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Page 1
Monte Carlo Strategies for Selecting Parameter Values in Simulation Experiments.
Leigh JW, Bryant D. Leigh JW, et al. Syst Biol. 2015 Sep;64(5):741-51. doi: 10.1093/sysbio/syv030. Epub 2015 May 25. Syst Biol. 2015. PMID: 26012871
Let them fall where they may: congruence analysis in massive phylogenetically messy data sets.
Leigh JW, Schliep K, Lopez P, Bapteste E. Leigh JW, et al. Mol Biol Evol. 2011 Oct;28(10):2773-85. doi: 10.1093/molbev/msr110. Epub 2011 Apr 27. Mol Biol Evol. 2011. PMID: 21527387
Evaluating phylogenetic congruence in the post-genomic era.
Leigh JW, Lapointe FJ, Lopez P, Bapteste E. Leigh JW, et al. Genome Biol Evol. 2011;3:571-87. doi: 10.1093/gbe/evr050. Epub 2011 Jun 28. Genome Biol Evol. 2011. PMID: 21712432 Free PMC article. Review.
Testing congruence in phylogenomic analysis.
Leigh JW, Susko E, Baumgartner M, Roger AJ. Leigh JW, et al. Syst Biol. 2008 Feb;57(1):104-15. doi: 10.1080/10635150801910436. Syst Biol. 2008. PMID: 18288620
A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the "brown algal crown radiation".
Silberfeld T, Leigh JW, Verbruggen H, Cruaud C, de Reviers B, Rousseau F. Silberfeld T, et al. Among authors: leigh jw. Mol Phylogenet Evol. 2010 Aug;56(2):659-74. doi: 10.1016/j.ympev.2010.04.020. Epub 2010 Apr 19. Mol Phylogenet Evol. 2010. PMID: 20412862
Invasion and persistence of a selfish gene in the Cnidaria.
Goddard MR, Leigh J, Roger AJ, Pemberton AJ. Goddard MR, et al. PLoS One. 2006 Dec 20;1(1):e3. doi: 10.1371/journal.pone.0000003. PLoS One. 2006. PMID: 17183657 Free PMC article.
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups".
Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ. Hampl V, et al. Among authors: leigh jw. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3859-64. doi: 10.1073/pnas.0807880106. Epub 2009 Feb 23. Proc Natl Acad Sci U S A. 2009. PMID: 19237557 Free PMC article.
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
Network analyses structure genetic diversity in independent genetic worlds.
Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E. Halary S, et al. Among authors: leigh jw. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):127-32. doi: 10.1073/pnas.0908978107. Epub 2009 Dec 10. Proc Natl Acad Sci U S A. 2010. PMID: 20007769 Free PMC article.
Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts.
Liu Y, Leigh JW, Brinkmann H, Cushion MT, Rodriguez-Ezpeleta N, Philippe H, Lang BF. Liu Y, et al. Among authors: leigh jw. Mol Biol Evol. 2009 Jan;26(1):27-34. doi: 10.1093/molbev/msn221. Epub 2008 Oct 14. Mol Biol Evol. 2009. PMID: 18922765
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