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"). In statistical terms, my research will be about prediction (say, predicting the chemical composition of grapevine berries based on information from the genome) and about estimation (say, reconstructing the genetic architecture underlying the chemical composition of grapevine berries).
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==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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* Timothée 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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* Affiliation 1: University of Chicago (Department of Human Genetics)
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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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* Affiliation 2: INRA (Department of Plant Breeding)
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* Address 1: CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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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]]
* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
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I am doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] 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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* 2007-2010, PhD, Université Paris Diderot ([http://www.aiv-paris.org/en/master-aiv/ FDV])
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* 2007-2010, PhD, Université Paris Diderot ([http://www.fdv-paris.org/en/ecole-doctorale-fdv FDV])
* 2006-2007, MS, Université Paris Diderot ([http://www.aiv-paris.org/en/master-aiv/ AIV])
* 2006-2007, MS, Université Paris Diderot ([http://www.aiv-paris.org/en/master-aiv/ AIV])
* 2003-2007, BS+MS, [http://www.agroparistech.fr/Presentation-of-AgroParisTech.html AgroParisTech]
* 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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# Genetics and genomics
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''to be updated...''
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# Transposable elements
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# Quantitative genomics (extend classical quantitative genetics with genomics data)
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# Transposable elements (bioinformatics analysis of newly-sequenced genomes)
# Statistical modeling (especially Bayesian)
# Statistical modeling (especially Bayesian)
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==Current work==
 
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* my [[User:Timothee_Flutre/Notebook|Notebook]]
 
==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] and [http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flutre%20T%22[Author] Pubmed]. When possible (that is, in agreement with my co-authors), my preprints are available on [http://arxiv.org/a/flutre_t_1 arXiv].
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* ''In search of lost trajectories: Recovering the diversification of transposable elements.''
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;11) The Genotype-Tissue Expression (GTEx) project.
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*: '''Flutre T''', Permal E, Quesneville H.
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: Lonsdale, ..., '''Flutre T''', ..., ''et al''.
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*: Mob Genet Elements. 2011 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/22016865 22016865])
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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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* ''Considering transposable element diversification in de novo annotation approaches.''
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;10) A statistical framework for joint eQTL analysis in multiple tissues.
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*: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
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: '''Flutre T'''*, Wen X*, Pritchard J, Stephens M.
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*: PLoS One. 2011 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/21304975 21304975])
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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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* ''Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.''
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;9) Transposable element annotation in completely sequenced eukaryote genomes.
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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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: '''Flutre T''', Permal E, Quesneville H.
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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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: 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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* ''Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.''
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;8) The ABO blood group is a trans-species polymorphism in primates.
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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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: 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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*: Nat. Biotechnol. 2008 (PMID=[http://www.ncbi.nlm.nih.gov/pubmed/18660804 18660804])
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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])
 +
 
 +
;5) 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.
 +
: '''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])
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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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;3) L'annotation des éléments transposables par la compréhension de leur diversification.
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: '''Flutre T''', supervised by Quesneville H and Feuillet C.
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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])
 +
 
 +
;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.
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: Proceedings of the National Academy of Sciences, 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 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.
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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])
==My useful links==
==My useful links==
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* current work: [[User:Timothee_Flutre/Notebook|Notebook]]
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* code: [http://github.com/timflutre/ Github]
* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
* bibliography: [http://www.citeulike.org/user/timflutre/ CiteULike]
* labs: [http://urgi.versailles.inra.fr/ PhD], [http://stephenslab.uchicago.edu/ postdoc]
* 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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==Other useful links==
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* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://www.scientificredcards.org/ Scientific Red Cards]
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*[[OpenWetWare:Welcome|Introductory tutorial]]
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*[[Help|OpenWetWare help pages]]
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Revision as of 11:31, 18 September 2013

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"). In statistical terms, my research will be about prediction (say, predicting the chemical composition of grapevine berries based on information from the genome) and about estimation (say, reconstructing the genetic architecture underlying the chemical composition of grapevine berries).

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 (especially Bayesian)

Publications

All my publications are listed below as well as on my CiteULike account, and can be retrieved via Google Scholar and Pubmed. When possible (that is, in agreement with my co-authors), my preprints are available 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

Personal tools