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The genome reduction hypothesis and the phylogeny of eukaryotes.
Bapteste E, Gribaldo S. Bapteste E, et al. Trends Genet. 2003 Dec;19(12):696-700. doi: 10.1016/j.tig.2003.10.004. Trends Genet. 2003. PMID: 14642750 Review. No abstract available.
On the conceptual difficulties in rooting the tree of life.
Bapteste E, Brochier C. Bapteste E, et al. Trends Microbiol. 2004 Jan;12(1):9-13. doi: 10.1016/j.tim.2003.11.002. Trends Microbiol. 2004. PMID: 14700546 Review.
Do orthologous gene phylogenies really support tree-thinking?
Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF. Bapteste E, et al. BMC Evol Biol. 2005 May 24;5:33. doi: 10.1186/1471-2148-5-33. BMC Evol Biol. 2005. PMID: 15913459 Free PMC article.
Evolution of genetic diversity using networks: the human gut microbiome as a case study.
Bapteste E, Bicep C, Lopez P. Bapteste E, et al. Clin Microbiol Infect. 2012 Jul;18 Suppl 4:40-3. doi: 10.1111/j.1469-0691.2012.03856.x. Clin Microbiol Infect. 2012. PMID: 22647047 Review.
Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny.
Bapteste E, Susko E, Leigh J, Ruiz-Trillo I, Bucknam J, Doolittle WF. Bapteste E, et al. Mol Biol Evol. 2008 Jan;25(1):83-91. doi: 10.1093/molbev/msm229. Epub 2007 Oct 16. Mol Biol Evol. 2008. PMID: 17940208
This application uses a hierarchical likelihood-ratio test framework to assess both the topological congruence between gene phylogenies (i.e., whether different genes share the same evolutionary history) and branch-length congruence (i.e., whether genes that share t …
This application uses a hierarchical likelihood-ratio test framework to assess both the topological congruence between gene phylogenies (i. …
Does the 'Ring of Life' ring true?
Bapteste E, Walsh DA. Bapteste E, et al. Trends Microbiol. 2005 Jun;13(6):256-61. doi: 10.1016/j.tim.2005.03.012. Trends Microbiol. 2005. PMID: 15936656 Review.
Phylogenetic reconstruction and lateral gene transfer.
Bapteste E, Boucher Y, Leigh J, Doolittle WF. Bapteste E, et al. Trends Microbiol. 2004 Sep;12(9):406-11. doi: 10.1016/j.tim.2004.07.002. Trends Microbiol. 2004. PMID: 15337161 Review.
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