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Number of documents

35

François Ehrenmann, Engineer


Information Systems Administrator - Databases - Web Development - Bioinformatics

Main activities

  • Administrator / Manager of information systems and databases
  • Management, development and maintenance of web applications / databases of the unit and in the framework of the EVOLTREE network (Quercus Portal, Pinus Portal)
  • Information system (IS) of interoperable databases covering different fields (genetics, genomics, ecology). Interoperability with databases and the GnpIS information system (URGI Versailles)
  • Data management plans (DMP) for projects and units
  • UMR Quality co-animator
  • Administrator of the BIOGECO unit dataverse
  • Member of the Computer Science Expertise Hub of the unit
  • Co-pilot of the SSI process of the Forêt RARe pillar

Participation in research infrastructures

  • National research infrastructure RARe (Ressources Agronomiques pour la Recherche) - Forest pillar
  • IN-SYLVA national infrastructure grouping together the research facilities of institutions working on forest management. Web : https://www6.inra.fr/in-sylva-france/


Journal articles20 documents

  • Cyril Dutech, N. Feau, Isabelle Lesur, François Ehrenmann, Thomas Letellier, et al.. An easy and robust method for isolation and validation of single-nucleotide polymorphic markers from a first Erysiphe alphitoides draft genome. Mycological Progress, Springer Verlag, 2020, 19 (6), pp.615-628. ⟨10.1007/s11557-020-01580-w⟩. ⟨hal-02768215⟩
  • Christophe Plomion, Jean-Marc Aury, Joelle Amselem, Thibault Leroy, Florent Murat, et al.. Oak genome reveals facets of long lifespan. Nature Plants, Nature Publishing Group, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩. ⟨hal-01820559⟩
  • Laura Truffaut, Emilie Chancerel, Alexis Ducousso, Jean-Luc Dupouey, Vincent Badeau, et al.. Fine-scale species distribution changes in a mixed oak stand over two successive generations. New Phytologist, Wiley, 2017, 215 (1), pp.126-139. ⟨10.1111/nph.14561⟩. ⟨hal-01604940⟩
  • Cuauhtémoc Saenz Romero, Jean-Baptiste Lamy, Alexis Ducousso, Brigitte Musch, François Ehrenmann, et al.. Adaptive and plastic responses of Quercus petraea populations to climate across Europe. Global Change Biology, Wiley, 2017, 23 (7), pp.2831-2847. ⟨10.1111/gcb.13576⟩. ⟨hal-01608713⟩
  • Catherine Bodénès, Emilie Chancerel, François Ehrenmann, Antoine Kremer, Christophe Plomion. High-density linkage mapping and distribution of segregation distortion regions in the oak genome. DNA Research, Oxford University Press (OUP), 2016, 23 (2), pp.115-124. ⟨10.1093/dnares/dsw001⟩. ⟨hal-02635371⟩
  • Christophe Plomion, Jérôme Bartholomé, Isabelle Lesur, Christophe Boury, Isabel Rodríguez-Quilón, et al.. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Molecular Ecology Resources, Wiley/Blackwell, 2016, 16 (2), pp.574-587. ⟨10.1111/1755-0998.12464⟩. ⟨hal-02640393⟩
  • Camille Lepoittevin, Catherine Bodénès, Emilie Chancerel, Laure Villate, Tiange Lang, et al.. Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks. Molecular Ecology Resources, Wiley/Blackwell, 2015, 15 (6), pp.1446-1459. ⟨10.1111/1755-0998.12407⟩. ⟨hal-02635881⟩
  • Marina de Miguel, Jérôme Bartholome, François Ehrenmann, Florent Murat, Yoshinari Moriguchi, et al.. Evidence of intense chromosomal shuffling during conifer evolution. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2015, 7 (10), pp.evv185. ⟨10.1093/gbe/evv185⟩. ⟨hal-02285512⟩
  • Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne da Silva, Jean-Charles Leplé, et al.. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics, BioMed Central, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩. ⟨hal-02285504⟩
  • Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Tina Alaeitabar, Valérie Barbe, et al.. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.. Molecular Ecology Resources, Wiley/Blackwell, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩. ⟨hal-01579667⟩
  • Javier Canales, Rocío Bautista, Philippe Label, Josefa Gómez-Maldonado, Isabelle Lesur, et al.. De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnology Journal, Wiley, 2014, 12 (3), pp.286-299. ⟨10.1111/pbi.12136⟩. ⟨hal-02640932⟩
  • Christophe Plomion, Emilie Chancerel, Jeffrey Endelman, Jean-Baptiste Lamy, Eric Mandrou, et al.. Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine. BMC Genomics, BioMed Central, 2014, 15, 17 p. ⟨10.1186/1471-2164-15-171⟩. ⟨hal-02636858⟩
  • Emilie Chancerel, Jean-Baptiste Lamy, Isabelle Lesur, Celine Noirot, Christophe Klopp, et al.. High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination. BMC Biology, BioMed Central, 2013, 11, 19 p. ⟨10.1186/1741-7007-11-50⟩. ⟨hal-00964786⟩
  • François Ehrenmann, Mp Lefranc. IMGT/DomainGapAlign: the IMGT® tool for the analysis of IG, TR, MH, IgSF, and MhSF domain amino acid polymorphism. Methods in Molecular Biology, Humana Press/Springer Imprint, 2012, 882, pp.605-633. ⟨10.1007/978-1-61779-842-9_33⟩. ⟨hal-00722914⟩
  • Mp Lefranc, François Ehrenmann, C. Ginestoux, V. Giudicelli, Patrice Duroux. Use of IMGT(®) databases and tools for antibody engineering and humanization. Methods in Molecular Biology, Humana Press/Springer Imprint, 2012, 907, pp.3-37. ⟨10.1007/978-1-61779-974-7_1⟩. ⟨hal-00742879⟩
  • Célia Dechavanne, François Guillonneau, Giovanni Chiappetta, Laïla Sago, Prisca Lévy, et al.. Mass spectrometry detection of G3m and IGHG3 alleles and follow-up of differential mother and neonate IgG3.. PLoS ONE, Public Library of Science, 2012, 7 (9), pp.e46097. ⟨10.1371/journal.pone.0046097⟩. ⟨hal-00858141⟩
  • François Ehrenmann, V. Giudicelli, Patrice Duroux, Mp Lefranc. IMGT/Collier de Perles: IMGT Standardized Representation f Domains (IG, TR, and IgSF Variable and Constant Domains, MH and MhSF Groove Domains). Cold Spring Harbor protocols, Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press, 2011, 6, pii: pdb.prot5635. doi: 10.1101/pdb.prot5635. ⟨10.1101/pdb.prot5635⟩. ⟨hal-00616472⟩
  • François Ehrenmann, Mp Lefranc. IMGT/3Dstructure-DB: Querying the IMGT Database for 3D Structures in Immunology and Immunoinformatics (IG or Antibodies, TR, MH, RPI, and FPIA). Cold Spring Harbor protocols, Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press, 2011, 6, pii: pdb.prot5637. doi: 10.1101/pdb.prot5637. ⟨10.1101/pdb.prot5637⟩. ⟨hal-00616465⟩
  • François Ehrenmann, Mp Lefranc. IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF).. Cold Spring Harbor protocols, Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press, 2011, 6, pii: pdb.prot5636. doi: 10.1101/pdb.prot5636. ⟨10.1101/pdb.prot5636⟩. ⟨hal-00616462⟩
  • Mp Lefranc, V. Giudicelli, C. Ginestoux, J. Jabado-Michaloud, G. Folch, et al.. IMGT(R), the international ImMunoGeneTics information system(R).. Nucleic Acids Research, Oxford University Press, 2009, 37 (Database issue), pp.D1006-12. ⟨10.1093/nar/gkn838⟩. ⟨hal-00357158⟩

Conference papers10 documents

  • Joëlle Amselem, Nicolas Francillonne, Célia Michotey, Thomas Letellier, Jean-Marc Aury, et al.. An integrated information system dedicated to oak genomics and genetics. PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides. ⟨hal-01839185⟩
  • Laurent Bouffier, Raphael Segura, François Ehrenmann, Jean-Marc Gion. Genetic parameters of maritime pine radial growth during a specific drought event. Forest Genetics 2017 - Forest Health and Productivity in Changing Environments, Jun 2017, Edmonton, Canada. ⟨hal-03341365⟩
  • Célia Michotey, Christel Anger, François Ehrenmann, Odile Rogier, Véronique Jorge, et al.. Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics. IUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France. ⟨hal-02740283⟩
  • Jerome Salse, Jean Marc Aury, Florent Murat, Sébastien Faye, Karine Labadie, et al.. Oak genome sequencing and evolution. Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p. ⟨hal-02741698⟩
  • Joelle Amselem, Jean Marc Aury, Nicolas Francillonne, Tina Alaeitabar, Corinne da Silva, et al.. Annotation of the oak genome sequence and associated bioinformatic resources. IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p. ⟨hal-02741128⟩
  • Marina de Miguel, Jérôme Bartholome, François Ehrenmann, Florent Murat, Yoshinari Moriguchi, et al.. Evidence of intense chromosomal shuffling during conifer evolution. ProCoGen final open conference, Promoting Conifer Genomic Resources, Nov 2015, Orléans, France. 75 p. ⟨hal-02741312⟩
  • Catherine Bodénès, Emilie Chancerel, Camille Lepoittevin, François Ehrenmann, Isabelle Lesur, et al.. Development of high density linkage maps in European oak for multi-objective genetic applications. IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-02805716⟩
  • François Ehrenmann, Antoine Kremer. Quercus portal: a web resource for genetics and genomics of oaks. IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-02804818⟩
  • Isabelle Lesur, Grégoire Le Provost, Céline Lalanne, François Ehrenmann, Céline Noirot, et al.. Sequencing and analysis of the oak transcriptome using RNA-seq technologies. IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-02806071⟩
  • Christophe Plomion, Joelle Amselem, Jean-Marc Aury, Catherine Bodenes, Emilie Chancerel, et al.. Development of genomic resources to study the structure, function and evolution of the oak genome. IUFRO working group "Genetics of Quercus and Nothofagus", Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-01019850⟩

Poster communications3 documents

  • Catherine Bodénès, Emilie Chancerel, François Ehrenmann, Meg Staton, Thomas Lane, et al.. High density genetic map in oak reveals segregation distortion in oak and allows comparative mapping between oak and chestnut. Genomics and Forest Tree Genetics Conference, May 2016, Arcachon, France. 134 p., 2016, Book of abstracts. ⟨hal-02741322⟩
  • Nicolas Francillonne, Catherine Bodénès, François Ehrenmann, Célia Michotey, Antoine Kremer, et al.. Detection of WUE positional candidate genes by combining QTL maps and BAC sequencing with the annotated oak genome sequence. Genomics and Forest Tree Genetics Conference, May 2016, Arcachon, France. 134 p., 2016, Book of abstracts. ⟨hal-02741266⟩
  • Célia Michotey, Christel Anger, François Ehrenmann, Odile Rogier, Véronique Jorge, et al.. Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics. 35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015. ⟨hal-02795537⟩

Book sections1 document

  • François Ehrenmann, Stephan Gaubitzer, Dieter Kopecky, Schmidt Johanna, Silvia Fluch, et al.. EVOLTREE ELAB - An information system for forest genetics. Evolution of trees and forest communities, PG Edition, 175 p., 2016, 978-2-9519296-3-9. ⟨hal-01603666⟩

Software1 document

  • . Evoltree, Audrey Jacques-Gustave, Antoine Kremer, Thierry Labbé, Mélina Millox, et al.. Quercus portal. 2012. ⟨hal-02809840⟩