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Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors.

Castrillo G, Turck F, Leveugle M, Lecharny A, Carbonero P, Coupland G, Paz-Ares J, Oñate-Sánchez L.

PLoS One. 2011;6(6):e21524. doi: 10.1371/journal.pone.0021524. Epub 2011 Jun 27.


Exploration of plant genomes in the FLAGdb++ environment.

Dèrozier S, Samson F, Tamby JP, Guichard C, Brunaud V, Grevet P, Gagnot S, Label P, Leplé JC, Lecharny A, Aubourg S.

Plant Methods. 2011 Mar 29;7:8. doi: 10.1186/1746-4811-7-8.


Improved detection of motifs with preferential location in promoters.

Bernard V, Lecharny A, Brunaud V.

Genome. 2010 Sep;53(9):739-52. doi: 10.1139/g10-042.


TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.

Bernard V, Brunaud V, Lecharny A.

BMC Genomics. 2010 Mar 12;11:166. doi: 10.1186/1471-2164-11-166.


Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis.

Deveaux Y, Toffano-Nioche C, Claisse G, Thareau V, Morin H, Laufs P, Moreau H, Kreis M, Lecharny A.

BMC Evol Biol. 2008 Oct 24;8:291. doi: 10.1186/1471-2148-8-291.


Unique genes in plants: specificities and conserved features throughout evolution.

Armisén D, Lecharny A, Aubourg S.

BMC Evol Biol. 2008 Oct 10;8:280. doi: 10.1186/1471-2148-8-280.


Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.

Aubourg S, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Lecharny A, Renou JP.

BMC Genomics. 2007 Nov 2;8:401.


CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform.

Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Aubourg S, Renou JP, Lecharny A, Brunaud V.

Nucleic Acids Res. 2008 Jan;36(Database issue):D986-90. Epub 2007 Oct 16.


The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P; French-Italian Public Consortium for Grapevine Genome Characterization.

Nature. 2007 Sep 27;449(7161):463-7. Epub 2007 Aug 26.


DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes.

Mingam A, Toffano-Nioche C, Brunaud V, Boudet N, Kreis M, Lecharny A.

Plant Biotechnol J. 2004 Sep;2(5):401-15.


Formation of the Arabidopsis pentatricopeptide repeat family.

Rivals E, Bruyère C, Toffano-Nioche C, Lecharny A.

Plant Physiol. 2006 Jul;141(3):825-39.


GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.

Aubourg S, Brunaud V, Bruyère C, Cock M, Cooke R, Cottet A, Couloux A, Déhais P, Deléage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlné G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J, Risler JL, Rivière S, Rombauts S, Rouzé P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M, Lecharny A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D641-6.


Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.

Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I.

Plant Cell. 2004 Aug;16(8):2089-103. Epub 2004 Jul 21.


FLAGdb++: a database for the functional analysis of the Arabidopsis genome.

Samson F, Brunaud V, Duchêne S, De Oliveira Y, Caboche M, Lecharny A, Aubourg S.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D347-50.


Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure.

Lecharny A, Boudet N, Gy I, Aubourg S, Kreis M.

J Struct Funct Genomics. 2003;3(1-4):111-6.


T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites.

Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Cruaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A.

EMBO Rep. 2002 Dec;3(12):1152-7. Epub 2002 Nov 21.


Genomic analysis of the terpenoid synthase ( AtTPS) gene family of Arabidopsis thaliana.

Aubourg S, Lecharny A, Bohlmann J.

Mol Genet Genomics. 2002 Aug;267(6):730-45. Epub 2002 Jun 29.


FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.

Samson F, Brunaud V, Balzergue S, Dubreucq B, Lepiniec L, Pelletier G, Caboche M, Lecharny A.

Nucleic Acids Res. 2002 Jan 1;30(1):94-7.


Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila.

Boudet N, Aubourg S, Toffano-Nioche C, Kreis M, Lecharny A.

Genome Res. 2001 Dec;11(12):2101-14.


Improved PCR-walking for large-scale isolation of plant T-DNA borders.

Balzergue S, Dubreucq B, Chauvin S, Le-Clainche I, Le Boulaire F, de Rose R, Samson F, Biaudet V, Lecharny A, Cruaud C, Weissenbach J, Caboche M, Lepiniec L.

Biotechniques. 2001 Mar;30(3):496-8, 502, 504. No abstract available.

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