User:Timothee Flutre: Difference between revisions

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==Publications==
==Publications==
All my published papers are listed on [http://www.citeulike.org/user/timflutre/publications CiteULike], as well as retrieved by [http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flutre%20T%22[Author] Pubmed] and [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 some preprints are available on [http://arxiv.org/a/flutre_t_1 arXiv].
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 (i.e. in agreement with my co-authors), my preprints are available on [http://arxiv.org/a/flutre_t_1 arXiv].


* ''The ABO blood group is a trans-species polymorphism in primates.''
;9) Transposable element annotation in completely sequenced eukaryote genomes.
*: 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.
: '''Flutre T''', Permal E, Quesneville H.
*: Proceedings of the National Academy of Sciences. 2012 ([http://arxiv.org/abs/1208.4613 arXiv], [http://dx.doi.org/10.1073/pnas.1210603109 DOI], [http://view.ncbi.nlm.nih.gov/pubmed/23091028 Pubmed], Open Access after 6 months)
: 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)


* ''Roadmap for annotating transposable elements in eukaryote genomes.''
;8) The ABO blood group is a trans-species polymorphism in primates.
*: Permal E, '''Flutre T''', Quesneville H.
: 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.
*: Mobile Genetics Elements: Protocols and Genomic Applications, Springer. 2012 ([http://dx.doi.org/10.1007/978-1-61779-603-6_3 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/22367865 Pubmed], Closed Access)
: 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)


* ''TriAnnot: A versatile and high performance pipeline for the automated annotation of plant genomes.''
;7) Roadmap for annotating transposable elements in eukaryote 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.
: Permal E, '''Flutre T''', Quesneville H.
*: 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])
: Mobile Genetics Elements: Protocols and Genomic Applications, Springer, 2012 ([http://dx.doi.org/10.1007/978-1-61779-603-6_3 DOI], Restricted Access)


* ''In search of lost trajectories: Recovering the diversification of transposable elements.''
;6) TriAnnot, a versatile and high performance pipeline for the automated annotation of plant genomes.
*: '''Flutre T''', Permal E, Quesneville H.
: 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.
*: Mobile Genetics Elements. 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/22016865 Pubmed], Open Access)
: 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])


* ''Considering transposable element diversification in de novo annotation approaches.''
;5) In search of lost trajectories, recovering the diversification of transposable elements.
*: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
: '''Flutre T''', Permal E, Quesneville H.
*: PLoS One. 2011 ([http://dx.doi.org/10.1371/journal.pone.0016526 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/21304975 Pubmed], Open Access: [http://creativecommons.org/licenses/by/2.5/ CC BY 2.5])
: Mobile Genetics Elements, 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], Open Access)


* ''L'annotation des éléments transposables par la compréhension de leur diversification''
;4) Considering transposable element diversification in de novo annotation approaches.
*: '''Flutre T''', supervised by Quesneville H and Feuillet C.
: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
*: PhD thesis, Université Paris Diderot. 2010 ([http://tel.archives-ouvertes.fr/tel-00560242 TEL], Accès Libre)
: 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])
: [http://urgi.versailles.inra.fr/Tools/REPET REPET] (free software under [http://en.wikipedia.org/wiki/CeCILL CeCILL])


* ''Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.''
;3) L'annotation des éléments transposables par la compréhension de leur diversification.
*: 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.
: '''Flutre T''', supervised by Quesneville H and Feuillet C.
*: Proceedings of the National Academy of Sciences. 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/20388903 Pubmed], Open Access)
: 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])


* ''Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.''
;2) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
*: 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.
: 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.
*: Nature Biotechnology. 2008 ([http://dx.doi.org/10.1038/nbt.1482 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/18660804 Pubmed], Open Access: [http://creativecommons.org/licenses/by-nc-sa/3.0/ CC BY-NC-SA 3.0])
: 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.
: 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==
* current work: [[User:Timothee_Flutre/Notebook|Notebook]]
* current work: [[User:Timothee_Flutre/Notebook|Notebook]]
* code: [https://github.com/timflutre/ Github]
* 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]
* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://www.scientificredcards.org/ Scientific Red Cards]
* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://www.scientificredcards.org/ Scientific Red Cards]

Revision as of 17:39, 31 January 2013

Contact Info

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

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