User:Timothee Flutre

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<!-- Delete this entire line as part of your first edit of your user page --> {{New user}}
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==Research interests==
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# develop and apply statistical models using genomic information to estimate genetic architectures and predict multiple traits jointly;
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# collaborate with researchers, farmers and citizens to breed new varieties of cultivated plants in a sustainable manner.
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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 Info==
==Contact Info==
[[Image:OWWEmblem.png|thumb|right|Timothee Flutre (an artistic interpretation)]]
[[Image:OWWEmblem.png|thumb|right|Timothee Flutre (an artistic interpretation)]]
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*Timothee Flutre
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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").
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*University of Chicago (Department of Human Genetics) - INRA (Department of Plant Breeding)
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* INRA, UMR AGAP - bâtiment 21 - 4e étage, 2 place Viala, 34070 Montpellier, France
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*Address 1: CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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* timothee.flutre[at]supagro.inra.fr
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*Address 2: URGI, Route de Saint Cyr, Versailles, 78026, France
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*[[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
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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.
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Until December 2013, I was doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago.
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* University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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* tflutre[at]uchicago.edu
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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.
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* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
==Education==
==Education==
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<!--Include info about your educational background-->
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* 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot ([http://cri-paris.org/doctoral-school-fdv/ FDV])
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* 2010, PhD, Université Paris Diderot
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* 2006-2007, MS, interdisciplinary, Université Paris Diderot ([http://cri-paris.org/master-aiv/ AIV])
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* 2007, MS, Université Paris Diderot
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* 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]
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==Research interests==
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See also my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
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<!-- Feel free to add brief descriptions to your research interests as well -->
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# Interest 1
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# Interest 2
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# Interest 3
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==Publications==
==Publications==
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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]).
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;11) The Genotype-Tissue Expression (GTEx) project.
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: Lonsdale, ..., '''Flutre T''', ..., ''et al''.
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: 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])
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;10) A statistical framework for joint eQTL analysis in multiple tissues.
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: '''Flutre T'''*, Wen X*, Pritchard J, Stephens M.
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: 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])
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: [http://github.com/timflutre/eqtlbma/wiki eQtlBma] (free software under [http://www.gnu.org/licenses/gpl.html GPL])
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;9) Transposable element annotation in completely sequenced eukaryote genomes.
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: '''Flutre T''', Permal E, Quesneville H.
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: 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)
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;8) The ABO blood group is a trans-species polymorphism in primates.
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: 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.
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: 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)
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;7) Roadmap for annotating transposable elements in eukaryote genomes.
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: Permal E, '''Flutre T''', Quesneville H.
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: Mobile Genetics Elements: Protocols and Genomic Applications, Springer, 2012 ([http://dx.doi.org/10.1007/978-1-61779-603-6_3 DOI], Restricted Access)
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;6) TriAnnot, a versatile and high performance pipeline for the automated annotation of plant genomes.
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: 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.
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: 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])
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;5) In search of lost trajectories, recovering the diversification of transposable elements.
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: '''Flutre T''', Permal E, Quesneville H.
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: Mobile Genetics Elements, 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], Open Access)
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* In search of lost trajectories: Recovering the diversification of transposable elements.
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;4) Considering transposable element diversification in de novo annotation approaches.
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*: '''Flutre T''', Permal E, Quesneville H.
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: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
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*: Mob Genet Elements. 2011 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/22016865 22016865])
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: 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])
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: [http://urgi.versailles.inra.fr/Tools/REPET REPET] (free software under [http://en.wikipedia.org/wiki/CeCILL CeCILL])
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* Considering transposable element diversification in de novo annotation approaches.
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;3) L'annotation des éléments transposables par la compréhension de leur diversification.
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*: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
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: '''Flutre T''', supervised by Quesneville H and Feuillet C.
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*: PLoS One. 2011 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/21304975 21304975])
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: 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])
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* Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
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;2) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
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*: 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.
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: 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.
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*: Proc Natl Acad Sci U S A. 2010 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/20388903 20388903])
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: Proceedings of the National Academy of Sciences, 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], Open Access)
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* Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
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;1) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
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*: 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.
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: 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.
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*: Nat. Biotechnol. 2008 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/18660804 18660804])
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: 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])
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==Useful links==
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==My useful links==
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*[[OpenWetWare:Welcome|Introductory tutorial]]
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* notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|Postdoc]], [[User:Timothee_Flutre/Notebook/CR_AGAP|CR AGAP]]
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*[[Help|OpenWetWare help pages]]
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* code: [http://github.com/timflutre/ Github]
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* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
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* labs: [http://urgi.versailles.inra.fr/ PhD], [http://stephenslab.uchicago.edu/ postdoc]
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* "social" CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn], [https://www.researchgate.net/profile/Timothee_Flutre/ ResearchGate]
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* 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 09:13, 1 May 2014

Contents

Research interests

  1. develop and apply statistical models using genomic information 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.

Here is an explanation of the difference between estimation and prediction by 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 Info

Timothee Flutre (an artistic interpretation)
Timothee Flutre (an artistic interpretation)

Since January 2014, I am a research scientist (Chargé de Rercherche 2e classe, CR2) at the INRA, in the team "Diversity, Adaptation and Breeding of Grapevine" 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 Google Scholar, Pubmed and 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 arXiv).

11) The Genotype-Tissue Expression (GTEx) project.
Lonsdale, ..., Flutre T, ..., et al.
Nature Genetics, 2013 (DOI, Open Access: CC BY-NC-SA 3.0)
10) 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)
9) 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)
8) 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)
7) 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)
6) 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)
5) In search of lost trajectories, recovering the diversification of transposable elements.
Flutre T, Permal E, Quesneville H.
Mobile Genetics Elements, 2011 (DOI, Open Access)
4) 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)
3) 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)
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)

My useful links

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