User:Timothee Flutre

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Starting in January 2014, I will be a research scientist (''Chargé de Rercherche 2e classe'', CR2) at the [http://www.inra.fr/en INRA], in the team "Diversity and Adaptation of Grapevine and Mediterranean Species" ([http://umr-agap.cirad.fr/en/equipes-scientifiques/diversite-et-adaptation-de-la-vigne-et-des-especes-mediterraneennes/objectif DAVEM]) of the lab "Genetic Improvement and Adaptation of Mediterranean and Tropical Plants" ([http://umr-agap.cirad.fr/en/ UMR AGAP]), part of the INRA division "Plant Biology and Breeding" (''Biologie et Amélioration des Plantes'', [http://www.bap.inra.fr/en BAP]). I will be based in the [http://www.montpellier.inra.fr/en INRA centre of Montpellier].
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==Research interests==
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# develop and apply statistical models using genomic information to estimate genetic architectures and predict multiple traits jointly;
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I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics"). In statistical terms, my research will be about prediction (say, predicting the chemical composition of grapevine berries based on information from the genome) and about estimation (say, reconstructing the genetic architecture underlying the chemical composition of grapevine berries).
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# collaborate with researchers, farmers and citizens to breed new varieties of cultivated plants in a sustainable manner.
==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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Until December 2013, I am doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago:
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Since January 2014, I am a research scientist (''Chargé de Rercherche'', CR) at the [http://www.inra.fr/en INRA], in the team "Diversity, Adaptation and Breeding of Grapevine" ([http://umr-agap.cirad.fr/en/scientific-teams/diversity-adaptation-and-breeding-of-grapevine/context-and-goals DAAV]) of the lab "Genetic Improvement and Adaptation of Mediterranean and Tropical Plants" ([http://umr-agap.cirad.fr/en/ UMR AGAP]), part of the INRA division "Plant Biology and Breeding" (''Biologie et Amélioration des Plantes'', [http://www.bap.inra.fr/en BAP]), based in the INRA center of [http://www.montpellier.inra.fr/en Montpellier]. I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics").
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* Affiliation: University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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* INRA, UMR AGAP - bâtiment 21 - 4e étage, 2 place Viala, 34070 Montpellier, France
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* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
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* timothee.flutre[at]supagro.inra.fr
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Until December 2013, I was doing a postdoc with [http://stephenslab.uchicago.edu/ Matthew Stephens] at the University of Chicago.
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* University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
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* tflutre[at]uchicago.edu
I learned about this website, [[OpenWetWare]], thanks to [http://igem.org/Team.cgi?id=18 friends] participating in [http://igem.org iGEM] a few years ago. I joined it because it seems to be a great project, and I like the idea of promoting more openness in science.
I learned about this website, [[OpenWetWare]], thanks to [http://igem.org/Team.cgi?id=18 friends] participating in [http://igem.org iGEM] a few years ago. I joined it because it seems to be a great project, and I like the idea of promoting more openness in science.
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* [[Special:Emailuser/Timothee Flutre|Email me through OpenWetWare]]
==Education==
==Education==
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* 2007-2010, PhD, Université Paris Diderot ([http://www.fdv-paris.org/en/ecole-doctorale-fdv FDV])
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* 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot ([http://cri-paris.org/doctoral-school-fdv/ FDV])
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* 2006-2007, MS, Université Paris Diderot ([http://www.aiv-paris.org/en/master-aiv/ AIV])
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* 2006-2007, MS, interdisciplinary, Université Paris Diderot ([http://cri-paris.org/master-aiv/ AIV])
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* 2003-2007, BS+MS, [http://www.agroparistech.fr/Presentation-of-AgroParisTech.html AgroParisTech]
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* 2003-2007, BS+MS in engineering and life sciences, [http://www.bginette.com/ lycée Sainte Geneviève] and [http://www.agroparistech.fr/Presentation-of-AgroParisTech.html AgroParisTech]
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More details on my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
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See also my [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 online CV].
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==Research interests==
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''to be updated...''
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# Quantitative genomics (extend classical quantitative genetics with genomics data)
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# Transposable elements (bioinformatics analysis of newly-sequenced genomes)
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# Statistical modeling (especially Bayesian)
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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[Author] Pubmed]. When possible (that is, in agreement with my co-authors), my preprints are available on [http://arxiv.org/a/flutre_t_1 arXiv].
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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://prodinra.inra.fr/?locale=en#!Result:%28au:%28Flutre%29%29+status:valid%C3%A9 ProdINRA], [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 (that is, in agreement with my co-authors), my preprints are available online (upon submission, that is before publication, for instance on [http://arxiv.org/a/flutre_t_1 arXiv]).
;11) The Genotype-Tissue Expression (GTEx) project.
;11) The Genotype-Tissue Expression (GTEx) project.
Line 73: Line 72:
: 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.
: 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])
: 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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==Funding==
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* 01/2015-12/2016: grant from metaprogram SelGen from INRA for the '''FruitSelGen project'''
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** topic: "Assessing genomic selection within bi-parental crosses for perennial fruit crops" (grapevine, apple, peach, apricot, cherry)
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** status: investigator and coordinator (6 different INRA labs involved)
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** amount: 114 k€ (no salary)
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* 06/2014-05/2018: grant from CASDAR for the '''EDGARR project'''
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** topic: "Exploitation De la sélection Génomique afin d’Accélérer la création de variétés Résistantes et qualitatives pour la filière viticole Rosé"
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** status: investigator (coordinator is Loïc Le Cunff)
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** amount: 220 k€ (no salary)
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* 06/2014-05/2016: starter grant from department BAP of INRA for the '''SELVI project'''
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** topic: "Genomic selection on grapevine, a feasibility study"
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** status: principal investigator
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** amount: 24 k€ (no salary)
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* 11/2010-08/2013: '''postdoc fellowship''' from INRA (ASC as well as ''Mission des Relations Internationales'', MRI)
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** topic: "Statistical methods for eQTL detection"
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** status: postdoc
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** amount: x k€ (salary only)
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* 09/2007-10/2010: '''PhD fellowship''' from INRA (''Assistant Scientifique Contractuel'', ASC)
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** topic: "The annotation of transposable elements through the understanding of their diversification"
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** status: PhD student
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** amount: x k€ (salary only)
==My useful links==
==My useful links==
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* current work: [[User:Timothee_Flutre/Notebook|Notebook]]
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* notebooks: [[User:Timothee_Flutre/Notebook/Postdoc|Postdoc]], [[User:Timothee_Flutre/Notebook/CR_AGAP|CR AGAP]]
* code: [http://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]
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* labs: [http://urgi.versailles.inra.fr/ PhD], [http://stephenslab.uchicago.edu/ postdoc]
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* labs: [http://umr-agap.cirad.fr/en current], [http://stephenslab.uchicago.edu/ postdoc], [http://urgi.versailles.inra.fr/ PhD]
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* CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn]
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* "social" CV: [http://www.linkedin.com/pub/timoth%C3%A9e-flutre/19/91/165 LinkedIn], [https://www.researchgate.net/profile/Timothee_Flutre/ ResearchGate], [http://orcid.org/0000-0003-4489-4782?lang=en ORCID]
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* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://www.scientificredcards.org/ Scientific Red Cards]
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* volunteering: [http://www.paris-montagne.org/ Paris-Montagne], [http://scientificredcards.wordpress.com/ Scientific Red Cards], [https://en.wikipedia.org/wiki/User:Timflutre Wikipedia]

Current revision

Contents

Research interests

  1. develop and apply statistical models using genomic information to estimate genetic architectures and predict multiple traits jointly;
  2. collaborate with researchers, farmers and citizens to breed new varieties of cultivated plants in a sustainable manner.

Contact Info

Timothee Flutre (an artistic interpretation)
Timothee Flutre (an artistic interpretation)

Since January 2014, I am a research scientist (Chargé de Rercherche, CR) at the INRA, in the team "Diversity, Adaptation and Breeding of Grapevine" (DAAV) of the lab "Genetic Improvement and Adaptation of Mediterranean and Tropical Plants" (UMR AGAP), part of the INRA division "Plant Biology and Breeding" (Biologie et Amélioration des Plantes, BAP), based in the INRA center of Montpellier. I have been recruited on the profile "Quantitative genetics and genomics" (topic "Genomic selection and grapevine genetics").

  • INRA, UMR AGAP - bâtiment 21 - 4e étage, 2 place Viala, 34070 Montpellier, France
  • timothee.flutre[at]supagro.inra.fr

Until December 2013, I was doing a postdoc with Matthew Stephens at the University of Chicago.

  • University of Chicago, Department of Human Genetics, CLSC, 5801 S Ellis Ave, Chicago, IL 60637, USA
  • tflutre[at]uchicago.edu

I learned about this website, OpenWetWare, thanks to friends participating in iGEM a few years ago. I joined it because it seems to be a great project, and I like the idea of promoting more openness in science.

Education

  • 2007-2010, PhD in bioinformatics and evolutionary genomics, Université Paris Diderot (FDV)
  • 2006-2007, MS, interdisciplinary, Université Paris Diderot (AIV)
  • 2003-2007, BS+MS in engineering and life sciences, lycée Sainte Geneviève and AgroParisTech

See also my online CV.

Publications

All my publications are listed below as well as on my CiteULike account, and can be retrieved via ProdINRA, Google Scholar and Pubmed. When possible (that is, in agreement with my co-authors), my preprints are available online (upon submission, that is before publication, for instance on arXiv).

11) The Genotype-Tissue Expression (GTEx) project.
Lonsdale, ..., Flutre T, ..., et al.
Nature Genetics, 2013 (DOI, Open Access: CC BY-NC-SA 3.0)
10) A statistical framework for joint eQTL analysis in multiple tissues.
Flutre T*, Wen X*, Pritchard J, Stephens M.
PLoS Genetics, 2013 (arXiv, DOI, Open Access: CC BY 2.5)
eQtlBma (free software under GPL)
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, Venkat A, 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)

Funding

  • 01/2015-12/2016: grant from metaprogram SelGen from INRA for the FruitSelGen project
    • topic: "Assessing genomic selection within bi-parental crosses for perennial fruit crops" (grapevine, apple, peach, apricot, cherry)
    • status: investigator and coordinator (6 different INRA labs involved)
    • amount: 114 k€ (no salary)
  • 06/2014-05/2018: grant from CASDAR for the EDGARR project
    • topic: "Exploitation De la sélection Génomique afin d’Accélérer la création de variétés Résistantes et qualitatives pour la filière viticole Rosé"
    • status: investigator (coordinator is Loïc Le Cunff)
    • amount: 220 k€ (no salary)
  • 06/2014-05/2016: starter grant from department BAP of INRA for the SELVI project
    • topic: "Genomic selection on grapevine, a feasibility study"
    • status: principal investigator
    • amount: 24 k€ (no salary)
  • 11/2010-08/2013: postdoc fellowship from INRA (ASC as well as Mission des Relations Internationales, MRI)
    • topic: "Statistical methods for eQTL detection"
    • status: postdoc
    • amount: x k€ (salary only)
  • 09/2007-10/2010: PhD fellowship from INRA (Assistant Scientifique Contractuel, ASC)
    • topic: "The annotation of transposable elements through the understanding of their diversification"
    • status: PhD student
    • amount: x k€ (salary only)

My useful links

Personal tools