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Philippe Lopez

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The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes

Shifu Aggarwal , Elaine Huang , Hackwon Do , Nishanth Makthal , Yanyan Li
Nature Communications, 2023, 14 (1), pp.5947. ⟨10.1038/s41467-023-41719-3⟩
Journal articles hal-04247659v1
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Interactomics: dozens of viruses, co-evolving with humans, including the influenza A virus, may actively distort human ageing

Jérôme Teulière , Charles Bernard , Hugo Bonnefous , Johannes Martens , Philippe Lopez
Molecular Biology and Evolution, 2023, ⟨10.1093/molbev/msad012⟩
Journal articles hal-03952038v1
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Aging at Evolutionary Crossroads: Longitudinal Gene Co-expression Network Analyses of Proximal and Ultimate Causes of Aging in Bats

Guillaume Bernard , Jérôme Teulière , Philippe Lopez , Eduardo Corel , François-Joseph Lapointe
Molecular Biology and Evolution, 2022, 39 (1), ⟨10.1093/molbev/msab302⟩
Journal articles hal-03820627v1
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Network analyses unveil ageing-associated pathways evolutionarily conserved from fungi to animals

Jérôme Teulière , Charles Bernard , Eduardo Corel , François-Joseph Lapointe , Johannes Martens
Journal articles hal-03917351v1
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Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome

Andrew Watson , Philippe Lopez , Eric Bapteste
Molecular Biology and Evolution, 2022, 39 (1), pp.msab329. ⟨10.1093/molbev/msab329⟩
Journal articles hal-03820636v1
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Proximate Drivers of Population-Level Lizard Gut Microbial Diversity: Impacts of Diet, Insularity, and Local Environment

Virginie Lemieux-Labonté , Chloé Vigliotti , Zoran Tadic , Beck Wehrle , Philippe Lopez
Microorganisms, 2022, 10 (8), pp.1550. ⟨10.3390/microorganisms10081550⟩
Journal articles hal-03820648v1
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The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View

Eric Bapteste , Philippe Gerard , Catherine Larose , Manuel Blouin , Fabrice Not
Biology, 2021, 10 (7), pp.651. ⟨10.3390/biology10070651⟩
Journal articles hal-03290801v1
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Retracing lineage history: time to emphasize genetic turn-over Authorship

Andrew K Watson , Philippe Lopez , Eric Bapteste
Trends in Microbiology, inPress, ⟨10.1016/j.tim.2021.08.001⟩
Journal articles hal-03341509v1
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Hundreds of out-of-frame remodelled gene families in the E. coli pangenome

Andrew K Watson , Philippe Lopez , Eric Bapteste
Molecular Biology and Evolution, 2021, pp.msab329. ⟨10.1093/molbev/msab329/6430988⟩
Journal articles hal-03451955v1
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Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication

Charles Bernard , Romain Lannes , Yanyan Li , Éric Bapteste , Philippe Lopez
mSystems, 2020, 5 (5), ⟨10.1128/mSystems.00414-20⟩
Journal articles hal-02967400v1
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Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur

Romain Lannes , Louise Cavaud , Philippe Lopez , Eric Bapteste
Genome Biology and Evolution, 2020, 13, ⟨10.1093/gbe/evaa261⟩
Journal articles hal-03380389v1
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Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms

Charles Bernard , Yanyan Li , Philippe Lopez , Eric Bapteste
The International Society of Microbiologial Ecology Journal, 2020, ⟨10.1038/s41396-020-00795-9⟩
Journal articles hal-02967396v1
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Carbon Fixation by Marine Ultrasmall Prokaryotes

Romain Lannes , Karen Olsson-Francis , Philippe Lopez , Eric Bapteste
Genome Biology and Evolution, 2019, 11 (4), pp.1166-1177. ⟨10.1093/gbe/evz050⟩
Journal articles hal-02277606v1
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Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data

Etienne Lord , Jananan S Pathmanathan , Eduardo L Corel , Vladimir Makarenkov , Philippe Lopez
Genome Biology and Evolution, 2019, ⟨10.1093/gbe/evz182⟩
Journal articles hal-02324769v1
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CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection

Jananan Sylvestre Pathmanathan , Philippe Lopez , Francois-Joseph Lapointe , Eric Bapteste
Molecular Biology and Evolution, 2018, 35 (1), pp.252-255. ⟨10.1093/molbev/msx283⟩
Journal articles hal-02057694v1
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Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny

Dominic Evangelista , France Thouzé , Manpreet Kaur Kohli , Philippe Lopez , Frédéric Legendre
Molecular Phylogenetics and Evolution, 2018, 128, pp.112-122. ⟨10.1016/j.ympev.2018.05.007⟩
Journal articles mnhn-02520951v1
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MultiTwin: A Software Suite to Analyze Evolution at Multiple Levels of Organization Using Multipartite Graphs

Eduardo L Corel , Jananan S Pathmanathan , Andrew B. Watson , Slim Karkar , Philippe Lopez
Genome Biology and Evolution, 2018, 10 (10), pp.2777-2784. ⟨10.1093/gbe/evy209⟩
Journal articles hal-01990830v1
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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
BMC Biology, 2018, 16, pp.30. ⟨10.1186/s12915-018-0500-0⟩
Journal articles hal-01761411v1
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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
Molecular Biology and Evolution, 2018, 35 (4), pp.899-913. ⟨10.1093/molbev/msy001⟩
Journal articles hal-01798030v1
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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
Genome Biology and Evolution, 2018, 10 (3), pp.707 - 715. ⟨10.1093/gbe/evy031⟩
Journal articles hal-01799304v1
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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
Genome Biology, 2018, 19, pp.75. ⟨10.1186/s13059-018-1454-9⟩
Journal articles hal-01830047v1
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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
Lingua Sinica, 2017, 3 (1), pp.5. ⟨10.1186/s40655-017-0021-8⟩
Journal articles hal-01555483v1
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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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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
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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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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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
BMC Biology, 2015, 13 (1), pp.16. ⟨10.1186/s12915-015-0125-5⟩
Journal articles hal-01144173v1

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

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

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

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
Bioinformatics, 2013, 29 (7), pp.837-844. ⟨10.1093/bioinformatics/btt049⟩
Journal articles hal-01544795v1

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

Eric Bapteste , Philippe Lopez , Frederic Bouchard , Fernando Baquero , James O. Mcinerney
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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Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

Lucie Bittner , Sébastien Halary , Claude Payri , Corinne Cruaud , Bruno de Reviers
Biology Direct, 2010, 5 (5), pp.47. ⟨10.1186/1745-6150-5-47⟩
Journal articles hal-02922363v1

First hsp70 from two hydrothermal vent shrimps, Mirocaris fortunata and Rimicaris exoculata: characterization and sequence analysis

Juliette Ravaux , Jean-Yves Toullec , Nelly Léger , Philippe Lopez , Françoise Gaill
Gene, 2007, 386, pp.162-172
Journal articles hal-00198962v1

Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes.

Romain Derelle , Philippe Lopez , Hervé Le Guyader , Michaël Manuel
Evolution and Development, 2007, 9 (3), pp.212-219
Journal articles hal-00607197v1