PubMed

Search for a 'Tree of Life' in the thicket of the phylogenetic forest.

Puigbò P, Wolf YI, Koonin EV.

J Biol. 2009;8(6):59. Epub 2009 Jul 13.PMID: 19594957 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

The Phylogenetic Forest and the Quest for the Elusive Tree of Life.

Koonin EV, Wolf YI, Puigbò P.

Cold Spring Harb Symp Quant Biol. 2009 Aug 17. [Epub ahead of print]PMID: 19687142 [PubMed - as supplied by publisher]Related articles

The Biological Big Bang model for the major transitions in evolution.

Koonin EV.

Biol Direct. 2007 Aug 20;2:21.PMID: 17708768 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome trees and the tree of life.

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

Trends Genet. 2002 Sep;18(9):472-9. Review.PMID: 12175808 [PubMed - indexed for MEDLINE]Related articles

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.

Mirkin BG, Fenner TI, Galperin MY, Koonin EV.

BMC Evol Biol. 2003 Jan 6;3:2. Epub 2003 Jan 6.PMID: 12515582 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.

Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV.

Genome Biol. 2003;4(9):R55. Epub 2003 Aug 29.PMID: 12952534 [PubMed - indexed for MEDLINE]Related articlesFree article

The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.

Koonin EV, Makarova KS, Rogozin IB, Davidovic L, Letellier MC, Pellegrini L.

Genome Biol. 2003;4(3):R19. Epub 2003 Feb 28.PMID: 12620104 [PubMed - indexed for MEDLINE]Related articlesFree article

Trees in the web of life.

Swithers KS, Gogarten JP, Fournier GP.

J Biol. 2009;8(6):54. Epub 2009 Jul 13. Review.PMID: 19664165 [PubMed - indexed for MEDLINE]Related articlesFree article

Universal trees based on large combined protein sequence data sets.

Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ.

Nat Genet. 2001 Jul;28(3):281-5.PMID: 11431701 [PubMed - indexed for MEDLINE]Related articles

Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4.

Chen K, Roberts E, Luthey-Schulten Z.

BMC Evol Biol. 2009 Jul 29;9:179.PMID: 19640295 [PubMed - indexed for MEDLINE]Related articlesFree article

Do orthologous gene phylogenies really support tree-thinking?

Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF.

BMC Evol Biol. 2005 May 24;5(1):33.PMID: 15913459 [PubMed - indexed for MEDLINE]Related articlesFree article

Estimation of phylogenetic inconsistencies in the three domains of life.

Soria-Carrasco V, Castresana J.

Mol Biol Evol. 2008 Nov;25(11):2319-29. Epub 2008 Aug 12.PMID: 18701430 [PubMed - indexed for MEDLINE]Related articlesFree article

Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract.

Nicolas P, Bessières P, Ehrlich SD, Maguin E, van de Guchte M.

BMC Evol Biol. 2007 Aug 20;7:141.PMID: 17708761 [PubMed - indexed for MEDLINE]Related articlesFree article

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO.

Proc Biol Sci. 2004 Dec 22;271(1557):2551-8.PMID: 15615680 [PubMed - indexed for MEDLINE]Related articlesFree article

The net of life: reconstructing the microbial phylogenetic network.

Kunin V, Goldovsky L, Darzentas N, Ouzounis CA.

Genome Res. 2005 Jul;15(7):954-9. Epub 2005 Jun 17.PMID: 15965028 [PubMed - indexed for MEDLINE]Related articlesFree article

Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers.

Brochier-Armanet C, Forterre P.

Archaea. 2007 May;2(2):83-93.PMID: 17350929 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogenetic identification of lateral genetic transfer events.

Beiko RG, Hamilton N.

BMC Evol Biol. 2006 Feb 11;6:15.PMID: 16472400 [PubMed - indexed for MEDLINE]Related articlesFree article

Dealing with incongruence in phylogenomic analyses.

Galtier N, Daubin V.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4023-9.PMID: 18852109 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome trees and the nature of genome evolution.

Snel B, Huynen MA, Dutilh BE.

Annu Rev Microbiol. 2005;59:191-209. Review.PMID: 16153168 [PubMed - indexed for MEDLINE]Related articles