User:Timothee Flutre

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)

• 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)

• In search of lost trajectories: Recovering the diversification of transposable elements.

  Flutre T, Permal E, Quesneville H.

  Mob Genet Elements. 2011 (DOI, Pubmed)

• Considering transposable element diversification in de novo annotation approaches.

  Flutre T, Duprat E, Feuillet C, Quesneville H.

  PLoS One. 2011 (DOI, Pubmed)

• 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)

• 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)

• 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)

My useful links

• current work: Notebook
• code: Github
• bibliography: CiteULike
• labs: PhD, postdoc
• volunteering: Paris-Montagne, Scientific Red Cards