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François EHRENMANN

François Ehrenmann, Engineer - Information systems and database administrator
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#### Administrateur de Systèmes d'informations - Bases de données - Développement Web - Bio-informatique **Activités principales** - Administrateur / Gestionnaire de systèmes d'informations et bases de données - Gestion, développement et maintenance des applications web / bases de données de l'unité et dans le cadre du réseau [EVOLTREE](http://www.evoltree.eu/) ([Quercus Portal](https://quercusportal.pierroton.inra.fr/), [Pinus Portal](https://pinusportal.pierroton.inra.fr/)) - Système d'Informations (SI) de bases interopérables couvrants différents champs (génétique, génomique, écologie). Interopérabilité avec les bases de données et le système d'information [GnpIS](https://urgi.versailles.inra.fr/gnpis/) (URGI Versailles) - Plans de gestions de données (PGD) de projets et [d'unité](https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/XS1RPM) - Référent Données Opérationnel (RDO) département ECODIV - Co-animateur Qualité de l'UMR - Administrateur du [dataverse d'unité BIOGECO](https://data.inrae.fr/dataverse/biogeco) - Membre du [Pôle de Compétence Métier Informatique](https://www6.bordeaux-aquitaine.inrae.fr/biogeco/Poles-de-Competences-Metiers/INFORMATIQUE) de l'unité PCM INFO - Co-pilote de processus SSI pilier Forêt RARe **Participation aux infrastructures de recherche** - Infrastructure de recherche nationale **RARe** (Ressources Agronomiques pour la Recherche) - Pilier Forêt - Infrastructure nationale **IN-SYLVA** regroupant les dispositifs de recherche des Établissements travaillant sur la gestion forestière. Web : https://www6.inra.fr/in-sylva-france/
#### 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](https://quercusportal.pierroton.inra.fr/), [Pinus Portal](https://pinusportal.pierroton.inra.fr/)) - 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 - Operational data referent of the ECODIV department - UMR Quality co-animator - Administrator of the [BIOGECO unit dataverse](https://data.inrae.fr/dataverse/biogeco) - Member of the [Computer Science Expertise Hub of the unit](https://www6.bordeaux-aquitaine.inrae.fr/biogeco_eng/Skill-Units/COMPUTER-SCIENCE) - 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/

Publications

Long-term and large-scale Quercus petraea population survey conducted in provenance tests installed in France

Alexis Ducousso , François Ehrenmann , Quentin Girard , Jean Baptiste Lamy , Jean Marc Louvet et al.
Annals of Forest Science, 2022, 79 (26), pp.1-10. ⟨10.1186/s13595-022-01141-z⟩
Journal articles hal-03724786v1
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SNP4OrphanSpecies: A bioinformatics pipeline to isolate molecular markers for studying genetic diversity of orphan species

Benjamin Penaud , Benoit Laurent , Marine Milhes , Camille Noûs , François Ehrenmann et al.
Biodiversity Data Journal, 2022, 10, pp.1-18. ⟨10.3897/BDJ.10.e85587⟩
Journal articles hal-03799044v1
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An easy and robust method for isolation and validation of single-nucleotide polymorphic markers from a first Erysiphe alphitoides draft genome

Cyril Dutech , N. Feau , Isabelle Lesur , François Ehrenmann , Thomas Letellier et al.
Mycological Progress, 2020, 19 (6), pp.615-628. ⟨10.1007/s11557-020-01580-w⟩
Journal articles hal-02768215v1
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Oak genome reveals facets of long lifespan

Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat et al.
Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩
Journal articles hal-01820559v1

Fine-scale species distribution changes in a mixed oak stand over two successive generations

Laura Truffaut , Emilie Chancerel , Alexis Ducousso , Jean-Luc Dupouey , Vincent Badeau et al.
New Phytologist, 2017, 215 (1), pp.126-139. ⟨10.1111/nph.14561⟩
Journal articles hal-01604940v1

Adaptive and plastic responses of Quercus petraea populations to climate across Europe

Cuauhtémoc Saenz Romero , Jean-Baptiste Lamy , Alexis Ducousso , Brigitte Musch , François Ehrenmann et al.
Global Change Biology, 2017, 23 (7), pp.2831-2847. ⟨10.1111/gcb.13576⟩
Journal articles hal-01608713v1
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High-density linkage mapping and distribution of segregation distortion regions in the oak genome

Catherine Bodenes-Brezard Bodénès , Emilie E. Chancerel , François Ehrenmann , Antoine Kremer , Christophe Plomion et al.
DNA Research, 2016, 23 (2), pp.115-124. ⟨10.1093/dnares/dsw001⟩
Journal articles hal-02635371v1

High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

Christophe Plomion , Jérôme Bartholomé , Isabelle Lesur Kupin Lesur , Christophe C. Boury , Isabel Rodríguez-Quilón et al.
Molecular Ecology Resources, 2016, 16 (2), pp.574-587. ⟨10.1111/1755-0998.12464⟩
Journal articles hal-02640393v1
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The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Isabelle Lesur , Grégoire G. Le Provost , Pascal Bento , Corinne da Silva , Jean-Charles Leplé et al.
BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩
Journal articles hal-02285504v1

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

Christophe Plomion , Jean-Marc Aury , Joëlle Amselem , Tina Alaeitabar , Valérie Barbe et al.
Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩
Journal articles hal-01579667v1

Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks

Camille Lepoittevin , Catherine Bodenes-Brezard Bodénès , Emilie E. Chancerel , Laure Villate , Tiange Lang et al.
Molecular Ecology Resources, 2015, 15 (6), pp.1446-1459. ⟨10.1111/1755-0998.12407⟩
Journal articles hal-02635881v1
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Evidence of intense chromosomal shuffling during conifer evolution

Marina de Miguel , Jérôme Bartholome , François Ehrenmann , Florent Murat , Yoshinari Moriguchi et al.
Genome Biology and Evolution, 2015, 7 (10), pp.evv185. ⟨10.1093/gbe/evv185⟩
Journal articles hal-02285512v1

De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology

Javier Canales , Rocío Bautista , Philippe Label , Josefa Gómez-Maldonado , Isabelle Lesur Kupin Lesur et al.
Plant Biotechnology Journal, 2014, 12 (3), pp.286-299. ⟨10.1111/pbi.12136⟩
Journal articles hal-02640932v1
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Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

Christophe Plomion , Emilie E. Chancerel , Jeffrey Endelman , Jean-Baptiste J.-B. Lamy , Eric Mandrou et al.
BMC Genomics, 2014, 15, 17 p. ⟨10.1186/1471-2164-15-171⟩
Journal articles hal-02636858v1
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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 E. Chancerel , Jean-Baptiste J.-B. Lamy , Isabelle Lesur Kupin Lesur , Celine C. Noirot , Christophe C. Klopp et al.
BMC Biology, 2013, 11, 19 p. ⟨10.1186/1741-7007-11-50⟩
Journal articles hal-00964786v1

IMGT/DomainGapAlign: the IMGT® tool for the analysis of IG, TR, MH, IgSF, and MhSF domain amino acid polymorphism

François Ehrenmann , Mp Lefranc
Methods in Molecular Biology, 2012, 882, pp.605-633. ⟨10.1007/978-1-61779-842-9_33⟩
Journal articles hal-00722914v1
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Mass spectrometry detection of G3m and IGHG3 alleles and follow-up of differential mother and neonate IgG3.

Célia Dechavanne , François Guillonneau , Giovanni Chiappetta , Laïla Sago , Prisca Lévy et al.
PLoS ONE, 2012, 7 (9), pp.e46097. ⟨10.1371/journal.pone.0046097⟩
Journal articles hal-00858141v1

Use of IMGT(®) databases and tools for antibody engineering and humanization

Mp Lefranc , François Ehrenmann , C. Ginestoux , V. Giudicelli , Patrice Duroux et al.
Methods in Molecular Biology, 2012, 907, pp.3-37. ⟨10.1007/978-1-61779-974-7_1⟩
Journal articles hal-00742879v1

IMGT/3Dstructure-DB: Querying the IMGT Database for 3D Structures in Immunology and Immunoinformatics (IG or Antibodies, TR, MH, RPI, and FPIA)

François Ehrenmann , Mp Lefranc
Cold Spring Harbor protocols, 2011, 6, pii: pdb.prot5637. doi: 10.1101/pdb.prot5637. ⟨10.1101/pdb.prot5637⟩
Journal articles hal-00616465v1

IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF).

François Ehrenmann , Mp Lefranc
Cold Spring Harbor protocols, 2011, 6, pii: pdb.prot5636. doi: 10.1101/pdb.prot5636. ⟨10.1101/pdb.prot5636⟩
Journal articles hal-00616462v1

IMGT/Collier de Perles: IMGT Standardized Representation f Domains (IG, TR, and IgSF Variable and Constant Domains, MH and MhSF Groove Domains)

François Ehrenmann , V. Giudicelli , Patrice Duroux , Mp Lefranc
Cold Spring Harbor protocols, 2011, 6, pii: pdb.prot5635. doi: 10.1101/pdb.prot5635. ⟨10.1101/pdb.prot5635⟩
Journal articles hal-00616472v1
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IMGT/3D Structure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF.

François Ehrenmann , Q. Kaas , Marie-Paule Lefranc
Nucleic Acids Research, 2010, 38 (Suppl 1), pp.D301-D307. ⟨10.1093/nar/gkp946⟩
Journal articles hal-00450668v1
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IMGT(R), the international ImMunoGeneTics information system(R).

Mp Lefranc , V. Giudicelli , C. Ginestoux , J. Jabado-Michaloud , G. Folch et al.
Nucleic Acids Research, 2009, 37 (Database issue), pp.D1006-12. ⟨10.1093/nar/gkn838⟩
Journal articles hal-00357158v1
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An integrated information system dedicated to oak genomics and genetics

Joëlle Amselem , Nicolas Francillonne , Célia Michotey , Thomas Letellier , Jean-Marc Aury et al.
PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides
Conference papers hal-01839185v1
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Genetic parameters of maritime pine radial growth during a specific drought event

Laurent Bouffier , Raphael Segura , François Ehrenmann , Jean-Marc Gion
Forest Genetics 2017 - Forest Health and Productivity in Changing Environments, Jun 2017, Edmonton, Canada
Conference papers hal-03341365v1

Oak genome sequencing and evolution

Jerome J. Salse , Jean Marc Aury , Florent Murat , Sébastien Faye , Karine Labadie et al.
Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Conference papers hal-02741698v1

Annotation of the oak genome sequence and associated bioinformatic resources

Joelle J. Amselem , Jean Marc Aury , Nicolas Francillonne , Tina Alaeitabar , Corinne da Silva et al.
IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Conference papers hal-02741128v1
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Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics

Célia Michotey , Christel Anger , François Ehrenmann , Odile Rogier , Véronique V. Jorge et al.
IUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France
Conference papers hal-02740283v1
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Evidence of intense chromosomal shuffling during conifer evolution

Marina de Miguel , Jérôme Bartholome , François Ehrenmann , Florent Murat , Yoshinari Moriguchi et al.
ProCoGen final open conference, Promoting Conifer Genomic Resources, Nov 2015, Orléans, France. 75 p
Conference papers hal-02741312v1

Quercus portal: a web resource for genetics and genomics of oaks

François Ehrenmann , Antoine Kremer
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
Conference papers hal-02804818v1

Development of high density linkage maps in European oak for multi-objective genetic applications

Catherine Bodenes-Brezard Bodénès , Emilie E. Chancerel , Camille Lepoittevin , François Ehrenmann , Isabelle Lesur Kupin Lesur et al.
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
Conference papers hal-02805716v1

Sequencing and analysis of the oak transcriptome using RNA-seq technologies

Isabelle Lesur Kupin Lesur , Grégoire G. Le Provost , Céline C. Lalanne , François Ehrenmann , Céline Noirot et al.
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
Conference papers hal-02806071v1

Development of genomic resources to study the structure, function and evolution of the oak genome

Christophe Plomion , Joelle J. Amselem , Jean-Marc Aury , Catherine Bodenes , Emilie Chancerel et al.
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
Conference papers hal-01019850v1
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EVOLTREE ELAB - An information system for forest genetics

François Ehrenmann , Stephan Gaubitzer , Dieter Kopecky , Schmidt Johanna , Silvia Fluch et al.
Evolution of trees and forest communities, PG Edition, 175 p., 2016, 978-2-9519296-3-9
Book sections hal-01603666v1