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Items: 1 to 20 of 53


Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance.

Kato H, Mori H, Maruyama F, Toyoda A, Oshima K, Endo R, Fuchu G, Miyakoshi M, Dozono A, Ohtsubo Y, Nagata Y, Hattori M, Fujiyama A, Kurokawa K, Tsuda M.

DNA Res. 2015 Dec;22(6):413-24. doi: 10.1093/dnares/dsv023. Epub 2015 Oct 1.


Genome-wide gene order distances support clustering the gram-positive bacteria.

House CH, Pellegrini M, Fitz-Gibbon ST.

Front Microbiol. 2015 Jan 20;5:785. doi: 10.3389/fmicb.2014.00785. eCollection 2014.


Archaea: the first domain of diversified life.

Caetano-Anollés G, Nasir A, Zhou K, Caetano-Anollés D, Mittenthal JE, Sun FJ, Kim KM.

Archaea. 2014 Jun 2;2014:590214. doi: 10.1155/2014/590214. eCollection 2014. Review.


Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments.

Seetharam AS, Stuart GW.

PeerJ. 2013 Dec 23;1:e226. doi: 10.7717/peerj.226. eCollection 2013 Dec 23.


The futalosine pathway played an important role in menaquinone biosynthesis during early prokaryote evolution.

Zhi XY, Yao JC, Tang SK, Huang Y, Li HW, Li WJ.

Genome Biol Evol. 2014 Jan;6(1):149-60. doi: 10.1093/gbe/evu007.


Phylo SI: a new genome-wide approach for prokaryotic phylogeny.

Shifman A, Ninyo N, Gophna U, Snir S.

Nucleic Acids Res. 2014 Feb;42(4):2391-404. doi: 10.1093/nar/gkt1138. Epub 2013 Nov 15.


Dialects of the DNA uptake sequence in Neisseriaceae.

Frye SA, Nilsen M, Tønjum T, Ambur OH.

PLoS Genet. 2013 Apr;9(4):e1003458. doi: 10.1371/journal.pgen.1003458. Epub 2013 Apr 18.


The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer.

Lücker S, Nowka B, Rattei T, Spieck E, Daims H.

Front Microbiol. 2013 Feb 21;4:27. doi: 10.3389/fmicb.2013.00027. eCollection 2013.


Phylogeny vs genome reshuffling: horizontal gene transfer.

Lal S, Cheema S, Kalia VC.

Indian J Microbiol. 2008 Jun;48(2):228-42. doi: 10.1007/s12088-008-0034-1. Epub 2008 Jul 27.


Reference-independent comparative metagenomics using cross-assembly: crAss.

Dutilh BE, Schmieder R, Nulton J, Felts B, Salamon P, Edwards RA, Mokili JL.

Bioinformatics. 2012 Dec 15;28(24):3225-31. doi: 10.1093/bioinformatics/bts613. Epub 2012 Oct 16.


The rhizome of life: what about metazoa?

Ramulu HG, Raoult D, Pontarotti P.

Front Cell Infect Microbiol. 2012 Apr 11;2:50. doi: 10.3389/fcimb.2012.00050. eCollection 2012. Review.


Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.

Meinel T, Krause A.

Evol Bioinform Online. 2012;8:489-525. doi: 10.4137/EBO.S9642. Epub 2012 Aug 7.


Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis.

Trindade-Silva AE, Rua C, Silva GG, Dutilh BE, Moreira AP, Edwards RA, Hajdu E, Lobo-Hajdu G, Vasconcelos AT, Berlinck RG, Thompson FL.

PLoS One. 2012;7(7):e39905. doi: 10.1371/journal.pone.0039905. Epub 2012 Jul 2.


Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales.

Andam CP, Harlow TJ, Papke RT, Gogarten JP.

BMC Evol Biol. 2012 Jun 13;12:85. doi: 10.1186/1471-2148-12-85.


Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts.

Kristensen DM, Cai X, Mushegian A.

J Bacteriol. 2011 Apr;193(8):1806-14. doi: 10.1128/JB.01311-10. Epub 2011 Feb 11.


The advantages and disadvantages of horizontal gene transfer and the emergence of the first species.

Vogan AA, Higgs PG.

Biol Direct. 2011 Jan 3;6:1. doi: 10.1186/1745-6150-6-1.


On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations.

Sangaralingam A, Susko E, Bryant D, Spencer M.

BMC Evol Biol. 2010 Nov 9;10:343. doi: 10.1186/1471-2148-10-343.


Mosaic-like sequences containing transposon, phage, and plasmid elements among Listeria monocytogenes plasmids.

Canchaya C, Giubellini V, Ventura M, de los Reyes-Gavilán CG, Margolles A.

Appl Environ Microbiol. 2010 Jul;76(14):4851-7. doi: 10.1128/AEM.02799-09. Epub 2010 May 28.


Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.

Jun SR, Sims GE, Wu GA, Kim SH.

Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):133-8. doi: 10.1073/pnas.0913033107. Epub 2009 Dec 14.


Modelling prokaryote gene content.

Spencer M, Susko E, Roger AJ.

Evol Bioinform Online. 2007 Feb 5;2:157-78.

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