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36

Marie Lefebvre


Bioinformatics engineer

Location: Bordeaux, France

I am a bioinformatics engineer in the Virology team at INRAE Fruit Biology and Pathology, Bordeaux. I am in charge of the software development for the analysis of high throughput sequencing (HTS) data of phytoviral metagenomics. I set up database and web interface via semantic web technologies.

Background & position

Since October 2017 - Bioinformatics ingineer permanent position at INRAe, Bordeaux, France
Development of virAnnot pipeline for viral metagenomic analyses. Databases and web interfaces development for plant viruses.

October 2020-March 2021 - Long term mission at the Bioinformatics Group, Wageningen University and Research, NL
I was awarded a Staff Exchange Grant from the ELIXIR project to:

  • integrate the virAnnot pipeline in the GALAXY environment to make viral metagenomics analyses easily accessible for all the community
  • develop a method to prioritize the genes of an eQTL region in order to identify more precisely the causal gene affecting trait, see AraQTL

2016-2017 - Bioinformatics ingineer - LS2N Combinatory and Informatic, Nantes, France
Algorithm and web interface development for heterogeneous data integration through linked open data and semantic web (BioPAX model). SyMeTRIC Project

2014-2016 - Bioinformatics ingineer - INRAe Biology of Fruit and Pathology, Bordeaux, France
Database and Web interface development for NMR spectra and metadata. Metabohub Project
Tool integration for Galaxy Workflow4Metabolomics

2014 - Internship - INRA Evolution and quantitative genetic, Paris-Sud, France
R package integration in a web interface for the analysis of wheat varietal selection data. SHiHeMaS Project

Education & training

2021 - IFB open science and PGD (IFB)

2020 - Hackaton Galaxy Interactive Tools (GEOC)

2017 - High-performance computing Course (Bordeaux Computing Center)

2015 - Tools integration for GALAXY (IFB Galaxy group)

2014 - Master’s degree: Bioinformatics (Nantes, France)

2012 - Licence’s degree: Biology, Geosciences, Chemistry (Nantes, france) Option: Environmental Biology


Journal articles15 documents

  • Marie Lefebvre, Alban Gaignard, Maxime Folschette, Jérémie Bourdon, Carito Guziolowski. Large-scale regulatory and signaling network assembly through linked open data. Database - The journal of Biological Databases and Curation, Oxford University Press, 2021, 2021, pp.baaa113. ⟨10.1093/database/baaa113⟩. ⟨hal-03107317v2⟩
  • Laurence Svanella-Dumas, Armelle Marais, Chantal Faure, Marie Lefebvre, Jonathan Gaudin, et al.. First report of lettuce necrotic leaf curl virus infecting cultivated lettuce in France. Plant Disease, American Phytopathological Society, 2021, 105 (4), 1 p. ⟨10.1094/PDIS-11-20-2348-PDN⟩. ⟨hal-03101398⟩
  • Armelle Marais, Sergio Murolo, Chantal Faure, Yoann Brans, Clement Larue, et al.. Sixty years from the first disease description, a novel badnavirus associated with chestnut mosaic disease. Phytopathology, American Phytopathological Society, 2021, 111 (6), pp.1051-1058. ⟨10.1094/PHYTO-09-20-0420-R⟩. ⟨hal-03036205⟩
  • Yuxin Ma, Tania Fort, Armelle Marais, Marie Lefebvre, Sébastien Theil, et al.. Leaf‐associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Plant-Environment Interactions, 2021, 2, pp.87-99. ⟨10.1002/pei3.10043⟩. ⟨hal-03182663⟩
  • Denis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, et al.. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms, MDPI, 2021, 9 (4), pp.841. ⟨10.3390/microorganisms9040841⟩. ⟨hal-03200602⟩
  • Yuxin Ma, Laurence Svanella-Dumas, Charlotte Julian, Serge Galzi, Emmanuel Fernandez, et al.. Genome characterization and diversity of trifolium virus 1: identification of a novel legume-infecting capulavirus. Archives of Virology, Springer Verlag, 2021, 166 (9), pp.2573-2578. ⟨10.1007/s00705-021-05135-6⟩. ⟨hal-03271050⟩
  • Jean-Sébastien Reynard, Justine Brodard, Eric Remoliff, Marie Lefebvre, Olivier Schumpp, et al.. A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris). Archives of Virology, Springer Verlag, 2020, 165 (12), pp.2999 - 3002. ⟨10.1007/s00705-020-04817-x⟩. ⟨hal-02983032⟩
  • Yuxin Ma, Armelle Marais, Marie Lefebvre, Chantal Faure, Thierry Candresse. Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum. Virology, Elsevier, 2020, 540, pp.38-44. ⟨10.1016/j.virol.2019.11.009⟩. ⟨hal-02625134⟩
  • Yuxin Ma, Armelle Marais, Marie Lefebvre, Sébastien Theil, Laurence Svanella-Dumas, et al.. Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches.. Journal of Virology, American Society for Microbiology, 2020, 94 (1), pp.e01462-9. ⟨10.1128/JVI.01462-19⟩. ⟨hal-02628250⟩
  • Thierry Candresse, Armelle Marais, Chantal Faure, Marie Lefebvre, Thierry Lacombe, et al.. Complete genome sequence of a novel grapevine-infecting member of the genus Polerovirus, grapevine polerovirus 1. Archives of Virology, Springer Verlag, 2020, 165 (7), pp.1683-1685. ⟨10.1007/s00705-020-04640-4⟩. ⟨hal-02565509⟩
  • Armelle Marais, Chantal Faure, Marie Lefebvre, Thierry Lacombe, Jean-Michel Boursiquot, et al.. Molecular diversity of grapevine Kizil Sapak virus and implications for its detection. Archives of Virology, Springer Verlag, 2020, 165, pp.1849-1853. ⟨10.1007/s00705-020-04673-9⟩. ⟨hal-02749957⟩
  • Laurence Svanella-Dumas, Armelle Marais, Flora Depasse, Marie Lefebvre, Yoann Brans, et al.. First report of Citrus virus A (CiVA) infecting pear (Pyrus communis) in France. Plant Disease, American Phytopathological Society, 2019, 103 (10), pp.2703. ⟨10.1094/PDIS-01-19-0028-PDN⟩. ⟨hal-02620798⟩
  • Marie Lefebvre, Sébastien Theil, Yuxin Ma, Thierry Candresse. The VirAnnot pipeline: a resource for automated viral diversity estimation and operational taxonomy units (OTU) assignation for virome sequencing data. Phytobiomes Journal, APS Publications, 2019, ⟨10.1094/PBIOMES-07-19-0037-A⟩. ⟨hal-02628298⟩
  • Laurence Svanella-Dumas, Armelle Marais, Chantal Faure, Sébastien Theil, Marie Lefebvre, et al.. Genome characterization of a divergent isolate of the mycovirus Botrytis virus F from a grapevine metagenome.. Archives of Virology, Springer Verlag, 2018, 163 (11), pp.3181-3183. ⟨10.1007/s00705-018-3975-7⟩. ⟨hal-02621857⟩
  • Daniel Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Annick Moing. NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. Metabolomics, Springer Verlag, 2017, 13 (4), pp.36. ⟨10.1007/s11306-017-1178-y⟩. ⟨hal-01606304⟩

Conference papers4 documents

  • Yuxin Ma, Armelle Marais, Marie Lefebvre, Sébastien Theil, Laurence Svanella-Dumas, et al.. Comparison of double-stranded RNA (dsRNA) and Virion-associated nucleic acids (VANA) targets for high-throughput sequencing analysis of phytoviral metagenomes. 17. Rencontres de Virologie Végétale (RVV 2019), Jan 2019, Aussois, France. ⟨hal-02737920⟩
  • Marie Lefebvre, Jérémie Bourdon, Carito Guziolowski, Alban Gaignard. Regulation and signalization graph assembly through Linked Open Data. JOBIM 2017, Jul 2017, Lille, France. ⟨hal-01768420⟩
  • Nils Paulhe, Pierrick Roger, Marie-Françoise Olivier, Marie Lefebvre, Christophe Duperier, et al.. PeakForest: a spectral reference database made from metabolomic experts for metabolomic analyses. 9. Journées scientifiques du RFMF, Réseau Francophone de Métabolomique et Fluxomique (RFMF). FRA., Jun 2015, Lille, France. ⟨hal-02742965⟩
  • Benjamin Provost, François Boussu, Marie Lefebvre, Julien Nussbaum. Comportement spécifique de structures 3D interlock tissées contre les impacts à haute vitesse. 17èmes Journées Nationales sur les Composites (JNC17), Jun 2011, Poitiers-Futuroscope, France. pp.39. ⟨hal-00597911⟩

Poster communications13 documents

  • Marie Lefebvre, Yuxin Ma, Sébastien Theil, Thierry Candresse. An automated strategy for viral diversity estimation and OTUs assignation implemented in the VirAnnot pipeline. 17. Rencontres de Virologie Végétale (RVV 2019), Jan 2019, Aussois, France. 2019. ⟨hal-02737922⟩
  • P. Gentit, Armelle Marais, Y. Brans, Jp Renvoisé, C Saison, et al.. Comparaison directe de la performance des techniques classiques avec Séquençage à haut débit (HTS) pour la détection des virus des arbres fruitiers. 17. Rencontres de Virologie Végétale (RVV 2019), Jan 2019, Aussois, France. 2019. ⟨hal-02737926⟩
  • Daniel Jacob, Catherine Deborde, Marie Lefebvre, Mickaël Maucourt, Annick Moing. NMRProcFlow: An easy GUI tool dedicated to 1D NMR spectra processing (1H & 13C) for Metabolomics. 11. Journées Scientifiques du RFMF, May 2018, Liège, Belgium. pp.P24, 2018, 11. Journées Scientifiques du RFMF. ⟨hal-03125691⟩
  • Daniel Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Annick Moing. NMRProcFlow: A graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.. EUROMAR - European Magnetic Resonance Meeting, Jul 2018, Nantes, France. 2018. ⟨hal-02733608⟩
  • Nils Paulhe, Christophe Duperier, Marie Lefebvre, Pierrick Roger-Mele, Christophe Junot, et al.. PeakForest: a spectral database and its toolbox, dedicated to the Metabolomics’ community. 12. annual conference of the Metabolomics Society, Jun 2016, Dublin, United Kingdom. 2016. ⟨hal-02744357⟩
  • Marie Lefebvre, Mickael Maucourt, Annick Moing, Dominique Rolin, Daniel Jacob, et al.. EMERODE: nuclEAR MagnEtic Resonance prOfiles DatabasE. 10. journées scientifiques du Réseau Francophone de Métabolomique et Fluxomique RFMF 2016, May 2016, Montpellier, France. 2016. ⟨hal-02741930⟩
  • Catherine Deborde, Patricia Ballias, Camille Bénard, Stéphane Bernillon, Thierry Berton, et al.. Plant Metabolomics at Bordeaux Metabolome Facility, a member of MetaboHUB and PHENOME IA projects. Tools and Applications. 10. journées scientifiques du Réseau Francophone de Métabolomique et Fluxomique RFMF 2016, May 2016, Montpellier, France. 2016. ⟨hal-02743906⟩
  • Catherine Deborde, Patricia Ballias, Camille Bénard, Stéphane Bernillon, Thierry Berton, et al.. Plant Metabolomics at Bordeaux Metabolome Facility, a member of MetaboHUB and PHENOME IA projects. Tools and Applications. Metabolomics 2016. 12. Annual Conference of the Metabolomics Society, Jun 2016, Dublin, United Kingdom. 2016. ⟨hal-02741696⟩
  • Yannick de Oliveira, Laura Burlot, Marie Lefebvre, Darkawi Madi, Pierre Riviere, et al.. SHiNeMaS : a database dedicated to seed lots genealogy, phenotyping and cultural practices.. Journées Ouvertes en Biologie, Informatique & Mathématiques 2015, Jul 2015, Clermont-Ferrand, France. ⟨hal-02417547⟩
  • Annick Moing, Catherine Deborde, Patricia Ballias, Camille Bénard, Stéphane Bernillon, et al.. Plant Metabolomics at Bordeaux Metabolome Facility, a member of MetaboHUB and PHENOME IA projects. Tools and Applications.. 9. Journées scientifiques du RFMF, Jun 2015, Lille, France. 2015. ⟨hal-02743630⟩
  • Nils Paulhe, Pierrick Roger, Marie-Françoise Olivier, Marie Lefebvre, Christophe Duperier, et al.. PeakForest: a spectral reference database made from metabolomic experts for metabolomic analyses. 9. Journées scientifiques du RFMF, Jun 2015, Lille, France. 2015. ⟨hal-02742964⟩
  • Marie Lefebvre, Julie Pinelli, Nils Paulhe, Vanessa Zhendre, Claire Lopez, et al.. Vers une annotation RMN 1D et 2D ciblée à partir de matrices de référence. 9. Journées scientifiques du RFMF, Jun 2015, Lille, France. 2015. ⟨hal-02743576⟩
  • Mélanie Petera, Gildas Le Corguille, Marion Landi, Misharl Monsoor, Marie Tremblay-Franco, et al.. Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. JOBIM 2015 (16. édition des Journées Ouvertes en Biologie, Informatique et Mathématiques ), Jul 2015, Clermont-Ferrand, France. 2015, JOBIM (16e édition des Journées Ouvertes en Biologie, Informatique et Mathématiques ). ⟨10.1093/bioinformatics/btu813⟩. ⟨hal-01214152⟩

Preprints, Working Papers, ...3 documents

  • Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, et al.. Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection. 2021. ⟨hal-03369187⟩
  • Caroline Meguerditchian, Ayse Ergun, Véronique Decroocq, Marie Lefebvre, Quynh-Trang Bui. A pipeline to detect the relationship between transposable elements and adjacent genes in host genomes. 2021. ⟨hal-03325096⟩
  • Daniel Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Annick Moing. NMRProcFlow: A graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. 2016. ⟨hal-01401241⟩

Software1 document