User:Timothee Flutre

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Starting in January 2014, I will be a research scientist (''Chargé de Rercherche 2e classe'', CR2) at the [http://www.inra.fr/en INRA], in the team "Diversity and Adaptation of Grapevine and Mediterranean Species" ([http://umr-agap.cirad.fr/en/equipes-scientifiques/diversite-et-adaptation-de-la-vigne-et-des-especes-mediterraneennes/objectif DAVEM]) 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]). I will be based in the [http://www.montpellier.inra.fr/en INRA centre of Montpellier].
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I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics"). My research will be about ''prediction'' of phenotypes as well as ''estimation'' of genetic architectures.
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("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.", from Andrew Gelman's [http://andrewgelman.com/2006/01/09/bayesian_parame/ blog].)
==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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Until December 2013, I am 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) - INRA (Department of Plant Breeding)
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* Affiliation: University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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*Address 1: CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
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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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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.
==Education==
==Education==
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<!--Include info about your educational background-->
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* 2007-2010, PhD, Université Paris Diderot ([http://www.fdv-paris.org/en/ecole-doctorale-fdv FDV])
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* 2010, PhD, Université Paris Diderot
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* 2006-2007, MS, Université Paris Diderot ([http://www.aiv-paris.org/en/master-aiv/ AIV])
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* 2007, MS, Université Paris Diderot
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* 2003-2007, BS+MS, [http://www.agroparistech.fr/Presentation-of-AgroParisTech.html AgroParisTech]
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More details on my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
==Research interests==
==Research interests==
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<!-- Feel free to add brief descriptions to your research interests as well -->
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''to be updated...''
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# Interest 1
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# Quantitative genomics (extend classical quantitative genetics with genomics data)
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# Interest 2
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# Transposable elements (bioinformatics analysis of newly-sequenced genomes)
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# Interest 3
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# Statistical modeling (Bayesian hierarchical models)
==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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* CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn]
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* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://scientificredcards.wordpress.com/ Scientific Red Cards]

Revision as of 04:10, 10 January 2014

Starting in January 2014, I will be a research scientist (Chargé de Rercherche 2e classe, CR2) at the INRA, in the team "Diversity and Adaptation of Grapevine and Mediterranean Species" (DAVEM) 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). I will be based in the INRA centre of Montpellier.

I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics"). My research will be about prediction of phenotypes as well as estimation of genetic architectures. ("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.", from Andrew Gelman's blog.)

Contents

Contact Info

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

Until December 2013, I am doing a postdoc with Matthew Stephens at the University of Chicago:

  • Affiliation: University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
  • Email me through OpenWetWare

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, Université Paris Diderot (FDV)
  • 2006-2007, MS, Université Paris Diderot (AIV)
  • 2003-2007, BS+MS, AgroParisTech

More details on my online CV.

Research interests

to be updated...

  1. Quantitative genomics (extend classical quantitative genetics with genomics data)
  2. Transposable elements (bioinformatics analysis of newly-sequenced genomes)
  3. Statistical modeling (Bayesian hierarchical models)

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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