User:Timothee Flutre: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(add PhD thesis + link)
(mention open access articles with their license)
Line 22: Line 22:
* ''Roadmap for annotating transposable elements in eukaryote genomes.''
* ''Roadmap for annotating transposable elements in eukaryote genomes.''
*: Permal E, '''Flutre T''', Quesneville H.
*: Permal E, '''Flutre T''', Quesneville H.
*: 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])
*: 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)


* ''TriAnnot: A versatile and high performance pipeline for the automated annotation of plant genomes.''
* ''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.
*: 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 ([http://dx.doi.org/10.3389/fpls.2012.00005 DOI])
*: 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])


* ''In search of lost trajectories: Recovering the diversification of transposable elements.''
* ''In search of lost trajectories: Recovering the diversification of transposable elements.''
*: '''Flutre T''', Permal E, Quesneville H.
*: '''Flutre T''', Permal E, Quesneville H.
*: Mob Genet Elements. 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/22016865 Pubmed])
*: Mob Genet Elements. 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/22016865 Pubmed], Open Access)


* ''Considering transposable element diversification in de novo annotation approaches.''
* ''Considering transposable element diversification in de novo annotation approaches.''
*: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
*: '''Flutre T''', Duprat E, Feuillet C, Quesneville H.
*: PLoS One. 2011 ([http://dx.doi.org/10.1371/journal.pone.0016526 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/21304975 Pubmed])
*: 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])


* ''L'annotation des éléments transposables par la compréhension de leur diversification''
* ''L'annotation des éléments transposables par la compréhension de leur diversification''
*: '''Flutre T''', supervised by Quesneville H and Feuillet C.
*: '''Flutre T''', supervised by Quesneville H and Feuillet C.
*: PhD thesis, Université Paris Diderot, 2010 ([http://tel.archives-ouvertes.fr/tel-00560242 TEL])
*: PhD thesis, Université Paris Diderot, 2010 ([http://tel.archives-ouvertes.fr/tel-00560242 TEL], Accès Libre)


* ''Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.''
* ''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.
*: 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.
*: Proc Natl Acad Sci U S A. 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/20388903 Pubmed])
*: Proc Natl Acad Sci U S A. 2010 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/20388903 Pubmed], Open Access)


* ''Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.''
* ''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.
*: 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.
*: Nat. Biotechnol. 2008 ([http://dx.doi.org/10.1038/nbt.1482 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/18660804 Pubmed])
*: Nat. Biotechnol. 2008 ([http://dx.doi.org/10.1038/nbt.1482 DOI], [http://www.ncbi.nlm.nih.gov/pubmed/18660804 Pubmed], Open Access: license [http://creativecommons.org/licenses/by-nc-sa/3.0/ CC BY-NC-SA 3.0])


==My useful links==
==My useful links==

Revision as of 07:02, 20 May 2012

Contact Info

Timothee Flutre (an artistic interpretation)
  • Timothée Flutre
  • Affiliation 1: University of Chicago (Department of Human Genetics), CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
  • Affiliation 2: INRA (Department of Plant Breeding), 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. Genetics and genomics
  2. Transposable elements
  3. Statistical modeling (especially Bayesian)

Publications

  • Roadmap for annotating transposable elements in eukaryote genomes.
    Permal E, Flutre T, Quesneville H.
    Mobile Genetics Elements: Protocols and Genomic Applications, Springer. 2012 (DOI, Pubmed, Closed Access)
  • 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)
  • In search of lost trajectories: Recovering the diversification of transposable elements.
    Flutre T, Permal E, Quesneville H.
    Mob Genet Elements. 2011 (DOI, Pubmed, Open Access)
  • Considering transposable element diversification in de novo annotation approaches.
    Flutre T, Duprat E, Feuillet C, Quesneville H.
    PLoS One. 2011 (DOI, Pubmed, Open Access: CC BY 2.5)
  • 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 (TEL, Accès Libre)
  • 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.
    Proc Natl Acad Sci U S A. 2010 (DOI, Pubmed, Open Access)
  • 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.
    Nat. Biotechnol. 2008 (DOI, Pubmed, Open Access: license CC BY-NC-SA 3.0)

My useful links

Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Timothee_Flutre&oldid=603427"