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1:

The global landscape of sequence diversity.

Peregrín-Alvarez JM, Parkinson J.

Genome Biol. 2007;8(11):R238.

PMID: 17996061 [PubMed - indexed for MEDLINE]

2:

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV.

Genome Res. 2001 Mar;11(3):356-72.

PMID: 11230160 [PubMed - indexed for MEDLINE]

3:

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

Chen B, Zhong D, Monteiro A.

BMC Genomics. 2006 Jun 17;7:156.

PMID: 16780600 [PubMed - indexed for MEDLINE]

4:

Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.

PMID: 11734060 [PubMed - indexed for MEDLINE]

5:

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Hahn P, Böse J, Edler S, Lengeling A.

BMC Genomics. 2008 Jun 18;9:293.

PMID: 18564434 [PubMed - indexed for MEDLINE]

6:

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.

PMID: 16729895 [PubMed - indexed for MEDLINE]

7:

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Pollock DD, Eisen JA, Doggett NA, Cummings MP.

Mol Biol Evol. 2000 Dec;17(12):1776-88. Review.

PMID: 11110893 [PubMed - indexed for MEDLINE]

8:

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF.

BMC Genomics. 2008 Feb 28;9:106.

PMID: 18307801 [PubMed - indexed for MEDLINE]

9:

Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus.

Gupta RS, Singh B.

Curr Biol. 1994 Dec 1;4(12):1104-14.

PMID: 7704574 [PubMed - indexed for MEDLINE]

10:

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV.

Genome Res. 1999 Jul;9(7):608-28.

PMID: 10413400 [PubMed - indexed for MEDLINE]

11:

Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes.

Jung S, Main D, Staton M, Cho I, Zhebentyayeva T, Arús P, Abbott A.

BMC Genomics. 2006 Apr 14;7:81.

PMID: 16615871 [PubMed - indexed for MEDLINE]

12:

Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications.

Siegel N, Hoegg S, Salzburger W, Braasch I, Meyer A.

BMC Genomics. 2007 Sep 6;8:312.

PMID: 17822543 [PubMed - indexed for MEDLINE]

13:

Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales.

Guerrero G, Peralta H, Aguilar A, Díaz R, Villalobos MA, Medrano-Soto A, Mora J.

BMC Evol Biol. 2005 Oct 17;5:55.

PMID: 16229745 [PubMed - indexed for MEDLINE]

14:

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.

Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

Genome Biol. 2004;5(2):R7. Epub 2004 Jan 15.

PMID: 14759257 [PubMed - indexed for MEDLINE]

15:

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.

Rasmussen MD, Kellis M.

Genome Res. 2007 Dec;17(12):1932-42. Epub 2007 Nov 7.

PMID: 17989260 [PubMed - indexed for MEDLINE]

16:

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

Xu J.

Mol Ecol. 2006 Jun;15(7):1713-31. Review.

PMID: 16689892 [PubMed - indexed for MEDLINE]

17:

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Hartmann S, Vision TJ.

BMC Evol Biol. 2008 Mar 26;8:95.

PMID: 18366758 [PubMed - indexed for MEDLINE]

18:

Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria.

Kuo CH, Kissinger JC.

BMC Evol Biol. 2008 Apr 11;8:108.

PMID: 18405380 [PubMed - indexed for MEDLINE]

19:

Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.

Andersson JO, Hirt RP, Foster PG, Roger AJ.

BMC Evol Biol. 2006 Mar 21;6:27.

PMID: 16551352 [PubMed - indexed for MEDLINE]

20:

Improvement of whole-genome annotation of cereals through comparative analyses.

Zhu W, Buell CR.

Genome Res. 2007 Mar;17(3):299-310. Epub 2007 Feb 6.

PMID: 17284677 [PubMed - indexed for MEDLINE]

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