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==Contact Info==
==Research interests==
[[Image:OWWEmblem.png|thumb|right|Timothee Flutre (an artistic interpretation)]]
# 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.
 
==Contact==
[[Image:TimothéeFlutre crop 40p.jpg|thumb|right|Timothée Flutre]]
 
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").
* INRA, UMR AGAP - bâtiment 21 - 4e étage, 2 place Viala, 34070 Montpellier, France
* timothee.flutre[at]supagro.inra.fr


* Timothée Flutre
Until December 2013, I was doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago.
* Affiliation 1: 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
* Affiliation 2: INRA (Department of Plant Breeding), URGI, Route de Saint Cyr, Versailles, 78026, France
* 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.
* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
I am doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago.  I learned about [[OpenWetWare]] thanks to [http://igem.org/Team.cgi?id=18 friends] participating in [http://igem.org iGEM] a few years ago. I joined OpenWetWare because it seems to be a great project, and I like the idea of promoting more openness in science.


==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 and C. Feuillet
* 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]


==Research interests==
See also my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
# Quantitative genomics (extend classical quantitative genetics with genomics data)
# Transposable elements (bioinformatics analysis of newly-sequenced genomes)
# Statistical modeling (especially Bayesian)


==Publications==
==Publications==
List on [http://www.citeulike.org/user/timflutre/publications CiteULike], as well as retrieved by [http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flutre%20T%22[Author] Pubmed] and [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].
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://prodinra.inra.fr/?locale=en#!Result:%28au:%28Flutre%29%29+status:valid%C3%A9 ProdINRA], [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 online (upon submission, that is before publication, for instance on [http://arxiv.org/a/flutre_t_1 arXiv]).
 
;13) 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])
 
;12) 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])
 
;11) 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)
 
;10) 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)
 
;9) 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)
 
;8) 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])
 
;7) Pilot scheme for misconduct database.
: '''Flutre T''', Julou T, Riboli-Sasco L, Ribrault C.
: Nature, 2011 ([http://dx.doi.org/10.1038/478037c DOI], Open Access)
 
;6) 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)


* ''The ABO blood group is a trans-species polymorphism in primates.''
;5) Considering transposable element diversification in de novo annotation approaches.
*: Ségurel L, Thompson E E, '''Flutre T''', Lovstad J, VenkatA , Margulis S W, Moyse J, Ross S, Gamble K, Sella G, Ober C, Przeworski M.
: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
*: Proceedings of the National Academy of Sciences. 2012 ([http://dx.doi.org/10.1073/pnas.1210603109 DOI], [http://view.ncbi.nlm.nih.gov/pubmed/23091028 Pubmed], Open Access after 6 months)
: 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])
: [http://urgi.versailles.inra.fr/Tools/REPET REPET] (free software under [http://en.wikipedia.org/wiki/CeCILL CeCILL])


* ''Roadmap for annotating transposable elements in eukaryote genomes.''
;4) L'annotation des éléments transposables par la compréhension de leur diversification.
*: Permal E, '''Flutre T''', Quesneville H.
: '''Flutre T''', advised by Quesneville H and Feuillet C.
*: Mobile Genetics Elements: Protocols and Genomic Applications, Springer. 2012 ([http://dx.doi.org/10.1007/978-1-61779-603-6_3 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/22367865 Pubmed], Closed Access)
: 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])


* ''TriAnnot: A versatile and high performance pipeline for the automated annotation of plant genomes.''
;3) Scientific Red Cards - a collaborative website for better communication between scientists and institutions about misconduct.
*: 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.
: '''Flutre T''', Julou T, Riboli-Sasco L, Ribrault 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])
: European Science Editing, 2010 ([http://www.ease.org.uk/sites/default/files/may_2010_362.pdf URL], Open Access)


* ''In search of lost trajectories: Recovering the diversification of transposable elements.''
;2) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
*: '''Flutre T''', Permal E, Quesneville H.
: 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.
*: Mobile Genetics Elements. 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/22016865 Pubmed], Open Access)
: Proceedings of the National Academy of Sciences, 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], Open Access)


* ''Considering transposable element diversification in de novo annotation approaches.''
;1) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
*: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
: 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.
*: PLoS One. 2011 ([http://dx.doi.org/10.1371/journal.pone.0016526 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/21304975 Pubmed], Open Access: [http://creativecommons.org/licenses/by/2.5/ CC BY 2.5])
: 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])


* ''L'annotation des éléments transposables par la compréhension de leur diversification''
==Teaching==
*: '''Flutre T''', supervised by Quesneville H and Feuillet C.
The french academic system requires researchers (with a PhD) to pass yet another exam to be granted the right to supervise PhD students. I still haven't done it, and thus can only officially supervise Master students:
*: PhD thesis, Université Paris Diderot. 2010 ([http://tel.archives-ouvertes.fr/tel-00560242 TEL], Accès Libre)
* 03/2015-08/2015: Dalel Ahmed, Master APIMET and SEPMET option from Montpellier SupAgro
** project: "Analyze the genetic architectures of traits of interest in a diversity panel of cultivated grapevines


* ''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:
*: 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], [http://www.ncbi.nlm.nih.gov/pubmed/20388903 Pubmed], Open Access)
* [https://github.com/timflutre/tuto-reproducible-research tutorial on reproducible research]
* tutorial on genotype-environment interactions (in french, with Nadine Hilgert)


* ''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.
* 01/2015-12/2016: grant from metaprogram SelGen from INRA for the '''FruitSelGen project'''
*: Nature Biotechnology. 2008 ([http://dx.doi.org/10.1038/nbt.1482 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/18660804 Pubmed], Open Access: license [http://creativecommons.org/licenses/by-nc-sa/3.0/ CC BY-NC-SA 3.0])
** 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)
* 2013-2015: '''Labo Hors Murs'''
** 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: [https://github.com/timflutre/ Github]
* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
* 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]]
* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://www.scientificredcards.org/ Scientific Red Cards]
* labs: [http://umr-agap.cirad.fr/en current], [http://stephenslab.uchicago.edu/ postdoc], [http://urgi.versailles.inra.fr/ PhD]
* "social" CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn], [https://www.researchgate.net/profile/Timothee_Flutre/ ResearchGate], [http://orcid.org/0000-0003-4489-4782?lang=en ORCID], [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]

Revision as of 11:32, 26 April 2015

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 and C. Feuillet
  • 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 below as well as on my CiteULike account, and can be retrieved via ProdINRA, 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).

13) The Genotype-Tissue Expression (GTEx) project.
Lonsdale, ..., Flutre T, ..., et al.
Nature Genetics, 2013 (DOI, Open Access: CC BY-NC-SA 3.0)
12) A statistical framework for joint eQTL analysis in multiple tissues.
Flutre T*, Wen X*, Pritchard J, Stephens M.
PLoS Genetics, 2013 (arXiv, DOI, Open Access: CC BY 2.5)
eQtlBma (free software under GPL)
11) 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 (DOI, Restricted Access)
10) 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 (arXiv, DOI, Open Access after 6 months)
9) Roadmap for annotating transposable elements in eukaryote genomes.
Permal E, Flutre T, Quesneville H.
Mobile Genetics Elements: Protocols and Genomic Applications, Springer, 2012 (DOI, Restricted Access)
8) 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 (DOI, Open Access: CC BY-NC 3.0)
7) Pilot scheme for misconduct database.
Flutre T, Julou T, Riboli-Sasco L, Ribrault C.
Nature, 2011 (DOI, Open Access)
6) In search of lost trajectories, recovering the diversification of transposable elements.
Flutre T, Permal E, Quesneville H.
Mobile Genetics Elements, 2011 (DOI, Open Access)
5) Considering transposable element diversification in de novo annotation approaches.
Flutre T, Duprat E, Feuillet C, Quesneville H.
PLoS One, 2011 (DOI, Open Access: CC BY 2.5)
REPET (free software under CeCILL)
4) L'annotation des éléments transposables par la compréhension de leur diversification.
Flutre T, advised by Quesneville H and Feuillet C.
PhD thesis, Université Paris Diderot, 2010 (downloadable on TEL and DART-Europe)
3) Scientific Red Cards - a collaborative website for better communication between scientists and institutions about misconduct.
Flutre T, Julou T, Riboli-Sasco L, Ribrault C.
European Science Editing, 2010 (URL, Open Access)
2) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
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.
Proceedings of the National Academy of Sciences, 2010 (DOI, Open Access)
1) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
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.
Nature Biotechnology, 2008 (DOI, Open Access: CC BY-NC-SA 3.0)

Teaching

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

  • 03/2015-08/2015: Dalel Ahmed, Master APIMET and SEPMET option from Montpellier SupAgro
    • project: "Analyze the genetic architectures of traits of interest in a diversity panel of cultivated grapevines

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

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)
  • 2013-2015: Labo Hors Murs
    • 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)

Links

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