Bioinformatics for Predictive Genomics

Group leader:
Sébastien Aubourg
aubourg@evry.inra.fr
+33 1 60 87 45 16

Sebastien Aubourg Portrait

Table of Contents
Prediction of gene networks involved in plant stress responses
Statistical methods for omics analysis
Data integration and gene family annotation
 
Publications
Previous Members

Veronique Brunaud Portrait

Véronique Brunaud
IR1 INRA
Veronique.Brunaud@evry.inra.fr
+33 1 60 87 45 14

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Cecile Guichard Portrait

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

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Guillem Rigaill

Guillem Rigaill
MCF UEVE-INRA
guillem.rigaill@evry.inra.fr
+33 1 60 87 45 18

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Jean-Phillipe Tamby Portrait

Jean-Phillipe Tamby
IE2 INRA
tamby@evry.inra.fr
+33 1 60 87 45 15

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Rim Zaag

Rim Zaag
PhD UEVE
Rim.zaag@evry.inra.fr
+33 1 60 87 45 37

Prediction of gene networks involved in plant stress responses

PI: S. Aubourg, ML Martin-Magniette
The objective of this running project is to take advantage of the transcription re-programming that occurs in stressed plants in order to assign orphan-of-function genes to plant responses to environment and to predict relational annotations between genes involved in stress adaptation. The meta-analysis of the high-quality transcriptome resource CATMA with an efficient model-based method of clustering is enriched by the integration of data including sequence analyses, bioinformatics predictions, functional annotation extracted from literature and interactome results. The concept of cluster improvement (from the co-expression clusters to the functional networks) is a key step of the project and its result will impact the density and the quality of the gene network obtained by the prediction of gene relationships through GGM approaches.
Keywords: predictive biology, biotic and abiotic stress, gene network, relational annotation
Main collaborators: G. Celeux’s Select team (INRIA, Orsay), S. Huet (INRA, Jouy-en-Josas), C. Ambroise and colleagues (IBGBI, Evry)...

Statistical methods for omics analysis

PI: ML Martin-Magniette, G. Rigaill
This project aims to develop original statistical methods oriented towards high-throughput technologies used in molecular biology and to propose analysis pipeline for the transcriptome platform of URGV. Skills are in model-based methods, linear models, algorithms for the analysis of omics data ... This project allows us to investigate genome activity (gene expression and control mechanisms). Main topics are (i) evaluation of normalization and differential analysis methods, (ii) development of model-based clustering for co-expression network and protein-DNA interaction and (iii) statistical methods for regulation networks
Keywords: modeling, mixture model, algorithms, transcriptome, chIP-chip
Main collaborators: S. Robin’s group (AgroParisTech/INRA), Department of Applied Mathematics and Informatics (MIA) of INRA, G. Celeux’s Select team (INRIA, Orsay), C. Maugis (IMT, Toulouse), the group of L. Wessels (CSBC)...

Data integration and gene family annotation

PI: V. Brunaud, S. Aubourg The bioinformatics group is involved in several integrative projects merging biological resources and bioinformatics predictions (see the tools and databases section). This data integration allows us to better understand the biological role of plant genes by considering them in a wide context: a multigene family, a topological environment, and/or a regulation network. In this way, we also work on the curated structural and functional annotation of gene families of interest (PPR, TPS, STS, CHS, RGA...), especially in Arabidopsis thaliana and Vitis vinifera, in order to study the relationships between gene structure, expression, evolution and physiological function.
Keywords: databases, integrative biology, gene family, evolution, annotation, FLAGdb++, CATdb.
Main collaborators: J. Bohlmann’s group (UBC, Vancouver), P. Hugueney (INRA, Colmar), I. Dry (CSIRO, Adelaide), J.-P. Bouchet (INRA, Avignon), C. Lurin’s group (INRA ,Evry)...

Publications of the Bioinformatics Group (Since 2001)

2012     2011     2010     2009     2008     2007     2006     2005     2004     2003     2002     2001

2012

Inférence de réseaux de régulation de gènes au travers de scores étendus dans les réseaux Bayésiens.

Vandel J, Mangin B, Vignes M, Leroux D, Loudet O, Martin-Magniette ML, de Givry S (2012)
Revue d’intelligence artificielle.

SelvarClustMV: Variable selection approach in model-based clustering allowing for missing values.

Maugis-Rabusseau C, Martin-Magniette ML, Pelletier S (2012)
Journal de la Société Française de Statistique.

Light-Regulated Genetic Module Was Recruited to Carpel Development in Arabidopsis following a Structural Change to SPATULA.

Reymond M, Brunoud G, Chauvet A, Martínez-Garcia J, Martin-Magniette ML, Monéger F, Scutt CP (2012)
Plant Cell. 24(7):2812-25.

A gene-phenotype network based on genetic variability of drought responses reveals key physiological processes in controlled and natural environments.

Rengel D, Arribat S, Maury P, Martin-Magniette ML, Hourlier T, Laporte M, Varès D, Carrère S, Grieu P, Balzergue S, Gouzy J, Vincourt P, Langlade NB (2012)
PLoS One, 7(10):e45249.

A regression model for estimating DNA copy number data applied to capture sequencing data.

Rigaill GJ, Cadot S, Kluin RJ, Xue Z, Bernards R, Majewski IJ, Wessels LF (2012)
Bioinformatics, 28(18):2357-65.

Structural, functional and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine (Vitis vinifera).

Parage C, Tavares R, Réty S, Baltenweck-Guyot R, Poutaraud A, Renault L, Heintz D, Lugan R, Marais G, Aubourg S, Hugueney P (2012)
Plant Physiol. 160(3):1407-19

Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures.

Cubillos FA, Yansouni J, Khalili H, Balzergue S, Elftieh S, Martin-Magniette ML, Serrand Y, Lepiniec L, Baud S, Dubreucq B, Renou JP, Camilleri C, Loudet O (2012).
BMC Genomics, 13(1), 117.

Mutations in the Arabidopsis Homolog of LST8/GβL, a Partner of the Target of Rapamycin Kinase, Impair Plant Growth, Flowering, and Metabolic Adaptation to Long Days.

Moreau M, Azzopardi M, Clément G, Dobrenel T, Marchive C, & Renne C, et al. (2012).
Plant Cell, 24(2):463-81

Variational Bayes approach for model aggregation in unsupervised classification with Markovian dependency.

Volant, S., Martin-Magniette, M.-L., & Robin, S. (2012).
Computational Statistics & Data Analysis.

2011

Genomic Approach to Study Floral Development Genes in Rosa sp.

Dubois A, Remay A, Raymond O, Balzergue S, Chauvet A, Maene M, Pécrix Y, Yang SH, Jeauffre J, Thouroude T, Boltz V, Martin-Magniette ML, Janczarski S, Legeai F, Renou JP, Vergne P, Le Bris M, Foucher F, Bendahmane M. (2011)
PLoS One. 6(12):e28455.

Invading Basement Membrane Matrix Is Sufficient for MDA-MB-231 Breast Cancer Cells to Develop a Stable In Vivo Metastatic Phenotype.

Abdelkarim M., Vintonenko N., Starzec A., Robles A., Aubert J., Martin M.-L., Mourah S., Podgorniak M.-P., Rodrigues-Ferreira S., Nahmias C., Couraud, P.-O., Doliger C., Sainte-Catherine O., Peyri N., Chen L., Mariau J., Etienne M., Perret G.-Y., Crepin M., Poyet J.-L., Khatib A.-M., Di Benedetto M. (2011)
PLoS One. 6(8):e23334.

Unsupervised Classification for Tiling Arrays: ChIP-chip and Transcriptome.

Bérard C, Martin-Magniette ML, Brunaud V, Aubourg S, Robin S (2011)
Statistical Applications in Genetics and Molecular Biology, 10: 50.

Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids.

Moghaddam AM, Roudier F, Seifert M, Bérard C, Martin-Magniette ML, Ashtiyani RK, Houben A, Colot V, Mette MF (2011)
Plant J. 67(4):691-700.

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 (2011)
PLoS ONE 6(6):e21524.

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis.

Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Després B, Drevensek S, Barneche F, Dèrozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V (2011)
EMBO J., 30:1928-1938.

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 (2011)
Plant Methods, 7: 8.

Variable selection in model-based discriminant analysis.

Maugis, C, Celeux, G, Martin-Magniette ML (2011)
Journal of Multivariate Analysis. 102(10):1374-1387.

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome.

Faivre-Rampant P, Lesur I, Boussardon C, Bitton F, Martin-Magniette ML, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C (2011).
BMC Genomics. 12(1):292.

2010

Annotation structurale et fonctionnelle des génomes.

Aubourg S (2010)
Bio-informatique, Principes d’utilisation des outils. Série Savoir-faire, Editions Quæ (D. Tagu, J.L Risler coord.) pp. 166-178.

A python module to normalize microarray data by the quantile adjustment method.

Baber I, Tamby JP, Manoukis NC, Sangaré D, Doumbia S, Traoré SF, Maiga MS, Dembélé D (2010)
Infect. Genet. Evol., 11(4):765-8.

Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes.

Cohen C, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I (2010)
BMC Genomics, 11:630.

Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays.

Martin S*, Aubourg S*, Schouwey M, Daviet L, Schalk M, Toub O, Lund S, Bohlmann J (2010)
BMC Plant Biol., 10: 226. (* co-premier auteur)

Improved detection of motifs with preferential location in promoters.

Bernard V, Lecharny A, Brunaud V (2010)
Genome, 9:739-752

Brain transcriptional stability upon prion protein-encoding gene invalidation in zygotic or adult mouse.

Chadi, S, Young R, Le Guillou S, Tilly G, Bitton F, Martin-Magniette ML, Soubigou-Taconnat L, Balzergue S, Vilotte M, Peyre C, Passet B, Beringue V, Renou JP, Le Provost F, Laude H, Vilotte JL. (2010)
BMC Genomics, 11(1): 448.

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

BMC Genomics. 2010 Mar 12;11:166. PMID: 20222994
Bernard V, Brunaud V, Lecharny A.

2009

Transcriptome analysis describing new immunity and defense genes in peripheral blood mononuclear cells of rheumatoid arthritis patients.

PLoS One. 2009 Aug 27;4(8):e6803. PMID: 19710928
Teixeira VH, Olaso R, Martin-Magniette ML, Lasbleiz S, Jacq L, Oliveira CR, Hilliquin P, Gut I, Cornelis F, Petit-Teixeira E.

Identification of germinal disk region derived genes potentially involved in hen fertility.

Mol Reprod Dev. 2009 Nov;76(11):1043-55. PMID: 19484757
Elis S, Blesbois E, Couty I, Balzergue S, Martin-Magniette ML, Batellier F, Govoroun MS.

Variable selection for clustering with Gaussian mixture models.

Biometrics. 2009 Sep;65(3):701-9. Epub 2009 Feb 4. PMID: 19210744
Maugis C, Celeux G, Martin-Magniette ML.

Variable selection in model-based clustering: A general variable role modeling.

Computational Statistics and Data Analysis, 53: 3872-3882. (2009)
Maugis C, Celeux G, Martin-Magniette, ML

Semi-parametric estimation of the hazard function in a model with covariate measurement error.

ESAIM Probability and Statistics, 13: 87-114. (2009)
Martin-Magniette ML, Taupin ML

Mélanges gaussiens bidimensionnels pour la comparaison de deux échantillons de chromatine immuno-précipitée.

Revue Modulad, 40: 53-68. (2009)
Bérard C, Martin-Magniette ML, To A, Roudier F, Colot V, Robin S

Sélection de variables pour la classification par mélanges gaussiens pour prédire la fonction des gènes orphelins

Revue Modulad, 40: 69-80. (2009)
Maugis C, Martin-Magniette ML, Tamby JP, Renou JP, Lecharny A, Aubourg S, Celeux G

2008

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

BMC Evol Biol. 2008 Oct 10;8:280. PMID: 18847470
Armisén D, Lecharny A, Aubourg S.

Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5.

Plant J. 2008 Jul 4. PMID: 18644002
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.

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
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

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
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.

Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection.

BMC Genomics. 2008 Jun 25;9:301. PMID: 18578863
Navajas M, Migeon A, Alaux C, Martin-Magniette M, Robinson G, Evans J, Cros-Arteil S, Crauser D, Le Conte Y.

Normalization for triple-target microarray experiments

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

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
Elis S, Batellier F, Couty I, Balzergue S, Martin-Magniette ML, Monget P, Blesbois E, Govoroun MS.

Transcriptional and metabolic adjustments in AGPase deficient bt2 maize kernels.

Plant Physiol. 2008 Feb 20 PMID: 18287491
Cossegal M, Chambrier P, Mbelo S, Balzergue S, Martin-Magniette ML, Moing A, Deborde C, Guyon V, Perez P, Rogowsky P.

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
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.

Contrasted Microcolinearity and Gene Evolution Within a Homoeologous Region of Wheat and Barley Species.

J Mol Evol. 2008 Feb 15 PMID: 18274696
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

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

2007

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
Ramel F, Sulmon C, Cabello-Hurtado F, Taconnat L, Martin-Magniette ML, Jean-Pierre Renou, Elamrani A, Couee I, Gouesbet G.

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
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

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
Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Christian Clepet, Sébastien Aubourg, Rameau C, Michel Caboche, Abdel Ihafid Bendahmane

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
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

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
Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G,Colot V.

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)

2005

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
Jammes F, Lecomte P, de Almeida-Engler J, Bitton F, Martin-Magniette ML, Renou JP, Abad P, Favery B.

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.

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
Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.

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
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

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
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

2004

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

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
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.

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
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.

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
Lescot M, Rombauts S, Zhang J, Aubourg S, Mathe C, Jansson S, Rouze P and Boerjan W

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

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D347-50. PMID: 14681431
Samson F, Brunaud V, Duchene S, De Oliveira Y, Caboche M, Lecharny A and Aubourg S

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)
Lecharny A.

2003

CATMA: a complete Arabidopsis GST database.

Nucleic Acids Res. 2003 Jan 1;31(1):156-8. PMID: 12519971
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.

Automatic design of gene-specific sequence tags for genome-wide functional studies.

Bioinformatics Vol. 19 no. 17 2003, pages 2191–2198 PMID: 14630647
Thareau V, Dehais P, Serizet C, Hilson P, Rouze P, Aubourg S.

2002

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
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.

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
Aubourg S, Lecharny A, Bohlmann J.

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

2001

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

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


Previous Members

We thank all the students, engineers, post-docs and collaborators for their works, ideas and enthusiasm during their position in the bioinformatics group.

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
Bentahar Nadia CDD ANR KBBE May 11-Aug 12 Annotation of Vitis RGA genes
Bernard Virginie Master professionnel de Bioinformatique (EGOISt – Rouen) and PhD Sept 04 - Jan 10 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
Cauchard Audrey Master Bioinformatics Rouen Sept 09 – Aug 11 Analyse of coexpression clusters
Dérozier Sandra CDD ANR Sept 08 – Sept 10 tiling-array design, FLAGdb++ update
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
Lecharny Alain DR2 CNRS 2000 - 2011 Team Leader, Principal investigator
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
Papastamoulis Panagiotis PostDoc INRA Aug 11-Aug 12 clustering of RNAseq data
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.
Rogier Odile CDD UE+CEA Jan 09 - Oct 11 ATOMEdb and RNAseq analysis
Samson Franck IE2 INRA (GAP) Computer Scientist 1999-2009 FLAGdb++ development
Serizet Carine POST-DOC INRA (BV) Oct 03 - Apr05 Study of Arabidopsis promoters at the genome scale
Zaag Rim Master2 and CDD KBBE Feb 11 – Oct 12 Data integration in Arabidopsis and melon