Publications

Publications

2021


  • Bapteste E, Gérard P, Larose C, Blouin M, Not F, Campos L, Aïdan G, Selosse MA, Adénis MS, Bouchard F, Dutreuil S, Corel E, Vigliotti C, Huneman P, Lapointe FJ, Lopez P: The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View. Biology 2021, 10, 651. https://doi.org/10.3390/biology10070651 [Article]
  • Dorrell RG, Villain A, Perez-Lamarque B, Audren de Kerdrel G, McCallum G, Watson AK, Ait-Mohamed O, Alberti A, Corre E, Frischkorn KR, Pierella Karlusich JJ, Pelletier E, Morlon H, Bowler C, Blanc G: Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. Proc Natl Acad Sci U S A. 2021;118(4).
  • Teulière J, Bernard C, Bapteste E: Interspecific interactions that affect ageing: age-distorters manipulate host ageing to their own evolutionary benefits. Ageing Res Rev. 2021 May 31:101375. doi: 10.1016/j.arr.2021.101375. Online ahead of print. [Article]
     

2020


  • Lannes R, Cavaud L, Lopez P, Bapteste E: Marine Ultra-small Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen and Sulfur. Genome Biol Evol. 2020 Dec 16
  • Bernard C, Lannes R, Li Y, Bapteste E, Lopez P: Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication. mSystems 2020 Oct; doi:  10.1128/mSystems.00414-20 [Article]
  • Bernard C, Li Y, Lopez P, Bapteste E: Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms. ISME J. 2020 Oct 7; doi: 10.1038/s41396-020-00795-9. [Article]
  • Teulière J, Bernard G, Bapteste E: The Distribution of Genes Associated With Regulated Cell Death Is Decoupled From the Mitochondrial Phenotypes Within Unicellular Eukaryotic Hosts. Frontiers in Cell and Developmental Biology. 2020 Sep 23; doi: 10.3389/fcell.2020.536389. [Article]
  • Arroyo AS, Lannes R, Bapteste E, Ruiz-Trillo I: Gene similarity networks unveil a potential novel unicellular group closely related to animals from the Tara Oceans expedition. Genome Biology and Evolution, 2020 Jun 13:evaa117. doi: 10.1093/gbe/evaa117. [Article]
  • Teulière J, Bhattacharya D, Bapteste E: Ancestral germen/soma distinction in microbes: Expanding the disposable soma theory of aging to all unicellular lineages. Ageing Res Rev. 2020 Jul;60:101064. doi: 10.1016/j.arr.2020.101064 [Article]
  • Bernard, C, Lopez P, Bapteste, E: Microbial Communication Networks: Sketching a Method for Analyzing the Communication of Bacteriophages Inside Environmental Communities, in ‘Biocommunication of Phages’, G. Witzany (ed), Springer, 2020, ISBN 978-3-030-45884-3, p.163-182. [Book]
  • Bapteste E, Papale F: Modeling the evolution of interconnected processes: It is the song and the singers. BioEsssays. 2020 [Article]

2019


 

  • Papale F, Saget J, Bapteste E: Networks Consolidate the Core Concepts of Evolution by Natural Selection. Trends Microbiol. 2019 Dec. doi: 10.1016/j.tim.2019.11.006. [Article]
  • Watson AK, Habib M, Bapteste E: Phylosystemics: Merging Phylogenomics, Systems Biology, and Ecology to Study Evolution.Trends Microbiol. 2019 Nov. doi: 10.1016/j.tim.2019.10.011. [Article]
  • Watson AK, Lannes R, Pathmanathan JS, Meheust R, Karkar S, Colson P, Corel E, Lopez P, Bapteste E: The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution. Methods Mol Biol 2019, 1910:271-308.
  • Lord E, Pathmanathan JS, Corel E, Makarenkov V, Lopez P, Bouchard F, Bhattacharya D, Antoine PO, Le Guyader H, Lapointe FJ, Bapteste E: Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data. Genome Biol Evol 2019, 11:2653-2665. [Article]
  • Lannes R, Olsson-Francis K, Lopez P, Bapteste E: Carbon fixation by marine ultra-small prokaryotes. Genome Biol Evol. 2019 Mar 23. [Article] Highlighted in Contribution of Ultra-Small Microbes to Global Carbon Cycles.

 

 

2018


  • 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. [Article]
  • 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. [Article]
  • 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. [Article]
  • Corel E, Pathmanathan JS, Watson AK, Karkar S, Lopez P, Bapteste E: MultiTwin: A Software Suite to Analyze Evolution at Multiple Levels of Organization Using Multipartite Graphs. Genome Biol Evol 2018, 10(10):2777-2784. [Article]
  • 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. [Article]
  • 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. [Article]
  • Bapteste E, Huneman P: Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory. BMC biology 2018, 16(1):56. [Article]

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). [Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]
  • Corel E, Lopez P, Meheust R, Bapteste E: Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends Microbiol 2016, 24(3):224-237. [Article]

 

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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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.[Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]

 

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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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. [Article]

 

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. [Article]
  • 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. [Article]

 

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. [Article]
  • 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. [Article]
  • Leigh JW, Lapointe FJ, Lopez P, Bapteste E: Evaluating phylogenetic congruence in the post-genomic era. Genome Biol Evol 2011, 3:571-587. [Article]
  • 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. [Article]

 

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. [Article]
  • 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. [Article]
  • 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. [Article]
  • 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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