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Items: 1 to 20 of 95


Pattern pluralism and the Tree of Life hypothesis.

Doolittle WF, Bapteste E.

Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2043-9. Epub 2007 Jan 29.


The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them.

Doolittle WF.

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2221-8. doi: 10.1098/rstb.2009.0032.


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;74:205-13. doi: 10.1101/sqb.2009.74.006. Epub 2009 Aug 17. Review.


Integrating horizontal gene transfer and common descent to depict evolution and contrast it with "common design".

Paz-Y-Miño C G, Espinosa A.

J Eukaryot Microbiol. 2010 Jan-Feb;57(1):11-8. doi: 10.1111/j.1550-7408.2009.00458.x. Epub 2009 Dec 18.


The Public Goods Hypothesis for the evolution of life on Earth.

McInerney JO, Pisani D, Bapteste E, O'Connell MJ.

Biol Direct. 2011 Aug 23;6:41. doi: 10.1186/1745-6150-6-41.


Prokaryotic evolution and the tree of life are two different things.

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W.

Biol Direct. 2009 Sep 29;4:34. doi: 10.1186/1745-6150-4-34.


Comparison of phylogenetic trees and search for a central trend in the "forest of life".

Koonin EV, Puigbò P, Wolf YI.

J Comput Biol. 2011 Jul;18(7):917-24. doi: 10.1089/cmb.2010.0185. Epub 2011 Apr 1.


The tree and net components of prokaryote evolution.

Puigbò P, Wolf YI, Koonin EV.

Genome Biol Evol. 2010;2:745-56. doi: 10.1093/gbe/evq062. Epub 2010 Oct 1.


The fundamental units, processes and patterns of evolution, and the tree of life conundrum.

Koonin EV, Wolf YI.

Biol Direct. 2009 Sep 29;4:33. doi: 10.1186/1745-6150-4-33.


Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

Beauregard-Racine J, Bicep C, Schliep K, Lopez P, Lapointe FJ, Bapteste E.

Biol Direct. 2011 Jul 20;6:39; discussion 39. doi: 10.1186/1745-6150-6-39.


Genome trees and the tree of life.

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

Trends Genet. 2002 Sep;18(9):472-9. Review.


Evaluating phylogenetic congruence in the post-genomic era.

Leigh JW, Lapointe FJ, Lopez P, Bapteste E.

Genome Biol Evol. 2011;3:571-87. doi: 10.1093/gbe/evr050. Epub 2011 Jun 28. Review.


Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin.

Merhej V, Raoult D.

Front Cell Infect Microbiol. 2012 Aug 28;2:113. doi: 10.3389/fcimb.2012.00113. eCollection 2012. Review.


Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws.

Altaba CR.

PLoS One. 2009;4(2):e4611. doi: 10.1371/journal.pone.0004611. Epub 2009 Feb 26.


The natural evolutionary relationships among prokaryotes.

Gupta RS.

Crit Rev Microbiol. 2000;26(2):111-31. Review.


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;5:33.


Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns.

Bapteste E, Bouchard F, Burian RM.

Methods Mol Biol. 2012;856:81-110. doi: 10.1007/978-1-61779-585-5_4.


The phylogenomics of protein structures: The backstory.

Kurland CG, Harish A.

Biochimie. 2015 Dec;119:284-302. doi: 10.1016/j.biochi.2015.07.027. Epub 2015 Jul 31. Review.


Universal scaling in the branching of the tree of life.

Herrada EA, Tessone CJ, Klemm K, Eguíluz VM, Hernández-García E, Duarte CM.

PLoS One. 2008 Jul 23;3(7):e2757. doi: 10.1371/journal.pone.0002757.

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