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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.
Nature, 2022, 609 (7928), pp.747-753. ⟨10.1038/s41586-022-05110-4⟩
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.
Evolutionary Genomics, pp.271-308, 2019, ⟨10.1007/978-1-4939-9074-0_9⟩
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.
Genome Biology, 2018, 19, pp.75. ⟨10.1186/s13059-018-1454-9⟩
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.
BMC Biology, 2018, 16, pp.30. ⟨10.1186/s12915-018-0500-0⟩
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.
Genome Biology and Evolution, 2018, 10 (3), pp.707 - 715. ⟨10.1093/gbe/evy031⟩
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.
Molecular Biology and Evolution, 2018, 35 (4), pp.899-913. ⟨10.1093/molbev/msy001⟩
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.
Lingua Sinica, 2017, 3 (1), pp.5. ⟨10.1186/s40655-017-0021-8⟩
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.
eLife, 2017, 6, pp.e23717. ⟨10.7554/eLife.23717⟩
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.
PLoS ONE, 2016, 11 (8), pp.e0161474. ⟨10.1371/journal.pone.0161474⟩
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
Trends in Microbiology, 2016, 24 (3), pp.224-237. ⟨10.1016/j.tim.2015.12.003⟩
Journal articles hal-01300043v1

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
Biology Direct, 2016, 11, pp.39. ⟨10.1186/s13062-016-0145-2⟩
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.
Genome Biology and Evolution, 2015, 7 (10), pp.2941-2954. ⟨10.1093/gbe/evv193⟩
Journal articles hal-01264332v1

Ladybirds from the Mercantour National Park (Coleoptera: Coccinellidae)

Jean-Pierre Coutanceau
Zoosystema, 2015, 37 (1), pp.193-205. ⟨10.5252/z2015n1a9⟩
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.
BMC Biology, 2015, 13 (1), pp.16. ⟨10.1186/s12915-015-0125-5⟩
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
Genome Biology and Evolution, 2015, 7 (2), pp.505-521. ⟨10.1093/gbe/evv002⟩
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
Biology Direct, 2015, 10, pp.64. ⟨10.1186/s13062-015-0092-3⟩
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
Genome Biology and Evolution, 2014, 6 (9), pp.2195-2205. ⟨10.1093/gbe/evu168⟩
Journal articles hal-01324848v1

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.
Molecular Biology and Evolution, 2014, 31 (3), pp.501-516. ⟨10.1093/molbev/mst228⟩
Journal articles hal-01544794v1

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.
Molecular Biology and Evolution, 2013, 30 (8), pp.1975-1986. ⟨10.1093/molbev/mst087⟩
Journal articles hal-01544800v1

EGN: a wizard for construction of gene and genome similarity networks

Sebastien Halary , James O. Mcinerney , Philippe Lopez , Eric Bapteste
BMC Evolutionary Biology, 2013, 13, pp.146. ⟨10.1186/1471-2148-13-146⟩
Journal articles hal-01544799v1

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

MosaicFinder: identification of fused gene families in sequence similarity networks

Pierre-Alain Jachiet , Romain Pogorelcnik , Anne Berry , Philippe Lopez , Eric Bapteste et al.
Bioinformatics, 2013, 29 (7), pp.837-844. ⟨10.1093/bioinformatics/btt049⟩
Journal articles hal-01544795v1

Towards a processual microbial ontology

Eric Bapteste , John Dupre
Biology and Philosophy, 2013, 28 (2, SI), pp.379-404. ⟨10.1007/s10539-012-9350-2⟩
Journal articles hal-01544796v1

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 of Phycology, 2013, 49 (1), pp.207-212. ⟨10.1111/jpy.12028⟩
Journal articles istex hal-01544797v1

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.
BioMed Research International , 2013, pp.243938. ⟨10.1155/2013/243938⟩
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.
PLoS ONE, 2013, 8 (8), pp.e68787. ⟨10.1371/journal.pone.0068787⟩
Journal articles mnhn-02921889v1

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

Evolution of genetic diversity using networks: the human gut microbiome as a case study

E. Bapteste , C. Bicep , P. Lopez
Clinical Microbiology and Infection, 2012, 18 (4, SI), pp.40-43. ⟨10.1111/j.1469-0691.2012.03856.x⟩
Journal articles hal-01544804v1

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⟩
Book sections hal-01544801v1