User:Timothee Flutre

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Contents

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
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, 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

  • 01/2015-12/2016: 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: 220 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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