Difference between revisions of "User:Timothee Flutre"

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Starting in January 2014, I will be a research scientist (''Chargé de Rercherche 2e classe'', CR2) at the [http://www.inra.fr/en INRA], in the team "Diversity and Adaptation of Grapevine and Mediterranean Species" ([http://umr-agap.cirad.fr/en/equipes-scientifiques/diversite-et-adaptation-de-la-vigne-et-des-especes-mediterraneennes/objectif DAVEM]) of the lab "Genetic Improvement and Adaptation of Mediterranean and Tropical Plants" ([http://umr-agap.cirad.fr/en/ UMR AGAP]), part of the INRA division "Plant Biology and Breeding" (''Biologie et Amélioration des Plantes'', [http://www.bap.inra.fr/en BAP]). I will be based in the [http://www.montpellier.inra.fr/en INRA centre of Montpellier].
+
==Research interests==
 +
# develop and apply statistical models to estimate genetic architectures and predict multiple traits jointly;
 +
# collaborate with researchers, farmers and citizens to breed new varieties of cultivated plants in a sustainable manner;
 +
# promote reproducibility with free/open tools to facilitate traceability, transparency, and collaborative improvement.
  
I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics"). In statistical terms, my research will be about prediction (say, predicting the chemical composition of grapevine berries based on information from the genome) and about estimation (say, reconstructing the genetic architecture underlying the chemical composition of grapevine berries).
+
==Contact==
 +
[[Image:TimothéeFlutre crop 40p.jpg|thumb|right|Timothée Flutre]]
  
==Contact Info==
+
Since January 2014, I am a research scientist (''Chargé de Rercherche'', CR) at the [http://www.inra.fr/en INRA], in the team "Diversity, Adaptation and Breeding of Grapevine" ([http://umr-agap.cirad.fr/en/scientific-teams/diversity-adaptation-and-breeding-of-grapevine/context-and-goals DAAV]) of the lab "Genetic Improvement and Adaptation of Mediterranean and Tropical Plants" ([http://umr-agap.cirad.fr/en/ UMR AGAP]), part of the INRA division "Plant Biology and Breeding" (''Biologie et Amélioration des Plantes'', [http://www.bap.inra.fr/en BAP]), based in the INRA center of [http://www.montpellier.inra.fr/en Montpellier]. I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics").
[[Image:OWWEmblem.png|thumb|right|Timothee Flutre (an artistic interpretation)]]
+
* INRA, UMR AGAP - bâtiment 21 - 4e étage, 2 place Viala, 34070 Montpellier, France
 +
* timothee.flutre[at]supagro.inra.fr
  
Until December 2013, I am doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago:
+
Until December 2013, I was doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago.
* Affiliation: University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
+
* University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
+
* tflutre[at]uchicago.edu
  
 
I learned about this website, [[OpenWetWare]], thanks to [http://igem.org/Team.cgi?id=18 friends] participating in [http://igem.org iGEM] a few years ago. I joined it because it seems to be a great project, and I like the idea of promoting more openness in science.
 
I learned about this website, [[OpenWetWare]], thanks to [http://igem.org/Team.cgi?id=18 friends] participating in [http://igem.org iGEM] a few years ago. I joined it because it seems to be a great project, and I like the idea of promoting more openness in science.
 +
* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
  
 
==Education==
 
==Education==
* 2007-2010, PhD, Université Paris Diderot ([http://www.fdv-paris.org/en/ecole-doctorale-fdv FDV])
+
* 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot ([http://cri-paris.org/doctoral-school-fdv/ FDV]); advisors: H. Quesneville (INRA Versailles) and C. Feuillet (INRA Clermont-Ferrand)
* 2006-2007, MS, Université Paris Diderot ([http://www.aiv-paris.org/en/master-aiv/ AIV])
+
* 2006-2007, MS, interdisciplinary, Université Paris Diderot ([http://cri-paris.org/master-aiv/ AIV])
* 2003-2007, BS+MS, [http://www.agroparistech.fr/Presentation-of-AgroParisTech.html AgroParisTech]
+
* 2003-2007, BS+MS in engineering and life sciences, [http://www.bginette.com/ lycée Sainte Geneviève] and [http://www.agroparistech.fr/Presentation-of-AgroParisTech.html AgroParisTech]
 
 
More details on my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
 
  
==Research interests==
+
See also my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
''to be updated...''
 
# Quantitative genomics (extend classical quantitative genetics with genomics data)
 
# Transposable elements (bioinformatics analysis of newly-sequenced genomes)
 
# Statistical modeling (especially Bayesian)
 
  
 
==Publications==
 
==Publications==
All my publications are listed below as well as on my [http://www.citeulike.org/user/timflutre/publications CiteULike] account, and can be retrieved via [http://scholar.google.com/scholar?as_q=&as_epq=&as_oq=&as_eq=&as_occt=any&as_sauthors=%22T+Flutre%22&as_publication=&as_ylo=&as_yhi=&hl=en&as_sdt=0%2C14 Google Scholar] and [http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flutre%20T%22[Author] Pubmed]. When possible (that is, in agreement with my co-authors), my preprints are available on [http://arxiv.org/a/flutre_t_1 arXiv].
+
All my publications are listed on [http://prodinra.inra.fr/?locale=en#!Result:%28au:%28Flutre%29%29+status:valid%C3%A9 ProdINRA], [https://hal.archives-ouvertes.fr/search/index/q/%2A/authIdHal_s/timothee-flutre/ HAL], [https://www.zotero.org/tflutre/ Zotero], [http://orcid.org/0000-0003-4489-4782?lang=en ORCID], [https://scholar.google.com/citations?user=FMrEOj8AAAAJ Google Scholar] and [http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flutre%20T%22[Author] Pubmed]. When possible (that is, in agreement with my co-authors), my preprints are available online (upon submission, that is before publication, for instance on [http://arxiv.org/a/flutre_t_1 arXiv]).
 
 
;11) The Genotype-Tissue Expression (GTEx) project.
 
: Lonsdale, ..., '''Flutre T''', ..., ''et al''.
 
: Nature Genetics, 2013 ([http://dx.doi.org/10.1038/ng.2653 DOI], Open Access: [http://creativecommons.org/licenses/by-nc-sa/3.0/ CC BY-NC-SA 3.0])
 
 
 
;10) A statistical framework for joint eQTL analysis in multiple tissues.
 
: '''Flutre T'''*, Wen X*, Pritchard J, Stephens M.
 
: PLoS Genetics, 2013 ([http://arxiv.org/abs/1212.4786 arXiv], [http://dx.doi.org/10.1371/journal.pgen.1003486 DOI], Open Access: [http://creativecommons.org/licenses/by/2.5/ CC BY 2.5])
 
: [http://github.com/timflutre/eqtlbma/wiki eQtlBma] (free software under [http://www.gnu.org/licenses/gpl.html GPL])
 
 
 
;9) Transposable element annotation in completely sequenced eukaryote genomes.
 
: '''Flutre T''', Permal E, Quesneville H.
 
: Plant Transposable Elements: Impact on Genome Structure and Function, Springer, 2012 ([http://dx.doi.org/10.1007/978-3-642-31842-9_2 DOI], Restricted Access)
 
 
 
;8) The ABO blood group is a trans-species polymorphism in primates.
 
: Ségurel L*, Thompson E E*, '''Flutre T''', Lovstad J, Venkat A, Margulis S W, Moyse J, Ross S, Gamble K, Sella G, Ober C, Przeworski M.
 
: Proceedings of the National Academy of Sciences, 2012 ([http://arxiv.org/abs/1208.4613 arXiv], [http://dx.doi.org/10.1073/pnas.1210603109 DOI], Open Access after 6 months)
 
 
 
;7) Roadmap for annotating transposable elements in eukaryote genomes.
 
: Permal E, '''Flutre T''', Quesneville H.
 
: Mobile Genetics Elements: Protocols and Genomic Applications, Springer, 2012 ([http://dx.doi.org/10.1007/978-1-61779-603-6_3 DOI], Restricted Access)
 
 
 
;6) TriAnnot, a versatile and high performance pipeline for the automated annotation of plant genomes.
 
: Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, '''Flutre T''', Pelegrin C, Ohyanagi H, Seidel M, Giacomoni F, Reichstadt M, Alaux M, Gicquello E, Legeai F, Cerutti L, Numa H, Tanaka T, Mayer K, Itoh T, Quesneville H, Feuillet C.
 
: Frontiers in Plant Science, 2012 ([http://dx.doi.org/10.3389/fpls.2012.00005 DOI], Open Access: [http://creativecommons.org/licenses/by-nc/3.0/ CC BY-NC 3.0])
 
 
 
;5) In search of lost trajectories, recovering the diversification of transposable elements.
 
: '''Flutre T''', Permal E, Quesneville H.
 
: Mobile Genetics Elements, 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], Open Access)
 
  
;4) Considering transposable element diversification in de novo annotation approaches.
+
==Teaching==
: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
+
The French academic system requires researchers (with a PhD) to pass yet another exam to be granted the right to be the main supervisor of PhD students. I still haven't done it, and thus can only officially co-supervise PhD students, or supervise Master students:
: PLoS One, 2011 ([http://dx.doi.org/10.1371/journal.pone.0016526 DOI], Open Access: [http://creativecommons.org/licenses/by/2.5/ CC BY 2.5])
+
* 12/2016-12/2019: Cathy Bouffartigue, PhD student at INRA Toulouse
: [http://urgi.versailles.inra.fr/Tools/REPET REPET] (free software under [http://en.wikipedia.org/wiki/CeCILL CeCILL])
+
** project: "Revalorisation du patrimoine génétique d'une espèce agroforestière : analyse de trois initiatives territoriales et co-­conception d’outils de gestion chez le châtaignier"
 +
** joint supervision with L. Hazard and N. Couix, both from INRA Toulouse
 +
* 06-07/2017: Rémi Bernhard, Master student from ENSIIE
 +
** project: "Analyze the genetic basis of grapevine response to water stress in a bi-parental progeny with LASSO-like variable selection methods"
 +
** joint supervision with J. Chiquet, T. Mary-Huard and L. Sansonnet, all from INRA Paris
 +
* 05/2015-12/2015: Pierre-Etienne Alary, Master student from Montpellier SupAgro
 +
** project: "QTL mapping for growth curve via stochastic differential equation"
 +
** joint supervision with B. Fontez (Montpellier SupAgro), P. Roumet (INRA) and A. Garcia (The Plant Accelerator, Univ. of Adelaide)
 +
* 03/2015-08/2015: Dalel Ahmed, Master student from Montpellier SupAgro
 +
** project: "Analyze the genetic architectures of traits of interest in a diversity panel of cultivated grapevines"
  
;3) L'annotation des éléments transposables par la compréhension de leur diversification.
+
I can however be part of the thesis committee of PhD students (once a year):
: '''Flutre T''', supervised by Quesneville H and Feuillet C.
+
* 01/2016-12/2018: Dalel Ahmed, PhD student at INRA Corse
: PhD thesis, Université Paris Diderot, 2010 (downloadable on [http://tel.archives-ouvertes.fr/tel-00560242 TEL] and [http://www.dart-europe.eu/full.php?id=629416 DART-Europe])
+
** project: "Genomic analysis of the impact of 2n gametes on the genetic structure and the expression of fruit quality from hybrids of triploid mandarins"
 +
* 10/2015-09/2018: Gaëlle van Frank, PhD student at INRA Versailles (Le Moulon)
 +
** project: "Participatory management of crop diversity and on-farm breeding for diverse wheat mixtures"
 +
* 09/2015-06/2016: Cathy Bouffartigue, PhD student at INRA Orléans
 +
** project: "Participatory breeding of oak and chestnut for agroforestery usage"
  
;2) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
+
As an INRA researcher, I am not required to teach, but I am sometimes asked by colleagues to speak in their class, or to present in seminars:
: d'Alençon E, Sezutsu H, Legeai F, Permal E, Bernard-Samain S, Gimenez S, Gagneur C, Cousserans F, Shimomura M, Brun-Barale A, '''Flutre T''', Couloux A, East P, Gordon K, Mita K, Quesneville H, Fournier P, Feyereisen R.
+
* [https://github.com/timflutre/atelier-prediction-genomique workshop on genomic predictions] (in french, with Jacques David)
: Proceedings of the National Academy of Sciences, 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], Open Access)
+
* [https://github.com/timflutre/tuto-tests-multiples tutorial on multiple testing] (in french)
 +
* [https://github.com/timflutre/tuto-reproducible-research tutorial on reproducible research]
 +
* tutorial on genotype-environment interactions (in french, with Nadine Hilgert)
  
;1) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
+
==Funding==
: Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud MC, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, '''Flutre T''', Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G, Poulain J, Robinson-Rechavi M, Sallet E, Ségurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P.
+
* 01/2018-12/2020: grant from CASDAR for the '''VITIRAMA''' project
: Nature Biotechnology, 2008 ([http://dx.doi.org/10.1038/nbt.1482 DOI], Open Access: [http://creativecommons.org/licenses/by-nc-sa/3.0/ CC BY-NC-SA 3.0])
+
** topic: "Characterization of grapevine genetic resources in relation to tolerance to pests and diseases"
 +
** status: investigator (coordinator is Thierry Lacombe)
 +
** amount: 77 k€ (no salary)
 +
* 01/2017-12/2019: grant from CASDAR for the '''SIGNE''' project
 +
** topic: "Spectroscopy, a tool for traceability and management of intra-variety variability in grapevine"
 +
** status: investigator (coordinator is Christophe Sereno)
 +
** amount: 89 k€ (no salary)
 +
* 01/2015-12/2016: grant from metaprogram SelGen from INRA for the '''FruitSelGen''' project
 +
** topic: "Assessing genomic selection within bi-parental crosses for perennial fruit crops" (grapevine, apple, peach, apricot, cherry)
 +
** status: investigator and coordinator (6 different INRA labs involved)
 +
** amount: 114 k€ (no salary)
 +
* 06/2014-05/2018: grant from CASDAR for the '''EDGARR''' project
 +
** topic: "Exploitation De la sélection Génomique afin d’Accélérer la création de variétés Résistantes et qualitatives pour la filière viticole Rosé"
 +
** status: investigator (coordinator is Loïc Le Cunff)
 +
** amount: 221 k€ (no salary)
 +
* 2013-2017: grant from metaprogram SelGen from INRA for the '''R2D2''' project
 +
** topic: "Network studying genetic and economic efficiency of genomic selection for about 20 animal and vegetal species"
 +
** status: participant (coordinators are Bruno Goffinet and Stéphane Lemarié for the v1; Stéphane Lemarié, Christèle Robert-Granié and Laurence Moreau for the v2)
 +
** amount: ? k€ (v1) and 76 k€ (v2)
 +
* 2013-2015: grant from Agropolis Fondation for the '''Labo Hors Murs''' project
 +
** topic: "participatory research for agricultural biodiversity"
 +
** status: participant (coordinators are Bob Brac de la Perrière and Pascal Moity-Maizi)
 +
** amount: ? k€
 +
* 06/2014-05/2016: starter grant from department BAP of INRA for the '''SelVi''' project
 +
** topic: "Genomic selection on grapevine, a feasibility study"
 +
** status: principal investigator
 +
** amount: 24 k€ (no salary)
 +
* 01/2014-: '''research scientist''' at INRA
 +
** topic: "Quantitative genetics and genomics" ("Genomic selection and grapevine genetics")
 +
** status: civil servant (permanent position)
 +
** amount: monthly salary of 2120 € (net)
 +
* 11/2010-08/2013: '''postdoc fellowship''' from INRA (ASC as well as from the ''Mission des Relations Internationales'', MRI); also the University of Chicago and the NIH (grant MH090951)
 +
** topic: "Statistical methods for eQTL detection"
 +
** status: postdoc
 +
** amount: monthly salary of 1990 € (net, INRA only)
 +
* 09/2007-10/2010: '''PhD fellowship''' from INRA (''Assistant Scientifique Contractuel'', ASC)
 +
** topic: "The annotation of transposable elements through the understanding of their diversification"
 +
** status: PhD student
 +
** amount: monthly salary of 1560-1990 € (net)
  
==My useful links==
+
==Links==
* current work: [[User:Timothee_Flutre/Notebook|Notebook]]
+
* code and teaching: [http://github.com/timflutre/ Github]
* code: [http://github.com/timflutre/ Github]
+
** contribution to other softwares: [https://cran.r-project.org/package=qtl R/qtl], [https://www.gnu.org/software/gsl/ GSL], [https://github.com/arq5x/bedtools2 bedtools], [https://github.com/Gregor-Mendel-Institute/mlmm R/mlmm], [https://github.com/jonesor/rcolony R/rcolony], [https://github.com/xqwen/IRLS IRLS], etc
* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
+
* bibliography: [https://www.zotero.org/tflutre/items Zotero]
* labs: [http://urgi.versailles.inra.fr/ PhD], [http://stephenslab.uchicago.edu/ postdoc]
+
* notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|Postdoc]], [[User:Timothee_Flutre/Notebook/CR_AGAP|CR AGAP]]
* CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn]
+
* labs: [http://umr-agap.cirad.fr/en current], [http://stephenslab.uchicago.edu/ postdoc], [http://urgi.versailles.inra.fr/ PhD]
* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://www.scientificredcards.org/ Scientific Red Cards]
+
* "social" CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn]
 +
** other websites: [https://www.researchgate.net/profile/Timothee_Flutre/ ResearchGate], [https://inra.academia.edu/TFlutre Academia], [http://loop.frontiersin.org/people/41072/overview Loop]
 +
* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://scientificredcards.wordpress.com/ Scientific Red Cards], [https://en.wikipedia.org/wiki/User:Timflutre Wikipedia], [http://www.openstreetmap.org/user/Timoth%C3%A9e%20Flutre OpenStreetMap]

Latest revision as of 00:34, 3 October 2017

Research interests

  1. develop and apply statistical models to estimate genetic architectures and predict multiple traits jointly;
  2. collaborate with researchers, farmers and citizens to breed new varieties of cultivated plants in a sustainable manner;
  3. promote reproducibility with free/open tools to facilitate traceability, transparency, and collaborative improvement.

Contact

Timothée Flutre

Since January 2014, I am a research scientist (Chargé de Rercherche, CR) at the INRA, in the team "Diversity, Adaptation and Breeding of Grapevine" (DAAV) of the lab "Genetic Improvement and Adaptation of Mediterranean and Tropical Plants" (UMR AGAP), part of the INRA division "Plant Biology and Breeding" (Biologie et Amélioration des Plantes, BAP), based in the INRA center of Montpellier. I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics").

  • INRA, UMR AGAP - bâtiment 21 - 4e étage, 2 place Viala, 34070 Montpellier, France
  • timothee.flutre[at]supagro.inra.fr

Until December 2013, I was doing a postdoc with Matthew Stephens at the University of Chicago.

  • University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
  • tflutre[at]uchicago.edu

I learned about this website, OpenWetWare, thanks to friends participating in iGEM a few years ago. I joined it because it seems to be a great project, and I like the idea of promoting more openness in science.

Education

  • 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot (FDV); advisors: H. Quesneville (INRA Versailles) and C. Feuillet (INRA Clermont-Ferrand)
  • 2006-2007, MS, interdisciplinary, Université Paris Diderot (AIV)
  • 2003-2007, BS+MS in engineering and life sciences, lycée Sainte Geneviève and AgroParisTech

See also my online CV.

Publications

All my publications are listed on ProdINRA, HAL, Zotero, ORCID, Google Scholar and Pubmed. When possible (that is, in agreement with my co-authors), my preprints are available online (upon submission, that is before publication, for instance on arXiv).

Teaching

The French academic system requires researchers (with a PhD) to pass yet another exam to be granted the right to be the main supervisor of PhD students. I still haven't done it, and thus can only officially co-supervise PhD students, or supervise Master students:

  • 12/2016-12/2019: Cathy Bouffartigue, PhD student at INRA Toulouse
    • project: "Revalorisation du patrimoine génétique d'une espèce agroforestière : analyse de trois initiatives territoriales et co-­conception d’outils de gestion chez le châtaignier"
    • joint supervision with L. Hazard and N. Couix, both from INRA Toulouse
  • 06-07/2017: Rémi Bernhard, Master student from ENSIIE
    • project: "Analyze the genetic basis of grapevine response to water stress in a bi-parental progeny with LASSO-like variable selection methods"
    • joint supervision with J. Chiquet, T. Mary-Huard and L. Sansonnet, all from INRA Paris
  • 05/2015-12/2015: Pierre-Etienne Alary, Master student from Montpellier SupAgro
    • project: "QTL mapping for growth curve via stochastic differential equation"
    • joint supervision with B. Fontez (Montpellier SupAgro), P. Roumet (INRA) and A. Garcia (The Plant Accelerator, Univ. of Adelaide)
  • 03/2015-08/2015: Dalel Ahmed, Master student from Montpellier SupAgro
    • project: "Analyze the genetic architectures of traits of interest in a diversity panel of cultivated grapevines"

I can however be part of the thesis committee of PhD students (once a year):

  • 01/2016-12/2018: Dalel Ahmed, PhD student at INRA Corse
    • project: "Genomic analysis of the impact of 2n gametes on the genetic structure and the expression of fruit quality from hybrids of triploid mandarins"
  • 10/2015-09/2018: Gaëlle van Frank, PhD student at INRA Versailles (Le Moulon)
    • project: "Participatory management of crop diversity and on-farm breeding for diverse wheat mixtures"
  • 09/2015-06/2016: Cathy Bouffartigue, PhD student at INRA Orléans
    • project: "Participatory breeding of oak and chestnut for agroforestery usage"

As an INRA researcher, I am not required to teach, but I am sometimes asked by colleagues to speak in their class, or to present in seminars:

Funding

  • 01/2018-12/2020: grant from CASDAR for the VITIRAMA project
    • topic: "Characterization of grapevine genetic resources in relation to tolerance to pests and diseases"
    • status: investigator (coordinator is Thierry Lacombe)
    • amount: 77 k€ (no salary)
  • 01/2017-12/2019: grant from CASDAR for the SIGNE project
    • topic: "Spectroscopy, a tool for traceability and management of intra-variety variability in grapevine"
    • status: investigator (coordinator is Christophe Sereno)
    • amount: 89 k€ (no salary)
  • 01/2015-12/2016: grant from metaprogram SelGen from INRA for the FruitSelGen project
    • topic: "Assessing genomic selection within bi-parental crosses for perennial fruit crops" (grapevine, apple, peach, apricot, cherry)
    • status: investigator and coordinator (6 different INRA labs involved)
    • amount: 114 k€ (no salary)
  • 06/2014-05/2018: grant from CASDAR for the EDGARR project
    • topic: "Exploitation De la sélection Génomique afin d’Accélérer la création de variétés Résistantes et qualitatives pour la filière viticole Rosé"
    • status: investigator (coordinator is Loïc Le Cunff)
    • amount: 221 k€ (no salary)
  • 2013-2017: grant from metaprogram SelGen from INRA for the R2D2 project
    • topic: "Network studying genetic and economic efficiency of genomic selection for about 20 animal and vegetal species"
    • status: participant (coordinators are Bruno Goffinet and Stéphane Lemarié for the v1; Stéphane Lemarié, Christèle Robert-Granié and Laurence Moreau for the v2)
    • amount: ? k€ (v1) and 76 k€ (v2)
  • 2013-2015: grant from Agropolis Fondation for the Labo Hors Murs project
    • topic: "participatory research for agricultural biodiversity"
    • status: participant (coordinators are Bob Brac de la Perrière and Pascal Moity-Maizi)
    • amount: ? k€
  • 06/2014-05/2016: starter grant from department BAP of INRA for the SelVi project
    • topic: "Genomic selection on grapevine, a feasibility study"
    • status: principal investigator
    • amount: 24 k€ (no salary)
  • 01/2014-: research scientist at INRA
    • topic: "Quantitative genetics and genomics" ("Genomic selection and grapevine genetics")
    • status: civil servant (permanent position)
    • amount: monthly salary of 2120 € (net)
  • 11/2010-08/2013: postdoc fellowship from INRA (ASC as well as from the Mission des Relations Internationales, MRI); also the University of Chicago and the NIH (grant MH090951)
    • topic: "Statistical methods for eQTL detection"
    • status: postdoc
    • amount: monthly salary of 1990 € (net, INRA only)
  • 09/2007-10/2010: PhD fellowship from INRA (Assistant Scientifique Contractuel, ASC)
    • topic: "The annotation of transposable elements through the understanding of their diversification"
    • status: PhD student
    • amount: monthly salary of 1560-1990 € (net)

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