User:Timothee Flutre: Difference between revisions

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==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.


==Contact Info==
==Contact==
[[Image:OWWEmblem.png|thumb|right|Timothee Flutre (an artistic interpretation)]]
[[Image:OWWEmblem.png|thumb|right|Timothee Flutre (an artistic interpretation)]]


*Timothee 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").
*University of Chicago (Department of Human Genetics) - INRA (Department of Plant Breeding)
* INRA, UMR AGAP - bâtiment 21 - 4e étage, 2 place Viala, 34070 Montpellier, France
*Address 1: CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
* timothee.flutre[at]supagro.inra.fr
*Address 2: URGI, Route de Saint Cyr, Versailles, 78026, France
 
*[[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
Until December 2013, I was doing a postdoc with [http://stephenslab.uchicago.edu/ 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 work in the [[Stephens lab]] at the University of Chicago.  I learned about [[OpenWetWare]] thanks to friends participating in iGEM a few years ago, and I've joined because OpenWetWare seems to be a great project, and I like the idea of promoting more openness in science. Thus I would like to give it a try.
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==
<!--Include info about your educational background-->
* 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot ([http://cri-paris.org/doctoral-school-fdv/ FDV])
* 2010, PhD, Université Paris Diderot
* 2006-2007, MS, interdisciplinary, Université Paris Diderot ([http://cri-paris.org/master-aiv/ AIV])
* 2007, MS, Université Paris Diderot
* 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].
<!-- Feel free to add brief descriptions to your research interests as well -->
# Interest 1
# Interest 2
# Interest 3


==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&#91;Author&#93; 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)
;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])


* In search of lost trajectories: Recovering the diversification of transposable elements.
;3) Scientific Red Cards - a collaborative website for better communication between scientists and institutions about misconduct.
*: '''Flutre T''', Permal E, Quesneville H.
: '''Flutre T''', Julou T, Riboli-Sasco L, Ribrault C.
*: Mob Genet Elements. 2011 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/22016865 22016865])
: European Science Editing, 2010 ([http://www.ease.org.uk/sites/default/files/may_2010_362.pdf URL], Open Access)


* Considering transposable element diversification in de novo annotation approaches.
;2) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
*: '''Flutre T''', Duprat E, Feuillet C, 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.
*: PLoS One. 2011 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/21304975 21304975])
: Proceedings of the National Academy of Sciences, 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], Open Access)


* Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
;1) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
*: 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.
: 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.
*: Proc Natl Acad Sci U S A. 2010 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/20388903 20388903])
: 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])


* 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'''
*: Nat. Biotechnol. 2008 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/18660804 18660804])
** 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)
* 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)
* 11/2010-08/2013: '''postdoc fellowship''' from INRA (ASC as well as ''Mission des Relations Internationales'', MRI)
** topic: "Statistical methods for eQTL detection"
** status: postdoc
** amount: x k€ (salary 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: x k€ (salary only)


==Useful links==
==Links==
*[[OpenWetWare:Welcome|Introductory tutorial]]
* code: [http://github.com/timflutre/ Github]
*[[Help|OpenWetWare help pages]]
* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
* 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]
* "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]
* 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 09:17, 31 January 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

Timothee Flutre (an artistic interpretation)

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)
  • 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, supervised 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)

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)
  • 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)
  • 11/2010-08/2013: postdoc fellowship from INRA (ASC as well as Mission des Relations Internationales, MRI)
    • topic: "Statistical methods for eQTL detection"
    • status: postdoc
    • amount: x k€ (salary 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: x k€ (salary only)

Links

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