2005-2009

 

 

7.                  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, 22(3):341-351.

8.                  Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C: Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A 2009, 106(35):14908-14913.

9.                  Pieretti I, Royer M, Barbe V, Carrere S, Koebnik R, Cociancich S, Couloux A, Darrasse A, Gouzy J, Jacques MA et al: The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics 2009, 10:616.

10.              Neron B, Menager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C: Mobyle: a new full web bioinformatics framework. Bioinformatics 2009, 25(22):3005-3011.

11.              Lelandais-Briere C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M: Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules. Plant Cell 2009, 21(9):2780-2796.

12.              Guidot A, Elbaz M, Carrere 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, 99(9):1105-1112.

13.              Gouzy J, Carrere S, Schiex T: FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics 2009, 25(5):670-671.

14.              Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A et al: Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform 2008, 9(3):220-231.

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

16.              Ruffel S, Freixes S, Balzergue S, Tillard P, Jeudy C, Martin-Magniette ML, van der Merwe MJ, Kakar K, Gouzy J, Fernie AR et al: Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula. Plant Physiol 2008, 146(4):2020-2035.

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

18.              Foissac S, Gouzy J, Rombauts S, Mathé C, Amselem J, Sterck L, Van de Peer Y, Rouzé P, Schiex T: Genome Annotation in Plants and Fungi: EuGène as a Model Platform. Current Bioinformatics 2008, 3(2):87-97.

19.              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, 36(Database issue):D485-490.

20.              Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, Carrere S, Cruveiller S, Dossat C, Lajus A et al: Genome sequence of the {beta}-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res 2008.

21.              Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC et al: Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol 2008, 26(8):909-915.

22.              Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R et al: New developments in the InterPro database. Nucleic Acids Res 2007, 35(Database issue):D224-228.

23.              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, 189(2):377-387.

24.              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, 20(3):321-332.

25.              Fremez R, Faraut T, Fichant G, Gouzy J, Quentin Y: Phylogenetic exploration of bacterial genomic rearrangements. Bioinformatics 2007, 23(9):1172-1174.

26.              Carrere S, Gouzy J: REMORA: a pilot in the ocean of BioMoby web-services. Bioinformatics 2006, 22(7):900-901.

27.              Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T et al: Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A 2006, 103(40):14959-14964.

28.              Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L et al: InterPro, progress and status in 2005. Nucleic Acids Res 2005, 33(Database issue):D201-205.

29.              Capela D, Carrere S, Batut J: Transcriptome-based identification of the Sinorhizobium meliloti NodD1 regulon. Appl Environ Microbiol 2005, 71(8):4910-4913.

30.              Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S, Kahn D: The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res 2005, 33(Database issue):D212-215.

31.              Bontemps C, Golfier G, Gris-Liebe C, Carrere S, Talini L, Boivin-Masson C: Microarray-based detection and typing of the Rhizobium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest. Appl Environ Microbiol 2005, 71(12):8042-8048.

 

 

2000-2004

 

 

32.              Kuster H, Hohnjec N, Krajinski F, El YF, Manthey K, Gouzy J, Dondrup M, Meyer F, Kalinowski J, Brechenmacher L et al: Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula. J Biotechnol 2004, 108(2):95-113.

33.              Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A et al: Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004, 431(7011):946-957.

34.              Ferrieres L, Francez-Charlot A, Gouzy J, Rouille S, Kahn D: FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti. Microbiology 2004, 150(Pt 7):2335-2345.

35.              El Yahyaoui F, Kuster H, Ben Amor B, Hohnjec N, Puhler A, Becker A, Gouzy J, Vernie T, Gough C, Niebel A et al: Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program. Plant Physiol 2004, 136(2):3159-3176.

36.              Schiex T, Gouzy J, Moisan A, de Oliveira Y: FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Research 2003, 31(13):3738-3741.

37.              Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P et al: The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 2003, 31(1):315-318.

38.              Gouet P, Robert X, Courcelle E: ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 2003, 31(13):3320-3323.

39.              Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS et al: Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. Journal of Bacteriology 2002, 184(11):3086-3095.

40.              Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D, Kahn D: ProDom: automated clustering of homologous domains. Brief Bioinform 2002, 3(3):246-251.

41.              Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L et al: Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 2002, 415(6871):497-502.

42.              Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P et al: InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform 2002, 3(3):225-235.

43.              Journet EP, van Tuinen D, Gouzy J, Crespeau H, Carreau V, Farmer MJ, Niebel A, Schiex T, Jaillon O, Chatagnier O et al: Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Research 2002, 30(24):5579-5592.

44.              Gouet P, Courcelle E: ENDscript: a workflow to display sequence and structure information. Bioinformatics 2002, 18(5):767-768.

45.              Journet EP, Carreau V, Gouzy J, Thoquet P, Rosenberg C, Barker D, Huguet T, Denarie J, Gamas P: The model legume Medicago truncatula: recent advances and perspectives in genomics. Ocl-Oleagineux Corps Gras Lipides 2001, 8(5):478-484.

46.              Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P et al: The composite genome of the legume symbiont Sinorhizobium meliloti. Science 2001, 293(5530):668-672.

47.              Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J et al: The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc Natl Acad Sci U S A 2001, 98(17):9889-9894.

48.              Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E et al: Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(17):9877-9882.

49.              Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J et al: Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(17):9883-9888.

50.              Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD et al: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001, 29(1):37-40.

51.              Galibert F, Barloy-Hubler F, Capela D, Gouzy J: Sequencing the Sinorhizobium meliloti genome. DNA Sequence 2000, 11(3-4):207-210.

52.              Corpet F, Servant F, Gouzy J, Kahn D: ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Research 2000, 28(1):267-269.

53.              Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD et al: InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 2000, 16(12):1145-1150.