User:Timothee Flutre

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 published papers are listed on CiteULike, as well as retrieved by Pubmed and Google Scholar, and some preprints are available on arXiv.

• 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, Pubmed, Open Access after 6 months)

• 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.

  Mobile Genetics 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)

  package REPET (free software under CeCILL)

• 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)

• 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, 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.

  Nature Biotechnology. 2008 (DOI, Pubmed, Open Access: CC BY-NC-SA 3.0)

My useful links

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