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Divergent genomic trajectories predate the origin of animals and fungi
Eduard Ocaña-Pallarès
,
Tom Williams
,
David López-Escardó
,
Alicia Arroyo
,
Jananan Pathmanathan
et al.
Journal articles
hal-03820663v1
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The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution
Andrew B. Watson
,
Romain Lannes
,
Jananan S Pathmanathan
,
Raphaël Méheust
,
Slim Karkar
et al.
Book sections
hal-02324786v1
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Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution
Raphaël Méheust
,
Andrew K Watson
,
Francois-Joseph Lapointe
,
R. Thane Papke
,
Philippe Lopez
et al.
Journal articles
hal-01830047v1
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Formation of chimeric genes with essential functions at the origin of eukaryotes
Raphaël Méheust
,
Debashish Bhattacharya
,
Jananan S Pathmanathan
,
James O Mcinerney
,
Philippe Lopez
et al.
Journal articles
hal-01761411v1
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Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery
Guillaume Bernard
,
Jananan S Pathmanathan
,
Romain Lannes
,
Philippe Lopez
,
Eric Bapteste
et al.
Journal articles
hal-01799304v1
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Bipartite Network Analysis of Gene Sharings in the Microbial World
Eduardo Corel
,
Raphaël Méheust
,
Andrew K Watson
,
James O Mcinerney
,
Philippe Lopez
et al.
Journal articles
hal-01798030v1
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Vowel purity and rhyme evidence in Old Chinese reconstruction
Johann-Mattis List
,
Jananan Sylvestre Pathmanathan
,
Nathan W. Hill
,
Eric Bapteste
,
Philippe Lopez
et al.
Journal articles
hal-01555483v1
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Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome
Richard G Dorrell
,
Gillian Gile
,
Giselle Mccallum
,
Raphaël Méheust
,
Eric P Bapteste
et al.
Journal articles
hal-01526828v1
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BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts
Etienne Lord
,
Margaux Le Cam
,
Éric Bapteste
,
Raphaël Méheust
,
Vladimir Makarenkov
et al.
Journal articles
hal-01361753v1
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Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution
Eduardo Corel
,
Philippe Lopez
,
Raphaël Méheust
,
Eric Bapteste
Journal articles
hal-01300043v1
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Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis
Raphael Meheust
,
Ehud Zelzion
,
Debashish Bhattacharya
,
Philippe Lopez
,
Eric Bapteste
et al.
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (13), pp.3579-3584. ⟨10.1073/pnas.1517551113⟩
Journal articles
hal-01544793v1
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Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics
Johann-Mattis List
,
Jananan Sylvestre Pathmanathan
,
Philippe Lopez
,
Eric Bapteste
Journal articles
hal-01378396v1
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The Dynamics of Genetic Interactions Between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment
Fabini Orata
,
Paul Kirchberger
,
Raphaël Méheust
,
E. Jed Barlow
,
Cheryl L. Tarr
et al.
Journal articles
hal-01264332v1
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Ladybirds from the Mercantour National Park (Coleoptera: Coccinellidae)
Jean-Pierre Coutanceau
Journal articles
hal-01544903v1
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Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms
Dominik Forster
,
Lucie Bittner
,
Slim Karkar
,
Micah Dunthorn
,
Sarah Romac
et al.
Journal articles
hal-01144173v1
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Studying Genome Heterogeneity within the Arbuscular Mycorrhizal Fungal Cytoplasm
Eva Boon
,
Sébastien Halary
,
Eric Bapteste
,
Mohamed Hijri
Journal articles
hal-01224215v1
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Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life
Philippe Lopez
,
Sébastien Halary
,
Eric Bapteste
Journal articles
hal-01257771v1
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Extensive Gene Remodeling in the Viral World: New Evidence for Nongradual Evolution in the Mobilome Network
Pierre-Alain Jachiet
,
Philippe Colson
,
Philippe Lopez
,
Eric Bapteste
Journal articles
hal-01324848v1
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A Pluralistic Account of Homology: Adapting the Models to the Data
Leanne S. Haggerty
,
Pierre-Alain Jachiet
,
William P. Hanage
,
David A. Fitzpatrick
,
Philippe Lopez
et al.
Journal articles
hal-01544794v1
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Sequence Comparative Analysis Using Networks: Software for Evaluating De Novo Transcript Assembly from Next-Generation Sequencing
Ian Misner
,
Cedric Bicep
,
Philippe Lopez
,
Sebastien Halary
,
Eric Bapteste
et al.
Journal articles
hal-01544800v1
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EGN: a wizard for construction of gene and genome similarity networks
Sebastien Halary
,
James O. Mcinerney
,
Philippe Lopez
,
Eric Bapteste
Journal articles
hal-01544799v1
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Gene similarity networks provide tools for understanding eukaryote origins and evolution
David Alvarez-Ponce
,
Philippe Lopez
,
Eric Bapteste
,
James O. Mcinerney
Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (17), pp.E1594-E1603. ⟨10.1073/pnas.1211371110⟩
Journal articles
hal-01544798v1
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MosaicFinder: identification of fused gene families in sequence similarity networks
Pierre-Alain Jachiet
,
Romain Pogorelcnik
,
Anne Berry
,
Philippe Lopez
,
Eric Bapteste
et al.
Journal articles
hal-01544795v1
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Towards a processual microbial ontology
Eric Bapteste
,
John Dupre
Journal articles
hal-01544796v1
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Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly
Debashish Bhattacharya
,
Dana C. Price
,
Cedric Bicep
,
Eric Bapteste
,
Mihir Sarwade
et al.
Journal articles
istex
hal-01544797v1
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In Situ Gene Mapping of Two Genes Supports Independent Evolution of Sex Chromosomes in Cold-Adapted Antarctic Fish
Laura Ghigliotti
,
C. -H. Christina Cheng
,
Celine Bonillo
,
Jean-Pierre Coutanceau
,
Eva Pisano
et al.
Journal articles
hal-01544911v1
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Is the Species Flock Concept Operational? The Antarctic Shelf Case
Guillaume Lecointre
,
Nadia Améziane
,
Marie-Catherine Boisselier
,
Céline P Bonillo
,
Frederic Busson
et al.
Journal articles
mnhn-02921889v1
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Evolutionary analyses of non-genealogical bonds produced by introgressive descent
Eric Bapteste
,
Philippe Lopez
,
Frederic Bouchard
,
Fernando Baquero
,
James O. Mcinerney
et al.
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (45), pp.18266-18272. ⟨10.1073/pnas.1206541109⟩
Journal articles
hal-01544803v1
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Evolution of genetic diversity using networks: the human gut microbiome as a case study
E. Bapteste
,
C. Bicep
,
P. Lopez
Journal articles
hal-01544804v1
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Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns
Eric Bapteste
,
Frederic Bouchard
,
Richard M. Burian
Anisimova, M. EVOLUTIONARY GENOMICS: STATISTICAL AND COMPUTATIONAL METHODS, VOL 2, 856 (2), HUMANA PRESS INC, pp.81-110, 2012, Methods in Molecular Biology, 978-1-61779-584-8. ⟨10.1007/978-1-61779-585-5_4⟩
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