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Eric Bapteste

Research Profile

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Physiology

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Evolution, Molecular

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Genes & Molecular Sequences

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Publications

TOP 3
David Alvarez-Ponce; Eric Bapteste; Philippe Lopez; James O McInerney
Gene similarity networks provide tools for understanding eukaryote origins and evolution.
Pierre-Alain Jachiet; Philippe Lopez; Romain Pogorelcnik; Anne Berry; Eric Bapteste
MosaicFinder: identification of fused gene families in sequence similarity networks.
Eric Bapteste; Fernando Baquero; Frédéric Bouchard; Philippe Lopez; James O McInerney; Richard M Burian
Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

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All Publications

2013: David Alvarez-Ponce; Eric Bapteste; Philippe Lopez; James O McInerney
Gene similarity networks provide tools for understanding eukaryote origins and evolution.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(17):E1594-603.
2013: Pierre-Alain Jachiet; Philippe Lopez; Romain Pogorelcnik; Anne Berry; Eric Bapteste
MosaicFinder: identification of fused gene families in sequence similarity networks.
Bioinformatics (Oxford, England) 2013;29(7):837-44.
2012: Eric Bapteste; Fernando Baquero; Frédéric Bouchard; Philippe Lopez; James O McInerney; Richard M Burian
Evolutionary analyses of non-genealogical bonds produced by introgressive descent.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(45):18266-72.
2012: Eric Bapteste; C Bicep; Philippe Lopez
Evolution of genetic diversity using networks: the human gut microbiome as a case study.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2012;18 Suppl 4():40-3.
2012: Eric Bapteste; Frédéric Bouchard; Richard M Burian
Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns.
Methods in molecular biology (Clifton, N.J.) 2012;856():81-110.
2011: Jessica W Leigh; Philippe Lopez; Klaus Schliep; Eric Bapteste
Let them fall where they may: congruence analysis in massive phylogenetically messy data sets.
Molecular biology and evolution 2011;28(10):2773-85.
2011: Klaus Schliep; Philippe Lopez; François-Joseph Lapointe; Eric Bapteste
Harvesting evolutionary signals in a forest of prokaryotic gene trees.
Molecular biology and evolution 2011;28(4):1393-405.
2011: James O McInerney; Eric Bapteste; Davide Pisani; Mary J O'Connell
The Public Goods Hypothesis for the evolution of life on Earth.
Biology direct 2011;6():41.
2011: Julie Beauregard-Racine; Cédric Bicep; François-Joseph Lapointe; Philippe Lopez; Klaus Schliep; Eric Bapteste
Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.
Biology direct 2011;6():39; discussion 39.
2011: Jessica W Leigh; Philippe Lopez; François-Joseph Lapointe; Eric Bapteste
Evaluating phylogenetic congruence in the post-genomic era.
Genome biology and evolution 2011;3():571-87.
2011: Yan Boucher; Otto X Cordero; Alison Takemura; Dana E Hunt; Klaus Schliep; Eric Bapteste; Philippe Lopez; Cheryl L Tarr; Martin F Polz
Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations.
mBio 2011;2(2):.
2010: François-Joseph Lapointe; Philippe Lopez; Yan Boucher; Jeremy Koenig; Eric Bapteste
Clanistics: a multi-level perspective for harvesting unrooted gene trees.
Trends in microbiology 2010;18(8):341-7.
2010: Sébastien Halary; Jessica W Leigh; Bachar Cheaib; Philippe Lopez; Eric Bapteste
Network analyses structure genetic diversity in independent genetic worlds.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(1):127-32.
2010: Lucie Bittner; Sébastien Halary; Claude Payri; Corinne Cruaud; Bruno de Reviers; Philippe Lopez; Eric Bapteste
Some considerations for analyzing biodiversity using integrative metagenomics and gene networks.
Biology direct 2010;5():47.
2009: Yan Boucher; Eric Bapteste
Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective.
BioEssays : news and reviews in molecular, cellular and developmental biology 2009;31(5):526-36.
2009: Camilla L Nesbø; Eric Bapteste; Bruce Curtis; Håkon Dahle; Philippe Lopez; Dave Macleod; Marlena Dlutek; Sharen Bowman; Olga Zhaxybayeva; Nils-Kåre Birkeland; W Ford Doolittle
The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.
Journal of bacteriology 2009;191(6):1974-8.
2009: Philippe Lopez; Eric Bapteste
Molecular phylogeny: reconstructing the forest.
Comptes rendus biologies 2009;332(2-3):171-82.
2009: Eric Bapteste; Maureen A O'Malley; Robert G Beiko; Marc Ereshefsky; J Peter Gogarten; Laura Franklin-Hall; François-Joseph Lapointe; John Dupré; Tal Dagan; Yan Boucher; William Martin
Prokaryotic evolution and the tree of life are two different things.
Biology direct 2009;4():34.
2009: Eric Bapteste; Yan Boucher
Epistemological impacts of horizontal gene transfer on classification in microbiology.
Methods in molecular biology (Clifton, N.J.) 2009;532():55-72.
2008: Elsa Denker; Eric Bapteste; Hervé Le Guyader; Michaël Manuel; Nicolas Rabet
Horizontal gene transfer and the evolution of cnidarian stinging cells.
Current biology : CB 2008;18(18):R858-9.
2008: Eric Bapteste; Yan Boucher
Lateral gene transfer challenges principles of microbial systematics.
Trends in microbiology 2008;16(5):200-7.
2008: J E Koenig; Yan Boucher; Robert L Charlebois; Camilla Nesbø; Olga Zhaxybayeva; Eric Bapteste; Matthew Spencer; Michael J Joss; H W Stokes; W Ford Doolittle
Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments.
Environmental microbiology 2008;10(4):1024-38.
2008: Eric Bapteste; Edward Susko; Jessica Leigh; Iñaki Ruiz-Trillo; J Bucknam; W Ford Doolittle
Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny.
Molecular biology and evolution 2008;25(1):83-91.
2007: W Ford Doolittle; Eric Bapteste
Pattern pluralism and the Tree of Life hypothesis.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(7):2043-9.
2007: Adrian K Sharma; David A Walsh; Eric Bapteste; Francisco Rodriguez-Valera; W Ford Doolittle; R Thane Papke
Evolution of rhodopsin ion pumps in haloarchaea.
BMC evolutionary biology 2007;7():79.
2006: Jonathan Filée; Eric Bapteste; Edward Susko; Henry M Krisch
A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes.
Molecular biology and evolution 2006;23(9):1688-96.
2006: Edward Susko; Jessica Leigh; W Ford Doolittle; Eric Bapteste
Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria.
Molecular biology and evolution 2006;23(5):1019-30.
2006: James Bucknam; Yan Boucher; Eric Bapteste
Refuting phylogenetic relationships.
Biology direct 2006;1():26.
2005: Emmanuel F Mongodin; Karen E Nelson; Sean C Daugherty; Robert T Deboy; J Wister; Hoda Khouri; Janice Weidman; David A Walsh; R Thane Papke; Gabino Sanchez-Perez; Adrian K Sharma; Camilla L Nesbø; Dave MacLeod; Eric Bapteste; W Ford Doolittle; Robert L Charlebois; Boris A Legault; Francisco Rodriguez-Valera
The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(50):18147-52.
2005: Uri Gophna; Eric Bapteste; W Ford Doolittle; Dvora Biran; Eliora Z Ron
Evolutionary plasticity of methionine biosynthesis.
Gene 2005;355():48-57.
2005: Eric Bapteste; David A Walsh
Does the 'Ring of Life' ring true?
Trends in microbiology 2005;13(6):256-61.
2005: Eric Bapteste; Céline Brochier; Yan Boucher
Higher-level classification of the Archaea: evolution of methanogenesis and methanogens.
Archaea (Vancouver, B.C.) 2005;1(5):353-63.
2005: Eric Bapteste; Robert L Charlebois; Dave MacLeod; Céline Brochier
The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure.
Genome biology 2005;6(10):R85.
2005: Eric Bapteste; Edward Susko; Jessica Leigh; Dave MacLeod; Robert L Charlebois; W Ford Doolittle
Do orthologous gene phylogenies really support tree-thinking?
BMC evolutionary biology 2005;5():33.
2005: Dave MacLeod; Robert L Charlebois; Ford Doolittle; Eric Bapteste
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.
BMC evolutionary biology 2005;5():27.
2004: Leila Equinet; Eric Bapteste; Marc Thellier; Meryem Ouarzane-Amara; Christian P Vivarès; Isabelle Desportes-Livage; Christian Doerig
The genes encoding cAMP-dependent protein kinase catalytic subunit homologues of the microsporidia Encephalitozoon intestinalis and E. cuniculi: molecular characterisation and phylogenetic analysis.
Parasitology international 2004;53(4):277-85.
2004: David A Walsh; Eric Bapteste; Masahiro Kamekura; W Ford Doolittle
Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene.
Molecular biology and evolution 2004;21(12):2340-51.
2004: Emmanuel J P Douzery; Elizabeth A Snell; Eric Bapteste; Frederic Delsuc; Hervé Philippe
The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?
Proceedings of the National Academy of Sciences of the United States of America 2004;101(43):15386-91.
2004: Eric Bapteste; Yan Boucher; Jessica Leigh; W Ford Doolittle
Phylogenetic reconstruction and lateral gene transfer.
Trends in microbiology 2004;12(9):406-11.
2004: Hervé Philippe; Elizabeth A Snell; Eric Bapteste; Philippe Lopez; Peter W H Holland; Didier Casane
Phylogenomics of eukaryotes: impact of missing data on large alignments.
Molecular biology and evolution 2004;21(9):1740-52.
2004: Eric Bapteste; Céline Brochier
On the conceptual difficulties in rooting the tree of life.
Trends in microbiology 2004;12(1):9-13.
2003: Eric Bapteste; Simonetta Gribaldo
The genome reduction hypothesis and the phylogeny of eukaryotes.
Trends in genetics : TIG 2003;19(12):696-700.
2003: Eric Bapteste; David Moreira; Hervé Philippe
Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase.
Gene 2003;318():185-91.
2002: Eric Bapteste; Hervé Philippe
The potential value of indels as phylogenetic markers: position of trichomonads as a case study.
Molecular biology and evolution 2002;19(6):972-7.
2002: Eric Bapteste; Henner Brinkmann; Jennifer A Lee; Dorothy V Moore; Christoph Wilhelm Sensen; Paul Gordon; Laure Duruflé; Terry Gaasterland; Philippe Lopez; Miklós Müller; Hervé Philippe
The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(3):1414-9.
2002: Céline Brochier; Eric Bapteste; David Moreira; Hervé Philippe
Eubacterial phylogeny based on translational apparatus proteins.
Trends in genetics : TIG 2002;18(1):1-5.