User:Timothee Flutre - Revision history

Timothee Flutre: /* Publications */ update eQtlBma paper

Timothee Flutre — Sat, 11 May 2013 17:26:46 GMT

Publications: update eQtlBma paper

←Older revision		Revision as of 17:26, 11 May 2013
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	;10) A statistical framework for joint eQTL analysis in multiple tissues.		;10) A statistical framework for joint eQTL analysis in multiple tissues.
	: '''Flutre T''', Xiaoquan Wen, Jonathan Pritchard, Matthew Stephens.		: '''Flutre T''', Xiaoquan Wen, Jonathan Pritchard, Matthew Stephens.
-	: PLoS Genetics, 2013, ~~accepted~~	+	: PLoS Genetics, 2013, ([http://arxiv.org/abs/1212.4786 arXiv], [http://dx.doi.org/10.1371/journal.pgen.1003486 DOI], Open Access: [http://creativecommons.org/licenses/by/2.5/ CC BY 2.5])
		+	: [http://github.com/timflutre/eqtlbma/wiki eQtlBma] (free software under [http://www.gnu.org/licenses/gpl.html GPL])

	;9) Transposable element annotation in completely sequenced eukaryote genomes.		;9) Transposable element annotation in completely sequenced eukaryote genomes.

Timothee Flutre: /* Publications */ add plos gen paper

Timothee Flutre — Thu, 02 May 2013 05:05:40 GMT

Publications: add plos gen paper

←Older revision		Revision as of 05:05, 2 May 2013
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	==Publications==		==Publications==
	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].		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].
		+
		+	;10) A statistical framework for joint eQTL analysis in multiple tissues.
		+	: '''Flutre T''', Xiaoquan Wen, Jonathan Pritchard, Matthew Stephens.
		+	: PLoS Genetics, 2013, accepted

	;9) Transposable element annotation in completely sequenced eukaryote genomes.		;9) Transposable element annotation in completely sequenced eukaryote genomes.
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	;8) The ABO blood group is a trans-species polymorphism in primates.		;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.	+	: 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 ([http://arxiv.org/abs/1208.4613 arXiv], [http://dx.doi.org/10.1073/pnas.1210603109 DOI], Open Access after 6 months)		: 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)

Timothee Flutre: /* My useful links */

Timothee Flutre — Fri, 01 Feb 2013 00:39:51 GMT

My useful links

←Older revision		Revision as of 00:39, 1 February 2013
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	==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]

Timothee Flutre: /* Publications */ use DOI of chapter instead of ISBN of book + rmv Pubmed IDs

Timothee Flutre — Fri, 01 Feb 2013 00:38:35 GMT

Publications: use DOI of chapter instead of ISBN of book + rmv Pubmed IDs

Timothee Flutre: /* Publications */ add book chapter + reformatting

Timothee Flutre — Fri, 01 Feb 2013 00:18:00 GMT

Publications: add book chapter + reformatting

←Older revision		Revision as of 00:18, 1 February 2013
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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 published papers and book chapters are listed on my [http://www.citeulike.org/user/timflutre/publications CiteULike] account, and can also be retrieved via [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]. 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://www.springer.com/life+sciences/plant+sciences/book/978-3-642-31841-2 ISBN], 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], [http://view.ncbi.nlm.nih.gov/pubmed/23091028 Pubmed], 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], [http://www.ncbi.nlm.nih.gov/pubmed/22367865 Pubmed], 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], [http://www.ncbi.nlm.nih.gov/pubmed/22016865 Pubmed], Open Access)
-	*: package [http://urgi.versailles.inra.fr/Tools/REPET REPET] (free software under [http://en.wikipedia.org/wiki/CeCILL CeCILL])	+

-	* ''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~~ (~~downloadable on~~ [http://~~tel~~.~~archives-ouvertes~~.fr/~~tel-00560242 TEL~~] ~~and~~ [http://www.~~dart-europe~~.eu/~~full~~.~~php?id=629416 DART-Europe~~])	+	: 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])
		+	: [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], [http://www.ncbi.nlm.nih.gov/pubmed/20388903 Pubmed], 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], [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])

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

Timothee Flutre: /* Publications */ add link to REPET and DART

Timothee Flutre — Thu, 17 Jan 2013 19:57:19 GMT

Publications: add link to REPET and DART

←Older revision		Revision as of 19:57, 17 January 2013
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	*: '''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], Open Access: [http://creativecommons.org/licenses/by/2.5/ CC BY 2.5])		*: 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])
		+	*: package [http://urgi.versailles.inra.fr/Tools/REPET REPET] (free software under [http://en.wikipedia.org/wiki/CeCILL CeCILL])

	* ''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]~~, Accès Libre~~)	+	*: 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])

	* ''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.''

Timothee Flutre: /* Publications */ add link to arxiv

Timothee Flutre — Thu, 03 Jan 2013 01:20:06 GMT

Publications: add link to arxiv

←Older revision		Revision as of 01:20, 3 January 2013
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	==Publications==		==Publications==
-	~~List~~ 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].	+	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].

	* ''The ABO blood group is a trans-species polymorphism in primates.''		* ''The ABO blood group is a trans-species polymorphism in primates.''

Timothee Flutre: /* Publications */ add link to arxiv

Timothee Flutre — Thu, 03 Jan 2013 01:10:14 GMT

Publications: add link to arxiv

←Older revision		Revision as of 01:10, 3 January 2013
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	* ''The ABO blood group is a trans-species polymorphism in primates.''		* ''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.		*: 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 ([http://dx.doi.org/10.1073/pnas.1210603109 DOI], [http://view.ncbi.nlm.nih.gov/pubmed/23091028 Pubmed], Open Access after 6 months)	+	*: 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)

	* ''Roadmap for annotating transposable elements in eukaryote genomes.''		* ''Roadmap for annotating transposable elements in eukaryote genomes.''
Line 51:		Line 51:
	* ''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.
-	*: Nature Biotechnology. 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])	+	*: 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])

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

Timothee Flutre: /* Contact Info */

Timothee Flutre — Thu, 03 Jan 2013 01:07:17 GMT

Contact Info

←Older revision		Revision as of 01:07, 3 January 2013
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	[[Image:OWWEmblem.png\|thumb\|right\|Timothee Flutre (an artistic interpretation)]]		[[Image:OWWEmblem.png\|thumb\|right\|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 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	+	* Affiliation 2: INRA (Department of Plant Genetics), URGI, Route de Saint Cyr, Versailles, 78026, France
	* [[Special:Emailuser/Timothee Flutre\|Email me through OpenWetWare]]		* [[Special:Emailuser/Timothee Flutre\|Email me through OpenWetWare]]

Timothee Flutre: /* Research interests */ add some eplanations

Timothee Flutre — Thu, 22 Nov 2012 16:24:39 GMT

Research interests: add some eplanations

←Older revision		Revision as of 16:24, 22 November 2012
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	==Research interests==		==Research interests==
-	# ~~Genetics and~~ genomics	+	# Quantitative genomics (extend classical quantitative genetics with genomics data)
-	# Transposable elements	+	# Transposable elements (bioinformatics analysis of newly-sequenced genomes)
	# Statistical modeling (especially Bayesian)		# Statistical modeling (especially Bayesian)

←Older revision		Revision as of 00:38, 1 February 2013
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	==Publications==		==Publications==
-	All my ~~published papers and book chapters~~ are listed on my [http://www.citeulike.org/user/timflutre/publications CiteULike] account, and can ~~also~~ be retrieved via ~~[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]. When possible (i.e. in agreement with my co-authors), my 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].

	;9) Transposable element annotation in completely sequenced eukaryote genomes.		;9) Transposable element annotation in completely sequenced eukaryote genomes.
	: '''Flutre T''', Permal E, Quesneville H.		: '''Flutre T''', Permal E, Quesneville H.
-	: Plant Transposable Elements: Impact on Genome Structure and Function, Springer, 2012 ([http://~~www~~.~~springer~~.~~com~~/~~life+sciences/plant+sciences/book~~/978-3-642-~~31841~~-~~2 ISBN~~], Restricted Access)	+	: 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)

	;8) The ABO blood group is a trans-species polymorphism in primates.		;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.		: 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 ([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)	+	: 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)

	;7) Roadmap for annotating transposable elements in eukaryote genomes.		;7) 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~~], Restricted Access)	+	: Mobile Genetics Elements: Protocols and Genomic Applications, Springer, 2012 ([http://dx.doi.org/10.1007/978-1-61779-603-6_3 DOI], Restricted Access)

	;6) TriAnnot, a versatile and high performance pipeline for the automated annotation of plant genomes.		;6) TriAnnot, a versatile and high performance pipeline for the automated annotation of plant genomes.
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	;5) In search of lost trajectories, recovering the diversification of transposable elements.		;5) In search of lost trajectories, recovering the diversification of transposable elements.
	: '''Flutre T''', Permal E, Quesneville H.		: '''Flutre T''', Permal E, Quesneville H.
-	: 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)	+	: Mobile Genetics Elements, 2011 ([http://dx.doi.org/10.4161/mge.1.2.17094 DOI], Open Access)

	;4) Considering transposable element diversification in de novo annotation approaches.		;4) 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~~], Open Access: [http://creativecommons.org/licenses/by/2.5/ CC BY 2.5])	+	: 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])		: [http://urgi.versailles.inra.fr/Tools/REPET REPET] (free software under [http://en.wikipedia.org/wiki/CeCILL CeCILL])

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	;2) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.		;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.		: 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 ([http://dx.doi.org/10.1073/pnas.0910413107 DOI~~], [http://www.ncbi.nlm.nih.gov/pubmed/20388903 Pubmed~~], Open Access)	+	: 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.		;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.		: 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~~], [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])	+	: 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==