cati-bbric

As-Sadi F, Carrere S, Gascuel Q, Hourlier T, Rengel D, Le Paslier MC, Bordat A, Boniface MC, Brunel D, Gouzy J, Godiard L, Vincourt P. Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences. BMC Genomics. 2011 Oct 11;12(1):498.

Amselem J, Cuomo C, van Kan J, Viaud M, Benito E, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quevillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Beever R, Anthouard V, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collemare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MA, Dickman MB. (2011). Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics. 2011 doi: pgen.1002230.

Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GH, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun. 2011 Feb;2:202.

Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Carle P, Saillard C, Carrère N, Carrère S, Duret S, Eveillard S, Gaurivaud P, Gourgues G, Gouzy J, Salar P, Verdin E, Breton M, Blanchard A, Laigret F, Bové JM, Renaudin J, Foissac X.Appl Environ Microbiol. 2010 Jun;76(11):3420-6.

Pieretti I, Royer M, Barbe V, Carrere S, Koebnik R, Cociancich S, Couloux A, Darrasse A, Gouzy J, Jacques MA, Lauber E, Manceau C, Mangenot S, Poussier S, Segurens B, Szurek B, Verdier V, Arlat M, Rott P. The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics. 2009 Dec 17.

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. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol. 2008 Jul 27

Saillard C, Carle P, Duret-Nurbel S, Henri R, Killiny N, Carrère S, Gouzy J, Bové JM, Renaudin J, Foissac X. The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome. BMC Genomics. 2008 Apr 28;9:195.

Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, Carrere S, Cruveiller S, Dossat C, Lajus A, Marchetti M, Poinsot V, Rouy Z, Servin B, Saad M, Schenowitz C, Barbe V, Batut J, Medigue C, Masson-Boivin C. Genome sequence of the {beta}-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res. 2008 May 19.

Paux E, Legeai F (co-author), Guilhot N, Adam-Blondon AF, Alaux M, Salse J, Sourdille P, Leroy P, Feuillet C. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics. 2008 Feb;8(1):29-32. Epub 2007 Nov 24.

Rispe C, Kutsukake M, Doublet V, Hudaverdian S, Legeai F, Simon JC, Tagu D, Fukatsu T. Large gene family expansion and variable selective pressures for cathepsin B in aphids. Mol Biol Evol. 2008 Jan;25(1):5-17. Epub 2007 Oct 13.

Rispe C, Legeai F, Gauthier JP, Tagu D. Strong heterogeneity in nucleotidic composition and codon bias in the pea aphid (Acyrthosiphon pisum) shown by EST-based coding genome reconstruction. J Mol Evol. 2007 Oct;65(4):413-24. Epub 2007 Oct 10.

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. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007 Sep 27;449(7161):463-7. Epub 2007 Aug 26.

Guidot A, Prior P, Schoenfeld J, Carrere S, Genin S, Boucher C.Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis. J Bacteriol. 2007 Jan;189(2):377-87. Epub 2006 Nov 3.

Sabater-Muñoz B, Legeai F, Rispe C, Bonhomme J, Dearden P, Dossat C, Duclert A, Gauthier JP, Ducray DG, Hunter W, Dang P, Kambhampati S, Martinez-Torres D, Cortes T, Moya A, Nakabachi A, Philippe C, Prunier-Leterme N, Rahbé Y, Simon JC, Stern DL, Wincker P, Tagu D. Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera). Genome Biol. 2006;7(3):R21. Epub 2006 Mar 10.

Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quétier F, Oldroyd GE, Debellé F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14959-64

Simon A, Dalmais B, Morgant G, Viaud M (2013). Screening of a Botrytis cinerea one-hybrid library reveals a Cys(2)His(2) transcription factor involved in the regulation of secondary metabolism gene clusters. Fungal Genet Biol. 2013 Feb 8. pii: S1087-1845(13)00020-0.

Schumacher J, Pradier JM, Simon A, Traeger S, Moraga J, Collado IG, Viaud M, Tudzynski B (2012). Natural Variation in the VELVET Gene bcvel1 Affects Virulence and Light-Dependent Differentiation in Botrytis cinerea. PLoS One. 2012;7(10):e47840.

Temme N, Oeser B, Massaroli M, Heller J, Simon A, González Collado I, Viaud M, Tudzynski P (2012). BcAtf1, a global regulator, controls various differentiation processes and phytotoxin production in Botrytis cinerea. Mol Plant Pathol. 2012 Feb 1. doi: 10.1111/j.1364-3703.2011.00778.x

Kebdani N, Pieuchot L, Deleury E, Panabières F, Le Berre J.Y, and Gourgues M. Cellular and molecular characterization of Phytophthora parasitica appressorium mediated penetration. New phytologist 2010. 185:248-257 doi:10.1111/j.1469-8137.2009.03048.x

Seddas PM, Arias CM, Arnould C, van Tuinen D, Godfroy O, Benhassou HA, Gouzy J, Morandi D, Dessaint F, Gianinazzi-Pearson V. Symbiosis-related plant genes modulate molecular responses in an arbuscular mycorrhizal fungus during early root interactions. Mol Plant Microbe Interact. 2009 Mar;22(3):341-51.

Sabourault C, Ganot P, Deleury E, Allemand D, and Furla P. Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis. BMC Genomics. 2009 10:333: doi:10.1189/1471-3164-1110-1333.

Garcia V, Stevens R, Gil L, Gilbert L, Gest N, Petit J, Faurobert M, Maucourt M, Deborde C, Moing A, Poessel JL, Jacob D, Bouchet JP, Giraudel JL, Gouble B, Page D, Alhagdow M, Massot C, Gautier H, Lemaire-Chamley M, de Daruvar A, Rolin D, Usadel B, Lahaye M, Causse M, Baldet P, Rothan C. An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato. C R Biol 2009 Nov;332(11):1007-21. PubMed PMID: 19909923.

Gilbert L, Alhagdow M, Nunes-Nesi A, Quemener B, Guillon F, Bouchet B, Faurobert M, Gouble B, Page D, Garcia V, Petit J, Stevens R, Causse M, Fernie AR, Lahaye M, Rothan C, Baldet P. GDP-D-mannose 3,5-epimerase (GME) plays a key role at the intersection of ascorbate and non-cellulosic cell-wall biosynthesis in tomato. Plant Journal 2009 Nov;60(3):499-508. PubMed PMID: 19619161.

Mounet F, Moing A, Garcia V, Petit J, Maucourt M, Deborde C, Bernillon S, Le Gall G, Colquhoun I, Defernez M, Giraudel JL, Rolin D, Rothan C, Lemaire-Chamley M. Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development. Plant Physiol. 2009 Mar;149(3):1505-28. PubMed PMID: 19144766.

Guidot A, Elbaz M, Carrère S, Siri MI, Pianzzola MJ, Prior P, Boucher C. Specific genes from the potato brown rot strains of Ralstonia solanacearum and their potential use for strain detection. Phytopathology 2009 Sep;99(9):1105-12.PMID: 19671014.

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 nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula. Plant Physiol. 2008 Apr;146(4):2020-35. Epub 2008 Feb 20.

Schumacher J, Viaud M, Simon A, and Tudzynski B. The Galpha subunit BCG1, the phospholipase C (BcPLC1) and the calcineurin phosphatase co-ordinately regulate gene expression in the grey mould fungus Botrytis cinerea. Mol Microbiol. 2008 Feb; 67(5): 1027-1050.

Choquer M, Fournier E, Kunz C, Levis C, Pradier JM, Simon A, Viaud M. Botrytis cinerea virulence factors: new insights into a necrotrophic and polyphageous pathogen. FEMS Microbiol Lett. 2007 Dec;277(1):1-10.

Dubreuil G, Magliano M, Deleury E, Abad P and Rosso M.N. Transcriptome analysis of root-knot nematode functions induced in the early stages of parasitism. New Pathologist. 2007 ;176: 426-436

Godiard L, Niebel A, Micheli F, Gouzy J, Ott T, Gamas P. Identification of new potential regulators of the Medicago truncatula-Sinorhizobium meliloti symbiosis using a large-scale suppression subtractive hybridization approach. Mol Plant Microbe Interact. 2007

Alhagdow M, Mounet F, Gilbert L, Nunes-Nesi A, Garcia V, Just D, Petit J, Beauvoit B, Fernie AR, Rothan C, Baldet P. Silencing of the mitochondrial ascorbate synthesizing enzyme L-galactono-1,4-lactone dehydrogenase affects plant and fruit development in tomato. Plant Physiol. 2007 Dec;145(4):1408-22. PubMed PMID: 17921340.

Gioti A, Simon A, Le Pêcheur P, Giraud C, Pradier JM, Viaud M, Levis C. Expression profiling of Botrytis cinerea genes identifies three patterns of up-regulation in planta and an FKBP12 protein affecting pathogenicity in J Mol Biol. 2006 Apr 28;358(2):372-86. Erratum in: J Mol Biol. 2006 Dec 1;364(3):550.

Barat-Houari M, Hilliou F, Jousset F.X, Sofer L, Deleury E, Rocher J, Ravallec M, Galibert L, Delobel P, Feyereisen R, Fournier P and Volkoff A.N. Gene expression profiling of Spodoptera frugiperda hemocytes and fat body using cDNA microarray reveals polydnavirus-associated variations in lepidopteran host genes transcript levels. BMC Genomics 2006, 7:160.

Simon M, Simon A, Martins F, Botran L, Tisné S, Granier F, Loudet O, Camilleri C (2012). DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions. Plant J. 2012 Mar;69(6):1094-101.

Simon A, Biot E. ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics. 2010 26(19):2468-9.

Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C. Mobyle: a new full web bioinformatics framework. Bioinformatics. 2009 Nov 15;25(22):3005-11.PMID: 19689959

Gouzy J, Carrere S, Schiex T. FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics. 2009 25(5):670-1.

Noirot C, Gaspin C, Schiex T, Gouzy J. LeARN: a platform for detecting, clustering and annotating non-coding RNAs. BMC Bioinformatics. 2008 Jan 14;9:21.

Courcelle E, Beausse Y, Letort S, Stahl O, Fremez R, Ngom-Bru C, Gouzy J, Faraut T. Narcisse: a mirror view of conserved syntenies. Nucleic Acids Res. 2008 Jan;36(Database issue):D485-90. Epub 2007 Nov 2.

Foissac S, Gouzy J, Rombauts S, Mathe C, Amselem J, Sterk L, van de Peer Y, Rouze P, Schiex T: Genome annotation in plants and fungi: eugene as a model platform. Current Bioinformatics 2008 May 3(2):87-97

BioMoby Consortium, Interoperability with Moby 1.0–it's better than sharing your toothbrush! Brief Bioinform. 2008 May;9(3):220-31. Epub 2008 Jan 31. Review.

Gauthier JP, Legeai F, Zasadzinski A, Rispe C, Tagu D. AphidBase: a database for aphid genomic resources. Bioinformatics. 2007 Mar 15;23(6):783-4.

Fremez R, Faraut T, Fichant G, Gouzy J, Quentin Y. Phylogenetic exploration of bacterial genomic rearrangements. Bioinformatics. 2007 May 1;23(9):1172-4

Carrere S, Gouzy J. Remora: a pilot in the ocean of BioMoby web-services. Bioinformatics. 2006 Apr 1;22(7):900-1.