User:Timothee Flutre: Difference between revisions

Revision as of 07:32, 21 March 2015

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

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.

Email me through OpenWetWare

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

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)

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 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: 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

code and teaching: Github
bibliography: CiteULike
notebooks: Postdoc, CR AGAP
labs: current, postdoc, PhD
"social" CV: LinkedIn, ResearchGate, ORCID, Loop
volunteering: Paris-Montagne, Scientific Red Cards, Wikipedia

@@ Line 1: / Line 1: @@
 ==Research interests==
-# develop and apply statistical models using genomic information to estimate genetic architectures and predict multiple traits jointly;
+# 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.
+# 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.
-Here is an explanation of the difference between ''estimation'' and ''prediction'' by [http://andrewgelman.com/2006/01/09/bayesian_parame/ Andrew Gelman]: "Basically, you estimate parameters and you predict observables. This is not just a semantic distinction. Parameters are those things that generalize to future studies, observables are ends in themselves. If the joint distribution of all the knowns and unknowns is written as a directed acycllic graph, the arrows go from parameters to observables and not the other way around. Or, to put it another way, one instance of a parameter can correspond to many observables.".
+==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)]]
-Since January 2014, I am a research scientist (''Chargé de Rercherche 2e classe'', CR2) at the [http://www.inra.fr/en INRA], in the team "Diversity, Adaptation and Breeding of Grapevine" 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
@@ Line 20: / Line 19: @@
 ==Education==
-* 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot ([http://cri-paris.org/doctoral-school-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, 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]
@@ Line 27: / Line 26: @@
 ==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], [http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flutre%20T%22&#91;Author&#93; Pubmed] and [http://prodinra.inra.fr/?locale=en#!Result:%28au:%28Flutre%29%29+status:valid%C3%A9 ProdINRA]. 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 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]).
-;11) The Genotype-Tissue Expression (GTEx) project.
+;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])
-;10) A statistical framework for joint eQTL analysis in multiple tissues.
+;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])
-;9) Transposable element annotation in completely sequenced eukaryote genomes.
+;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)
-;8) The ABO blood group is a trans-species polymorphism in primates.
+;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)
-;7) Roadmap for annotating transposable elements in eukaryote genomes.
+;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)
-;6) TriAnnot, a versatile and high performance pipeline for the automated annotation of plant genomes.
+;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])
-;5) In search of lost trajectories, recovering the diversification of transposable elements.
+;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)
-;4) Considering transposable element diversification in de novo annotation approaches.
+;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])
-;3) L'annotation des éléments transposables par la compréhension de leur diversification.
+;4) L'annotation des éléments transposables par la compréhension de leur diversification.
-: '''Flutre T''', supervised by Quesneville H and Feuillet C.
+: '''Flutre T''', advised 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.
@@ Line 75: / Line 82: @@
 : 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])
-==My useful links==
+==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 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: 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==
+* code and teaching: [http://github.com/timflutre/ Github]
+* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
 * notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|Postdoc]], [[User:Timothee_Flutre/Notebook/CR_AGAP|CR AGAP]]
-* code: [http://github.com/timflutre/ Github]
+* labs: [http://umr-agap.cirad.fr/en current], [http://stephenslab.uchicago.edu/ postdoc], [http://urgi.versailles.inra.fr/ PhD]
-* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
+* "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]
-* labs: [http://urgi.versailles.inra.fr/ PhD], [http://stephenslab.uchicago.edu/ postdoc]
+* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://scientificredcards.wordpress.com/ Scientific Red Cards], [https://en.wikipedia.org/wiki/User:Timflutre Wikipedia]
-* 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]

User:Timothee Flutre: Difference between revisions

Revision as of 07:32, 21 March 2015

Contents

Research interests

Contact

Education

Publications

Funding

Links

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

research

Tools