User:Timothee Flutre

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All my publications are listed below as well as on my [ CiteULike] account, and can be retrieved via [ Google Scholar] and [[Author] Pubmed]. When possible (that is, in agreement with my co-authors), my preprints are available on [ arXiv].
All my publications are listed below as well as on my [ CiteULike] account, and can be retrieved via [ Google Scholar], [[Author] Pubmed] and [!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 [ arXiv]).
;11) The Genotype-Tissue Expression (GTEx) project.
;11) The Genotype-Tissue Expression (GTEx) project.
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==My useful links==
==My useful links==
* notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|postdoc]]
* notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|Postdoc]], [[User:Timothee_Flutre/Notebook/CR_AGAP|CR AGAP]]
* code: [ Github]
* code: [ Github]
* bibliography: [ CiteULike]
* bibliography: [ CiteULike]

Revision as of 05:10, 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.)


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.


  • 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)


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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