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Carbon Fixation by Marine Ultrasmall Prokaryotes.

Lannes R, Olsson-Francis K, Lopez P, Bapteste E.

Genome Biol Evol. 2019 Apr 1;11(4):1166-1177. doi: 10.1093/gbe/evz050.


MultiTwin: A Software Suite to Analyze Evolution at Multiple Levels of Organization Using Multipartite Graphs.

Corel E, Pathmanathan JS, Watson AK, Karkar S, Lopez P, Bapteste E.

Genome Biol Evol. 2018 Oct 1;10(10):2777-2784. doi: 10.1093/gbe/evy209.


Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.

Méheust R, Watson AK, Lapointe FJ, Papke RT, Lopez P, Bapteste E.

Genome Biol. 2018 Jun 7;19(1):75. doi: 10.1186/s13059-018-1454-9.


Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.

Bapteste E, Huneman P.

BMC Biol. 2018 May 29;16(1):56. doi: 10.1186/s12915-018-0531-6. Review.


Tracking the Rules of Transmission and Introgression with Networks.

Vigliotti C, Bicep C, Bapteste E, Lopez P, Corel E.

Microbiol Spectr. 2018 Apr;6(2). doi: 10.1128/microbiolspec.MTBP-0008-2016. Review.


Formation of chimeric genes with essential functions at the origin of eukaryotes.

Méheust R, Bhattacharya D, Pathmanathan JS, McInerney JO, Lopez P, Bapteste E.

BMC Biol. 2018 Mar 13;16(1):30. doi: 10.1186/s12915-018-0500-0.


Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery.

Bernard G, Pathmanathan JS, Lannes R, Lopez P, Bapteste E.

Genome Biol Evol. 2018 Mar 1;10(3):707-715. doi: 10.1093/gbe/evy031.


Bipartite Network Analysis of Gene Sharings in the Microbial World.

Corel E, Méheust R, Watson AK, McInerney JO, Lopez P, Bapteste E.

Mol Biol Evol. 2018 Apr 1;35(4):899-913. doi: 10.1093/molbev/msy001. Erratum in: Mol Biol Evol. 2018 Jul 1;35(7):1821.


CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection.

Pathmanathan JS, Lopez P, Lapointe FJ, Bapteste E.

Mol Biol Evol. 2018 Jan 1;35(1):252-255. doi: 10.1093/molbev/msx283.


Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome.

Dorrell RG, Gile G, McCallum G, Méheust R, Bapteste EP, Klinger CM, Brillet-Guéguen L, Freeman KD, Richter DJ, Bowler C.

Elife. 2017 May 12;6. pii: e23717. doi: 10.7554/eLife.23717.


BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts.

Lord E, Le Cam M, Bapteste É, Méheust R, Makarenkov V, Lapointe FJ.

PLoS One. 2016 Aug 31;11(8):e0161474. doi: 10.1371/journal.pone.0161474. eCollection 2016.


Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

List JM, Pathmanathan JS, Lopez P, Bapteste E.

Biol Direct. 2016 Aug 20;11:39. doi: 10.1186/s13062-016-0145-2. Review.


Bipartite graph analyses reveal interdomain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins.

Jaffe AL, Corel E, Pathmanathan JS, Lopez P, Bapteste E.

Environ Microbiol. 2016 Dec;18(12):5072-5081. doi: 10.1111/1462-2920.13477. Epub 2016 Aug 25.


Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis.

Méheust R, Zelzion E, Bhattacharya D, Lopez P, Bapteste E.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3579-84. doi: 10.1073/pnas.1517551113. Epub 2016 Mar 14.


Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.

Corel E, Lopez P, Méheust R, Bapteste E.

Trends Microbiol. 2016 Mar;24(3):224-237. doi: 10.1016/j.tim.2015.12.003. Epub 2016 Jan 13. Review.


Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life.

Lopez P, Halary S, Bapteste E.

Biol Direct. 2015 Oct 26;10:64. doi: 10.1186/s13062-015-0092-3.


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.


Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly.

Bhattacharya D, Price DC, Bicep C, Bapteste E, Sarwade M, Rajah VD, Yoon HS.

J Phycol. 2013 Feb;49(1):207-12. doi: 10.1111/jpy.12028. Epub 2013 Jan 10.


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.


Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations.

Boucher Y, Cordero OX, Takemura A, Hunt DE, Schliep K, Bapteste E, Lopez P, Tarr CL, Polz MF.

MBio. 2011 Apr 12;2(2). pii: e00335-10. doi: 10.1128/mBio.00335-10. Print 2011.


Harvesting evolutionary signals in a forest of prokaryotic gene trees.

Schliep K, Lopez P, Lapointe FJ, Bapteste E.

Mol Biol Evol. 2011 Apr;28(4):1393-405. doi: 10.1093/molbev/msq323. Epub 2010 Dec 20.


Some considerations for analyzing biodiversity using integrative metagenomics and gene networks.

Bittner L, Halary S, Payri C, Cruaud C, de Reviers B, Lopez P, Bapteste E.

Biol Direct. 2010 Jul 30;5:47. doi: 10.1186/1745-6150-5-47.


Clanistics: a multi-level perspective for harvesting unrooted gene trees.

Lapointe FJ, Lopez P, Boucher Y, Koenig J, Bapteste E.

Trends Microbiol. 2010 Aug;18(8):341-7. doi: 10.1016/j.tim.2010.03.009. Epub 2010 May 31.


Network analyses structure genetic diversity in independent genetic worlds.

Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E.

Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):127-32. doi: 10.1073/pnas.0908978107. Epub 2009 Dec 10.


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.


Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective.

Boucher Y, Bapteste E.

Bioessays. 2009 May;31(5):526-36. doi: 10.1002/bies.200800216.


Molecular phylogeny: reconstructing the forest.

Lopez P, Bapteste E.

C R Biol. 2009 Feb-Mar;332(2-3):171-82. doi: 10.1016/j.crvi.2008.07.003. Epub 2008 Nov 29. Review.


Epistemological impacts of horizontal gene transfer on classification in microbiology.

Bapteste E, Boucher Y.

Methods Mol Biol. 2009;532:55-72. doi: 10.1007/978-1-60327-853-9_4. Review.


The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.

Nesbø CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, Doolittle WF.

J Bacteriol. 2009 Mar;191(6):1974-8. doi: 10.1128/JB.01448-08. Epub 2009 Jan 5.


Horizontal gene transfer and the evolution of cnidarian stinging cells.

Denker E, Bapteste E, Le Guyader H, Manuel M, Rabet N.

Curr Biol. 2008 Sep 23;18(18):R858-9. doi: 10.1016/j.cub.2008.07.031. No abstract available.


Lateral gene transfer challenges principles of microbial systematics.

Bapteste E, Boucher Y.

Trends Microbiol. 2008 May;16(5):200-7. doi: 10.1016/j.tim.2008.02.005. Epub 2008 Apr 15.


Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments.

Koenig JE, Boucher Y, Charlebois RL, Nesbø C, Zhaxybayeva O, Bapteste E, Spencer M, Joss MJ, Stokes HW, Doolittle WF.

Environ Microbiol. 2008 Apr;10(4):1024-38. doi: 10.1111/j.1462-2920.2007.01524.x. Epub 2008 Jan 7.


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