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Reccent publications

Lord E, Le Cam M, Bapteste É, Méheust R, Makarenkov V, Lapointe FJ. BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts. PLoS One. 2016 Aug 31;11(8):e0161474. doi: 10.1371/journal.pone.0161474.

List JM, Pathmanathan JS, Lopez P, Bapteste E. Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics. Biol Direct. 2016 Aug 20;11:39. doi: 10.1186/s13062-016-0145-2.

Jaffe AL, Corel E, Pathmanathan JS, Lopez P, Bapteste E. Bipartite graph analyses reveal interdomain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins. Environ Microbiol. 2016 Aug 3. doi: 10.1111/1462-2920.13477.

Méheust R, Zelzion E, Bhattacharya D, Lopez P, Bapteste E. Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis. Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3579-84. doi: 10.1073/pnas.1517551113.

Corel E, Lopez P, Méheust R, Bapteste E. Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends Microbiol. 2016 Mar;24(3):224-37. doi: 10.1016/j.tim.2015.12.003.

Lopez P, Halary S, Bapteste E. Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life. Biol Direct. 2015 Oct 26;10:64. doi: 10.1186/s13062-015-0092-3.

Orata, F. D., Kirchberger, P. C., Méheust, R., Barlow, E. J., Tarr, C. L., & Boucher, Y. (2015). The Dynamics of Genetic Interactions Between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment. Genome Biology and Evolution. doi:10.1093/gbe/evv193

Forster, D., Bittner, L., Karkar, S., Dunthorn, M., Romac, S., Audic, S., … Bapteste, E. (2015). Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biology, 13, 16. doi:10.1186/s12915-015-0125-5

Méheust, R., Lopez, P., & Bapteste, E. (2015). Metabolic bacterial genes and the construction of high-level composite lineages of life. Trends in Ecology & Evolution. doi:10.1016/j.tree.2015.01.001

Dagan T, Bapteste E, McInerney JO, Martin WF.SMBE Satellite Meeting on Reticulated Microbial Evolution 2014 - Meeting Report. Genome Biol Evol. 2014 Aug 12. [Epub ahead of print]

Jachiet P, Colson P, Lopez P, Bapteste E. Extensive gene remodeling in the viral world : new evidence for non-gradual evolution in the mobilome network. Genome Biol Evol. 2014 Aug 7. [Epub ahead of print]

Bapteste E. The origins of microbial adaptations: how introgressive descent, egalitarian evolutionary transitions and expanded kin selection shape the network of life. Front. Microbiol. 2014. 5:83

Bapteste E. Les gènes voyageurs: l'odyssée de l'évolution. Belin. 2013. 192 pages.

Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ,Pisani D, Wilkinson M, Bapteste E, McInerney JO. A Pluralistic Account of Homology: Adapting the Models to the Data. Mol Biol Evol. 2013 Dec 18.

Halary S, McInerney JO, Lopez P, Bapteste E. EGN: a wizard for construction of gene and genome similarity networks. BMC Evol Biol. 2013 Jul 11;13:146.

Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitfield J. Networks: expanding evolutionary thinking. Trends Genet. 2013Aug;29(8):439-41.

Misner I, Bicep C, Lopez P, Halary S, Bapteste E, Lane CE. Sequence comparative analysis using networks: software for evaluating de novo transcript assembly from next-generation sequencing. Mol Biol Evol. 2013 Aug;30(8):1975-86.

Alvarez-Ponce D, Lopez P, Bapteste E, McInerney JO. Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1594-603.

Bapteste E, Dupré J. Towards a processual microbial ontology. Biol Philos. 2013 Mar;28(2):379-404.

Jachiet PA, Pogorelcnik R, Berry A, Lopez P, Bapteste E. MosaicFinder: identification of fused gene families in sequence similarity networks. Bioinformatics. 2013 Apr 1;29(7):837-44.

Bapteste E, Lopez P, Bouchard F, Baquero F, McInerney JO, Burian RM. Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18266-72.

Bapteste E, Bicep C, Lopez P. Evolution of genetic diversity using networks: the human gut microbiome as a case study. Clin Microbiol Infect. 2012 Jul;18 Suppl 4:40-3.

Bapteste E, Bouchard F, Burian RM. Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns. Methods Mol Biol. 2012;856:81-110.

McInerney JO, Pisani D, Bapteste E, O'Connell MJ. The Public Goods Hypothesis for the evolution of life on Earth. Biol Direct. 2011 Aug 23;6:41.

Beauregard-Racine J, Bicep C, Schliep K, Lopez P, Lapointe FJ, Bapteste E. Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol Direct. 2011 Jul 20;6:39; discussion 39.

Leigh JW, Lapointe FJ, Lopez P, Bapteste E. Evaluating Phylogenetic Congruence in the Post-Genomic Era. Genome Biol Evol. 2011; 3:571-87.

Leigh JW, Schliep K, Lopez P, Bapteste E. Let Them Fall Where They May: Congruence Analysis in Massive, Phylogenetically Messy Datasets. Mol Biol Evol. 2011; 28(10):2773-85

Boucher Y, Cordero OX, Takemura A, Hunt DE, Schliep K, Bapteste E, Lopez P, Tarr CL, Polz MF. Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio. 2011 Apr 12;2(2). pii: e00335-10. doi: 10.1128/mBio.00335-10. Print 2011.

Schliep K, Lopez P, Lapointe FJ, Bapteste E. Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol. 2011 Apr;28(4):1393-405.

Bittner L, Halary S, Payri C, Cruaud C, de Reviers B, Lopez P, Bapteste E. Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biol Direct. 2010 Jul 30;5:47.

Lapointe FJ, Lopez P, Boucher Y, Koenig J, Bapteste E. Clanistics: a multi-level perspective for harvesting unrooted gene trees. Trends Microbiol. 2010 Aug;18(8):341-7.

Bapteste E and Burian R.M. On the need for integrative phylogenomics, and some steps toward its creation. Biology and Philosophy. 2010. Volume 25, Number 4, 711-736.

Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E. Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):127-32.

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W. Prokaryotic evolution and the tree of life are two different things. Biol Direct. 2009 Sep 29;4:34.

Boucher Y, Bapteste E. Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. Bioessays. 2009 May;31(5):526-36.

Lopez P, Bapteste E. Molecular phylogeny: reconstructing the forest. C R Biol. 2009 Feb-Mar;332(2-3):171-82.

Bapteste E, Boucher Y. Epistemological impacts of horizontal gene transfer on classification in microbiology. Methods Mol Biol. 2009;532:55-72.

Nesbø CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, Doolittle WF. The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol. 2009 Mar;191(6):1974-8.