Publications

Publications

2018

 


  • Watson AK, Lannes R, Pathmanathan JS, Méheust R, Karkar S, Colson P, Corel E, Lopez  P, Bapteste E: The Methodology Behind Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution in Evolutionary Genomics. In: Statistical and Computational Methods. Edited by Anisimova M: Springer; 2018: in press.
  • Vigliotti C, Bicep C, Bapteste E, Lopez P, Corel E: Tracking the Rules of Transmission and Introgression with Networks. Microbiol Spectr 2018, 6(2).
  • Pathmanathan JS, Lopez P, Lapointe FJ, Bapteste E: CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection. Mol Biol Evol 2018, 35(1):252-255.
  • Meheust R, Watson AK, Lapointe FJ, Papke RT, Lopez P, Bapteste E: Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. Genome Biol 2018, 19(1):75.
  • Meheust R, Bhattacharya D, Pathmanathan JS, McInerney JO, Lopez P, Bapteste E: Formation of chimeric genes with essential functions at the origin of eukaryotes. BMC biology 2018, 16(1):30.
  • Evangelista D, Thouze F, Kohli MK, Lopez P, Legendre F: Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny. Molecular phylogenetics and evolution 2018, 128:112-122.
  • Corel E, Meheust R, Watson AK, McInerney JO, Lopez P, Bapteste E: Bipartite Network Analysis of Gene Sharings in the Microbial World. Mol Biol Evol 2018, 35(4):899-913.
  • Bernard G, Pathmanathan JS, Lannes R, Lopez P, Bapteste E: Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. Genome Biol Evol 2018, 10(3):707-715.
  • Bapteste E, Huneman P: Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory. BMC biology 2018, 16(1):56.

 

2017

 


  • Vigliotti C, Lopez P, Bapteste E: Analyse de la diversité microbienne : de la difficulté (paradoxale) de voir large en métagénomique. In: Evolution et Biodiversité. Edited by Grandcolas P, Maurel MC, ISTE Editions edn; 2017.
  • Vigliotti C, Bicep C, bapteste E, Lopez P, Corel E: Tracking the rules of transmission and introgression with networks. In: Experimental and Theoretical Modes of Transmission. Edited by Baquero F, Coque TM: ASM Press; 2017.
  • List JM, Pathmanathan JS, Hill NW, Bapteste E, Lopez P: Vowel purity and rhyme evidence in Old Chinese reconstruction. Lingua Sinica 2017, 3(5).
  • Dorrell RG, Gile G, McCallum G, Meheust R, Bapteste EP, Klinger CM, Brillet-Gueguen L, Freeman KD, Richter DJ, Bowler C: Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife 2017, 6.
  • Bapteste E, Lopez P: Comment les Big Data font évoluer les recherches en phylogénie. In: Les Big Data à découvert. Edited by Editions C. Paris: CNRS Editions; 2017: 226-227.
  • Bapteste E, Campos L: Raconter le virus : Dialogue interdisciplinaire sur la transposition narrative du discours biologique. Epistémocritique 2017, in press.
  • Bapteste E, Anderson G: Intersecting processes are necessary explanantia for evolutionary biology, but challenge retrodiction. In: Everything Flows: Towards a Processual Philosophy of Biology. Edited by Nicholson DJ, Dupré J. Oxford: Oxford University Press; 2017.

2016

 


  • Völkel F, Bapteste E, Habib M, Lopez P, Vigliotti C: Read networks and k-laminar graphs. In.: arXiv.org; 2016.
  • Meheust 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, 113(13):3579-3584.
  • Lord E, Le Cam M, Bapteste E, Meheust 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, 11(8):e0161474.
  • 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, 11:39.
  • List JM, Lopez P, Bapteste E: Using sequence similarity networks to identify partial cognates in multilingual wordlists. In: Proceedings of the Association of Computational Linguistics: 2016. 599-605.
  • 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, 18(12):5072-5081.
  • Corel E, Lopez P, Meheust R, Bapteste E: Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends Microbiol 2016, 24(3):224-237.

2015

 


  • Orata FD, Kirchberger PC, Meheust R, Barlow EJ, Tarr CL, Boucher Y: The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment. Genome Biol Evol 2015, 7(10):2941-2954.
  • Meheust R, Lopez P, Bapteste E: Metabolic bacterial genes and the construction of high-level composite lineages of life. Trends in ecology & evolution 2015, 30(3):127-129. PDF
  • Lopez P, Halary S, Bapteste E: Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life. Biol Direct 2015, 10(1):64.
  • Forster D, Bittner L, Karkar S, Dunthorn M, Romac S, Audic S, Lopez P, Stoeck T, Bapteste E: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC biology 2015, 13:16.
  • Boon E, Halary S, Bapteste E, Hijri M: Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm. Genome Biol Evol 2015, 7(2):505-521.
  • Bapteste E: Conflits intérieurs. Fable scientifique.: Editions Matériologiques-Essais; 2015.

2014

 


  • Jachiet PA, Colson P, Lopez P, Bapteste E: Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Genome Biol Evol 2014, 6(9):2195-2205. PDF
  • 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 2014, 31(3):501-516.
  • Dagan T, Bapteste E, McInerney JO, Martin WF: SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report. Genome Biol Evol 2014, 6(9):2206-2209.
  • Cheng S, Karkar S, Bapteste E, Yee N, Falkowski P, Bhattacharya D: Sequence similarity network reveals the imprints of major diversification events in the evolution of microbial life. Frontiers in Ecology and Evolution 2014, 2:72.
  • Bapteste E: Pluralisme et évolution réticulée en microbiologie évolutive. In: PRÉCIS DE PHILOSOPHIE DE LA BIOLOGIE. Edited by Merlin F, Hoquet T; 2014: 321.
  • 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.

2013

 


  • 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, 30(8):1975-1986.
  • Lopez P, List J, Bapteste E: A preliminary case for exploratory networks in biology and linguistics: the phonetic network of Chinese words as a case-study. In: Classification and Evolution in Biology, Linguistics and the History of Science. Edited by Heiner Fangerau HG, Thorsten Halling and William Martin. Stuttgart: Franz Steiner Verlag; 2013: 181-196.
  • Jachiet PA, Pogorelcnik R, Berry A, Lopez P, Bapteste E: MosaicFinder: identification of fused gene families in sequence similarity networks. Bioinformatics 2013, 29(7):837-844.
  • Halary S, McInerney JO, Lopez P, Bapteste E: EGN: a wizard for construction of gene and genome similarity networks. BMC Evol Biol 2013, 13:146.
  • Bhattacharya D, Price DC, Bicep C, Bapteste E, Sarwade M, Rajah VD, Yoon HS: Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly. Journal of Phycology 2013, 49(1):207-212.
  • Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L et al: Networks: expanding evolutionary thinking. Trends Genet 2013, 29(8):439-441.
  • Bapteste E, Dupre J: Towards a processual microbial ontology. Biology & philosophy 2013, 28(2):379-404.
  • Bapteste E: Les gènes voyageurs: l'odyssée de l'évolution: Belin-Pour la Science; 2013.
  • 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, 110(17):E1594-1603.

2012

 


  • 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, 109(45):18266-18272.
  • 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.
  • Bapteste E, Bicep C, Lopez P: 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 4:40-43.

2011

 


  • Schliep KP: phangorn: phylogenetic analysis in R. Bioinformatics 2011, 27(4):592-593.
  • Schliep K, Lopez P, Lapointe FJ, Bapteste E: Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol 2011, 28(4):1393-1405.
  • McInerney JO, Pisani D, Bapteste E, O'Connell MJ: The Public Goods Hypothesis for the evolution of life on Earth. Biol Direct 2011, 6:41.
  • Leigh JW, Schliep K, Lopez P, Bapteste E: Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol 2011, 28(10):2773-2785.
  • Leigh JW, Lapointe FJ, Lopez P, Bapteste E: Evaluating phylogenetic congruence in the post-genomic era. Genome Biol Evol 2011, 3:571-587.
  • 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, 2(2).
  • 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, 6:39; discussion 39.

2010

 


  • Silberfeld T, Leigh JW, Verbruggen H, Cruaud C, de Reviers B, Rousseau F: A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the "brown algal crown radiation". Molecular phylogenetics and evolution 2010, 56(2):659-674.
  • Lapointe FJ, Lopez P, Boucher Y, Koenig J, Bapteste E: Clanistics: a multi-level perspective for harvesting unrooted gene trees. Trends Microbiol 2010, 18(8):341-347.
  • 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, 107(1):127-132.
  • 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, 5:47.
  • Bapteste E, Burian RM: On the need for integrative phylogenomics, and some steps toward its creation. Biology & philosophy 2010, 25(4):711-736.

2009

 


  • Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Queinnec E et al: Phylogenomics revives traditional views on deep animal relationships. Curr Biol 2009, 19(8):706-712.
  • Nesbo CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK et al: The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol 2009, 191(6):1974-1978.
  • Lopez P, Bapteste E: Molecular phylogeny: reconstructing the forest. C R Biol 2009, 332(2-3):171-182.
  • Boucher Y, Bapteste E: Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. Bioessays 2009, 31(5):526-536.
  • Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupre J, Dagan T, Boucher Y et al: Prokaryotic evolution and the tree of life are two different things. Biol Direct 2009, 4:34.
  • Bapteste E, Boucher Y: Epistemological impacts of horizontal gene transfer on classification in microbiology. Methods Mol Biol 2009, 532:55-72.

 

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