Philippe Lopez

Publications

Article dans une revue (41)

Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes Miguel Gomez-Raya-Vilanova,Jérôme Teulière,Sofia Medvedeva,Yuping Dai,Eduardo Corelet al. Nature Communications, 2025, 16 (1), pp.5697. ⟨10.1038/s41467-025-60613-8⟩ Article dans une revue pasteur-05141107v1
New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean Duncan Sussfeld,Romain Lannes,Eduardo Corel,Guillaume Bernard,Pierre Martinet al. Environmental Microbiome, 2025, 20, pp.65. ⟨10.1186/s40793-025-00697-3⟩ Article dans une revue hal-05347054v1
Interspecific interactions and aging: Prediction of gerogenic bacteria and critical human protein targets of microbial infections Yuping Dai,Ni Boussaguet,Jérôme Teulière,Hugo Bonnefous,Elphège Budzinskiet al. Mechanisms of Ageing and Development, 2025, 226, pp.112076. ⟨10.1016/j.mad.2025.112076⟩ Article dans une revue hal-05347044v1
Gene expression and co-expression heterogeneity patterns and biodemography analyses during the cell cycle encourage aging studies in archaea Yuping Dai,Miguel Gomez-Raya-Vilanova,Jérôme Teulière,Mouhammad Toucourou,Eduardo Corelet al. GeroScience, In press, ⟨10.1007/s11357-025-01769-5⟩ Article dans une revue hal-05347051v1
The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes Shifu Aggarwal,Elaine Huang,Hackwon Do,Nishanth Makthal,Yanyan Liet al. Nature Communications, 2023, 14 (1), pp.5947. ⟨10.1038/s41467-023-41719-3⟩ Article dans une revue hal-04247659v1
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 Lopezet al. Molecular Biology and Evolution, 2023, ⟨10.1093/molbev/msad012⟩ Article dans une revue hal-03952038v1
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⟩ Article dans une revue hal-03820636v1
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 Lopezet al. Microorganisms, 2022, 10 (8), pp.1550. ⟨10.3390/microorganisms10081550⟩ Article dans une revue hal-03820648v1
Network analyses unveil ageing-associated pathways evolutionarily conserved from fungi to animals Jérôme Teulière,Charles Bernard,Eduardo Corel,François-Joseph Lapointe,Johannes Martenset al. GeroScience, 2022, ⟨10.1007/s11357-022-00704-2⟩ Article dans une revue hal-03917351v1
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 Lapointeet al. Molecular Biology and Evolution, 2022, 39 (1), ⟨10.1093/molbev/msab302⟩ Article dans une revue hal-03820627v1
The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View Eric Bapteste,Philippe Gérard,Catherine Larose,Manuel Blouin,Fabrice Notet al. Biology, 2021, 10 (7), pp.651. ⟨10.3390/biology10070651⟩ Article dans une revue hal-03290801v1
Retracing lineage history: time to emphasize genetic turn-over Authorship Andrew K Watson,Philippe Lopez,Eric Bapteste Trends in Microbiology, In press, ⟨10.1016/j.tim.2021.08.001⟩ Article dans une revue hal-03341509v1
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⟩ Article dans une revue hal-03451955v1
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⟩ Article dans une revue hal-02967400v1
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⟩ Article dans une revue hal-03380389v1
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⟩ Article dans une revue hal-02967396v1
Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data Etienne Lord,Jananan S Pathmanathan,Eduardo L Corel,Vladimir Makarenkov,Philippe Lopezet al. Genome Biology and Evolution, 2019, ⟨10.1093/gbe/evz182⟩ Article dans une revue hal-02324769v1
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⟩ Article dans une revue hal-02277606v1
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 Lopezet al. Genome Biology and Evolution, 2018, 10 (10), pp.2777-2784. ⟨10.1093/gbe/evy209⟩ Article dans une revue hal-01990830v1
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⟩ Article dans une revue mnhn-02520951v1
Bipartite Network Analysis of Gene Sharings in the Microbial World Eduardo Corel,Raphaël Méheust,Andrew K Watson,James O Mcinerney,Philippe Lopezet al. Molecular Biology and Evolution, 2018, 35 (4), pp.899-913. ⟨10.1093/molbev/msy001⟩ Article dans une revue hal-01798030v1
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 Lopezet al. Genome Biology, 2018, 19, pp.75. ⟨10.1186/s13059-018-1454-9⟩ Article dans une revue hal-01830047v1
Formation of chimeric genes with essential functions at the origin of eukaryotes Raphaël Méheust,Debashish Bhattacharya,Jananan S Pathmanathan,James O Mcinerney,Philippe Lopezet al. BMC Biology, 2018, 16, pp.30. ⟨10.1186/s12915-018-0500-0⟩ Article dans une revue hal-01761411v1
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⟩ Article dans une revue hal-01799304v1
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⟩ Article dans une revue hal-02057694v1
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⟩ Article dans une revue hal-01555483v1
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⟩ Article dans une revue 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⟩ Article dans une revue hal-01544793v1
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⟩ Article dans une revue hal-01378396v1
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⟩ Article dans une revue hal-01257771v1
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 Romacet al. BMC Biology, 2015, 13 (1), pp.16. ⟨10.1186/s12915-015-0125-5⟩ Article dans une revue 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 Lopezet al. Molecular Biology and Evolution, 2014, 31 (3), pp.501-516. ⟨10.1093/molbev/mst228⟩ Article dans une revue hal-01544794v1
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⟩ Article dans une revue hal-01324848v1
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 Baptesteet al. Molecular Biology and Evolution, 2013, 30 (8), pp.1975-1986. ⟨10.1093/molbev/mst087⟩ Article dans une revue 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⟩ Article dans une revue 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⟩ Article dans une revue 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⟩ Article dans une revue hal-01544795v1
Evolutionary analyses of non-genealogical bonds produced by introgressive descent Eric Bapteste,Philippe Lopez,Frederic Bouchard,Fernando Baquero,James O. Mcinerneyet al. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (45), pp.18266-18272. ⟨10.1073/pnas.1206541109⟩ Article dans une revue hal-01544803v1
Some considerations for analyzing biodiversity using integrative metagenomics and gene networks Lucie Bittner,Sébastien Halary,Claude Payri,Corinne Cruaud,Bruno de Revierset al. Biology Direct, 2010, 5 (5), pp.47. ⟨10.1186/1745-6150-5-47⟩ Article dans une revue hal-02922363v1
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 Article dans une revue hal-00607197v1
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 Gaillet al. Gene, 2007, 386, pp.162-172 Article dans une revue hal-00198962v1

Pré-publication, Document de travail (3)

RRNPP_detector: a tool to detect RRNPP quorum sensing systems in chromosomes, plasmids and phages of gram-positive bacteria Charles Bernard,Yanyan Li,Eric Bapteste,Philippe Lopez 2021 Pré-publication, Document de travail hal-03384406v1
Large-scale identification of viral quorum sensing systems reveals density-dependent sporulation-hijacking mechanisms in bacteriophages Charles Bernard,Yanyan Li,Philippe Lopez,Eric Bapteste 2021 Pré-publication, Document de travail hal-03384404v1
Read networks and k-laminar graphs Finn Völkel,Eric Bapteste,Michel Habib,Philippe Lopez,Chloe Vigliotti 2016 Pré-publication, Document de travail hal-01282715v1

Chapitre d'ouvrage (3)

Microbial Communication Networks: Sketching a Method for Analyzing the Communication of Bacteriophages Inside Environmental Communities Charles Bernard,Philippe Lopez,Eric Bapteste Biocommunication of Phages, Springer International Publishing, pp.163-181, 2020, ⟨10.1007/978-3-030-45885-0_8⟩ Chapitre d'ouvrage hal-02918305v1
The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution Andrew B. Watson,Romain Lannes,Jananan S Pathmanathan,Raphaël Méheust,Slim Karkaret al. Evolutionary Genomics, pp.271-308, 2019, ⟨10.1007/978-1-4939-9074-0_9⟩ Chapitre d'ouvrage hal-02324786v1
Analyse de la diversité microbienne : de la difficulté (paradoxale) de voir large en métagénomique Chloé Vigliotti,Eric Bapteste,Philippe Lopez Biodiversité et Evolution, 2018 Chapitre d'ouvrage hal-02367812v1

Communication dans un congrès (1)

DEM-based model for reconstructing volcano's morphology from primary volcanic landforms Eric Gayer,Philippe Lopez,Laurent Michon EGU 2014, Apr 2014, Vienna, Austria. pp.2014 - 10701 Communication dans un congrès hal-01386609v1