User:Timothee Flutre: Difference between revisions

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==Contact==
==Contact==
[[Image:OWWEmblem.png|thumb|right|Timothee Flutre (an artistic interpretation)]]
Since February 2019, I am a research scientist (''Chargé de Rercherche'', CR) at the [http://www.inra.fr/en INRA], in the team "Diversity, Evolution and Adaptation of Populations" ([http://moulon.inra.fr/index.php/fr/equipes/deap DEAP]) of the lab "Quantiative Genetics and Evolution" ([http://moulon.inra.fr/ UMR GQE-Le Moulon]), 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.versailles-grignon.inra.fr/ Versailles-Grignon]. I have been recruited on the profile "Harness intra-specific diversity for Agroecology" (domain "Genetics, Mathematics and Informatics for Life and the Environment").
* Génétique Quantitative et Évolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Ferme du Moulon; 91190 Gif-sur-Yvette, France
* timothee.flutre[at]inra.fr


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").
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").
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* 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
* tflutre[at]uchicago.edu
* 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]]


==Education==
==Education==
* 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot ([http://cri-paris.org/doctoral-school-fdv/ FDV])
See my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
* 2006-2007, MS, interdisciplinary, Université Paris Diderot ([http://cri-paris.org/master-aiv/ AIV])
* 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]
 
See also my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].


==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://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]).
All my publications are listed on [http://prodinra.inra.fr/?locale=en#!Result:%28au:%28Flutre%29%29+status:valid%C3%A9 ProdINRA]. See also my [http://orcid.org/0000-0003-4489-4782?lang=en ORCID] account.
 
;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)
 
;5) Considering transposable element diversification in de novo annotation approaches.
: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
: 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])
 
;4) L'annotation des éléments transposables par la compréhension de leur diversification.
: '''Flutre T''', supervised by Quesneville H and Feuillet C.
: 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])
 
;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 ([http://www.ease.org.uk/sites/default/files/may_2010_362.pdf 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 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], Open Access)


;1) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
==Teaching==
: 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.
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:
: 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])
* [https://github.com/timflutre/atelier-prediction-genomique workshop on genomic predictions] (in french, with Jacques David)
* [https://github.com/timflutre/tuto-tests-multiples tutorial on multiple testing] (in french)
* [https://github.com/timflutre/tuto-reproducible-research tutorial on reproducible research]


==Funding==
==Funding==
* 01/2015-12/2016: grant from metaprogram SelGen from INRA for the '''FruitSelGen project'''
* 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)
** 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)
** status: investigator and coordinator (6 different INRA labs involved)
** amount: 114 k€ (no salary)
** amount: 114 k€ (no salary)
* 06/2014-05/2018: grant from CASDAR for the '''EDGARR project'''
* 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"
** 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)
** status: investigator (coordinator is Loïc Le Cunff)
** amount: 220 k€ (no salary)
** amount: 221 k€ (no salary)
* 2013-2015: '''Labo Hors Murs'''
* 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"
** topic: "participatory research for agricultural biodiversity"
** status: participant (coordinators are Bob Brac de la Perrière and Pascal Moity-Maizi)
** status: participant (coordinators are Bob Brac de la Perrière and Pascal Moity-Maizi)
* 06/2014-05/2016: starter grant from department BAP of INRA for the '''SELVI project'''
** 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"
** topic: "Genomic selection on grapevine, a feasibility study"
** status: principal investigator
** status: principal investigator
** amount: 24 k€ (no salary)
** amount: 24 k€ (no salary)
* 11/2010-08/2013: '''postdoc fellowship''' from INRA (ASC as well as ''Mission des Relations Internationales'', MRI)
* 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 2100-2400 € (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"
** topic: "Statistical methods for eQTL detection"
** status: postdoc
** status: postdoc
** amount: x k€ (salary only)
** amount: monthly salary of 1990 € (net, INRA only)
* 09/2007-10/2010: '''PhD fellowship''' from INRA (''Assistant Scientifique Contractuel'', ASC)
* 09/2007-10/2010: '''PhD fellowship''' from INRA (''Assistant Scientifique Contractuel'', ASC)
** topic: "The annotation of transposable elements through the understanding of their diversification"
** topic: "The annotation of transposable elements through the understanding of their diversification"
** status: PhD student
** status: PhD student
** amount: x k€ (salary only)
** amount: monthly salary of 1560-1990 € (net)


==Links==
==Links==
* code: [http://github.com/timflutre/ Github]
* code and teaching: [http://github.com/timflutre/ Github]
* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
** 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], [https://github.com/famuvie/breedR R/breedR], [https://github.com/stephenturner/qqman R/qqman], etc
** contribution to open data repositories: [https://master.bioconductor.org/ Bioconductor], [https://urgi.versailles.inra.fr/ephesis/ Ephesis]
** contribution to online communities: [https://stackoverflow.com/users/597069/tflutre StackOverflow], [https://en.wikipedia.org/wiki/User:Timflutre Wikipedia], [http://www.openstreetmap.org/user/Timoth%C3%A9e%20Flutre OpenStreetMap]
* bibliography: [https://www.zotero.org/tflutre/items Zotero]
* notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|Postdoc]], [[User:Timothee_Flutre/Notebook/CR_AGAP|CR AGAP]]
* notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|Postdoc]], [[User:Timothee_Flutre/Notebook/CR_AGAP|CR AGAP]]
* labs: [http://umr-agap.cirad.fr/en current], [http://stephenslab.uchicago.edu/ postdoc], [http://urgi.versailles.inra.fr/ PhD]
* 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]
* online CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn]
* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://scientificredcards.wordpress.com/ Scientific Red Cards], [https://en.wikipedia.org/wiki/User:Timflutre Wikipedia]
** 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]

Latest revision as of 06:53, 5 February 2019

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

Since February 2019, I am a research scientist (Chargé de Rercherche, CR) at the INRA, in the team "Diversity, Evolution and Adaptation of Populations" (DEAP) of the lab "Quantiative Genetics and Evolution" (UMR GQE-Le Moulon), part of the INRA division "Plant Biology and Breeding" (Biologie et Amélioration des Plantes, BAP), based in the INRA center of Versailles-Grignon. I have been recruited on the profile "Harness intra-specific diversity for Agroecology" (domain "Genetics, Mathematics and Informatics for Life and the Environment").

  • Génétique Quantitative et Évolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Ferme du Moulon; 91190 Gif-sur-Yvette, France
  • timothee.flutre[at]inra.fr

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

Education

See my online CV.

Publications

All my publications are listed on ProdINRA. See also my ORCID account.

Teaching

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 2100-2400 € (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

Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Timothee_Flutre&oldid=1058796"