PLoS One. 2013 Jul 1;8(7):e67337. doi: 10.1371/journal.pone.0067337. Print 2013.

3.

Codon bias signatures, organization of microorganisms in codon space, and lifestyle.

Carbone A, Képès F, Zinovyev A.

Mol Biol Evol. 2005 Mar;22(3):547-61. Epub 2004 Nov 10. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1158.

PMID:
15537809
4.

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
5.

The BISMiS 2011 special issue on prokaryotic systematics, a vital discipline entering a period of transition.

Sutcliffe IC, Trujillo ME, Goodfellow M.

Antonie Van Leeuwenhoek. 2012 Jan;101(1):1-2. doi: 10.1007/s10482-011-9674-y. Epub 2011 Nov 12. No abstract available.

PMID:
22080412
6.

Analysis of tRNA composition and folding in psychrophilic, mesophilic and thermophilic genomes: indications for thermal adaptation.

Dutta A, Chaudhuri K.

FEMS Microbiol Lett. 2010 Apr;305(2):100-8. doi: 10.1111/j.1574-6968.2010.01922.x. Epub 2010 Feb 5.

7.

Adding genomic 'foliage' to the tree of life.

Walker A.

Nat Rev Microbiol. 2014 Feb;12(2):78. doi: 10.1038/nrmicro3203. No abstract available.

PMID:
24429416
8.

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Wu M, Scott AJ.

Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.

PMID:
22332237
9.

Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content.

Sandberg R, Bränden CI, Ernberg I, Cöster J.

Gene. 2003 Jun 5;311:35-42.

PMID:
12853136
10.

Thermophiles like hot T.

Lieph R, Veloso FA, Holmes DS.

Trends Microbiol. 2006 Oct;14(10):423-6. Epub 2006 Aug 28.

PMID:
16934982
11.

Origin and fate of repeats in bacteria.

Achaz G, Rocha EP, Netter P, Coissac E.

Nucleic Acids Res. 2002 Jul 1;30(13):2987-94.

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.

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.

Biol Direct. 2007 Nov 27;2:33.

14.

The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life.

Koonin EV.

J Mol Evol. 2015 Jun;80(5-6):244-50. doi: 10.1007/s00239-015-9679-7. Epub 2015 Apr 18. Review.

15.

Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation.

Sabath N, Ferrada E, Barve A, Wagner A.

Genome Biol Evol. 2013;5(5):966-77. doi: 10.1093/gbe/evt050.

16.

Informatics for unveiling hidden genome signatures.

Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T.

Genome Res. 2003 Apr;13(4):693-702.

17.

Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea.

Groussin M, Gouy M.

Mol Biol Evol. 2011 Sep;28(9):2661-74. doi: 10.1093/molbev/msr098. Epub 2011 Apr 15.

PMID:
21498602
18.

CRISPI: a CRISPR interactive database.

Rousseau C, Gonnet M, Le Romancer M, Nicolas J.

Bioinformatics. 2009 Dec 15;25(24):3317-8. doi: 10.1093/bioinformatics/btp586. Epub 2009 Oct 21.

19.

Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes.

Lee KH, Shin KS, Lim D, Kim WC, Chung BC, Han GB, Roh J, Cho DH, Cho K.

Genomics. 2015 Jul;106(1):30-42. doi: 10.1016/j.ygeno.2015.04.004. Epub 2015 Apr 23.

PMID:
25918033

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