2010-2014

1.            Sallet E, Gouzy J, Schiex T: EuGene-PP: A Next Generation Automated Annotation Pipeline for Prokaryotic Genomes. Bioinformatics 2014.

2.            Roux B, Rodde N, Jardinaud MF, Timmers T, Sauviac L, Cottret L, Carrere S, Sallet E, Courcelle E, Moreau S et al: An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing. Plant J 2014, 77(6):817-83

3.           Bustos-Sanmamed P, Hudik E, Laffont C, Reynes C, Sallet E, Wen J, Mysore K, Camproux A, Hartmann C, Gouzy J et al: A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development. Plant Biotechnology Journal 2014.

4.            Cheeseman K, Ropars J, Renault P, Dupont J, Gouzy J, Branca A, Abraham AL, Ceppi M, Conseiller E, Debuchy R et al: Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nat Commun 2014, 5:2876.

5.            Khafif M, Cottret L, Balagué C, Raffaele S: Identification and phylogenetic analyses of VASt, an uncharacterized  protein domain associated with lipid-binding domains in Eukaryotes. BMC Bioinformatics 2014.

6.            Milreu PV, Klein CC, Cottret L, Acuna V, Birmele E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L et al: Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. Bioinformatics 2014, 30(1):61-70.

7.            Ramesh R, Gaitonde S, Achari G, Asolkar T, Singh NP, Carrere S, Genin S, Peeters N: Genome Sequencing of Ralstonia solanacearum Biovar 3, Phylotype I, Strains Rs-09-161 and Rs-10-244, Isolated from Eggplant and Chili in India. Genome Announc 2014, 2(3).

8.            Arrieta-Ortiz ML, Rodriguez RL, Perez-Quintero A, Poulin L, Diaz AC, Arias Rojas N, Trujillo C, Restrepo Benavides M, Bart R, Boch J et al: Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151. PLoS One 2013, 8(11):e79704.

9.            Bolot S, Roux B, Carrere S, Jiang BL, Tang JL, Arlat M, Noel LD: Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16. Genome Announc 2013, 1(4).

10.          Bolot S, Munoz Bodnar A, Cunnac S, Ortiz E, Szurek B, Noel LD, Arlat M, Jacques MA, Gagnevin L, Portier P et al: Draft Genome Sequence of the Xanthomonas cassavae Type Strain CFBP 4642. Genome Announc 2013, 1(4).

11.          Bolot S, Guy E, Carrere S, Barbe V, Arlat M, Noel LD: Genome Sequence of Xanthomonas campestris pv. campestris Strain Xca5. Genome Announc 2013, 1(1).

12.          Cadic E, Coque M, Vear F, Grezes-Besset B, Pauquet J, Piquemal J, Lippi Y, Blanchard P, Romestant M, Pouilly N et al: Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.). Theor Appl Genet 2013, 126(5):1337-1356.

13.          Cunnac S, Bolot S, Forero Serna N, Ortiz E, Szurek B, Noel LD, Arlat M, Jacques MA, Gagnevin L, Carrere S et al: High-Quality Draft Genome Sequences of Two Xanthomonas citri pv. malvacearum Strains. Genome Announc 2013, 1(4).

14.          Darrasse A, Bolot S, Serres-Giardi L, Charbit E, Boureau T, Fisher-Le Saux M, Briand M, Arlat M, Gagnevin L, Koebnik R et al: High-Quality Draft Genome Sequences of Xanthomonas axonopodis pv. glycines Strains CFBP 2526 and CFBP 7119. Genome Announc 2013, 1(6).

15.          Darrasse A, Carrere S, Barbe V, Boureau T, Arrieta-Ortiz ML, Bonneau S, Briand M, Brin C, Cociancich S, Durand K et al: Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads. BMC Genomics 2013, 14:761.

16.          Dejean G, Blanvillain-Baufume S, Boulanger A, Darrasse A, de Bernonville TD, Girard AL, Carrere S, Jamet S, Zischek C, Lautier M et al: The xylan utilization system of the plant pathogen Xanthomonas campestris pv campestris controls epiphytic life and reveals common features with oligotrophic bacteria and animal gut symbionts. New Phytol 2013, 198(3):899-915.

17.          Guy E, Genissel A, Hajri A, Chabannes M, David P, Carrere S, Lautier M, Roux B, Boureau T, Arlat M et al: Natural genetic variation of Xanthomonas campestris pv. campestris pathogenicity on arabidopsis revealed by association and reverse genetics. MBio 2013, 4(3):e00538-00512.

18.          Jacques MA, Bolot S, Charbit E, Darrasse A, Briand M, Arlat M, Gagnevin L, Koebnik R, Noel LD, Portier P et al: High-Quality Draft Genome Sequence of Xanthomonas alfalfae subsp. alfalfae Strain CFBP 3836. Genome Announc 2013, 1(6).

19.          Lanois A, Ogier JC, Gouzy J, Laroui C, Rouy Z, Givaudan A, Gaudriault S: Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1. Genome Announc 2013, 1(3).

20.          Loridon K, Burgarella C, Chantret N, Martins F, Gouzy J, Prosperi JM, Ronfort J: Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. Mol Ecol Resour 2013.

21.          Peeters N, Carrere S, Anisimova M, Plener L, Cazale AC, Genin S: Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics 2013, 14:859.

22.          Royer M, Koebnik R, Marguerettaz M, Barbe V, Robin GP, Brin C, Carrere S, Gomez C, Hugelland M, Voller GH et al: Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides. BMC Genomics 2013, 14(1):658.

23.          Sallet E, Roux B, Sauviac L, Jardinaud MF, Carrere S, Faraut T, de Carvalho-Niebel F, Gouzy J, Gamas P, Capela D et al: Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011. DNA Res 2013.

24.          Verdier J, Lalanne D, Pelletier S, Torres-Jerez I, Righetti K, Bandyopadhyay K, Leprince O, Chatelain E, Ly Vu B, Gouzy J et al: A regulatory network-based approach dissects late maturation processes related to the acquisition of desiccation tolerance and longevity of Medicago truncatula seeds. Plant Physiol 2013.

25.          Acuna V, Milreu PV, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot MF: Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Bioinformatics 2012, 28(19):2474-2483.

26.          Ariel F, Brault-Hernandez M, Laffont C, Huault E, Brault M, Plet J, Moison M, Blanchet S, Ichante JL, Chabaud M et al: Two Direct Targets of Cytokinin Signaling Regulate Symbiotic Nodulation in Medicago truncatula. Plant Cell 2012.

27.          Deleury E, Dubreuil G, Elangovan N, Wajnberg E, Reichhart JM, Gourbal B, Duval D, Baron OL, Gouzy J, Coustau C: Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study. PLoS One 2012, 7(3):e32512.

28.          Dubois A, Carrere S, Raymond O, Pouvreau B, Cottret L, Roccia A, Onesto JP, Sakr S, Atanassova R, Baudino S et al: Transcriptome database resource and gene expression atlas for the rose. BMC Genomics 2012, 13:638.

29.          Klein CC, Cottret L, Kielbassa J, Charles H, Gautier C, Ribeiro de Vasconcelos AT, Lacroix V, Sagot MF: Exploration of the core metabolism of symbiotic bacteria. BMC Genomics 2012, 13:438.

30.          Pieretti I, Royer M, Barbe V, Carrere S, Koebnik R, Couloux A, Darrasse A, Gouzy J, Jacques MA, Lauber E et al: Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels. BMC Genomics 2012, 13:658.

31.          Rengel D, Arribat S, Maury P, Martin-Magniette ML, Hourlier T, Laporte M, Vares D, Carrere S, Grieu P, Balzergue S et al: A gene-phenotype network based on genetic variability for drought responses reveals key physiological processes in controlled and natural environments. PLoS One 2012, 7(10):e45249.

32.          Rouxel M, Papura D, Nogueira M, Machefer V, Dezette D, Richard-Cervera S, Carrere S, Mestre P, Delmotte F: Microsatellite markers for characterization of native and introduced populations of Plasmopara viticola, the causal agent of grapevine downy mildew. Appl Environ Microbiol 2012, 78(17):6337-6340.

33.          Vincourt P, As-Sadi F, Bordat A, Langlade NB, Gouzy J, Pouilly N, Lippi Y, Serre F, Godiard L, Tourvieille de Labrouhe D et al: Consensus mapping of major resistance genes and independent QTL for quantitative resistance to sunflower downy mildew. Theor Appl Genet 2012, 125(5):909-920.

34.          Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H et al: The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480(7378):520-524.

35.          Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN et al: The genome of Theobroma cacao. Nat Genet 2011.

36.          As-sadi F, Carrere S, Gascuel Q, Hourlier T, Rengel D, Le Paslier MC, Bordat A, Boniface MC, Brunel D, Gouzy J et al: Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences. BMC Genomics 2011, 12:498.

37.          Moreau S, Verdenaud M, Ott T, Letort S, de Billy F, Niebel A, Gouzy J, de Carvalho-Niebel F, Gamas P: Transcription reprogramming during root nodule development in Medicago truncatula. PLoS One 2011, 6(1):e16463.

38.          Charles H, Balmand S, Lamelas A, Cottret L, Perez-Brocal V, Burdin B, Latorre A, Febvay G, Colella S, Calevro F et al: A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: reduced transporter sets and variable membrane organisations. PLoS One 2011, 6(12):e29096.

39.          Vellozo AF, Veron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbe Y, Douglas AE, Gabaldon T et al: CycADS: an annotation database system to ease the development and update of BioCyc databases. Database (Oxford) 2011, 2011:bar008.

40.          Carle P, Saillard C, Carrere N, Carrere S, Duret S, Eveillard S, Gaurivaud P, Gourgues G, Gouzy J, Salar P et al: Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Appl Environ Microbiol 2010, 76(11):3420-3426.

41.          Cottret L, Jourdan F: Graph methods for the investigation of metabolic networks in parasitology. Parasitology 2010, 137(9):1393-1407.

42.          Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F: MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res 2010, 38(Web Server issue):W132-137.

43.          Cottret L, Milreu PV, Acuna V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF: Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata. PLoS Comput Biol 2010, 6(9).

44.          Jourdan F, Cottret L, Huc L, Wildridge D, Scheltema R, Hillenweck A, Barrett MP, Zalko D, Watson DG, Debrauwer L: Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining. Metabolomics 2010, 6(2):312-321.

-2009