User:Timothee Flutre

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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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*Timothee Flutre
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* Affiliation 1: University of Chicago (Department of Human Genetics), CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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*University of Chicago (Department of Human Genetics) - INRA (Department of Plant Breeding)
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* Affiliation 2: INRA (Department of Plant Genetics), URGI, Route de Saint Cyr, Versailles, 78026, France
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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 am doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago.  I learned about [[OpenWetWare]] thanks to [http://igem.org/Team.cgi?id=18 friends] participating in [http://igem.org iGEM] a few years ago. I joined OpenWetWare 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]
==Research interests==
==Research interests==
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<!-- Feel free to add brief descriptions to your research interests as well -->
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# Quantitative genomics (extend classical quantitative genetics with genomics data)
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# Interest 1
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# Transposable elements (bioinformatics analysis of newly-sequenced genomes)
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# Interest 2
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# Statistical modeling (especially Bayesian)
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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] and [http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flutre%20T%22&#91;Author&#93; Pubmed]. When possible (i.e. in agreement with my co-authors), my preprints are available on [http://arxiv.org/a/flutre_t_1 arXiv].
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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, VenkatA , 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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* current work: [[User:Timothee_Flutre/Notebook|Notebook]]
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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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* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://www.scientificredcards.org/ Scientific Red Cards]

Revision as of 19:39, 31 January 2013

Contents

Contact Info

Timothee Flutre (an artistic interpretation)
Timothee Flutre (an artistic interpretation)
  • Affiliation 1: University of Chicago (Department of Human Genetics), CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
  • Affiliation 2: INRA (Department of Plant Genetics), URGI, Route de Saint Cyr, Versailles, 78026, France
  • Email me through OpenWetWare

I am doing a postdoc with Matthew Stephens at the University of Chicago. I learned about OpenWetWare thanks to friends participating in iGEM a few years ago. I joined OpenWetWare 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

Research interests

  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 (i.e. in agreement with my co-authors), my preprints are available on arXiv.

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, VenkatA , 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