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Wood, Genomes and Anthropogenic selection team (XYLOMES)

Information Systems Administrator - Databases - Web Development - Bioinformatics

François EHRENMANN

UMR 1202 Biodiversité Gènes & Communautés
INRA
69 route d'Arcachon
33610 CESTAS Cedex – France

Tel. : + 33 5 35 38 53 35

Courriel : francois.ehrenmann_at_inrae.fr

Formation

1998 Master's degree in Chemistry - François Rabelais University, Tours

1999 DEA Chemistry of biomolecules - University of Montpellier II

2005 DESS in Bioinformatics - University of Montpellier II

Activities

• Database administrator / manager
• 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 the databases and the GnpIS information system developed by the Genomics Info Research Unit (URGI Versailles)
• Co-development with GENOTOUL bioinformatics platform GENOTOUL (INRA Toulouse-Auzeville)
• Data management plans (DMP) for projects and units
• Co-leader of the UMR Quality cell
• Member of the Pôle de Compétence Métier Informatique de l'unité
• Co-pilot of the SSI process of the RARe Forest pillar
• Sharepoint site administration
  • Electronic Document Manager of the unit GED GED
  • Team website XYLOMES
  • IN-SYLVA national infrastructure website
• BIOGECO unit dataverse administrator
• CIRON Research Action Group (database group, action in database development and web application)

Areas of expertise

• DBMS management and maintenance (PostGreSQL, MySQL, MongoDB), web servers, Linux administration.
• Web application development: Ruby On Rails, PHP, PERL/cgi, JAVA, PYTHON, Javascript.
• Data management / Data management plan
• Bioinformatics tools for sequence analysis (BLAST, FASTA, CLUSTAL, etc.), 3D visualisation software (Jmol, QuickPDB).
• GENOTOUL (INRA Toulouse-Auzeville) / MIGALE (INRA Jouy-en-Josas) computing cluster
• NGSPipelines user (integrates pipelines and user interfaces to help biologists to analyse data outputted from biological applications such as RNAseq, sRNAseq, ChipSeq, BS-seq, ...)
• Quality assurance
• Administration of sharepoint sites

Participation in ongoing research projects

• 2021 - 2025 FORGENIUS : Improving access to FORest GENetic resources Information and services for end-USers
• 2019 - 2021 SPNA : Sylviculture de Précision en Nouvelle-Aquitaine
• 2018 - 2022 HOMED : Holistic management of emerging forest pests and disease. Coordonné par Hervé Jactel. Web : http://homed-project.eu/
• 2018-2021 ANR EpiTree: Evolutionary and functional impact of EPIgenetic variation in forest TREEs. Coordonné par Stéphane Maury. Web : https://www6.inra.fr/epitree-project/
• 2014-2019 7PCRD (ERC advanced grant), TREEPEACE: From holocene to anthropocene: the pace of microevolution in trees. Coordonné par Antoine Kremer. Web : http://www.treepeace.fr/
• Advances in oak genome sequencing : http://www.oakgenome.fr/

Participation in research infrastructures

• National research infrastructure RARe (Ressources Agronomiques pour la Recherche) / Forêt pillar (CRB Forêts: 1 CRB managed by INRA, 15 species, 10,000 samples)
• IN-SYLVA national infrastructure grouping together the research facilities of establishments working on forest management. Web : https://www6.inra.fr/in-sylva-france/

Selected publications

2020

• 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⟩

2018

• Lefranc MP., Ehrenmann F., Kossida S., Giudicelli V., Duroux P. (2018) Use of IMGT^® Databases and Tools for Antibody Engineering and Humanization. In: Nevoltris D., Chames P. (eds) Antibody Engineering. Methods in Molecular Biology, vol 1827. Humana Press, New York, NY. DOI: https://doi.org/10.1007/978-1-4939-8648-4_3

• Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé B, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne A, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. Nature Plants 4: 440-452. DOI: https://doi.org/10.1038/s41477-018-0172-3

2017

• Fine-scale species distribution changes in a mixed oak stand over two successive generations.
  Truffaut L, Chancerel E, Ducousso A, Dupouey JL, Badeau V, Ehrenmann F, Kremer A.
  New Phytol. 2017 Jul;215(1):126-139. doi: 10.1111/nph.14561. Epub 2017 Apr 26.
  PMID: 28444962

• Adaptive and plastic responses of Quercus petraea populations to climate across Europe.
  Sáenz-Romero C, Lamy JB, Ducousso A, Musch B, Ehrenmann F, Delzon S, Cavers S, Chałupka W, Dağdaş S, Hansen JK, Lee SJ, Liesebach M, Rau HM, Psomas A, Schneck V, Steiner W, Zimmermann NE, Kremer A.
  Glob Chang Biol. 2017 Jul;23(7):2831-2847. doi: 10.1111/gcb.13576. Epub 2017 Jan 25.
  PMID: 27885754

2016

• High-density linkage mapping and distribution of segregation distortion regions in the oak genome.
  Bodénès C, Chancerel E, Ehrenmann F, Kremer A, Plomion C.
  DNA Res. 2016 Apr;23(2):115-24. doi: 10.1093/dnares/dsw001.
  PMID: 27013549

• High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).
  Plomion C, Bartholomé J, Lesur I, Boury C, Rodríguez-Quilón I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, de Miguel M, de María N, Cervera MT, Bagnoli F, Isik F, Vendramin GG, González-Martínez SC.
  Mol Ecol Resour. 2016 Mar;16(2):574-87. doi: 10.1111/1755-0998.12464.
  PMID: 26358548

• Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.
  Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A.
  Mol Ecol Resour. 2016 Jan;16(1):254-65. doi: 10.1111/1755-0998.12425.
  PMID: 25944057

2015

• Evidence of intense chromosomal shuffling during conifer evolution.
  de Miguel M, Bartholomé J, Ehrenmann F, Murat F, Moriguchi Y, Uchiyama K, Ueno S, Tsumura Y, Lagraulet H, de Maria N, Cabezas JA, Cervera MT, Gion JM, Salse J, Plomion C.
  Genome Biol Evol. 2015 Sep 23. pii: evv185. [Epub ahead of print]
  PMID: 26400405

• Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks.
  Lepoittevin C, Bodénès C, Chancerel E, Villate L, Lang T, Lesur I, Boury C, Ehrenmann F, Zelenica D, Boland A, Besse C, Garnier-Géré P, Plomion C, Kremer A.
  Mol Ecol Resour. 2015 Nov;15(6):1446-59. doi: 10.1111/1755-0998.12407.
  PMID: 25818027

• The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release.
  Lesur I, Le Provost G, Bento P, Da Silva C, Leplé JC, Murat F, Ueno S, Bartholomé J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Léger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C.
  BMC Genomics. 2015 Feb 21;16:112. doi: 10.1186/s12864-015-1331-9.
  PMID: 25765701

2014

• Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine.
  Christophe Plomion, Emilie Chancerel, Jeffrey Endelman, Jean-Baptiste Lamy, Eric Mandrou, Isabelle Lesur, François Ehrenmann, Fikret Isik, Marco Cam Bink, Joost van Heerwaarden, Laurent Bouffier
  BMC Genomics 03/2014; 15(1):171.

• De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology
  Canales, J. ; Bautista, R. ; Label, P. ; Gómez-Maldonado, J. ; Lesur, I. ; Fernández-Pozo, N. ; Rueda-López, M. ; Guerrero-Fernández, D. ; Castro-Rodríguez, V. ; Benzekri, H. ; Cañas, R. A. ; Guevara, M.-A. ; Rodrigues, A. ; Seoane, P. ; Teyssier, C. ; Morel, A. ; Ehrenmann, F. ; Le Provost, G. ; Lalanne, C. ; Noirot, C. ; Klopp, C. ; Reymond, I. ; García-Gutiérrez, A. ; Trontin, J.-F. ; Lelu-Walter, M.-A. ; Miguel, C. ; Cervera, M. T. ; Cantón, F. R. ; Plomion, C. ; Harvengt, L. ; Avila, C. ; Gonzalo Claros, M. ; Cánovas, F. M.
  Plant Biotechnology Journal, 2014, 12 (3) : 286-299.

2013

• 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.
  Emilie Chancerel, Jean-Baptiste Lamy, Isabelle Lesur, Céline Noirot, Christophe Klopp, François Ehrenmann, Christophe Boury, Grégoire Le Provost, Philippe Label, Céline Lalanne, Valérie Léger, Franck Salin, Jean-Marc Gion, Christophe Plomion
  BMC Biology 04/2013; 11(1):50.

Présentations orales

• Development of high density linkage maps in European oak for multi-objective genetic applications
  Bodenes, C. ; Chancerel, E. ; Lepoittevin, C. ; Ehrenmann, F. ; Lesur, I. ; Roussel, G. ; Kremer, A. ; Plomion, C.
  IUFRO working group “Genetics of Quercus and Nothofagus” (2012-10-09-2012-10-12) Bordeaux (FRA). 2012. 1 p.
• Sequencing and analysis of the oak transcriptome using RNA-seq technologies
  Lesur, I. ; Le Provost, G. ; Lalanne, C. ; Ehrenmann, F. ; Noirot, C. ; Klopp, C. ; Kremer, A. ; Buscot, F. ; Tarkka, M. ; Aury, J.-M. ; Plomion, C.
  IUFRO working group “Genetics of Quercus and Nothofagus” (2012-10-09-2012-10-12) Bordeaux (FRA). 2012. 1 p.
• Quercus portal: a web resource for genetics and genomics of oaks
  Ehrenmann, F. ; Kremer, A.
  IUFRO working group “Genetics of Quercus and Nothofagus” (2012-10-09-2012-10-12) Bordeaux (FRA). 2012. 1 p.
• Development of genomic resources to study the structure, function and evolution of the oak genome
  Plomion, C. ; Amselem, J. ; Aury, J.-M. ; Bodenes, C. ; Chancerel, E. ; Dencausse, B. ; Duplessis, S. ; Ehrenmann, F. ; Faivre-Rampant, P. ; Jamilloux, V. ; Klopp, C. ; Kremer, A. ; Lalanne, C. ; Leroy, P. ; Lesur, I. ; Luyten, I. ; Martin, F. ; Noirot, C. ; Pavy, N. ; Le Provost, G. ; Quesneville, H. ; Roussel, G. ; Salin, F. ; Salse, J. ; Steinbach, D. ; Zytnicki, M.
  IUFRO working group “Genetics of Quercus and Nothofagus” (2012-10-09-2012-10-12) Bordeaux (FRA). 2012. 1 p.

Posters

• Forest Tree Genomics: genomic resources, bioinformatics, databases and research questions
  F Ehrenmann, I Lesur, J Bartholomé, L Bouffier, JM Gion, A Kremer, G Le Provost, T Leroy, C Plomion
  Bordeaux Computational Biology and Bioinformatics (2014)
• De novo assembly of Fagus sylvatica transcriptome based on Sanger and 454 ESTs: application in transcriptome-scale analysis of bud phenology and markers development
  Lesur, I. ; Le Provost, G. ; Lalanne, C. ; Ehrenman, F. ; Noirot, C. ; Klopp, C. ; Kremer, A. ; Plomion, C.
  IUFRO working group “Genetics of Quercus and Nothofagus” (2012-10-09-2012-10-12) Bordeaux (FRA). 2012. 1 p.