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Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms.

Forster D, Bittner L, Karkar S, Dunthorn M, Romac S, Audic S, Lopez P, Stoeck T, Bapteste E.

BMC Biol. 2015 Feb 24;13:16. doi: 10.1186/s12915-015-0125-5.


Metabolic bacterial genes and the construction of high-level composite lineages of life.

Méheust R, Lopez P, Bapteste E.

Trends Ecol Evol. 2015 Mar;30(3):127-9. doi: 10.1016/j.tree.2015.01.001. Epub 2015 Jan 16.


Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm.

Boon E, Halary S, Bapteste E, Hijri M.

Genome Biol Evol. 2015 Jan 7;7(2):505-21. doi: 10.1093/gbe/evv002.


SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report.

Dagan T, Bapteste E, McInerney JO, Martin WF.

Genome Biol Evol. 2014 Aug 12;6(9):2206-9. doi: 10.1093/gbe/evu173. No abstract available.


Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network.

Jachiet PA, Colson P, Lopez P, Bapteste E.

Genome Biol Evol. 2014 Aug 7;6(9):2195-205. doi: 10.1093/gbe/evu168.


The origins of microbial adaptations: how introgressive descent, egalitarian evolutionary transitions and expanded kin selection shape the network of life.

Bapteste E.

Front Microbiol. 2014 Mar 4;5:83. doi: 10.3389/fmicb.2014.00083. eCollection 2014. No abstract available.


A pluralistic account of homology: adapting the models to the data.

Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO.

Mol Biol Evol. 2014 Mar;31(3):501-16. doi: 10.1093/molbev/mst228. Epub 2013 Nov 22. Review.


EGN: a wizard for construction of gene and genome similarity networks.

Halary S, McInerney JO, Lopez P, Bapteste E.

BMC Evol Biol. 2013 Jul 11;13:146. doi: 10.1186/1471-2148-13-146.


Networks: expanding evolutionary thinking.

Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitfield J.

Trends Genet. 2013 Aug;29(8):439-41. doi: 10.1016/j.tig.2013.05.007. Epub 2013 Jun 11.


Sequence comparative analysis using networks: software for evaluating de novo transcript assembly from next-generation sequencing.

Misner I, Bicep C, Lopez P, Halary S, Bapteste E, Lane CE.

Mol Biol Evol. 2013 Aug;30(8):1975-86. doi: 10.1093/molbev/mst087. Epub 2013 May 10.


Gene similarity networks provide tools for understanding eukaryote origins and evolution.

Alvarez-Ponce D, Lopez P, Bapteste E, McInerney JO.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1594-603. doi: 10.1073/pnas.1211371110. Epub 2013 Apr 1.


Towards a processual microbial ontology.

Bapteste E, Dupré J.

Biol Philos. 2013 Mar;28(2):379-404. Epub 2012 Nov 6.


MosaicFinder: identification of fused gene families in sequence similarity networks.

Jachiet PA, Pogorelcnik R, Berry A, Lopez P, Bapteste E.

Bioinformatics. 2013 Apr 1;29(7):837-44. doi: 10.1093/bioinformatics/btt049. Epub 2013 Jan 30.


Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

Bapteste E, Lopez P, Bouchard F, Baquero F, McInerney JO, Burian RM.

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18266-72. doi: 10.1073/pnas.1206541109. Epub 2012 Oct 22.


Evolution of genetic diversity using networks: the human gut microbiome as a case study.

Bapteste E, Bicep C, Lopez P.

Clin Microbiol Infect. 2012 Jul;18 Suppl 4:40-3. doi: 10.1111/j.1469-0691.2012.03856.x. Review.


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 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.


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.


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.


Let them fall where they may: congruence analysis in massive phylogenetically messy data sets.

Leigh JW, Schliep K, Lopez P, Bapteste E.

Mol Biol Evol. 2011 Oct;28(10):2773-85. doi: 10.1093/molbev/msr110. Epub 2011 Apr 27.

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