Hélène Chiapello
Présentation
Professional experience • INRAE: research engineer in microbial bioinformatics at the Microbiology and the food chain (MICA) scientific division, MaIAGE (Applied Mathematics and Computer Science, from Genomes to Environment) research unit, INRAE Jouy-en-Josas, France • SFBI (French Society of Bioinformatics): member of the board (2014-2020) and deputy president (2016-2020) • IFB (French Institute of Bioinformatics): co-coordinator of Training (since 2017), member of the steering committee ( 2020-2023) • DUBii (University Diploma in Integrative Bioinformatics): Co-head of the diploma (2018, 2019, 2020) Education • 2016: HDR - Paul Sabatier university (Toulouse 3) • 1999: PhD - Pierre & Marie Curie university (Paris 6) • 1990: Master in Biochemistry - Pierre & Marie Curie university (Paris 6)
Publications
Publications
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Community detection in a plant-based fermentation knowledge graphFOODSIM 2026 - 14th biennial FOODSIM'2026, EUROSIS, Apr 2026, Gand, Belgium |
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Feedback from EvoGT LEGO - Journées du GDR BIMMM, GDR BIMMM, Nov 2025, Nantes, France |
Unveiling Integrative Conjugative Elements: detection and annotation in Bacillota genomesINTERNATIONAL CONFERENCE ON TYPE IV SECRETION SYSTEM, Feb 2025, Nancy, France |
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Prevalence and diversity of Integrative and Conjugative or Mobilizable Elements carrying antimicrobial resistance genes in Streptococcus suisInternational Conference on type IV secretion system, UMR1128 DynAMic; PROPULS', Feb 2025, Nancy, France |
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IFB/ELIXIR-FR, the french node of ELIXIRISMB ECCB 2023, International Society for Computational Biology, Jul 2023, Lyon, France |
EMERGEN-BioInfo The digital platform for the French SARS-CoV-2 genomic surveillance and research programJOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. ⟨10.5281/ZENODO.6778707⟩ |
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ICEscreen: a valuable tool for automatic detection of ICEs and IMEs in FirmicutesRéunion du GDR3546 Eléments transposables, Dec 2022, Paris, France |
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Microbial transfers at the crossroads of agro-ecological transitions in dairy systemsCarrefours de l’innovation agronomique (CIAG) Les indicateurs de qualité des sols et leur usage dans un contexte de transitions agricoles, Nov 2022, Orléans, France |
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Mobile Genetic Elements transferring by conjugation in the human commensal bacterium Streptococcus salivarius: abundance, diversity and role in the adaptation to environment.Réunion du GDR3546 Eléments transposables, Dec 2021, Paris, France |
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A workflow to build a relevant and reduced bacterial dataset from NCBIJOBIM : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France |
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The ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus.8th symposium on Antimicrobial Resistance in Animal and Environment, Jul 2019, Tours, France |
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Evolution et co-évolution des petits ARNs régulateurs et des gènes codants chez les bactériesANSES - Séminaire DEBUG, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES). FRA., Jun 2018, Toulouse, France |
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Integrating Tara oceans data sets using multiple kernels15th European Conference on Computational Biology (ECCB 2016), Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2016, The Hague, Netherlands. pp.3 |
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Evolution of the pan-secretome among lineages of Magnaporthe oryzae attacking different host-plants27. Fungal Genetics Conference, Mar 2013, Asilomar, United States. pp.281 |
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Genome evolution of fungal pathogens from the Magnaporthe oryzae/grisea clade.27 Fungal Genetics Conference, Mar 2013, Asilomar, United States. p.76 |
Genomic comparison within Xenorhabdus genus: X. poinarii species characterized by a small genome and attenuated virulence toward insects5. Congress of European Microbiologists (FEMS 2013), Jul 2013, Leipzig, Allemagne |
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Deciphering why <em>Salmonella</em> Gallinarum is less invasive in vitro than <em>Salmonella</em> EnteritidisI3S International Symposium Salmonella and Salmonellosis, Institut National de la Recherche Agronomique (INRA). FRA., May 2013, Saint Malo, France |
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GEMO project: Genetic bases of pathogenicity and host specificity analyzed through comparative and evolutionary genomics in the model fungus Magnaporthe9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.82-82 |
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The GEMO project: Analysis and comparison of genomes of the fungal pathogen Magnaporthe oryzaeJOBIM-Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.379-380 |
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Alignement de génomes bactériens : méthodes, évaluation et exemples d'applications.Seminaire IRISA ( Symbiose ), Jan 2012, Rennes, France |
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Evaluation et comparaison de logiciels de visualisation et d’exploration de génomesSeminaire Institut Pasteur, 2011, Paris, France |
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Comparaison et annotation de 9 génomes de MagnaportheRéunion du groupe Champignons du REID, Nov 2011, Paris, France |
Genomic diversity of 24 Propionibacterium freudenreichii 1 strains6 Conference on Functional Genomics of Gram-positive Microorganisms 16 International Conference on Bacilli, Jun 2011, Montecatini, Italy |
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The GEMO project: Analysis and comparison of genomes of the fungal pathogen Magnaporthe oryzaeConférence EMBO, Nov 2011, Sant Feliu de Guixols, Spain. pp.1 |
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GEMO: an innovative project on Evolutionary Genomics of Magnaporthe oryzae8. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2010, Aussois, France |
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Evaluating Genome Browsers Using a Software Qualification Method EvaluationJOBIM 2010, Sep 2010, Montpellier, France. pp.196 |
Assessing the robustness of complete bacterial genomeRECOMB-CG 2010, Oct 2010, Ottawa, Canada. ⟨10.1007/978-3-642-16181-0_15⟩ |
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Comparison and evolution of closely related genomes: methods and examples of applications in bacteria and fungiSéminaire du LIPM, Institut National de Recherche Agronomique (INRA). UMR Interactions Plantes - Microorganismes (0441)., Nov 2010, Toulouse, France |
Web services for microbial genome annotation using data integrationJOBIM 2010 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France |
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Origine des Spécificités Phénotypiques de la Levure œnologique a travers une Approche GénomiqueJOBIM 2010 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France. pp.184 |
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Improved sensitivity and reliability of anchor based genome alignmentJOBIM - Journées Ouvertes en Biologie Informatique Mathématiques2009 - Nantes :, Jun 2009, Nantes, France. 259 p |
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How to measure the robustness of bacterial genome comparisons?10èmes Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2009, Nantes, France. pp.257 |
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Improved Sensitivity And Reliability Of Anchor Based Genome AlignmentJOBIM 2009 - 10es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36 |
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BReIF: une e-infrastructure pour accélérer l'utilisation de ressources biologiques diversifiéesTrans Numériques 2026, Feb 2026, Rennes, France. |
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IFB/ELIXIR-FR contributions to the ELIXIR Training Platform ProgrammeJOBIM 2025, Jul 2025, Bordeaux, France |
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Intra-species diversity in metagenomic datasetsJOBIM 2024, Jun 2024, Toulouse, France. , 2024 |
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To the species level and beyond A rationalized approach to study pangenomesJournées Ouvertes de Biologie, Informatique et Mathématiques 2024, Jun 2024, Toulouse, France. , Nextcloud, https://nextcloud.inrae.fr/s/An986qpn6CqCQek |
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Understanding taxonomic diversity and functional signatures of fermented vegetables microbiomeFood System Microbiomes, May 2024, Torino, Italy. |
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A Unix competency framework for learning bioinformaticsJOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France. |
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Design and production of a plug-in tool facilitating the submission of microbial meta-omics data to an international repositoryJOBIM 2023, Jun 2023, Nancy, France. |
Factors contributing to the prevalence of Integrative and Conjugative or Mobilizable Elements carrying antimicrobial resistance genes in Streptococcus suis5th International Workshop on Streptococcus suis, Jun 2023, Bangkok / Thailand, Thailand |
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Abundance and diversity of Mobile Genetic Elements carrying antibiotic resistance genes and transferring by conjugation in the human commensal bacterium Streptococcus salivarius.5th International Caparica Congress in Antibiotic Resistance (IC2AR 2022), Sep 2022, Caparica, Lisbon, Portugal |
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Precise detection of antibiotic resistance genes in chicken microbiotaJournées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM - colloque virtuel, Jul 2021, Paris, France. |
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The IFB e-Learning Working GroupJOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques) 2021, Jul 2021, Paris, France. |
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Characterization of the genomic diversity and gene content of a lactobacilli collectionJOBIM 2021, Jul 2021, Paris, France. |
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2020, Montpellier, France. 2020 |
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Plateforme bioinformatique MIGALEJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2019, Nantes, France. 2019 |
The ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus4th International Workshop on Streptococcus suis, Jun 2019, Montréal, Canada. |
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Whole metagenome analysis with metagWGSJOBIM 2019, Jul 2019, Nantes, France. , 2019 |
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Groupe de travail sur les Métiers de la Bioinformatique (MetBIF)JOBIM 2018, Jul 2018, Marseille, France |
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Towards an integrated approach for the annotation of ICEs and IMEs in bacterial genomesJOBIM 2018, Jul 2018, Marseille, France |
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Host tropism and host-pathogen interplay of typhoidal Salmonella entericaJOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. , 2017, Journées Ouvertes en Biologie, Informatique et Mathématiques. JOBIM 2017 |
Investigating mycoplasma small non-coding RNAs using synthetic biology toolsColloque Biologie synthétique et systémique, BioSynSys, Jun 2016, Bordeaux, France. 2016 |
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The GEMO project: Hitchhiking DNA in Magnaporthe oryzaeJOBIM 2015. Meeting of working Group Medicago sativa, Jul 2015, Clermont-Ferrand, France. , 1123 p., 2015 |
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Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of <i>Propionibacterium freudenreichii</i>JOBIM 16. Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015, ⟨10.1186/s12864-015-1467-7⟩ |
Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. , 2015 |
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Comparative analysis of transposable elements in the Magnaporthe oryzae/grisea cladePAG - Plant Animal Genome,, Jan 2013, San Diego, United States. 2013 |
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IGO, Integration from Genomes to OrganismsJOBIM 2013, Jul 2013, Toulouse, France. , pp.246, 2013, JOBIM TOULOUSE 2013 - RÉSUMÉS COURTS (affiches) |
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Distribution and evolution of transposable elements in the Magnaporthe oryzae/grisea clade27. Fungal Genetics Conference, Mar 2013, Asilomar, United States. 2013 |
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Genome evolution of fungal pathoens from Magnaporthe oryzae/grisea clade15. International congress on Molecular plant-microbe interactions, Jul 2012, Kyoto, Japan. , 2012, Poster session 21 - Structural biology |
FAIR training handbook2023 |
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SPiD: a subtilis protein interaction database5 p., 2000 |
Banques et bases de données en biologieBio-Informatique - principes d'utilisation des outils, Editions Quae, 2010 |
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Gene predictionFunctional plant genomics, Science Publishers, 2007, 978-1-57808-506-4 |
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Databases in biologyFunctional Plant Genomics, Science Publishers, 2007, 978-1-57808-506-4 |
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Introduction to bioinformaticsFunctional Plant Genomics, Science Publishers, 2007, 978-1-57808-506-4 |
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Banques et bases de données en biologieLa génomique en biologie végétale, INRA Editions, 2004, Science Update, 2-7380-1167-5 |
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Annotation and databases : status and prospectsDatabase annotation in molecular biology : principles and practice, Wiley, 2004, 978-0-470-85681-9 |
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Prédiction de gènesLa génomique en biologie végétale, INRA Editions, 2004, Science Update, 2-7380-1167-5 |
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Guide simplifié - Gestion des données de vos recherches à l'usage des porteurs de projets2025, ⟨10.17180/0ezn-aq96⟩ |
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Sandbox.bio tutorials – Linux basics training modules (IFB ELIXIR-FR)École thématique. France. 2026 |