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Items: 1 to 20 of 38

1.

Impact of small repeat sequences on bacterial genome evolution.

Delihas N.

Genome Biol Evol. 2011;3:959-73. doi: 10.1093/gbe/evr077. Epub 2011 Jul 29.

2.

Evolutionary rewiring and reprogramming of bacterial transcription regulation.

Wang L, Wang FF, Qian W.

J Genet Genomics. 2011 Jul 20;38(7):279-88. doi: 10.1016/j.jgg.2011.06.001. Epub 2011 Jun 17. Review.

PMID:
21777852
3.

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.

Treangen TJ, Rocha EP.

PLoS Genet. 2011 Jan 27;7(1):e1001284. doi: 10.1371/journal.pgen.1001284.

4.

The transposon-like Correia elements encode numerous strong promoters and provide a potential new mechanism for phase variation in the meningococcus.

Siddique A, Buisine N, Chalmers R.

PLoS Genet. 2011 Jan 20;7(1):e1001277. doi: 10.1371/journal.pgen.1001277.

5.

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes.

Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T.

Genome Res. 2011 Apr;21(4):599-609. doi: 10.1101/gr.115592.110. Epub 2011 Jan 26.

6.

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.

Kuzniar A, Dhir S, Nijveen H, Pongor S, Leunissen JA.

Bioinformatics. 2010 Oct 1;26(19):2482-3. doi: 10.1093/bioinformatics/btq435. Epub 2010 Aug 2. Erratum in: Bioinformatics. 2015 Oct 1;31(19):3240.

7.

Comparison of 61 sequenced Escherichia coli genomes.

Lukjancenko O, Wassenaar TM, Ussery DW.

Microb Ecol. 2010 Nov;60(4):708-20. doi: 10.1007/s00248-010-9717-3. Epub 2010 Jul 11. Review.

8.

Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.

Lee DH, Palsson BØ.

Appl Environ Microbiol. 2010 Jul;76(13):4158-68. doi: 10.1128/AEM.00373-10. Epub 2010 Apr 30. Erratum in: Appl Environ Microbiol. 2010 Sep;76(18):6327.

9.

The effect of mobile element IS10 on experimental regulatory evolution in Escherichia coli.

Stoebel DM, Dorman CJ.

Mol Biol Evol. 2010 Sep;27(9):2105-12. doi: 10.1093/molbev/msq101. Epub 2010 Apr 16.

10.

CD-HIT Suite: a web server for clustering and comparing biological sequences.

Huang Y, Niu B, Gao Y, Fu L, Li W.

Bioinformatics. 2010 Mar 1;26(5):680-2. doi: 10.1093/bioinformatics/btq003. Epub 2010 Jan 6.

11.

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E.

PLoS One. 2009 Oct 19;4(10):e7526. doi: 10.1371/journal.pone.0007526.

12.

A novel mechanism of transposon-mediated gene activation.

Zhang Z, Saier MH Jr.

PLoS Genet. 2009 Oct;5(10):e1000689. doi: 10.1371/journal.pgen.1000689. Epub 2009 Oct 16.

13.

Lateral genetic transfer: open issues.

Ragan MA, Beiko RG.

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2241-51. doi: 10.1098/rstb.2009.0031. Review.

14.

Genesis, effects and fates of repeats in prokaryotic genomes.

Treangen TJ, Abraham AL, Touchon M, Rocha EP.

FEMS Microbiol Rev. 2009 May;33(3):539-71. Review.

15.

Infernal 1.0: inference of RNA alignments.

Nawrocki EP, Kolbe DL, Eddy SR.

Bioinformatics. 2009 May 15;25(10):1335-7. doi: 10.1093/bioinformatics/btp157. Epub 2009 Mar 23. Erratum in: Bioinformatics. 2009 Jul 1;25(13):1713.

16.

Transcription factor function and promoter architecture govern the evolution of bacterial regulons.

Perez JC, Groisman EA.

Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4319-24. doi: 10.1073/pnas.0810343106. Epub 2009 Feb 27.

18.

Rfam: updates to the RNA families database.

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766. Epub 2008 Oct 25.

19.

The emergence and fate of horizontally acquired genes in Escherichia coli.

van Passel MW, Marri PR, Ochman H.

PLoS Comput Biol. 2008 Apr 11;4(4):e1000059. doi: 10.1371/journal.pcbi.1000059.

20.

Evolution of eukaryotic transcription circuits.

Tuch BB, Li H, Johnson AD.

Science. 2008 Mar 28;319(5871):1797-9. doi: 10.1126/science.1152398.

PMID:
18369141

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