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Patrice Baa-Puyoulet

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At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica

François Renoz , Vincent Foray , Jérôme Ambroise , Patrice Baa-Puyoulet , Bertrand Bearzatto et al.
Frontiers in Cellular and Infection Microbiology, 2021, 11, pp.660007. ⟨10.3389/fcimb.2021.660007⟩
Journal articles hal-03297041v1
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The transposable element-rich genome of the cereal pest Sitophilus oryzae

Nicolas Parisot , Carlos Vargas-Chávez , Clément Goubert , Patrice Baa-Puyoulet , Severine Balmand et al.
BMC Biology, 2021, 19 (1), pp.1-29. ⟨10.1186/s12915-021-01158-2⟩
Journal articles hal-03432029v1

At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica

Vincent Foray , François Renoz , Jérôme Ambroise , Patrice Baa-Puyoulet , Bertrand Bearzatto et al.
Frontiers in Cellular and Infection Microbiology, 2021, 11, ⟨10.3389/fcimb.2021.660007⟩
Journal articles hal-03562624v1
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Draft Genome Sequences of Two Cultivable Strains of the Bacterial Symbiont Serratia symbiotica

François Renoz , Jérôme Ambroise , Bertrand Bearzatto , Patrice Baa-Puyoulet , Federica Calevro et al.
Microbiology Resource Announcements, 2020, 9 (10), pp.e01579-19. ⟨10.1128/MRA.01579-19⟩
Journal articles hal-02505875v1
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The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Claude Rispe , Fabrice Legeai , Paul Nabity , Rosa Fernández , Arinder Arora et al.
BMC Biology, 2020, 18 (1), pp.90. ⟨10.1186/s12915-020-00820-5⟩
Journal articles hal-02917617v1
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Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera

Jan Philip Oeyen , Patrice Baa-Puyoulet , Joshua Benoit , Leo Beukeboom , Erich Bornberg-Bauer et al.
Genome Biology and Evolution, 2020, 12 (7), pp.1099-1118. ⟨10.1093/gbe/evaa106⟩
Journal articles hal-02618254v1
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Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth

Jessika Consuegra , Théodore Grenier , Patrice Baa-Puyoulet , Isabelle Rahioui , Houssam Akherraz et al.
PLoS Biology, 2020, 18 (3), pp.e3000681. ⟨10.1371/journal.pbio.3000681⟩
Journal articles hal-02919023v1
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Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Kristen Panfilio , Iris Vargas Jentzsch , Joshua Benoit , Deniz Erezyilmaz , Yuichiro Suzuki et al.
Genome Biology, 2019, 20 (1), pp.64. ⟨10.1186/s13059-019-1660-0⟩
Journal articles hal-02139052v1
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Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum

Stefano Colella , Nicolas Parisot , Pierre Simonet , Karen Gaget , Gabrielle Duport et al.
Frontiers in Physiology, 2018, 9, pp.1498. ⟨10.3389/fphys.2018.01498⟩
Journal articles hal-01905508v1
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Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford et al.
Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩
Journal articles hal-01500475v1
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Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford et al.
Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩
Journal articles hal-01588181v1
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ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods

Patrice Baa-Puyoulet , Nicolas Parisot , Gérard Febvay , Jaime Huerta-Cepas , Augusto F Vellozo et al.
Database - The journal of Biological Databases and Curation, 2016, pp.1-9. ⟨10.1093/database/baw081⟩
Journal articles hal-01352558v1
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Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development

Andréane Rabatel , Gérard Febvay , Karen Gaget , Gabrielle Duport , Patrice Baa-Puyoulet et al.
BMC Genomics, 2013, 14 (1), pp.235. ⟨10.1186/1471-2164-14-235⟩
Journal articles hal-00824527v1
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CycADS: an annotation database system to ease the development and update of BioCyc databases.

Augusto F Vellozo , Amélie S Véron , Patrice Baa-Puyoulet , Jaime Huerta-Cepas , Ludovic Cottret et al.
Database - The journal of Biological Databases and Curation, 2011, 2011, pp.bar008. ⟨10.1093/database/bar008⟩
Journal articles hal-00632965v1

Intégration de données multi-omiques pour l’identification d’enzymes clés du métabolisme lipidique chez l’espèce sentinelle Gammarus fossarum

Natacha Koenig , Patrice Baa-Puyoulet , Maxime Leprêtre , Jean-Charles Gaillard , J. Armengaud et al.
GDR Ecotoxicologie, Nov 2021, Rennes, France
Conference papers hal-03810311v1

Analysis of the inhibitor of aPoptosis (IAP) repertoire in insects reveals a complex pattern of gene losses and amplifications

Mélanie Ribeiro Lopes , Jousselin Emmanuelle , Patrice Baa-Puyoulet , C. Huygens , Karen Gaget et al.
Incontri di diversità delle forme e degli animali, Università di Pisa, 2021, Pisa, Italy
Conference papers hal-03514196v1

The challenge of annotating and reconstructing metabolic networks for the comprehension of the physiology of aphids and other insects

Hubert Charles , Patrice Baa-Puyoulet
2. Annual meeting of Japan-France Plant-Insect-Symbiont Interaction network (PISI-net), Nov 2019, Le Rheu, France
Conference papers hal-03513078v1

Bacteriocyte reprogramming to cope with nutritional stress in a phloem sap feeding hemipteran, the pea aphid Acyrthosiphon pisum

Nicolas Parisot , Stefano Colella , Mélanie Ribeiro Lopes , Karen Gaget , Marie-Gabrielle Duport et al.
International Partner Days, Oct 2018, Villeurbanne (INSA-Lyon), France
Conference papers hal-03514034v1

Bacteriocyte reprogramming to cope with nutritional stress in a phloem sap feeding hemipteran, the pea aphid Acyrthosiphon pisum

Nicolas Parisot , Mélanie Ribeiro Lopes , Karen Gaget , Marie-Gabrielle Duport , Patrice Baa-Puyoulet et al.
France-Israel PRC Meeting – The role of metabolic interactions in shaping the bacterial endosymbiotic community of Hemyptera, Nov 2018, Villeurbanne, France
Conference papers hal-03514051v1

Atelier Bases de données génomiques et métaboliques : présentation des bases BioCyc développées dans l’UMR BF2I

Hubert Charles , Patrice Baa-Puyoulet
11ème Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA),, Nov 2018, Rennes, France
Conference papers hal-03510598v1

AphidCyc, une collection de bases de données métaboliques dédiée à l'étude et la comparaison du métabolisme chez les pucerons

Patrice Baa-Puyoulet , Hubert Charles , Federica Calevro
11ème Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), Nov 2018, Rennes, France
Conference papers hal-03510642v1

Rôle clé du bactériocyte dans la résilience du puceron aux stress nutritionnels

Federica Calevro , Nicolas Parisot , Mélanie Ribeiro Lopes , Stefano Colella , Karen Gaget et al.
11ème Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), Nov 2018, Rennes, France
Conference papers hal-03514026v1

Effecteurs et inhibiteurs de l’apoptose chez le puceron du pois : annotation et implication dans la mort cellulaire bactériocytaire

Mélanie Ribeiro Lopes , Pierre Simonet , Karen Gaget , Marie-Gabrielle Duport , Severine Balmand et al.
10. Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), Nov 2017, Colmar, France
Conference papers hal-03506807v1

Life history traits and tissue-specific gene expression changes underlying the symbiotic pea aphid resilience to a tyrosine and phenylalanine depleted diet

Nicolas Parisot , Pierre Simonet , Karen Gaget , Marie-Gabrielle Duport , Patrice Baa-Puyoulet et al.
9. Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), Nov 2016, Amiens, France
Conference papers hal-03506796v1

Systems biology of symbiosis: from partners’ genomics to physiology of interactions

Hubert Charles , Federica Calevro , Gérard Febvay , Patrice Baa-Puyoulet , Marie-Gabrielle Duport et al.
First Meeting of the PRC Israel-France, Sep 2016, Villeurbanne, France
Conference papers hal-03506791v1
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From SymbAphidBase to SymbAphidCyc: two companion databases to study and compare aphid symbionts from genomes to metabolic pathways

Patrice Baa-Puyoulet , Mathieu Labernardiere , Nicolas Parisot , Jean-Pierre Gauthier , Gérard Febvay et al.
JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Université d'Auvergne - Clermont-Ferrand I (UdA). FRA., Jul 2015, Clermont-Ferrand, France. 1 p
Conference papers hal-01208786v1

SymbAphidBase : une base de données nouvelle dédiée aux symbiotes de pucerons pour stocker et visualiser les génomes séquencés en standardisant leurs annotations

Mathieu Labernardiere , Patrice Baa-Puyoulet , Jean-Pierre Gauthier , Gérard Febvay , Federica Calevro et al.
7. Rencontres du réseau Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). Le Rheu, FRA., Nov 2014, Avignon, France. 1 p
Conference papers hal-01208785v1

Symbiose puceron – Buchnera : approche métabolomique chez Acyrthosiphon pisum

Marjolaine Rey , Floriant Bellvert , Marie-Gabrielle Duport , Patrice Baa-Puyoulet , Federica Calevro et al.
6èmes journées du Réseau BAPOA (Biologie Adaptative des Pucerons et Organismes Associés, Oct 2013, Montpellier, France
Conference papers hal-03506758v1

Analyse métabolomique de la symbiose entre le puceron Acyrthosiphon pisum et la bactérie Buchnera aphidicola

Marjolaine Rey , Floriant Bellvert , Marie-Gabrielle Duport , Patrice Baa-Puyoulet , Federica Calevro et al.
7èmes Journées Scientifiques du Réseau Français de Métabolomique et Fluxomique, Jun 2013, Amiens, France
Conference papers hal-03506751v1

The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

Patrice Baa-Puyoulet , Augusto F. Vellozo , Jaime Huerta-Cepas , Gérard Febvay , Toni Gabaldon et al.
13. Journées Ouvertes en Biologie, Informatique et Mathématiques, Institut National de Recherche en Informatique et en Automatique (INRIA). Rennes, FRA., Jul 2012, Rennes, France. Pagination multiple
Conference papers hal-02747415v1

ArthropodaCyc: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Patrice Baa-Puyoulet , Augusto F Vellozo , Jaime Huerta-Cepas , Gérard Febvay , T. Gabaldon et al.
5th Annual Arthropod Genomics Symposium "Arthropod Genomics 2011: Exploring Diversity, Relating Similarity", Jun 2011, Kansas City, United States
Conference papers hal-00748601v1

Integration of metabolic pathways and host regulation in symbiosis: tyrosine and cuticular protein biosynthesis during the pea aphid embryonic development

Andréane Rabatel , Gérard Febvay , Karen Gaget , Gabrielle Duport , Nadia Bendridi et al.
Sixth International Symposium on Molecular Insect Science, 2011, Amsterdam, Netherlands
Conference papers hal-00748785v1

Exploration génomique et fonctionnelle des insectes et de leurs partenaires symbiotiques

Hubert Charles , Stefano Colella , Federica Calevro , Gérard Febvay , Yvan Rahbé et al.
Journée Sciences Croisées "Modélisation et Sciences Numériques : nouveaux instruments et opportunités", Institut National des Sciences Appliquées de Lyon (INSA Lyon). Conseil Scientifique de l'INSA, Villeurbanne, FRA., Oct 2010, Villeurbanne, France. n. p
Conference papers hal-02804281v1

CycADS: an annotation management system for the development and update of BioCyc metabolic network databases

A. Vellozo , Patrice Baa-Puyoulet , A. Veron , Jaime Huerta-Cepas , Ludovic Cottret et al.
1st International Workshop on Information Systems for Insect Pests, Rennes, FRANCE, 2009, France
Conference papers hal-00496032v1

High-throughput genomics and transcriptomics to decipher host-symbiont molecular dialogue in the cereal weevil Sitophilus oryzae andSodalis pierantonius endosymbiotic association

Nicolas Parisot , Mariana Galvão Ferrarini , Clément Goubert , Carlos Vargas-Chávez , Agnès Vallier et al.
ISS 2022 - 10th Congress of the International Symbiosis Society, Jul 2022, Lyon, France
Conference poster hal-03810657v1

From genomes to metabolism reconstruction: companion collections of databases to study symbiotic interactions between insects and their bacterial symbionts.

Patrice Baa-Puyoulet , Nicolas Parisot , Sergio Peignier , Federica Calevro , Hubert Charles et al.
12. Rencontre du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), May 2022, Nice, France
Conference poster hal-03810352v1

From genomes to metabolism reconstruction: companion collections of databases to study symbiotic interactions between insects and their bacterial symbionts

Patrice Baa-Puyoulet , Nicolas Parisot , Sergio Peignier , Federica Calevro , Hubert Charles et al.
13. Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), 2020, Nice (virtuel), France
Conference poster hal-03514174v1

Bacteriocyte reprogramming to maintain organismal homeostasis under nutritional stress in aphid symbiosis

Nicolas Parisot , Stefano Colella , Pierre Simonet , Karen Gaget , Marie-Gabrielle Duport et al.
UK-France joint Meeting Aphid Special Interest Group – BAPOA, Apr 2019, Rothamsted, United Kingdom
Conference poster hal-03513048v1

Bacteriocyte reprogramming to cope with nutritional stress in a phloem sap feeding hemipteran, the pea aphid Acyrthosiphon pisum

Nicolas Parisot , Mélanie Ribeiro Lopes , Karen Gaget , Marie-Gabrielle Duport , Patrice Baa-Puyoulet et al.
UK-France joint Meeting Aphid Special Interest Group – BAPOA, Apr 2019, Harpenden, United Kingdom
Conference poster hal-03741333v1

Evaluating the essentiality of the primary endosymbiont of the rice weevil Sitophilus oryzae through genome analysis

Carlos Vargas-Chavez , Nicolas Parisot , C. Goubert , Patrice Baa-Puyoulet , Severine Balmand et al.
VI Meeting of the Spanish Society for Evolutionary Biology (SESBE), Jan 2018, Palma de Mallorca, Spain
Conference poster hal-03514015v1

Bacteriocyte reprogramming to maintain organismal homeostasis under nutritional stress in aphid symbiosis

Nicolas Parisot , Stefano Colella , Pierre Simonet , Karen Gaget , Marie-Gabrielle Duport et al.
XIth European Congress of Entomology, Jul 2018, Naples, Italy
Conference poster hal-03509885v1

The draft genome sequence of the rice weevil Sitophilus oryzae as a model to explore the host-symbiont interactions in a nascent stage of endosymbiosis

Carlos Vargas-Chavez , Nicolas Parisot , Clément Goubert , Patrice Baa-Puyoulet , Severine Balmand et al.
Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Jun 2016, Lyon, France
Conference poster hal-03506786v1
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SymbAphidBase: a new database dedicated to aphid symbionts to store novel sequenced genomes and standardize their annotations

Mathieu Labernardiere , Patrice Baa-Puyoulet , Jean-Pierre Gauthier , Gérard Febvay , Federica Calevro et al.
13. European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. , 1 p., 2014
Conference poster hal-02798649v1
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Annotating arthropods genome to study and compare their metabolism: the ArthropodaCyc collection of Cyc databases powered by CycADS

Patrice Baa-Puyoulet , Augusto Vellozo , Jaime Huerta-Cepas , Gérard Febvay , Federica Calevro et al.
13. European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. , 1 p., 2014
Conference poster hal-02798101v1

The CycADS annotation database system to support the development and update of enriched BioCyc databases: development of ad hoc BioCyc DB (AcypiCyc, ArthropodaCyc

Patrice Baa-Puyoulet , Augusto Vellozo , Jaime Huerta-Cepas , Gérard Febvay , Federica Calevro et al.
8. Meeting of the International Aphid Genomics Consortium, Jan 2013, Harpenden, United Kingdom
Conference poster hal-03506707v1

« ArthropodaCyc » : une collection de bases de données enrichies à l’aide de CycADS pour étudier et comparer le métabolisme des arthropodes.

Patrice Baa-Puyoulet , Stefano Colella , Augusto Vellozo , Jaime Huerta-Cepas , Gérard Febvay et al.
17. Colloque de Biologie de l’Insecte - CBI-2013, Oct 2013, Montpellier, France
Conference poster hal-03506713v1

The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

Patrice Baa-Puyoulet , Augusto Vellozo , Jaime Huerta-Cepas , Gérard Febvay , Toni Gabaldon et al.
5. Réunion Réseau BAPOA, Nov 2012, Villeurbanne, France. 2012
Conference poster hal-02806092v1

“ArthropodaCyc”: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Patrice Baa-Puyoulet , Augusto Vellozo , Jaime Huerta-Cepas , Gérard Febvay , Toni Gabaldon et al.
5. Annual Arthropod Genomics Symposium “Arthropod Genomics 2011: Exploring Diversity, Relating Similarity”, Jun 2011, Kansas City, United States. , 33 p., 2011, Fifth Annual Arthropod Genomics Symposium
Conference poster hal-02749029v1

Integration of metabolic pathways and host regulation in symbiosis: tyrosine and cuticular protein biosynthesis during the pea aphid embryonic development

Andréane Rabatel , Gérard Febvay , Karen Gaget , Marie-Gabrielle Duport , Nadia Bendridi et al.
4. Réunion Réseau BAPOA, Nov 2011, Paris, France. 1 p., 2011
Conference poster hal-02805925v1

Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

Patrice Baa-Puyoulet , Augusto Vellozo , Jaime Huerta-Cepas , Gérard Febvay , Toni Gabaldon et al.
Rencontres bioinformaticiens et statisticiens de l’INRA, Mar 2011, Versailles, France. 1 p., 2011
Conference poster hal-02806205v1

Integration of metabolic pathways and host regulation in symbiosis: tyrosine and cuticular protein biosynthesis during the pea aphid embryonic development

Andréane Rabatel , Gérard Febvay , Karen Gaget , Marie-Gabrielle Duport , Nadia Bendridi et al.
6. International Symposium on Molecular Insect Science, Oct 2011, Amsterdam, Netherlands. Elsevier, 2011,  
Conference poster hal-02747829v1
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A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources

Fabrice Legeai , Stefano Colella , Jaime Huerta-Cepas , Jean-Pierre Gauthier , Augusto Vellozo et al.
10. Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom. 1 p., 2010
Conference poster hal-01231276v1

Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

Augusto Vellozo , Patrice Baa-Puyoulet , Jaime Huerta-Cepas , Gérard Febvay , Federica Calevro et al.
4. Annual Arthropod Genomics Symposium on “Arthropod Genomics: New Approaches and Outcomes”, Jun 2010, Kansas City, United States. 45 p., 2010, Fourth Annual Arthropod Genomics Symposium
Conference poster hal-02753908v1