Bioinformatics

Group leader:
Alain Lecharny »
lecharny@evry.inra.fr
+33 1 60 87 45 18 and
+33 1 69 15 34 04

Table of Content

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Running Projects
Genome wide characterization of gene expression regulation in plants

Topological organization of regulatory sequences in promoters - Véronique Brunaud
Orphan and orthologous genes in plants - Sébastien Aubourg
Statistical methods for microarray data - Marie-Laure Martin Magniette

Structural and functional plant genome annotation

Prediction of protein-protein interactions in Arabidopsis - Sébastien Aubourg
Annotation of grape genome - Sébastien Aubourg
Improvement of the Arabidopsis genome annotation – Sébastien Aubourg

Other Projects

A model for T-DNA integration in Arabidopsis thaliana - Véronique Brunaud
The terpenoid synthase gene family in Arabidopsis - Sébastien Aubourg
Transcription factors in REGULATORS -Alain Lecharny

Publications

Publications of the Bioinformatics Group

Miscellaneous

Previous Members

Sébastien Aubourg
CR 1 INRA
Sebastien.Aubourg@...
+33 1 60 87 45 16

Virginie Bernard
PhD
Virginie.Bernard@...
+33 1 60 87 45 18

Véronique Brunaud
IR2 INRA
Veronique.Brunaud@...
+33 1 60 87 45 14

Sandra Derozier
CDD INRA
sandra.derozier@...
+33 1 60 87 45 37

Cécile Guichard
IE2 INRA
Cecile.Guichard@...
+33 1 60 87 45 37

Marie-Laure Martin-Magniette
CR1 INRA
Marie-Laure.Martin@...
+33 1 60 87 45 18

Franck Samson
IE2 INRA
Franck.Samson@...
+33 1 60 87 45 15

Jean-Phillipe Tamby
IE2 INRA
tamby@versailles.inra.fr
+33 1 60 87 45 16

Goals

We use topological organization of genomic components, T-DNA integration sites, genes, regulatory elements and protein modules, as a likely source of information on their function. We build databases to integrate genomic data around the Arabidopsis genome and develop bioinformatics tools to help in data mining and data sharing between Arabidopsis and the plants of agronomical interest studied at the URGV.

From the topological organization towards the mechanisms of regulation of gene transcription. Microarray data may be analysed in two directions:

(a) starting from hierarchical clusters of genes to make a syntaxical analysis of promoters;
(b) starting by a topological description of regulatory elements then used to explain the hierarchical clusters of genes.

topological organization of genomic components

Topological organization of regulatory sequences in promoters

Group leader: Alain Lecharny
PI: Véronique Brunaud (IR2-INRA)
Participants :
Virginie Bernard (MASTER-P, PhD grant, MENRS),
Alain Lecharny (DR2-CNRS)
Key words: cartography of promoters

A new tool for the detection of short motifs potentially involved in the control of gene expression has been developed. The originality of this approach is based on the concept that some regulatory elements should have preferred positions in regard to the transcription start site. This method, applied to the Arabidopsis thaliana genome, defines automatically a list of candidate motifs in three steps. We validate the set of promoters by the preferential position of TATA boxes and evaluate the method by its application to an example of biological interest, the motifs present in a family of genes, the DEAD-box RNA helicases.

Publications

Sélection de motifs candidates pour la régulation des gènes chez Arabidopsis thaliana sur des critères topologiques.

JOBIM 2006 external Journées Ouvertes Biologie Informatique et Mathématiques. Bordeaux, France. 5-7 juillet 2006, Actes Session 1, 17-28
224cp Bernard V., Brunaud V., Serizet C., Martin-Magniette M.-L., Caboche M., Aubourg S. & Lecharny A.

Mingam A, Toffano-Nioche C, Brunaud V, Boudet N, Kreis M, Lecharny A
DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes.
Plant Biotechnol J. 2004 Sep;2(5):401-15. PMID : 17168887

Orphan and orthologous genes in plants

PI: Sébastien Aubourg (CR1-INRA)
Participants : David Armisen PhD, Marie Curie grant external
Alain Lecharny
Key words: orphan genes, orthologues, Arabidopsis, rice

In a moment where several species genome had been completely sequenced and many on going projects are at work to increase the number of available sequenced species, it becomes necessary to apply approaches that permit to use the available information of sequencing and characterization of plant model to infer knowledge on plants with agronomical interests. Orthologous relationships can play a key role on this knowledge transfer as can be used to define genes pairs that have evolved directly from an ancestral gene following a speciation event while conserving, often, a similar biological functions and expression patterns. Following a "phylogenetic footprinting" approach, an idea firstly introduced by Tagle et al (1988), the expected conservation of cis-elements responsible of transcriptional regulation on these genes promoters would have a higher selective pressure and, therefore, a lower divergence rate than the rest of promoter regions. The identification of cis-elements responsible for specific patterns of transcriptional regulation would permit then, to link unknown to known genes and infer their hypothetical functions, expression levels, etc. by an inverse search or "reverse phylogenetic footprinting". However, the identification of these cis-elements is not easy as their positions normally vary up to ~1 kb from TSS and many times the promoter’s divergence is not big enough, specially on closely related species, to distinguish between cis-elements and conserved non-functional non-coding regions.

Statistical methods for microarray data

PI: Marie-Laure Martin-Magniette
The need of statistical methods to analyze the data of DNA microarray appeared very quickly. The abundance of the data requires automatic methods which take their technical and biological variabilities into account. The objective of this project is to develop statistical methods to analyse microarray data.

Analysis of CATMA arrays produced by the team 'Analyse Of Transcriptome' led by Jean Pierre Renou . Software in R was written to normalise raw data and to determine genes differentially expressed using statistical tests. This work is a collaboration with the Statistics and Genome team of UMR AgroParisTech/INRA MIA 518 .
All functions were generalized for other arrays and are in a R package named anapuce.
All these C A T M A data are stored in a database C A T d b and are used to investigate gene functional analysis.
In collaboration with the Select team of INRIA Futurs . We study model-based clustering to determine co-expressed genes (PhD of Cathy Maugis).
Analysis of the tiling array of chromosome 4 produced by the team 'Functional Genomics and Epigenetics' led by Vincent Colot. For expression data, Software in R was written to normalise raw data and to determine genes differentially expressed using statistical tests. The tiling array is also used to perform ChIP-chip experiments and we devise statistical methods to interpret them.

Other external collaboration: MIA-Jouy team.

Publications:

Marie-Laure Martin-Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, Frederic Magniette, Jean-Pierre Renou and Jean-Jacques Daudin
Normalization for triple-target microarray experiments
BMC Bioinformatics. 2008 Apr 28;9(1):216 PMID: 18442385

Ramel F, Sulmon C, Cabello-Hurtado F, Taconnat L, Martin-Magniette ML, Jean-Pierre Renou, Elamrani A, Couee I, Gouesbet G.
Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance.
BMC Genomics. 2007 Dec 5;8(1):450 PMID: 18053238

1569 1855 Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.
Evaluation of the gene-specific dye bias in cDNA microarray experiments.
Bioinformatics. 2005 May 1;21(9):1995-2000. Epub 2005 Feb 2. PMID: 15691855

Prediction of protein-protein interactions in Arabidopsis

PI: Sébastien Aubourg
Collaborations: Claire Lurin
Funding: This project APPI (2003-2005) is financed by the ACI IMP Bio external (Informatique, Mathématiques, Physique en Biologie moléculaire)
Keywords : interactions, Rosetta Stone, positional regulation, PFAM motifs, evolution, relationship structure-function

As for prokaryotes, the topological organization of genes along the chromosomes of eukaryotes is under a positive selection depending on the nature of gene function. A particular case is when two sequences coding two different protein domains are observed both separately in two genes, the component genes, and together in one gene, the composite gene. These situations may be efficiently used for the functional annotation of genomes. In plants, rare occurrences of evolutionary or functional relationships between genes either duplicated in tandem or merged have been described. For instance, we have characterized the multigene family of terpene synthases in Arabidopsis thaliana and showed some occurrences of genes in tandem and coding for two enzymes, TPS and GGPS, involved in the same metabolic pathway. In this project, we use an exhaustive approach of the topological associations of protein domains to contribute to the study of the interactome of the model plant Arabidopsis thaliana. The bioinformatics part of the project is an exhaustive search of the conserved organizations of topologically associated genes and of composite genes.

Bioinformatics - Prediction of protein-protein interactions in Arabidopsis

The bioinformatics prediction step is ended and the experimental validation of the protein-protein interactions is in progress in the team of Claire Lurin. The confirmed results will be available through the database FLAGdb++ external .

Annotation of grape genome

PI: Sébastien Aubourg (CR1-INRA)
Participants: Cécile Guichard, Franck Samson

Collaboration:

Coordination of the grapevine project: Anne-Françoise Adam-Blondon
Sequencing : Francis Quétier quetier@genoscope.cnrs.fr
Annotation in Genoscope : Olivier Jaillon ojaillon@genoscope.cns.fr
EuGène support: Thomas Schiex tschiex@toulouse.inra.fr
and Jérome Gouzy gouzy@toulouse.inra.fr
cDNA project : Christian Clépet
MIGALE platform, INRA-MIG team: Christophe Caron christophe.caron@jouy.inra.fr

Links:

Grapevine and Forest Trees Genomics team at URGV
Vitis vinifera at Genoscope
EuGène at BIA
The Vitis genome in FLAGdb++
The MIGALE platform

The genomic sequences generated and clustered by GENOSCOPE external will be annotated using different approaches. The annotation will be carried out at GENOSCOPE by a pipeline including the EXOFISH tool and at URGV by the integrated predictions of the EuGène software (collaboration B I A, INRA Toulouse) The final annotation and the results of the different predictive approaches will be available at Genoscope (Genome Browser) and at URGV through the FLAGdb++ external application allowing data navigation and analysis at the genomic scale. The annotation release will be synchronised with the availability of the full-length cDNA clones and sequences obtained in this project.

The storage of the grape genomic sequences and annotations in FLAGdb++ external should also help in the functional interpretation of transcriptome data obtained from the URGV-Affymetrix platform and for which a grape DNA chip is available.

We have also characterized the Vitis Terpene Synthase and the Stilbene Synthase families in collaboration with Philippe Hugueney, hugueney@colmar.inra.fr and compared them with Arabidopsis: The terpenoid synthase gene family in Arabidopsis - Sébastien Aubourg.

Publications:

Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain, Clémence Bruyère, Alain Billault, Béatrice Segurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattonaro, Véronique Anthouard, Virginie Vico, Cristian Del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny , Claude Scarpelli, François Artiguenave, M. Enrico Pè, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier & Patrick Wincker
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
Nature 449, 463-467 (27 September 2007) | doi:10.1038/nature06148; Received 5 April 2007; Accepted 7 August 2007; Published online 26 August 2007 PMID: 17721507

Improvement of the Arabidopsis genome annotation

PI : Sébastien Aubourg (CR1-INRA)
Participants:
Véronique Brunaud, Marie-Laure Martin-Magniette, Alain Lecharny, Jean-Pierre Renou and his group, Vincent Thareau and all the GeneFarm Network

GeneFarm db external
Swiss-Prot plant section

Publications:

Sébastien Aubourg, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Alain Lecharny, Jean-Pierre Renou
Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.
BMC Genomics. 2007 Nov 2;8(1):401 PMID: 17980019

Aubourg S, Brunaud V, Bruyere C, Cock M, Cooke R, Cottet A, Couloux A, Dehais P, Deleage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlne 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, Riviere S, Rombauts S, Rouze P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M and Lecharny A
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D641-6. PMID: 15608279

A model for T-DNA integration in Arabidopsis thaliana

PI: Véronique Brunaud
Participants:
Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Curaud C, DeRose R, Pelletier G, Lecharny A. Lepiniec L.
Funding: The FLAGdb/FST project is supported by Génoplante external .
FLAGdb/FST has been registered at APP under the key IDDN.FR.001.380012.00.R.P.2001.000.10300.
Keywords : Arabidopsis, database, FST (Flanking Sequence Tag), genome, T-DNA, insertion mutant.

ADT 29 FST Poster (.ppt 301KB)

A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France. The molecular characterisation of the insertion sites is currently performed by sequencing genomic regions flanking the inserted T-DNA (FST). The almost complete sequence of the nuclear genome of A.thaliana provides the framework for organising FSTs in a genome oriented database, FLAGdb/FST. The main scope of FLAGdb/FST is to help biologists to find the FSTs that interrupt the genes in which they are interested. FSTs are anchored to the genome sequences of A.thaliana and positions of both predicted genes and FSTs are shown graphically on sequences. Requests to locate the genomic position of a query sequence are made using BLAST programs. The response delivered by FLAGdb/FST is a graphical representation of the putative FSTs and of predicted genes in a 20 kb region.

FST data are now acessible in F L A G d b + + external

The thousands of FST produced have been used to characterize and understand the different molecular steps of the T-DNA integration in the genome. The unsolved question of preferential insertion sites is approached, in collaboration with the L. Lepiniec team (INRA-Versailles). The high number of FST and the available whole Arabidopsis genome allow one of the first statistical study on the nature of the T-DNA insertion sites. The localization of the sites is correlated to other features such the base composition, the gene density and the sequence nature (coding/uncoding, intron/exon, repeat sequences, promoter, UTR...). Results show that T-DNA insertion involves sequence microhomologies and clarify the molecular model described by Tinland (1995).

Publications

Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Curaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A.
T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites.
EMBO Rep. 2002 Dec;3(12):1152-7. Epub 2002 Nov 21. PMID: 12446565

Samson F, Brunaud V, Balzergue S, Dubreucq B, Lepiniec L, Pelletier G, Caboche M, Lecharny A.
FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.
Nucleic Acids Res. 2002 Jan 1;30(1):94-7. PMID: 11752264

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

Biotechniques. 2001 Mar;30(3):496-8, 502, 504. PMID: 11252785
141 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.
INRA, Evry, France.

The terpenoid synthase gene family in Arabidopsis

PI: Sébastien Aubourg
Collaboration: Jörg Bohlmann external
Keywords : gene evolution, secondary metabolism, isoprenoid, terpene cyclase, prenyl transferase.

The Arabidopsis thaliana genome contains 40 terpenoid synthases (AtTPS). Surprisingly, thirty AtTPS closely resemble in all aspects of gene architecture, sequence relatedness and phylogenetic placement the plant monoterpene synthases, sesquiterpene synthases or diterpene synthases, characteristic of secondary metabolism. Several AtTPS genes are organized in tandem repeats and some AtTPS are localized with prenyltransferase genes in contiguous genomic clusters of consecutive steps of terpenoid biosynthesis. Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of the TPS gene family.

Bioinformatics - The terpenoid synthase gene family in Arabidopsis - AtTPS

Intron-exon structure of the AtTPS genes

Topological organization of the AtTPS gene family

Predicted Sequences of the AtTPS Family

Publications

Aubourg S, Lecharny A, Bohlmann J.
Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana.
Mol Genet Genomics. 2002 Aug;267(6):730-45. Epub 2002 Jun 29. PMID: 12207221

Bohlmann J, Gershenzon J, Aubourg S
Biochemical, molecular genetic and evolutionary aspects of defense-related terpenoid metabolism in conifers.
EVOLUTION OF METABOLIC PATHWAYS Elsevier Science, Amsterdam, pp. 109-149 JUN-2000 ISBN-13: 978-0-08-043860-3 ISBN-10: 0-08-043860-1

Transcription factors in REGULATORS

PI: Alain Lecharny (DR2-CNRS)
Participants: Magalie Leveugle (Post-doctoral grant, GENOPLANTE Trilateral)
Key words: transcription factors, binding sites
Funding: GENOPLANTE external
Collaborators: George Coupland (Coordinator) , Detlef Weigel , Javier Paz Ares, Pilar Carbonero and Vincent Colot.

The REGULATORS programme exploits inter-species conservation in promoter sequences to identify regulators of agronomic performance. We re-evaluated the Arabidopsis genes that encode potential or known TF. Results will be available soon through a web site (Regulators-TF) allowing queries by family or single locus names or keywords. Gene and family names are linked to detailed information (such as sequence, gene structure) in the FLAGdb++ database external .

Publications of the Bioinformatics Group (Since 2001)

2008 2007 2006 2005 2004 2003 2002 2001

Armisén D, Lecharny A, Aubourg S.
Unique genes in plants: specificities and conserved features throughout evolution.
BMC Evol Biol. 2008 Oct 10;8:280. PMID: 18847470

Benhamed M, Martin-Magniette ML, Taconnat L, Bitton F, Servet C, De Clercq R, De Meyer B, Buysschaert C, Rombauts S, Villarroel R, Aubourg S, Beynon J, Bhalerao RP, Coupland G, Gruissem W, Menke FL, Weisshaar B, Renou JP, Zhou DX, Hilson P.
Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5.
Plant J. 2008 Jul 4. PMID: 18644002

Marion Dalmais, Julien Schmidt, Christine Le Signor, Francoise Moussy, Judith Burstin, Vincent Savois, Gregoire Aubert, Veronique Brunaud, Yannick de Oliveira, Cecile Guichard, Richard Thompson and Abdelhafid Bendahmane
UTILLdb, a Pisum sativum in silico forward and reverse genetics tool
Genome Biology 2008, 9:R43 doi:10.1186/gb-2008-9-2-r43 PMID: 18302733

Moroldo M, Paillard S, Marconi R, Fabrice L, Canaguier A, Cruaud C, De Berardinis V, Guichard C, Brunaud V, Le Clainche I, Scalabrin S, Testolin R, Di Gaspero G, Morgante M, Adam-Blondon AF.
A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.
BMC Plant Biol. 2008 Jun 13;8:66. PMID: 18554400

Navajas M, Migeon A, Alaux C, Martin-Magniette M, Robinson G, Evans J, Cros-Arteil S, Crauser D, Le Conte Y.
Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection.
BMC Genomics. 2008 Jun 25;9:301. PMID: 18578863

Marie-Laure Martin-Magniette*¹², Julie Aubert¹, Avner Bar-Hen ⁴, Samira Elftieh² , Frederic Magniette³, Jean-Pierre Renou² and Jean-Jacques Daudin¹
Normalization for triple-target microarray experiments
BMC Bioinformatics. 2008 Apr 28;9(1):216 PMID: 18442385

Elis S, Batellier F, Couty I, Balzergue S, Martin-Magniette ML, Monget P, Blesbois E, Govoroun MS.
Search for the genes involved in oocyte maturation and early embryo development in the hen.
BMC Genomics. 2008 Feb 29;9(1):110 PMID: 18312645

Cossegal M, Chambrier P, Mbelo S, Balzergue S, Martin-Magniette ML, Moing A, Deborde C, Guyon V, Perez P, Rogowsky P.
Transcriptional and metabolic adjustments in AGPase deficient bt2 maize kernels.
Plant Physiol. 2008 Feb 20 PMID: 18287491

Ruffel S, Freixes S, Balzergue S, Tillard P, Jeudy C, Martin-Magniette ML, van der Merwe MJ, Kakar K, Gouzy J, Fernie AR, Udvardi M, Salon C, Gojon A, Lepetit M.
Systemic signaling of the plant N status triggers specific transcriptome responses depending on the N source in Medicago truncatula.
Plant Physiol. 2008 Feb 20 PMID: 18287487

Chantret N, Salse J, Sabot F, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Leroy P, Bernard M, Boulos Chalhoub
Contrasted Microcolinearity and Gene Evolution Within a Homoeologous Region of Wheat and Barley Species.
J Mol Evol. 2008 Feb 15 PMID: 18274696

Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Sébastien Aubourg, Alain Lecharny, Jean-Pierre Renou, Brunaud V.
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform.
Nucleic Acids Res. 2008 Jan;36(Database issue):D986-90. Epub 2007 Oct 16. PMID: 17940091

2007

Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Christian Clepet, Sébastien Aubourg, Rameau C, Michel Caboche, Abdel Ihafid Bendahmane
Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea.
Plant J. 2007 Sep;51(6):1116-25. Epub 2007 Jul 25. PMID: 17651368

Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain, Clémence Bruyère, Alain Billault, Béatrice Segurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattonaro, Véronique Anthouard, Virginie Vico, Cristian Del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny, Claude Scarpelli, François Artiguenave, M. Enrico Pè, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier & Patrick Wincker
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
Nature 449, 463-467 (27 September 2007) | doi:10.1038/nature06148; Received 5 April 2007; Accepted 7 August 2007; Published online 26 August 2007 PMID: 17721507

Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G,Colot V.
Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27.
PLoS Genet. 2007 Jun;3(6):e86. Epub 2007 Apr 17. PMID: 17542647

2006

L'organisation des génomes végétaux révélée par leur annotation.

Biofutur, Vol 25/265 - 2006 - pp.33-37
Aubourg S., Delseny M. and Lecharny A. (2006)
Depuis une dizaine d'années, la communauté internationale des génomistes a considérablement investi dans la caractérisation d'une sélection de génomes végétaux modèles. Les connaissances déduites des séquences génomiques servent maintenant de socle à la compréhension de l'organisation et de l'évolution des génomes, à l'obtention de données fonctionnelles et à leur analyse intégrative.
Biofutur,(Subscribers Only) external

2005

Jammes F, Lecomte P, de Almeida-Engler J, Bitton F, Martin-Magniette ML, Renou JP, Abad P, Favery B.
Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis.
Plant J. 2005 Nov;44(3):447-58. PMID: 16236154

Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'.

Bioinformatics. 2005 Jul 15;21(14):3065. Epub 2005 Jun 7. PMID: 15941744
Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.

Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.
Evaluation of the gene-specific dye bias in cDNA microarray experiments.
Bioinformatics. 2005 May 1;21(9):1995-2000. Epub 2005 Feb 2. PMID: 15691855

Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier M-F, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P and Chalhoub B
Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (triticum and aegilops).
Plant Cell. 2005 Apr;17(4):1033-45. Epub 2005 Mar 4. PMID: 15749759

2004

Mingam A, Toffano-Nioche C, Brunaud V, Boudet N, Kreis M and Lecharny A
DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes
Plant Biotechnol J. 2004 Sep;2(5):401-15. PMID: 17168887

Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, Bhalerao RP, Bitton F, Caboche M, Cannoot B, Chardakov V, Cognet-Holliger C, Colot V, Crowe M, Darimont C, Durinck S, Eickhoff H, de Longevialle AF, Farmer EE, Grant M, Kuiper MT, Lehrach H, Leon C, Leyva A, Lundeberg J, Lurin C, Moreau Y, Nietfeld W, Paz-Ares J, Reymond P, Rouze P, Sandberg G, Segura MD, Serizet C, Tabrett A, Taconnat L, Thareau V, Van Hummelen P, Vercruysse S, Vuylsteke M, Weingartner M, Weisbeek PJ, Wirta V, Wittink FR, Zabeau M, Small I.
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.
Genome Res. 2004 Oct;14(10B):2176-89. PMID: 15489341

Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere 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.
Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.
Plant Cell. 2004 Aug;16(8):2089-103. Epub 2004 Jul 21. PMID: 15269332

Lescot M, Rombauts S, Zhang J, Aubourg S, Mathe C, Jansson S, Rouze P and Boerjan W
Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements.
Theor Appl Genet. 2004 Jun;109(1):10-22. Epub 2004 Apr 14. PMID: 15085260

Samson F, Brunaud V, Duchene S, De Oliveira Y, Caboche M, Lecharny A and Aubourg S
FLAGdb++, a database for the functional analysis of the Arabidopsis genome.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D347-50. PMID: 14681431

Un modèle statistique pour l'intégration de l'ADN-T dans le génome d'Arabidopsis thaliana. In « La fluidité des génomes et ses conséquences »

Ed. Commission du Génie Biomoléculaire. (2004)
282 Lecharny A.

2003

Crowe ML, Serizet C, Thareau V, Aubourg S, Rouze P, Hilson P, Beynon J, Weisbeek P, van Hummelen P, Reymond P, Paz-Ares J, Nietfeld W, Trick M.
CATMA: a complete Arabidopsis GST database.
Nucleic Acids Res. 2003 Jan 1;31(1):156-8. PMID: 12519971

Thareau V, Dehais P, Serizet C, Hilson P, Rouze P, Aubourg S.
Automatic design of gene-specific sequence tags for genome-wide functional studies.
Bioinformatics Vol. 19 no. 17 2003, pages 2191–2198 PMID: 14630647

2002

Aubourg S, Lecharny A, Bohlmann J.
Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana.
Mol Genet Genomics. 2002 Aug;267(6):730-45. Epub 2002 Jun 29. PMID: 12207221

2001

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

Previous Members

Armisen, David	PhD (EU grants) GAO Doctoral School UEVE	Oct 06 – Dec 08	Unique genes in plants : Evolution and features
Bailly, Nathalie	Master professionnel Ingenierie en Génomique Fonctionnelle - Paris VII	Mar 05 - Sept 05	Bioinformatics prediction of protein-protein interactions
Balzergue, Sandrine	DESS Ingenierie en Génomique Fonctionnelle - Paris 7	Apr 03 - Aug 03	Improvement of the CATdb database
Bernard, Virginie	Master professionnel de Bioinformatique EGOISt - Rouen	Sept 04 - Sept 06	Study of promoters in Arabidopsis
Blanchet, Marion	DESS Génie Physiologique et Bioinformatique - Poitiers	Feb 03 - Jul 03	Phenotypic database for Arabidopsis seed mutants
Bourgognon, Aȉcha	Training period	Feb 06 - Aug 06	FLAGdb data control
Bruyère, Clémence	DESS Compétences Complémentaires en Informatique - Evry CDD ANR	Apr 02 - Sept 02 Feb 06 - Mar 08	Development of interfaces for the FLAGdb++ database Grapevine genome annotation
Duchene, Sylvain	CDD Genoplante	Jun 02 - Jun 04	Integration of data and development of interfaces for the FLAGdb++ database
Filippi, Ghislain	CDD Genoplante	Apr 02 - Oct 03	The GeneFarm database
Gagnot, Séverine	IE2 CNRS	Nov 07 - Jul 08	CATdb and FLAGdb
Guichard, Cécile	CDD Genoplante CDD ANR	Apr 02 - Oct 03 Sep 04 - Nov 04	Development of tools for comparative genomics UTILLdb
Leveugle, Magalie	Post-Doc trilateral	May 05 - Oct 07	Arabidopsis transcription factors (REGULATORs)
Luyten, Isabelle	Master Spécialisé en Bioinformatique - Evry	Apr 02 - Oct 02	Improvement of the FLAGdb++ database
Martinez, Kelly	DESS Bioinformatique pour la Génomique -Clermont-Ferrand	Apr 02 - Sept 02	Integration of structural annotations in the FLAGdb++ database
Moukthasser, Sonia	DESS Informatique et Applications aux Sciences de la Vie- Paris V	Apr 04 - Sept 04	Implementation of CATdb interfaces and data export
de Oliveira, Yannick	DESS Etude des Génomes, Outils Informatiques et Statistiques - Rouen CDD Genoplante	Oct 02 - Oct04 Dec 04 - May 05	Integration of PFAM motifs and protein families in the FLAGdb++ database and their exploitation Updating of FLAGdb++ data
Ory-Salam, Christine	Master Compétence Complémentaire en Informatique –Evry	Mar 06 – Sept 06	Development of information system for Vitis genetic markers
Poidevin, Laetitia	DESS Ressources Génomique et Traitements Informatiques - Nancy	Mar 04 - Sept 04	Integration of organit genomes in the FLAGdb++ database
Pommier, Cyril	DEA Application des Mathématiques et de l'Informatique à la Biologie - Evry CDD Genoplante	Feb 03 - Jun 03 May 04 - Oct 04	Relationships between topology and gene function in Arabidopsis Improvement of the GeneFarm database.
Serizet, Carine	POST-DOC INRA (BV)	Oct 03 - Apr05	Study of Arabidopsis promoters at the genome scale