Publications

See also Google scholar LABGeM page.

2020

  • Vallenet, D., Calteau, A., Dubois, M., Amours, P., Bazin, A., Beuvin, M., Burlot, L., Bussell, X., Fouteau, S., Gautreau, G., & others. (2020). Microscope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic acids research, 48(D1), D579–D589.
    [BibTeX]
    @article{vallenet2020microscope,
    title={MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis},
    author={Vallenet, David and Calteau, Alexandra and Dubois, Mathieu and Amours, Paul and Bazin, Adelme and Beuvin, Myl{\`e}ne and Burlot, Laura and Bussell, Xavier and Fouteau, St{\'e}phanie and Gautreau, Guillaume and others},
    journal={Nucleic acids research},
    volume={48},
    number={D1},
    pages={D579--D589},
    year={2020},
    publisher={Oxford University Press}
    }

  • Gautreau, G., Bazin, A., Gachet, M., Planel, R., Burlot, L., Dubois, M., Perrin, A., Médigue, C., Calteau, A., Cruveiller, S., & others. (2020). Ppanggolin: depicting microbial diversity via a partitioned pangenome graph. Plos computational biology, 16(3), e1007732.
    [BibTeX]
    @article{gautreau2020ppanggolin,
    title={PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph},
    author={Gautreau, Guillaume and Bazin, Adelme and Gachet, Mathieu and Planel, R{\'e}mi and Burlot, Laura and Dubois, Mathieu and Perrin, Amandine and M{\'e}digue, Claudine and Calteau, Alexandra and Cruveiller, St{\'e}phane and others},
    journal={PLOS Computational Biology},
    volume={16},
    number={3},
    pages={e1007732},
    year={2020},
    publisher={Public Library of Science San Francisco, CA USA}
    }

  • Bazin, A., Gautreau, G., Médigue, C., Vallenet, D., & Calteau, A.. (2020). Panrgp: a pangenome-based method to predict genomic islands and explore their diversity. Biorxiv.
    [BibTeX]
    @article{bazin2020panrgp,
    title={panRGP: a pangenome-based method to predict genomic islands and explore their diversity},
    author={Bazin, Adelme and Gautreau, Guillaume and M{\'e}digue, Claudine and Vallenet, David and Calteau, Alexandra},
    journal={bioRxiv},
    year={2020},
    publisher={Cold Spring Harbor Laboratory}
    }

2019

  • Médigue, C., Calteau, A., Cruveiller, S., Gachet, M., Gautreau, G., Josso, A., Lajus, A., Langlois, J., Pereira, H., Planel, R., & others. (2019). Microscope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. Briefings in bioinformatics, 20(4), 1071–1084.
    [BibTeX]
    @article{medigue2019microscope,
    title={MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data},
    author={M{\'e}digue, Claudine and Calteau, Alexandra and Cruveiller, St{\'e}phane and Gachet, Mathieu and Gautreau, Guillaume and Josso, Adrien and Lajus, Aur{\'e}lie and Langlois, Jordan and Pereira, Hugo and Planel, R{\'e}mi and others},
    journal={Briefings in bioinformatics},
    volume={20},
    number={4},
    pages={1071--1084},
    year={2019},
    publisher={Oxford University Press}
    }

  • Le Quéré, A., Gully, D., Teulet, A., Navarro, E., Gargani, D., Fardoux, J., Cruveiller, S., Neyra, M., Giraud, E., & Wade, T. K.. (2019). Complete genome sequence of bradyrhizobium sp. strain ors3257, an efficient nitrogen-fixing bacterium isolated from cowpea in senegal. Microbiol resour announc, 8(3), e01449–18.
    [BibTeX]
    @article{le2019complete,
    title={Complete Genome Sequence of Bradyrhizobium sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal},
    author={Le Qu{\'e}r{\'e}, Antoine and Gully, Djamel and Teulet, Albin and Navarro, Elisabeth and Gargani, Daniel and Fardoux, Jo{\"e}l and Cruveiller, St{\'e}phane and Neyra, Marc and Giraud, Eric and Wade, Tatiana Krasova},
    journal={Microbiol Resour Announc},
    volume={8},
    number={3},
    pages={e01449--18},
    year={2019},
    publisher={Am Soc Microbiol}
    }

  • Li, M., Calteau, A., Semchonok, D. A., Witt, T. A., Nguyen, J. T., Sassoon, N., Boekema, E. J., Whitelegge, J., Gugger, M., & Bruce, B. D.. (2019). Physiological and evolutionary implications of tetrameric photosystem i in cyanobacteria. Nature plants, 5(12), 1309–1319.
    [BibTeX]
    @article{li2019physiological,
    title={Physiological and evolutionary implications of tetrameric photosystem I in cyanobacteria},
    author={Li, Meng and Calteau, Alexandra and Semchonok, Dmitry A and Witt, Thomas A and Nguyen, Jonathan T and Sassoon, Nathalie and Boekema, Egbert J and Whitelegge, Julian and Gugger, Muriel and Bruce, Barry D},
    journal={Nature Plants},
    volume={5},
    number={12},
    pages={1309--1319},
    year={2019},
    publisher={Nature Publishing Group}
    }

  • Bourrel, A. S., Poirel, L., Royer, G., Darty, M., Vuillemin, X., Kieffer, N., Clermont, O., Denamur, E., Nordmann, P., Decousser, J., & others. (2019). Colistin resistance in parisian inpatient faecal escherichia coli as the result of two distinct evolutionary pathways. Journal of antimicrobial chemotherapy, 74(6), 1521–1530.
    [BibTeX]
    @article{bourrel2019colistin,
    title={Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways},
    author={Bourrel, Anne Sophie and Poirel, Laurent and Royer, Guilhem and Darty, M{\'e}lanie and Vuillemin, Xavier and Kieffer, Nicolas and Clermont, Olivier and Denamur, Erick and Nordmann, Patrice and Decousser, Jean-Winoc and others},
    journal={Journal of Antimicrobial Chemotherapy},
    volume={74},
    number={6},
    pages={1521--1530},
    year={2019},
    publisher={Oxford University Press}
    }

  • Mayol, O., Bastard, K., Beloti, L., Frese, A., Turkenburg, J. P., Petit, J., Mariage, A., Debard, A., Pellouin, V., Perret, A., & others. (2019). A family of native amine dehydrogenases for the asymmetric reductive amination of ketones. Nature catalysis, 2(4), 324–333.
    [BibTeX]
    @article{mayol2019family,
    title={A family of native amine dehydrogenases for the asymmetric reductive amination of ketones},
    author={Mayol, Ombeline and Bastard, Karine and Beloti, Lilian and Frese, Amina and Turkenburg, Johan P and Petit, Jean-Louis and Mariage, Aline and Debard, Adrien and Pellouin, Virginie and Perret, Alain and others},
    journal={Nature Catalysis},
    volume={2},
    number={4},
    pages={324--333},
    year={2019},
    publisher={Nature Publishing Group}
    }

  • Pujic, P., Alloisio, N., Fournier, P., Roche, D., Sghaier, H., Miotello, G., Armengaud, J., Berry, A. M., & Normand, P.. (2019). Omics of the early molecular dialogue between frankia alni and alnus glutinosa and the cellulase synton. Environmental microbiology, 21(9), 3328–3345.
    [BibTeX]
    @article{pujic2019omics,
    title={Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton},
    author={Pujic, Petar and Alloisio, Nicole and Fournier, Pascale and Roche, David and Sghaier, Haitham and Miotello, Guylaine and Armengaud, Jean and Berry, Alison M and Normand, Philippe},
    journal={Environmental microbiology},
    volume={21},
    number={9},
    pages={3328--3345},
    year={2019},
    publisher={John Wiley \& Sons, Inc. Hoboken, USA}
    }

  • Monteil, C. L., Vallenet, D., Menguy, N., Benzerara, K., Barbe, V., Fouteau, S., Cruaud, C., Floriani, M., Viollier, E., Adryanczyk, G., & others. (2019). Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist. Nature microbiology, 4(7), 1088–1095.
    [BibTeX]
    @article{monteil2019ectosymbiotic,
    title={Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist},
    author={Monteil, Caroline L and Vallenet, David and Menguy, Nicolas and Benzerara, Karim and Barbe, Val{\'e}rie and Fouteau, St{\'e}phanie and Cruaud, Corinne and Floriani, Magali and Viollier, Eric and Adryanczyk, G{\'e}raldine and others},
    journal={Nature microbiology},
    volume={4},
    number={7},
    pages={1088--1095},
    year={2019},
    publisher={Nature Publishing Group}
    }

  • Billard-Pomares, T., Clermont, O., Castellanos, M., Magdoud, F., Royer, G., Condamine, B., Fouteau, S., Barbe, V., Roche, D., Cruveiller, S., & others. (2019). The arginine deiminase operon is responsible for a fitness trade-off in extended-spectrum-$\beta$-lactamase-producing strains of escherichia coli. Antimicrobial agents and chemotherapy, 63(8), e00635–19.
    [BibTeX]
    @article{billard2019arginine,
    title={The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-$\beta$-Lactamase-Producing Strains of Escherichia coli},
    author={Billard-Pomares, Typhaine and Clermont, Olivier and Castellanos, Miguel and Magdoud, Fatma and Royer, Guilhem and Condamine, B{\'e}n{\'e}dicte and Fouteau, St{\'e}phanie and Barbe, Val{\'e}rie and Roche, David and Cruveiller, St{\'e}phane and others},
    journal={Antimicrobial agents and chemotherapy},
    volume={63},
    number={8},
    pages={e00635--19},
    year={2019},
    publisher={American Society for Microbiology Journals}
    }

  • Belkhelfa, S., Roche, D., Dubois, I., Berger, A., Delmas, V. A., Cattolico, L., Perret, A., Labadie, K., Perdereau, A. C., Darii, E., & others. (2019). Continuous culture adaptation of methylobacterium extorquens am1 and tk 0001 to very high methanol concentrations. Frontiers in microbiology, 10, 1313.
    [BibTeX]
    @article{belkhelfa2019continuous,
    title={Continuous culture adaptation of Methylobacterium extorquens AM1 and TK 0001 to very high methanol concentrations},
    author={Belkhelfa, Sophia and Roche, David and Dubois, Ivan and Berger, Anne and Delmas, Val{\'e}rie Anne and Cattolico, Laurence and Perret, Alain and Labadie, Karine and Perdereau, Aude C{\'e}cile and Darii, Ekaterina and others},
    journal={Frontiers in Microbiology},
    volume={10},
    pages={1313},
    year={2019},
    publisher={Frontiers}
    }

  • Branger, C., Ledda, A., Billard-Pomares, T., Doublet, B., Barbe, V., Roche, D., Médigue, C., Arlet, G., & Denamur, E.. (2019). Specialization of small non-conjugative plasmids in escherichia coli according to their family types. Microbial genomics, 5(9).
    [BibTeX]
    @article{branger2019specialization,
    title={Specialization of small non-conjugative plasmids in Escherichia coli according to their family types},
    author={Branger, Catherine and Ledda, Alice and Billard-Pomares, Typhaine and Doublet, Beno{\^\i}t and Barbe, Val{\'e}rie and Roche, David and M{\'e}digue, Claudine and Arlet, Guillaume and Denamur, Erick},
    journal={Microbial genomics},
    volume={5},
    number={9},
    year={2019},
    publisher={Microbiology Society}
    }

  • Royer, G., Melloul, E., Roisin, L., Courbin, V., Jacquier, H., Lepeule, R., Coutte, L., Darty, M., Fihman, V., Lim, P., & others. (2019). Complete genome sequencing of enterococcus faecalis strains suggests role of ebp deletion in infective endocarditis relapse.. Clinical microbiology and infection: the official publication of the european society of clinical microbiology and infectious diseases, 25(12), 1565.
    [BibTeX]
    @article{royer2019complete,
    title={Complete genome sequencing of Enterococcus faecalis strains suggests role of Ebp deletion in infective endocarditis relapse.},
    author={Royer, G and Melloul, E and Roisin, L and Courbin, V and Jacquier, H and Lepeule, R and Coutte, L and Darty, M and Fihman, V and Lim, P and others},
    journal={Clinical microbiology and infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
    volume={25},
    number={12},
    pages={1565},
    year={2019}
    }

  • Mahérault, A., Kemble, H., Magnan, M., Gachet, B., Roche, D., Le Nagard, H., Tenaillon, O., Denamur, E., Branger, C., & Landraud, L.. (2019). Advantage of the f2: a1: b-incf pandemic plasmid over incc plasmids in in vitro acquisition and evolution of blactx-m gene-bearing plasmids in escherichia coli. Antimicrobial agents and chemotherapy, 63(10), e01130–19.
    [BibTeX]
    @article{maherault2019advantage,
    title={Advantage of the F2: A1: B-IncF pandemic plasmid over IncC plasmids in in vitro acquisition and evolution of blaCTX-M gene-bearing plasmids in Escherichia coli},
    author={Mah{\'e}rault, Anne-Claire and Kemble, Harry and Magnan, M{\'e}lanie and Gachet, Benoit and Roche, David and Le Nagard, Herv{\'e} and Tenaillon, Olivier and Denamur, Erick and Branger, Catherine and Landraud, Luce},
    journal={Antimicrobial agents and chemotherapy},
    volume={63},
    number={10},
    pages={e01130--19},
    year={2019},
    publisher={Am Soc Microbiol}
    }

  • Royer, G., Fourreau, F., Gomart, C., Maurand, A., Hacquin, B., Ducellier, D., Cizeau, F., Lo, S., Cordonnier-Jourdin, C., Mercier-Darty, M., & others. (2019). Outbreak of an uncommon rifampin-resistant blandm-1citrobacter amalonaticus strain in a digestive rehabilitation center: the putative role of rifaximin. Clinical infectious diseases.
    [BibTeX]
    @article{royer2019outbreak,
    title={Outbreak of an Uncommon Rifampin-resistant blaNDM-1Citrobacter amalonaticus Strain in a Digestive Rehabilitation Center: The Putative Role of Rifaximin},
    author={Royer, Guilhem and Fourreau, Fr{\'e}deric and Gomart, Camille and Maurand, Audrey and Hacquin, Bruno and Ducellier, David and Cizeau, Florence and Lo, St{\'e}phane and Cordonnier-Jourdin, Catherine and Mercier-Darty, M{\'e}lanie and others},
    journal={Clinical Infectious Diseases},
    year={2019}
    }

  • Kieffer, N., Royer, G., Decousser, J., Bourrel, A., Palmieri, M., De La Rosa, J. O., Jacquier, H., Denamur, E., Nordmann, P., & Poirel, L.. (2019). Mcr-9, an inducible gene encoding an acquired phosphoethanolamine transferase in escherichia coli, and its origin. Antimicrobial agents and chemotherapy, 63(9), e00965–19.
    [BibTeX]
    @article{kieffer2019mcr,
    title={mcr-9, an inducible gene encoding an acquired phosphoethanolamine transferase in Escherichia coli, and its origin},
    author={Kieffer, Nicolas and Royer, Guilhem and Decousser, Jean-Winoc and Bourrel, Anne-Sophie and Palmieri, Mattia and De La Rosa, Jose-Manuel Ortiz and Jacquier, Herv{\'e} and Denamur, Erick and Nordmann, Patrice and Poirel, Laurent},
    journal={Antimicrobial agents and chemotherapy},
    volume={63},
    number={9},
    pages={e00965--19},
    year={2019},
    publisher={American Society for Microbiology Journals}
    }

2018

  • Borriss, R., Danchin, A., Harwood, C. R., Médigue, C., Rocha, E. P., Sekowska, A., & Vallenet, D.. (2018). Bacillus subtilis, the model gram-positive bacterium: 20 years of annotation refinement. Microbial biotechnology, 11(1), 3–17.
    [BibTeX]
    @article{borriss2018bacillus,
    title={Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement},
    author={Borriss, Rainer and Danchin, Antoine and Harwood, Colin R and M{\'e}digue, Claudine and Rocha, Eduardo PC and Sekowska, Agnieszka and Vallenet, David},
    journal={Microbial biotechnology},
    volume={11},
    number={1},
    pages={3--17},
    year={2018},
    publisher={Wiley Online Library}
    }

  • Dias, G., Bidault, A., Le Chevalier, P., Choquet, G., Der Sarkissian, C., Orlando, L., Medigue, C., Barbe, V., Thompson, F., Thompson, C. C., & others. (2018). Vibrio tapetis displays an original type iv secretion system in strains pathogenic for bivalve molluscs. Frontiers in microbiology, 9, 227.
    [BibTeX]
    @article{dias2018vibrio,
    title={Vibrio tapetis displays an original type IV secretion system in strains pathogenic for bivalve molluscs},
    author={Dias, Graciela and Bidault, Adeline and Le Chevalier, Patrick and Choquet, Gwenaelle and Der Sarkissian, Clio and Orlando, Ludovic and Medigue, Claudine and Barbe, Valerie and Thompson, Fabiano and Thompson, Cristiane Carneiro and others},
    journal={Frontiers in Microbiology},
    volume={9},
    pages={227},
    year={2018},
    publisher={Frontiers}
    }

  • Turpin, W., Weiman, M., Guyot, J., Lajus, A., Cruveiller, S., & Humblot, C.. (2018). The genomic and transcriptomic basis of the potential of lactobacillus plantarum a6 to improve the nutritional quality of a cereal based fermented food. International journal of food microbiology, 266, 346–354.
    [BibTeX]
    @article{turpin2018genomic,
    title={The genomic and transcriptomic basis of the potential of Lactobacillus plantarum A6 to improve the nutritional quality of a cereal based fermented food},
    author={Turpin, Williams and Weiman, Marion and Guyot, Jean-Pierre and Lajus, Aur{\'e}lie and Cruveiller, St{\'e}phane and Humblot, Christ{\`e}le},
    journal={International journal of food microbiology},
    volume={266},
    pages={346--354},
    year={2018},
    publisher={Elsevier}
    }

  • Clerissi, C., Touchon, M., Capela, D., Tang, M., Cruveiller, S., Genthon, C., Lopez-Roques, C., Parker, M. A., Moulin, L., Masson-Boivin, C., & others. (2018). Parallels between experimental and natural evolution of legume symbionts. Nature communications, 9(1), 1–13.
    [BibTeX]
    @article{clerissi2018parallels,
    title={Parallels between experimental and natural evolution of legume symbionts},
    author={Clerissi, Camille and Touchon, Marie and Capela, Delphine and Tang, Mingxing and Cruveiller, St{\'e}phane and Genthon, Cl{\'e}mence and Lopez-Roques, C{\'e}line and Parker, Matthew A and Moulin, Lionel and Masson-Boivin, Catherine and others},
    journal={Nature communications},
    volume={9},
    number={1},
    pages={1--13},
    year={2018},
    publisher={Nature Publishing Group}
    }

  • Belkhelfa, S., Labadie, K., Cruaud, C., Aury, J., Roche, D., Bouzon, M., Salanoubat, M., & Döring, V.. (2018). Complete genome sequence of the facultative methylotroph methylobacterium extorquens tk 0001 isolated from soil in poland. Genome announcements, 6(8), e00018–18.
    [BibTeX]
    @article{belkhelfa2018complete,
    title={Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland},
    author={Belkhelfa, Sophia and Labadie, Karine and Cruaud, Corinne and Aury, Jean-Marc and Roche, David and Bouzon, Madeleine and Salanoubat, Marcel and D{\"o}ring, Volker},
    journal={Genome announcements},
    volume={6},
    number={8},
    pages={e00018--18},
    year={2018},
    publisher={Am Soc Microbiol}
    }

  • Mercier, J., Josso, A., Medigue, C., & Vallenet, D.. (2018). Grools: reactive graph reasoning for genome annotation through biological processes. Bmc bioinformatics, 19(1), 132.
    [BibTeX]
    @article{mercier2018grools,
    title={GROOLS: reactive graph reasoning for genome annotation through biological processes},
    author={Mercier, Jonathan and Josso, Adrien and Medigue, Claudine and Vallenet, David},
    journal={BMC Bioinformatics},
    volume={19},
    number={1},
    pages={132},
    year={2018},
    publisher={BioMed Central}
    }

  • Desroches, M., Royer, G., Roche, D., Mercier-Darty, M., Vallenet, D., Médigue, C., Bastard, K., Rodriguez, C., Clermont, O., Denamur, E., & others. (2018). The odyssey of the ancestral escherich strain through culture collections: an example of allopatric diversification. Msphere, 3(1), e00553–17.
    [BibTeX]
    @article{desroches2018odyssey,
    title={The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification},
    author={Desroches, M and Royer, G and Roche, D and Mercier-Darty, M and Vallenet, D and M{\'e}digue, C and Bastard, K and Rodriguez, C and Clermont, O and Denamur, E and others},
    journal={mSphere},
    volume={3},
    number={1},
    pages={e00553--17},
    year={2018},
    publisher={Am Soc Microbiol}
    }

  • Krin, E., Pierlé, S. A., Sismeiro, O., Jagla, B., Dillies, M., Varet, H., Irazoki, O., Campoy, S., Rouy, Z., Cruveiller, S., & others. (2018). Expansion of the sos regulon of vibrio cholerae through extensive transcriptome analysis and experimental validation. Bmc genomics, 19(1), 373.
    [BibTeX]
    @article{krin2018expansion,
    title={Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation},
    author={Krin, Evelyne and Pierl{\'e}, Sebastian Aguilar and Sismeiro, Odile and Jagla, Bernd and Dillies, Marie-Agn{\`e}s and Varet, Hugo and Irazoki, Oihane and Campoy, Susana and Rouy, Zo{\'e} and Cruveiller, St{\'e}phane and others},
    journal={BMC genomics},
    volume={19},
    number={1},
    pages={373},
    year={2018},
    publisher={BioMed Central}
    }

  • Partensky, F., Six, C., Ratin, M., Garczarek, L., Vaulot, D., Probert, I., Calteau, A., Gourvil, P., Marie, D., Grébert, T., & others. (2018). A novel species of the marine cyanobacterium acaryochloris with a unique pigment content and lifestyle. Scientific reports, 8(1), 1–13.
    [BibTeX]
    @article{partensky2018novel,
    title={A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle},
    author={Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Ratin, Morgane and Garczarek, Laurence and Vaulot, Daniel and Probert, Ian and Calteau, Alexandra and Gourvil, Priscillia and Marie, Dominique and Gr{\'e}bert, Th{\'e}ophile and others},
    journal={Scientific reports},
    volume={8},
    number={1},
    pages={1--13},
    year={2018},
    publisher={Nature Publishing Group}
    }

  • Gully, D., Czernic, P., Cruveiller, S., Mahé, F., Longin, C., Vallenet, D., François, P., Nidelet, S., Rialle, S., Giraud, E., & others. (2018). Transcriptome profiles of nod factor-independent symbiosis in the tropical legume aeschynomene evenia. Scientific reports, 8(1), 1–12.
    [BibTeX]
    @article{gully2018transcriptome,
    title={Transcriptome profiles of Nod factor-independent symbiosis in the tropical legume Aeschynomene evenia},
    author={Gully, Djamel and Czernic, Pierre and Cruveiller, St{\'e}phane and Mah{\'e}, Fr{\'e}d{\'e}ric and Longin, Cyrille and Vallenet, David and Fran{\c{c}}ois, Philippe and Nidelet, Sabine and Rialle, St{\'e}phanie and Giraud, Eric and others},
    journal={Scientific reports},
    volume={8},
    number={1},
    pages={1--12},
    year={2018},
    publisher={Nature Publishing Group}
    }

  • Duchemin, W., Gence, G., Arigon Chifolleau, A., Arvestad, L., Bansal, M. S., Berry, V., Boussau, B., Chevenet, F., Comte, N., Dav{‘i}n, A. A., & others. (2018). Recphyloxml: a format for reconciled gene trees. Bioinformatics, 34(21), 3646–3652.
    [BibTeX]
    @article{duchemin2018recphyloxml,
    title={RecPhyloXML: a format for reconciled gene trees},
    author={Duchemin, Wandrille and Gence, Guillaume and Arigon Chifolleau, Anne-Muriel and Arvestad, Lars and Bansal, Mukul S and Berry, Vincent and Boussau, Bastien and Chevenet, Fran{\c{c}}ois and Comte, Nicolas and Dav{\'\i}n, Adri{\'a}n A and others},
    journal={Bioinformatics},
    volume={34},
    number={21},
    pages={3646--3652},
    year={2018},
    publisher={Oxford University Press}
    }

  • Monteil, C. L., Perrière, G., Menguy, N., Ginet, N., Alonso, B., Waisbord, N., Cruveiller, S., Pignol, D., & Lefèvre, C. T.. (2018). Genomic study of a novel magnetotactic alphaproteobacteria uncovers the multiple ancestry of magnetotaxis. Environmental microbiology, 20(12), 4415–4430.
    [BibTeX]
    @article{monteil2018genomic,
    title={Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis},
    author={Monteil, Caroline L and Perri{\`e}re, Guy and Menguy, Nicolas and Ginet, Nicolas and Alonso, B{\'e}atrice and Waisbord, Nicolas and Cruveiller, St{\'e}phane and Pignol, David and Lef{\`e}vre, Christopher T},
    journal={Environmental microbiology},
    volume={20},
    number={12},
    pages={4415--4430},
    year={2018},
    publisher={John Wiley \& Sons, Inc. Hoboken, USA}
    }

  • Branger, C., Ledda, A., Billard-Pomares, T., Doublet, B., Fouteau, S., Barbe, V., Roche, D., Cruveiller, S., Médigue, C., Castellanos, M., & others. (2018). Extended-spectrum $\beta$-lactamase-encoding genes are spreading on a wide range of escherichia coli plasmids existing prior to the use of third-generation cephalosporins. Microbial genomics, 4(9).
    [BibTeX]
    @article{branger2018extended,
    title={Extended-spectrum $\beta$-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins},
    author={Branger, Catherine and Ledda, Alice and Billard-Pomares, Typhaine and Doublet, Beno{\^\i}t and Fouteau, St{\'e}phanie and Barbe, Val{\'e}rie and Roche, David and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Castellanos, Miguel and others},
    journal={Microbial genomics},
    volume={4},
    number={9},
    year={2018},
    publisher={Microbiology Society}
    }

  • Royer, G., Decousser, J., Branger, C., Dubois, M., Médigue, C., Denamur, E., & Vallenet, D.. (2018). Plascope: a targeted approach to assess the plasmidome from genome assemblies at the species level. Microbial genomics, 4(9).
    [BibTeX]
    @article{royer2018plascope,
    title={PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level},
    author={Royer, G and Decousser, JW and Branger, C and Dubois, M and M{\'e}digue, C and Denamur, E and Vallenet, D},
    journal={Microbial Genomics},
    volume={4},
    number={9},
    year={2018},
    publisher={Microbiology Society}
    }

  • Gobet, A., Barbeyron, T., Matard-Mann, M., Magdelenat, G., Vallenet, D., Duchaud, E., & Michel, G.. (2018). Evolutionary evidence of algal polysaccharide degradation acquisition by pseudoalteromonas carrageenovora 9t to adapt to macroalgal niches. Frontiers in microbiology, 9, 2740.
    [BibTeX]
    @article{gobet2018evolutionary,
    title={Evolutionary evidence of algal polysaccharide degradation acquisition by Pseudoalteromonas carrageenovora 9T to adapt to macroalgal niches},
    author={Gobet, Ang{\'e}lique and Barbeyron, Tristan and Matard-Mann, Maria and Magdelenat, Ghislaine and Vallenet, David and Duchaud, Eric and Michel, Gurvan},
    journal={Frontiers in microbiology},
    volume={9},
    pages={2740},
    year={2018},
    publisher={Frontiers}
    }

  • Bastard, K., Isabet, T., Stura, E. A., Legrand, P., & Zaparucha, A.. (2018). Structural studies based on two lysine dioxygenases with distinct regioselectivity brings insights into enzyme specificity within the clavaminate synthase-like family. Scientific reports, 8(1), 1–11.
    [BibTeX]
    @article{bastard2018structural,
    title={Structural studies based on two lysine dioxygenases with distinct regioselectivity brings insights into enzyme specificity within the clavaminate synthase-like family},
    author={Bastard, Karine and Isabet, Tatiana and Stura, Enrico A and Legrand, Pierre and Zaparucha, Anne},
    journal={Scientific reports},
    volume={8},
    number={1},
    pages={1--11},
    year={2018},
    publisher={Nature Publishing Group}
    }

2017

  • Tran, T. T., Mangenot, S., Magdelenat, G., Payen, E., Rouy, Z., Belahbib, H., Grail, B. M., Johnson, B. D., Bonnefoy, V., & Talla, E.. (2017). Comparative genome analysis provides insights into both the lifestyle of acidithiobacillus ferrivorans strain cf27 and the chimeric nature of the iron-oxidizing acidithiobacilli genomes. Frontiers in microbiology, 8, 1009.
    [BibTeX]
    @article{tran2017comparative,
    title={Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes},
    author={Tran, Tam TT and Mangenot, Sophie and Magdelenat, Ghislaine and Payen, Emilie and Rouy, Zoe and Belahbib, Hassiba and Grail, Barry M and Johnson, D Barrie and Bonnefoy, Violaine and Talla, Emmanuel},
    journal={Frontiers in microbiology},
    volume={8},
    pages={1009},
    year={2017},
    publisher={Frontiers}
    }

  • Pancrace, C., Gugger, M., & Calteau, A.. (2017). Genomics of nrps/pks biosynthetic gene clusters in cyanobacteria. Cyanobacteria: omics and manipulation. caister academic press, 32, 55–74.
    [BibTeX]
    @article{pancrace2017genomics,
    title={Genomics of NRPS/PKS Biosynthetic Gene Clusters in Cyanobacteria},
    author={Pancrace, Claire and Gugger, Muriel and Calteau, Alexandra},
    journal={Cyanobacteria: Omics and Manipulation. CAISTER ACADEMIC PRESS},
    volume={32},
    pages={55--74},
    year={2017}
    }

  • Rochat, T., Fujiwara-Nagata, E., Calvez, S., Dalsgaard, I., Madsen, L., Calteau, A., Lunazzi, A., Nicolas, P., Wiklund, T., Bernardet, J., & others. (2017). Genomic characterization of flavobacterium psychrophilum serotypes and development of a multiplex pcr-based serotyping scheme. Frontiers in microbiology, 8, 1752.
    [BibTeX]
    @article{rochat2017genomic,
    title={Genomic characterization of Flavobacterium psychrophilum serotypes and development of a multiplex PCR-based serotyping scheme},
    author={Rochat, Tatiana and Fujiwara-Nagata, Erina and Calvez, S{\'e}gol{\`e}ne and Dalsgaard, Inger and Madsen, Lone and Calteau, Alexandra and Lunazzi, Aur{\'e}lie and Nicolas, Pierre and Wiklund, Tom and Bernardet, Jean-Fran{\c{c}}ois and others},
    journal={Frontiers in Microbiology},
    volume={8},
    pages={1752},
    year={2017},
    publisher={Frontiers}
    }

  • Capela, D., Marchetti, M., Clérissi, C., Perrier, A., Guetta, D., Gris, C., Valls, M., Jauneau, A., Cruveiller, S., Rocha, E. P., & others. (2017). Recruitment of a lineage-specific virulence regulatory pathway promotes intracellular infection by a plant pathogen experimentally evolved into a legume symbiont. Molecular biology and evolution, 34(10), 2503–2521.
    [BibTeX]
    @article{capela2017recruitment,
    title={Recruitment of a lineage-specific virulence regulatory pathway promotes intracellular infection by a plant pathogen experimentally evolved into a legume symbiont},
    author={Capela, Delphine and Marchetti, Marta and Cl{\'e}rissi, Camille and Perrier, Anthony and Guetta, Dorian and Gris, Carine and Valls, Marc and Jauneau, Alain and Cruveiller, St{\'e}phane and Rocha, Eduardo PC and others},
    journal={Molecular biology and evolution},
    volume={34},
    number={10},
    pages={2503--2521},
    year={2017},
    publisher={Oxford University Press}
    }

  • Lassalle, F., Planel, R., Penel, S., Chapulliot, D., Barbe, V., Dubost, A., Calteau, A., Vallenet, D., Mornico, D., Bigot, T., & others. (2017). Ancestral genome estimation reveals the history of ecological diversification in agrobacterium. Genome biology and evolution, 9(12), 3413–3431.
    [BibTeX]
    @article{lassalle2017ancestral,
    title={Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium},
    author={Lassalle, Florent and Planel, R{\'e}mi and Penel, Simon and Chapulliot, David and Barbe, Val{\'e}rie and Dubost, Audrey and Calteau, Alexandra and Vallenet, David and Mornico, Damien and Bigot, Thomas and others},
    journal={Genome biology and evolution},
    volume={9},
    number={12},
    pages={3413--3431},
    year={2017},
    publisher={Oxford University Press}
    }

  • Mouammine, A., Pages, S., Lanois, A., Gaudriault, S., Jubelin, G., Bonabaud, M., Cruveiller, S., Dubois, E., Roche, D., Legrand, L., & others. (2017). An antimicrobial peptide-resistant minor subpopulation of photorhabdus luminescens is responsible for virulence. Scientific reports, 7, 43670.
    [BibTeX]
    @article{mouammine2017antimicrobial,
    title={An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence},
    author={Mouammine, Annabelle and Pages, Sylvie and Lanois, Anne and Gaudriault, Sophie and Jubelin, Gregory and Bonabaud, Maurine and Cruveiller, St{\'e}phane and Dubois, Emeric and Roche, David and Legrand, Ludovic and others},
    journal={Scientific reports},
    volume={7},
    pages={43670},
    year={2017},
    publisher={Nature Publishing Group}
    }

  • Gully, D., Teulet, A., Busset, N., Nouwen, N., Fardoux, J., Rouy, Z., Vallenet, D., Cruveiller, S., & Giraud, E.. (2017). Complete genome sequence of bradyrhizobium sp. ors285, a photosynthetic strain able to establish nod factor-dependent or nod factor-independent symbiosis with aeschynomene legumes. Genome announcements, 5(30), e00421–17.
    [BibTeX]
    @article{gully2017complete,
    title={Complete Genome Sequence of Bradyrhizobium sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with Aeschynomene Legumes},
    author={Gully, Djamel and Teulet, Albin and Busset, Nicolas and Nouwen, Nico and Fardoux, Jo{\"e}l and Rouy, Zoe and Vallenet, David and Cruveiller, St{\'e}phane and Giraud, Eric},
    journal={Genome announcements},
    volume={5},
    number={30},
    pages={e00421--17},
    year={2017},
    publisher={Am Soc Microbiol}
    }

  • Galia, W., Leriche, F., Cruveiller, S., Garnier, C., Navratil, V., Dubost, A., Blanquet-Diot, S., & Thevenot-Sergentet, D.. (2017). Strand-specific transcriptomes of enterohemorrhagic escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat. Bmc genomics, 18(1), 574.
    [BibTeX]
    @article{galia2017strand,
    title={Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat},
    author={Galia, Wessam and Leriche, Francoise and Cruveiller, St{\'e}phane and Garnier, Cindy and Navratil, Vincent and Dubost, Audrey and Blanquet-Diot, St{\'e}phanie and Thevenot-Sergentet, Delphine},
    journal={BMC genomics},
    volume={18},
    number={1},
    pages={574},
    year={2017},
    publisher={BioMed Central}
    }

  • Payelleville, A., Lanois, A., Gislard, M., Dubois, E., Roche, D., Cruveiller, S., Givaudan, A., & Brillard, J.. (2017). Dna adenine methyltransferase (dam) overexpression impairs photorhabdus luminescens motility and virulence. Frontiers in microbiology, 8, 1671.
    [BibTeX]
    @article{payelleville2017dna,
    title={DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence},
    author={Payelleville, Amaury and Lanois, Anne and Gislard, Marie and Dubois, Emeric and Roche, David and Cruveiller, St{\'e}phane and Givaudan, Alain and Brillard, Julien},
    journal={Frontiers in microbiology},
    volume={8},
    pages={1671},
    year={2017},
    publisher={Frontiers}
    }

  • Dupont, H., Choinier, P., Roche, D., Adiba, S., Sookdeb, M., Branger, C., Denamur, E., & Mammeri, H.. (2017). Structural alteration of ompr as a source of ertapenem resistance in a ctx-m-15-producing escherichia coli o25b: h4 sequence type 131 clinical isolate. Antimicrobial agents and chemotherapy, 61(5), e00014–17.
    [BibTeX]
    @article{dupont2017structural,
    title={Structural alteration of OmpR as a source of ertapenem resistance in a CTX-M-15-producing Escherichia coli O25b: H4 sequence type 131 clinical isolate},
    author={Dupont, Herv{\'e} and Choinier, Pascaline and Roche, David and Adiba, Sandine and Sookdeb, Megan and Branger, Catherine and Denamur, Erick and Mammeri, Hedi},
    journal={Antimicrobial agents and chemotherapy},
    volume={61},
    number={5},
    pages={e00014--17},
    year={2017},
    publisher={Am Soc Microbiol}
    }

  • Pérez-Pascual, D., Lunazzi, A., Magdelenat, G., Rouy, Z., Roulet, A., Lopez-Roques, C., Larocque, R., Barbeyron, T., Gobet, A., Michel, G., & others. (2017). The complete genome sequence of the fish pathogen tenacibaculum maritimum provides insights into virulence mechanisms. Frontiers in microbiology, 8, 1542.
    [BibTeX]
    @article{perez2017complete,
    title={The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms},
    author={P{\'e}rez-Pascual, David and Lunazzi, Aurelie and Magdelenat, Ghislaine and Rouy, Zoe and Roulet, Alain and Lopez-Roques, Celine and Larocque, Robert and Barbeyron, Tristan and Gobet, Ang{\'e}lique and Michel, Gurvan and others},
    journal={Frontiers in Microbiology},
    volume={8},
    pages={1542},
    year={2017},
    publisher={Frontiers}
    }

  • Blanchard, L., Guérin, P., Roche, D., Cruveiller, S., Pignol, D., Vallenet, D., Armengaud, J., & De Groot, A.. (2017). Conservation and diversity of the irre/ddro-controlled radiation response in radiation-resistant deinococcus bacteria. Microbiologyopen, 6(4), e00477.
    [BibTeX]
    @article{blanchard2017conservation,
    title={Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria},
    author={Blanchard, Laurence and Gu{\'e}rin, Philippe and Roche, David and Cruveiller, St{\'e}phane and Pignol, David and Vallenet, David and Armengaud, Jean and De Groot, Arjan},
    journal={MicrobiologyOpen},
    volume={6},
    number={4},
    pages={e00477},
    year={2017}
    }

  • Marchetti, M., Clerissi, C., Yousfi, Y., Gris, C., Bouchez, O., Rocha, E., Cruveiller, S., Jauneau, A., Capela, D., & Masson-Boivin, C.. (2017). Experimental evolution of rhizobia may lead to either extra-or intracellular symbiotic adaptation depending on the selection regime. Molecular ecology, 26(7), 1818–1831.
    [BibTeX]
    @article{marchetti2017experimental,
    title={Experimental evolution of rhizobia may lead to either extra-or intracellular symbiotic adaptation depending on the selection regime},
    author={Marchetti, Marta and Clerissi, Camille and Yousfi, Yasmine and Gris, Carine and Bouchez, Olivier and Rocha, Eduardo and Cruveiller, St{\'e}phane and Jauneau, Alain and Capela, Delphine and Masson-Boivin, Catherine},
    journal={Molecular ecology},
    volume={26},
    number={7},
    pages={1818--1831},
    year={2017},
    publisher={Wiley Online Library}
    }

  • Pancrace, C., Barny, M., Ueoka, R., Calteau, A., Scalvenzi, T., Pédron, J., Barbe, V., Piel, J., Humbert, J., & Gugger, M.. (2017). Insights into the planktothrix genus: genomic and metabolic comparison of benthic and planktic strains. Scientific reports, 7(1), 1–10.
    [BibTeX]
    @article{pancrace2017insights,
    title={Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains},
    author={Pancrace, Claire and Barny, Marie-Anne and Ueoka, Reiko and Calteau, Alexandra and Scalvenzi, Thibault and P{\'e}dron, Jacques and Barbe, Val{\'e}rie and Piel, Joern and Humbert, Jean-Fran{\c{c}}ois and Gugger, Muriel},
    journal={Scientific reports},
    volume={7},
    number={1},
    pages={1--10},
    year={2017},
    publisher={Nature Publishing Group}
    }

  • Bastard, K., Perret, A., Mariage, A., Bessonnet, T., Pinet-Turpault, A., Petit, J., Darii, E., Bazire, P., Vergne-Vaxelaire, C., Brewee, C., & others. (2017). Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nature chemical biology, 13(8), 858.
    [BibTeX]
    @article{bastard2017parallel,
    title={Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis},
    author={Bastard, Karine and Perret, Alain and Mariage, Aline and Bessonnet, Thomas and Pinet-Turpault, Agn{\`e}s and Petit, Jean-Louis and Darii, Ekaterina and Bazire, Pascal and Vergne-Vaxelaire, Carine and Brewee, Cl{\'e}mence and others},
    journal={Nature chemical biology},
    volume={13},
    number={8},
    pages={858},
    year={2017},
    publisher={Nature Publishing Group}
    }

  • Pancrace, C., Jokela, J., Sassoon, N., Ganneau, C., Desnos-Ollivier, M., Wahlsten, M., Humisto, A., Calteau, A., Bay, S., Fewer, D. P., & others. (2017). Rearranged biosynthetic gene cluster and synthesis of hassallidin e in planktothrix serta pcc 8927. Acs chemical biology, 12(7), 1796–1804.
    [BibTeX]
    @article{pancrace2017rearranged,
    title={Rearranged biosynthetic gene cluster and synthesis of hassallidin E in Planktothrix serta PCC 8927},
    author={Pancrace, Claire and Jokela, Jouni and Sassoon, Nathalie and Ganneau, Christelle and Desnos-Ollivier, Marie and Wahlsten, Matti and Humisto, Anu and Calteau, Alexandra and Bay, Sylvie and Fewer, David P and others},
    journal={ACS chemical biology},
    volume={12},
    number={7},
    pages={1796--1804},
    year={2017},
    publisher={ACS Publications}
    }

  • Bringel, F., Postema, C. P., Mangenot, S., Bibi-Triki, S., Chaignaud, P., Haque, M. F. U., Gruffaz, C., Hermon, L., Louhichi, Y., Maucourt, B., & others. (2017). Genome sequence of the dichloromethane-degrading bacterium hyphomicrobium sp. strain gj21. Genome announcements, 5(30), e00622–17.
    [BibTeX]
    @article{bringel2017genome,
    title={Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21},
    author={Bringel, Fran{\c{c}}oise and Postema, Christiaan P and Mangenot, Sophie and Bibi-Triki, Sabrina and Chaignaud, Pauline and Haque, Muhammad Farhan Ul and Gruffaz, Christelle and Hermon, Louis and Louhichi, Yousra and Maucourt, Bruno and others},
    journal={Genome announcements},
    volume={5},
    number={30},
    pages={e00622--17},
    year={2017},
    publisher={Am Soc Microbiol}
    }

  • Chaignaud, P., Maucourt, B., Weiman, M., Alberti, A., Kolb, S., Cruveiller, S., Vuilleumier, S., & Bringel, F.. (2017). Genomic and transcriptomic analysis of growth-supporting dehalogenation of chlorinated methanes in methylobacterium. Frontiers in microbiology, 8, 1600.
    [BibTeX]
    @article{chaignaud2017genomic,
    title={Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium},
    author={Chaignaud, Pauline and Maucourt, Bruno and Weiman, Marion and Alberti, Adriana and Kolb, Steffen and Cruveiller, St{\'e}phane and Vuilleumier, St{\'e}phane and Bringel, Fran{\c{c}}oise},
    journal={Frontiers in microbiology},
    volume={8},
    pages={1600},
    year={2017},
    publisher={Frontiers}
    }

  • Ji, B., Zhang, S., Zhang, W., Rouy, Z., Alberto, F., Santini, C., Mangenot, S., Gagnot, S., Philippe, N., Pradel, N., & others. (2017). The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of proteobacteria. Environmental microbiology, 19(3), 1103–1119.
    [BibTeX]
    @article{ji2017chimeric,
    title={The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria},
    author={Ji, Boyang and Zhang, Sheng-Da and Zhang, Wei-Jia and Rouy, Zoe and Alberto, Fran{\c{c}}ois and Santini, Claire-Lise and Mangenot, Sophie and Gagnot, S{\'e}verine and Philippe, Nad{\`e}ge and Pradel, Nathalie and others},
    journal={Environmental microbiology},
    volume={19},
    number={3},
    pages={1103--1119},
    year={2017},
    publisher={Wiley Online Library}
    }

  • Ficko-Blean, E., Préchoux, A., Thomas, F., Rochat, T., Larocque, R., Zhu, Y., Stam, M., Génicot, S., Jam, M., Calteau, A., & others. (2017). Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. Nature communications, 8(1), 1–17.
    [BibTeX]
    @article{ficko2017carrageenan,
    title={Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria},
    author={Ficko-Blean, Elizabeth and Pr{\'e}choux, Aur{\'e}lie and Thomas, Fran{\c{c}}ois and Rochat, Tatiana and Larocque, Robert and Zhu, Yongtao and Stam, Mark and G{\'e}nicot, Sabine and Jam, Murielle and Calteau, Alexandra and others},
    journal={Nature communications},
    volume={8},
    number={1},
    pages={1--17},
    year={2017},
    publisher={Nature Publishing Group}
    }

  • De Berardinis, V., Guérard-Hélaine, C., Darii, E., Bastard, K., Hélaine, V., Mariage, A., Petit, J., Poupard, N., Sánchez-Moreno, I., Stam, M., & others. (2017). Expanding the reaction space of aldolases using hydroxypyruvate as a nucleophilic substrate. Green chemistry, 19(2), 519–526.
    [BibTeX]
    @article{de2017expanding,
    title={Expanding the reaction space of aldolases using hydroxypyruvate as a nucleophilic substrate},
    author={De Berardinis, V{\'e}ronique and Gu{\'e}rard-H{\'e}laine, Christine and Darii, Ekaterina and Bastard, Karine and H{\'e}laine, Virgil and Mariage, Aline and Petit, Jean-Louis and Poupard, Nicolas and S{\'a}nchez-Moreno, Israel and Stam, Mark and others},
    journal={Green Chemistry},
    volume={19},
    number={2},
    pages={519--526},
    year={2017},
    publisher={Royal Society of Chemistry}
    }

2016

  • Bisch, G., Ogier, J., Medigue, C., Rouy, Z., Vincent, S., Tailliez, P., Givaudan, A., & Gaudriault, S.. (2016). Comparative genomics between two xenorhabdus bovienii strains highlights differential evolutionary scenarios within an entomopathogenic bacterial species. Genome biology and evolution, 8(1), 148–160.
    [BibTeX]
    @article{bisch2016comparative,
    title={Comparative genomics between two Xenorhabdus bovienii strains highlights differential evolutionary scenarios within an entomopathogenic bacterial species},
    author={Bisch, Gaelle and Ogier, Jean-Claude and Medigue, Claudine and Rouy, Zoe and Vincent, Stephanie and Tailliez, Patrick and Givaudan, Alain and Gaudriault, Sophie},
    journal={Genome biology and evolution},
    volume={8},
    number={1},
    pages={148--160},
    year={2016},
    publisher={Oxford University Press}
    }

  • Gerbore, J., Brutel, A., Lemainque, A., Mairey, B., Médigue, C., Vallenet, D., Lefort, F., & Grizard, D.. (2016). Complete genome sequence of bacillus methylotrophicus strain b25, a potential plant growth-promoting rhizobacterium. Genome announcements, 4(2), e00058–16.
    [BibTeX]
    @article{gerbore2016complete,
    title={Complete genome sequence of Bacillus methylotrophicus strain B25, a potential plant growth-promoting rhizobacterium},
    author={Gerbore, Jonathan and Brutel, Aline and Lemainque, Arnaud and Mairey, Barbara and M{\'e}digue, Claudine and Vallenet, David and Lefort, Francois and Grizard, Damien},
    journal={Genome announcements},
    volume={4},
    number={2},
    pages={e00058--16},
    year={2016},
    publisher={Am Soc Microbiol}
    }

  • Redko, Y., Galtier, E., Arnion, H., Darfeuille, F., Sismeiro, O., Coppée, J., Médigue, C., Weiman, M., Cruveiller, S., & De Reuse, H.. (2016). Rnase j depletion leads to massive changes in mrna abundance in helicobacter pylori. Rna biology, 13(2), 243–253.
    [BibTeX]
    @article{redko2016rnase,
    title={RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori},
    author={Redko, Yulia and Galtier, Elo{\"\i}se and Arnion, H{\'e}l{\`e}ne and Darfeuille, Fabien and Sismeiro, Odile and Copp{\'e}e, Jean-Yves and M{\'e}digue, Claudine and Weiman, Marion and Cruveiller, St{\'e}phane and De Reuse, Hilde},
    journal={RNA biology},
    volume={13},
    number={2},
    pages={243--253},
    year={2016},
    publisher={Taylor \& Francis}
    }

  • Vallenet, D., Calteau, A., Cruveiller, S., Gachet, M., Lajus, A., Josso, A., Mercier, J., Renaux, A., Rollin, J., Rouy, Z., & others. (2016). Microscope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. Nucleic acids research, 45(D1), D517–D528.
    [BibTeX]
    @article{vallenet2016microscope,
    title={MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes},
    author={Vallenet, David and Calteau, Alexandra and Cruveiller, St{\'e}phane and Gachet, Mathieu and Lajus, Aur{\'e}lie and Josso, Adrien and Mercier, Jonathan and Renaux, Alexandre and Rollin, Johan and Rouy, Zoe and others},
    journal={Nucleic acids research},
    volume={45},
    number={D1},
    pages={D517--D528},
    year={2016},
    publisher={Oxford University Press}
    }

  • Vanhove, A. S., Rubio, T. P., Nguyen, A. N., Lemire, A., Roche, D., Nicod, J., Vergnes, A., Poirier, A. C., Disconzi, E., Bachère, E., & others. (2016). Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics. Environmental microbiology, 18(3), 875–888.
    [BibTeX]
    @article{vanhove2016copper,
    title={Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics},
    author={Vanhove, Audrey S and Rubio, Tristan P and Nguyen, An N and Lemire, Astrid and Roche, David and Nicod, Julie and Vergnes, Agn{\`e}s and Poirier, Aurore C and Disconzi, Elena and Bach{\`e}re, Evelyne and others},
    journal={Environmental microbiology},
    volume={18},
    number={3},
    pages={875--888},
    year={2016},
    publisher={Wiley Online Library}
    }

  • Bronnec, V., Haddad, N., Cruveiller, S., Hernould, M., Tresse, O., & Zagorec, M.. (2016). Draft genome sequence of campylobacter jejuni bf, an atypical strain able to grow under aerobiosis. Genome announcements, 4(2), e00120–16.
    [BibTeX]
    @article{bronnec2016draft,
    title={Draft genome sequence of Campylobacter jejuni Bf, an atypical strain able to grow under aerobiosis},
    author={Bronnec, Vicky and Haddad, Nabila and Cruveiller, St{\'e}phane and Hernould, Mathieu and Tresse, Odile and Zagorec, Monique},
    journal={Genome announcements},
    volume={4},
    number={2},
    pages={e00120--16},
    year={2016},
    publisher={Am Soc Microbiol}
    }

  • Remenant, B., Borges, F., Cailliez-Grimal, C., Revol-Junelles, A., Marché, L., Lajus, A., Médigue, C., Pilet, M., Prévost, H., & Zagorec, M.. (2016). Draft genome sequence of carnobacterium divergens v41, a bacteriocin-producing strain. Genome announcements, 4(5), e01109–16.
    [BibTeX]
    @article{remenant2016draft,
    title={Draft genome sequence of Carnobacterium divergens V41, a bacteriocin-producing strain},
    author={Remenant, Beno{\^\i}t and Borges, Fr{\'e}d{\'e}ric and Cailliez-Grimal, Catherine and Revol-Junelles, Anne-Marie and March{\'e}, Laurent and Lajus, Aur{\'e}lie and M{\'e}digue, Claudine and Pilet, Marie-France and Pr{\'e}vost, Herv{\'e} and Zagorec, Monique},
    journal={Genome announcements},
    volume={4},
    number={5},
    pages={e01109--16},
    year={2016},
    publisher={Am Soc Microbiol}
    }

  • Plucain, J., Suau, A., Cruveiller, S., Médigue, C., Schneider, D., & Le Gac, M.. (2016). Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria. Bmc evolutionary biology, 16(1), 86.
    [BibTeX]
    @article{plucain2016contrasting,
    title={Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria},
    author={Plucain, Jessica and Suau, Antonia and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Schneider, Dominique and Le Gac, Micka{\"e}l},
    journal={BMC evolutionary biology},
    volume={16},
    number={1},
    pages={86},
    year={2016},
    publisher={BioMed Central}
    }

  • Ailloud, F., Lowe, T. M., Robène, I., Cruveiller, S., Allen, C., & Prior, P.. (2016). In planta comparative transcriptomics of host-adapted strains of ralstonia solanacearum. Peerj, 4, e1549.
    [BibTeX]
    @article{ailloud2016planta,
    title={In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum},
    author={Ailloud, Florent and Lowe, Tiffany M and Rob{\`e}ne, Isabelle and Cruveiller, St{\'e}phane and Allen, Caitilyn and Prior, Philippe},
    journal={PeerJ},
    volume={4},
    pages={e1549},
    year={2016},
    publisher={PeerJ Inc.}
    }

  • Bronnec, V., Turoňová, H., Bouju, A., Cruveiller, S., Rodrigues, R., Demnerova, K., Tresse, O., Haddad, N., & Zagorec, M.. (2016). Adhesion, biofilm formation, and genomic features of campylobacter jejuni bf, an atypical strain able to grow under aerobic conditions. Frontiers in microbiology, 7, 1002.
    [BibTeX]
    @article{bronnec2016adhesion,
    title={Adhesion, biofilm formation, and genomic features of Campylobacter jejuni Bf, an atypical strain able to grow under aerobic conditions},
    author={Bronnec, Vicky and Turo{\v{n}}ov{\'a}, Hana and Bouju, Agn{\`e}s and Cruveiller, St{\'e}phane and Rodrigues, Ramila and Demnerova, Katerina and Tresse, Odile and Haddad, Nabila and Zagorec, Monique},
    journal={Frontiers in microbiology},
    volume={7},
    pages={1002},
    year={2016},
    publisher={Frontiers}
    }

  • Belda, E., Van Heck, R. G., José Lopez-Sanchez, M., Cruveiller, S., Barbe, V., Fraser, C., Klenk, H., Petersen, J., Morgat, A., Nikel, P. I., & others. (2016). The revisited genome of pseudomonas putida kt2440 enlightens its value as a robust metabolic chassis. Environmental microbiology, 18(10), 3403–3424.
    [BibTeX]
    @article{belda2016revisited,
    title={The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis},
    author={Belda, Eugeni and Van Heck, Ruben GA and Jos{\'e} Lopez-Sanchez, Maria and Cruveiller, St{\'e}phane and Barbe, Val{\'e}rie and Fraser, Claire and Klenk, Hans-Peter and Petersen, J{\"o}rn and Morgat, Anne and Nikel, Pablo I and others},
    journal={Environmental microbiology},
    volume={18},
    number={10},
    pages={3403--3424},
    year={2016},
    publisher={Wiley Online Library}
    }

  • Zhang, S., Santini, C., Zhang, W., Barbe, V., Mangenot, S., Guyomar, C., Garel, M., Chen, H., Li, X., Yin, Q., & others. (2016). Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea photobacterium phosphoreum ant-2200. Extremophiles, 20(3), 301–310.
    [BibTeX]
    @article{zhang2016genomic,
    title={Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200},
    author={Zhang, Sheng-Da and Santini, Claire-Lise and Zhang, Wei-Jia and Barbe, Val{\'e}rie and Mangenot, Sophie and Guyomar, Charlotte and Garel, Marc and Chen, Hai-Tao and Li, Xue-Gong and Yin, Qun-Jian and others},
    journal={Extremophiles},
    volume={20},
    number={3},
    pages={301--310},
    year={2016},
    publisher={Springer}
    }

  • Tenaillon, O., Barrick, J. E., Ribeck, N., Deatherage, D. E., Blanchard, J. L., Dasgupta, A., Wu, G. C., Wielgoss, S., Cruveiller, S., Médigue, C., & others. (2016). Tempo and mode of genome evolution in a 50,000-generation experiment. Nature, 536(7615), 165.
    [BibTeX]
    @article{tenaillon2016tempo,
    title={Tempo and mode of genome evolution in a 50,000-generation experiment},
    author={Tenaillon, Olivier and Barrick, Jeffrey E and Ribeck, Noah and Deatherage, Daniel E and Blanchard, Jeffrey L and Dasgupta, Aurko and Wu, Gabriel C and Wielgoss, S{\'e}bastien and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and others},
    journal={Nature},
    volume={536},
    number={7615},
    pages={165},
    year={2016},
    publisher={Nature Publishing Group}
    }

2015

  • Goudenège, D., Travers, M. A., Lemire, A., Petton, B., Haffner, P., Labreuche, Y., Tourbiez, D., Mangenot, S., Calteau, A., Mazel, D., & others. (2015). A single regulatory gene is sufficient to alter vibrio aestuarianus pathogenicity in oysters. Environmental microbiology, 17(11), 4189–4199.
    [BibTeX]
    @article{goudenege2015single,
    title={A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters},
    author={Gouden{\`e}ge, David and Travers, Marie Agn{\`e}s and Lemire, Astrid and Petton, Bruno and Haffner, Philippe and Labreuche, Yannick and Tourbiez, Delphine and Mangenot, Sophie and Calteau, Alexandra and Mazel, Didier and others},
    journal={Environmental microbiology},
    volume={17},
    number={11},
    pages={4189--4199},
    year={2015},
    publisher={Wiley Online Library}
    }

  • Fahy, A., Giloteaux, L., Bertin, P., Le Paslier, D., Médigue, C., Weissenbach, J., Duran, R., & Lauga, B.. (2015). 16s rrna and as-related functional diversity: contrasting fingerprints in arsenic-rich sediments from an acid mine drainage. Microbial ecology, 70(1), 154–167.
    [BibTeX]
    @article{fahy201516s,
    title={16S rRNA and As-related functional diversity: contrasting fingerprints in arsenic-rich sediments from an acid mine drainage},
    author={Fahy, Anne and Giloteaux, Ludovic and Bertin, Philippe and Le Paslier, Denis and M{\'e}digue, Claudine and Weissenbach, Jean and Duran, Robert and Lauga, B{\'e}atrice},
    journal={Microbial ecology},
    volume={70},
    number={1},
    pages={154--167},
    year={2015},
    publisher={Springer}
    }

  • Sorokina, M., Medigue, C., & Vallenet, D.. (2015). A new network representation of the metabolism to detect chemical transformation modules. Bmc bioinformatics, 16(1), 385.
    [BibTeX]
    @article{sorokina2015new,
    title={A new network representation of the metabolism to detect chemical transformation modules},
    author={Sorokina, Maria and Medigue, Claudine and Vallenet, David},
    journal={BMC bioinformatics},
    volume={16},
    number={1},
    pages={385},
    year={2015},
    publisher={BioMed Central}
    }

  • Gordon, J. L., Lefeuvre, P., Escalon, A., Barbe, V., Cruveiller, S., Gagnevin, L., & Pruvost, O.. (2015). Comparative genomics of 43 strains of xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. Bmc genomics, 16(1), 1098.
    [BibTeX]
    @article{gordon2015comparative,
    title={Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges},
    author={Gordon, Jonathan L and Lefeuvre, Pierre and Escalon, Aline and Barbe, Val{\'e}rie and Cruveiller, St{\'e}phane and Gagnevin, Lionel and Pruvost, Olivier},
    journal={BMC genomics},
    volume={16},
    number={1},
    pages={1098},
    year={2015},
    publisher={BioMed Central}
    }

  • Ailloud, F., Lowe, T., Cellier, G., Roche, D., Allen, C., & Prior, P.. (2015). Comparative genomic analysis of ralstonia solanacearum reveals candidate genes for host specificity. Bmc genomics, 16(1), 270.
    [BibTeX]
    @article{ailloud2015comparative,
    title={Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity},
    author={Ailloud, Florent and Lowe, Tiffany and Cellier, Gilles and Roche, David and Allen, Caitilyn and Prior, Philippe},
    journal={BMC genomics},
    volume={16},
    number={1},
    pages={270},
    year={2015},
    publisher={BioMed Central}
    }

  • Maddamsetti, R., Hatcher, P. J., Cruveiller, S., Médigue, C., Barrick, J. E., & Lenski, R. E.. (2015). Synonymous genetic variation in natural isolates of escherichia coli does not predict where synonymous substitutions occur in a long-term experiment. Molecular biology and evolution, 32(11), 2897–2904.
    [BibTeX]
    @article{maddamsetti2015synonymous,
    title={Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment},
    author={Maddamsetti, Rohan and Hatcher, Philip J and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Barrick, Jeffrey E and Lenski, Richard E},
    journal={Molecular biology and evolution},
    volume={32},
    number={11},
    pages={2897--2904},
    year={2015},
    publisher={Oxford University Press}
    }

  • Belda, E., Vallenet, D., & Médigue, C.. (2015). Accurate microbial genome annotation using an integrated and user-friendly environment for community expertise of gene functions: the microscope platform. In Hydrocarbon and lipid microbiology protocols (pp. 141–169). Springer.
    [BibTeX]
    @incollection{belda2015accurate,
    title={Accurate microbial genome annotation using an integrated and user-friendly environment for community expertise of gene functions: the microscope platform},
    author={Belda, Eugeni and Vallenet, David and M{\'e}digue, Claudine},
    booktitle={Hydrocarbon and Lipid Microbiology Protocols},
    pages={141--169},
    year={2015},
    publisher={Springer}
    }

  • Persson, T., Battenberg, K., Demina, I. V., Vigil-Stenman, T., Heuvel, B. V., Pujic, P., Facciotti, M. T., Wilbanks, E. G., O’Brien, A., Fournier, P., & others. (2015). Candidatus frankia datiscae dg1, the actinobacterial microsymbiont of datisca glomerata, expresses the canonical nod genes nodabc in symbiosis with its host plant. Plos one, 10(5), e0127630.
    [BibTeX]
    @article{persson2015candidatus,
    title={Candidatus Frankia datiscae Dg1, the actinobacterial microsymbiont of Datisca glomerata, expresses the canonical nod genes nodABC in symbiosis with its host plant},
    author={Persson, Tomas and Battenberg, Kai and Demina, Irina V and Vigil-Stenman, Theoden and Heuvel, Brian Vanden and Pujic, Petar and Facciotti, Marc T and Wilbanks, Elizabeth G and O'Brien, Anna and Fournier, Pascale and others},
    journal={PLoS One},
    volume={10},
    number={5},
    pages={e0127630},
    year={2015},
    publisher={Public Library of Science}
    }

  • Lemire, A., Goudenège, D., Versigny, T., Petton, B., Calteau, A., Labreuche, Y., & Le Roux, F.. (2015). Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. The isme journal, 9(7), 1523–1531.
    [BibTeX]
    @article{lemire2015populations,
    title={Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters},
    author={Lemire, Astrid and Gouden{\`e}ge, David and Versigny, Typhaine and Petton, Bruno and Calteau, Alexandra and Labreuche, Yannick and Le Roux, Fr{\'e}d{\'e}rique},
    journal={The ISME journal},
    volume={9},
    number={7},
    pages={1523--1531},
    year={2015},
    publisher={Nature Publishing Group}
    }

2014

  • de Groot, A., Roche, D., Fernandez, B., Ludanyi, M., Cruveiller, S., Pignol, D., Vallenet, D., Armengaud, J., & Blanchard, L.. (2014). Rna sequencing and proteogenomics reveal the importance of leaderless mrnas in the radiation-tolerant bacterium deinococcus deserti. Genome biology and evolution, 6(4), 932–948.
    [BibTeX]
    @article{de2014rna,
    title={RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti},
    author={de Groot, Arjan and Roche, David and Fernandez, Bernard and Ludanyi, Monika and Cruveiller, Stephane and Pignol, David and Vallenet, David and Armengaud, Jean and Blanchard, Laurence},
    journal={Genome biology and evolution},
    volume={6},
    number={4},
    pages={932--948},
    year={2014},
    publisher={Oxford University Press}
    }

  • Plucain, J., Hindré, T., Le Gac, M., Tenaillon, O., Cruveiller, S., Médigue, C., Leiby, N., Harcombe, W. R., Marx, C. J., Lenski, R. E., & others. (2014). Epistasis and allele specificity in the emergence of a stable polymorphism in escherichia coli. Science, 343(6177), 1366–1369.
    [BibTeX]
    @article{plucain2014epistasis,
    title={Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli},
    author={Plucain, Jessica and Hindr{\'e}, Thomas and Le Gac, Micka{\"e}l and Tenaillon, Olivier and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Leiby, Nicholas and Harcombe, William R and Marx, Christopher J and Lenski, Richard E and others},
    journal={Science},
    volume={343},
    number={6177},
    pages={1366--1369},
    year={2014},
    publisher={American Association for the Advancement of Science}
    }

  • Ogier, J., Pagès, S., Bisch, G., Chiapello, H., Médigue, C., Rouy, Z., Teyssier, C., Vincent, S., Tailliez, P., Givaudan, A., & others. (2014). Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, xenorhabdus poinarii. Genome biology and evolution, 6(6), 1495–1513.
    [BibTeX]
    @article{ogier2014attenuated,
    title={Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii},
    author={Ogier, Jean-Claude and Pag{\`e}s, Sylvie and Bisch, Ga{\"e}lle and Chiapello, H{\'e}l{\`e}ne and M{\'e}digue, Claudine and Rouy, Zo{\'e} and Teyssier, Corinne and Vincent, St{\'e}phanie and Tailliez, Patrick and Givaudan, Alain and others},
    journal={Genome biology and evolution},
    volume={6},
    number={6},
    pages={1495--1513},
    year={2014},
    publisher={Oxford University Press}
    }

  • Raeside, C., Gaffé, J., Deatherage, D. E., Tenaillon, O., Briska, A. M., Ptashkin, R. N., Cruveiller, S., Médigue, C., Lenski, R. E., Barrick, J. E., & others. (2014). Large chromosomal rearrangements during a long-term evolution experiment with escherichia coli. Mbio, 5(5), e01377–14.
    [BibTeX]
    @article{raeside2014large,
    title={Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli},
    author={Raeside, Colin and Gaff{\'e}, Jo{\"e}l and Deatherage, Daniel E and Tenaillon, Olivier and Briska, Adam M and Ptashkin, Ryan N and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Lenski, Richard E and Barrick, Jeffrey E and others},
    journal={MBio},
    volume={5},
    number={5},
    pages={e01377--14},
    year={2014},
    publisher={Am Soc Microbiol}
    }

  • Ji, B., Zhang, S., Arnoux, P., Rouy, Z., Alberto, F., Philippe, N., Murat, D., Zhang, W., Rioux, J., Ginet, N., & others. (2014). Comparative genomic analysis provides insights into the evolution and niche adaptation of marine magnetospira sp. qh-2 strain. Environmental microbiology, 16(2), 525–544.
    [BibTeX]
    @article{ji2014comparative,
    title={Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain},
    author={Ji, Boyang and Zhang, Sheng-Da and Arnoux, Pascal and Rouy, Zoe and Alberto, Fran{\c{c}}ois and Philippe, Nad{\`e}ge and Murat, Doroth{\'e}e and Zhang, Wei-Jia and Rioux, Jean-Baptiste and Ginet, Nicolas and others},
    journal={Environmental microbiology},
    volume={16},
    number={2},
    pages={525--544},
    year={2014},
    publisher={Wiley Online Library}
    }

  • Bastard, K., Smith, A. A. T., Vergne-Vaxelaire, C., Perret, A., Zaparucha, A., De Melo-Minardi, R., Mariage, A., Boutard, M., Debard, A., Lechaplais, C., & others. (2014). Revealing the hidden functional diversity of an enzyme family. Nature chemical biology, 10(1), 42.
    [BibTeX]
    @article{bastard2014revealing,
    title={Revealing the hidden functional diversity of an enzyme family},
    author={Bastard, Karine and Smith, Adam Alexander Thil and Vergne-Vaxelaire, Carine and Perret, Alain and Zaparucha, Anne and De Melo-Minardi, Raquel and Mariage, Aline and Boutard, Magali and Debard, Adrien and Lechaplais, Christophe and others},
    journal={Nature chemical biology},
    volume={10},
    number={1},
    pages={42},
    year={2014},
    publisher={Nature Publishing Group}
    }

  • Stuani, L., Lechaplais, C., Salminen, A. V., Ségurens, B., Durot, M., Castelli, V., Pinet, A., Labadie, K., Cruveiller, S., Weissenbach, J., & others. (2014). Novel metabolic features in acinetobacter baylyi adp1 revealed by a multiomics approach. Metabolomics, 10(6), 1223–1238.
    [BibTeX]
    @article{stuani2014novel,
    title={Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach},
    author={Stuani, Lucille and Lechaplais, Christophe and Salminen, Aaro V and S{\'e}gurens, B{\'e}atrice and Durot, Maxime and Castelli, Vanina and Pinet, Agn{\`e}s and Labadie, Karine and Cruveiller, St{\'e}phane and Weissenbach, Jean and others},
    journal={Metabolomics},
    volume={10},
    number={6},
    pages={1223--1238},
    year={2014},
    publisher={Springer}
    }

  • Gomez-Valero, L., Rusniok, C., Rolando, M., Neou, M., Dervins-Ravault, D., Demirtas, J., Rouy, Z., Moore, R. J., Chen, H., Petty, N. K., & others. (2014). Comparative analyses of legionella species identifies genetic features of strains causing legionnaires’ disease. Genome biology, 15(11), 505.
    [BibTeX]
    @article{gomez2014comparative,
    title={Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires’ disease},
    author={Gomez-Valero, Laura and Rusniok, Christophe and Rolando, Monica and Neou, Mario and Dervins-Ravault, Delphine and Demirtas, Jasmin and Rouy, Zoe and Moore, Robert J and Chen, Honglei and Petty, Nicola K and others},
    journal={Genome biology},
    volume={15},
    number={11},
    pages={505},
    year={2014},
    publisher={BioMed Central}
    }

  • Bordier, F., Stam, M., Darii, E., Tricot, S., Fossey, A., Rohault, J., Debard, A., Mariage, A., Pellouin, V., Petit, J., & others. (2014). Large $\alpha$-aminonitrilase activity screening of nitrilase superfamily members: access to conversion and enantiospecificity by lc–ms. Journal of molecular catalysis b: enzymatic, 107, 79–88.
    [BibTeX]
    @article{bordier2014large,
    title={Large $\alpha$-aminonitrilase activity screening of nitrilase superfamily members: access to conversion and enantiospecificity by LC--MS},
    author={Bordier, Franck and Stam, Mark and Darii, Ekaterina and Tricot, Sabine and Fossey, Aurelie and Rohault, Johanna and Debard, Adrien and Mariage, Aline and Pellouin, Virginie and Petit, Jean-Louis and others},
    journal={Journal of Molecular Catalysis B: Enzymatic},
    volume={107},
    pages={79--88},
    year={2014},
    publisher={Elsevier}
    }

  • Zhang, S., Barbe, V., Garel, M., Zhang, W., Chen, H., Santini, C., Murat, D., Jing, H., Zhao, Y., Lajus, A., & others. (2014). Genome sequence of luminous piezophile photobacterium phosphoreum ant-2200. Genome announcements, 2(2), e00096–14.
    [BibTeX]
    @article{zhang2014genome,
    title={Genome sequence of luminous piezophile Photobacterium phosphoreum ANT-2200},
    author={Zhang, Sheng-Da and Barbe, Val{\'e}rie and Garel, Marc and Zhang, Wei-Jia and Chen, Haitao and Santini, Claire-Lise and Murat, Doroth{\'e}e and Jing, Hongmei and Zhao, Yuan and Lajus, Aur{\'e}lie and others},
    journal={Genome announcements},
    volume={2},
    number={2},
    pages={e00096--14},
    year={2014},
    publisher={Am Soc Microbiol}
    }

  • Ramos, P. I. P., Picão, R. C., de Almeida, L. G. P., Lima, N. C. B., Girardello, R., Vivan, A. C. P., Xavier, D. E., Barcellos, F. G., Pelisson, M., Vespero, E. C., & others. (2014). Comparative analysis of the complete genome of kpc-2-producing klebsiella pneumoniae kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms. Bmc genomics, 15(1), 54.
    [BibTeX]
    @article{ramos2014comparative,
    title={Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms},
    author={Ramos, Pablo Ivan Pereira and Pic{\~a}o, Renata Christina and de Almeida, Luiz Gonzaga Paula and Lima, Nicholas Costa B and Girardello, Raquel and Vivan, Ana Carolina P and Xavier, Danilo E and Barcellos, Fernando G and Pelisson, Marsileni and Vespero, Eliana C and others},
    journal={BMC genomics},
    volume={15},
    number={1},
    pages={54},
    year={2014},
    publisher={BioMed Central}
    }

  • Calteau, A., Fewer, D. P., Latifi, A., Coursin, T., Laurent, T., Jokela, J., Kerfeld, C. A., Sivonen, K., Piel, J., & Gugger, M.. (2014). Phylum-wide comparative genomics unravel the diversity of secondary metabolism in cyanobacteria. Bmc genomics, 15(1), 977.
    [BibTeX]
    @article{calteau2014phylum,
    title={Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria},
    author={Calteau, Alexandra and Fewer, David P and Latifi, Amel and Coursin, Th{\'e}r{\`e}se and Laurent, Thierry and Jokela, Jouni and Kerfeld, Cheryl A and Sivonen, Kaarina and Piel, J{\"o}rn and Gugger, Muriel},
    journal={BMC genomics},
    volume={15},
    number={1},
    pages={977},
    year={2014},
    publisher={BioMed Central}
    }

  • Billard-Pomares, T., Fouteau, S., Jacquet, M. E., Roche, D., Barbe, V., Castellanos, M., Bouet, J. Y., Cruveiller, S., Médigue, C., Blanco, J., & others. (2014). Characterization of a p1-like bacteriophage carrying an shv-2 extended-spectrum $\beta$-lactamase from an escherichia coli strain. Antimicrobial agents and chemotherapy, 58(11), 6550–6557.
    [BibTeX]
    @article{billard2014characterization,
    title={Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum $\beta$-lactamase from an Escherichia coli strain},
    author={Billard-Pomares, Typhaine and Fouteau, St{\'e}phanie and Jacquet, Marie Elise and Roche, David and Barbe, Val{\'e}rie and Castellanos, Miguel and Bouet, Jean Yves and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Blanco, Jorge and others},
    journal={Antimicrobial agents and chemotherapy},
    volume={58},
    number={11},
    pages={6550--6557},
    year={2014},
    publisher={Am Soc Microbiol}
    }

  • Trujillo, M. E., Bacigalupe, R., Pujic, P., Igarashi, Y., Benito, P., Riesco, R., Médigue, C., & Normand, P.. (2014). Genome features of the endophytic actinobacterium micromonospora lupini strain lupac 08: on the process of adaptation to an endophytic life style?. Plos one, 9(9), e108522.
    [BibTeX]
    @article{trujillo2014genome,
    title={Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?},
    author={Trujillo, Martha E and Bacigalupe, Rodrigo and Pujic, Petar and Igarashi, Yasuhiro and Benito, Patricia and Riesco, Ra{\'u}l and M{\'e}digue, Claudine and Normand, Philippe},
    journal={PloS one},
    volume={9},
    number={9},
    pages={e108522},
    year={2014},
    publisher={Public Library of Science}
    }

  • Remigi, P., Capela, D., Clerissi, C., Tasse, L., Torchet, R., Bouchez, O., Batut, J., Cruveiller, S., Rocha, E. P., & Masson-Boivin, C.. (2014). Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer. Plos biology, 12(9), e1001942.
    [BibTeX]
    @article{remigi2014transient,
    title={Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer},
    author={Remigi, Philippe and Capela, Delphine and Clerissi, Camille and Tasse, L{\'e}na and Torchet, Rachel and Bouchez, Olivier and Batut, Jacques and Cruveiller, St{\'e}phane and Rocha, Eduardo PC and Masson-Boivin, Catherine},
    journal={PLoS biology},
    volume={12},
    number={9},
    pages={e1001942},
    year={2014},
    publisher={Public Library of Science}
    }

  • Sorokina, M., Stam, M., Médigue, C., Lespinet, O., & Vallenet, D.. (2014). Profiling the orphan enzymes. Biology direct, 9(1), 10.
    [BibTeX]
    @article{sorokina2014profiling,
    title={Profiling the orphan enzymes},
    author={Sorokina, Maria and Stam, Mark and M{\'e}digue, Claudine and Lespinet, Olivier and Vallenet, David},
    journal={Biology direct},
    volume={9},
    number={1},
    pages={10},
    year={2014},
    publisher={BioMed Central}
    }

  • Lescat, M., Reibel, F., Pintard, C., Dion, S., Glodt, J., Gateau, C., Launay, A., Ledda, A., Cruvellier, S., Tourret, J., & others. (2014). The conserved nhaar operon is drastically divergent between b2 and non-b2 escherichia coli and is involved in extra-intestinal virulence. Plos one, 9(9), e108738.
    [BibTeX]
    @article{lescat2014conserved,
    title={The conserved nhaAR operon is drastically divergent between B2 and non-B2 Escherichia coli and is involved in extra-intestinal virulence},
    author={Lescat, Mathilde and Reibel, Florence and Pintard, Coralie and Dion, Sara and Glodt, Jeremy and Gateau, Cecile and Launay, Adrien and Ledda, Alice and Cruvellier, Stephane and Tourret, J{\'e}r{\^o}me and others},
    journal={PLoS One},
    volume={9},
    number={9},
    pages={e108738},
    year={2014},
    publisher={Public Library of Science}
    }

2013

  • Kristiansen, R., Nguyen, H. T. T., Saunders, A. M., Nielsen, J. L., Wimmer, R., Le, V. Q., McIlroy, S. J., Petrovski, S., Seviour, R. J., Calteau, A., & others. (2013). A metabolic model for members of the genus tetrasphaera involved in enhanced biological phosphorus removal. The isme journal, 7(3), 543–554.
    [BibTeX]
    @article{kristiansen2013metabolic,
    title={A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal},
    author={Kristiansen, Rikke and Nguyen, Hien Thi Thu and Saunders, Aaron Marc and Nielsen, Jeppe Lund and Wimmer, Reinhard and Le, Vang Quy and McIlroy, Simon Jon and Petrovski, Steve and Seviour, Robert J and Calteau, Alexandra and others},
    journal={The ISME journal},
    volume={7},
    number={3},
    pages={543--554},
    year={2013},
    publisher={Nature Publishing Group}
    }

  • Kits, D. K., Kalyuzhnaya, M. G., Klotz, M. G., Jetten, M. S., den Camp, H. J. O., Vuilleumier, S., Bringel, F., DiSpirito, A. A., Murrell, C. J., Bruce, D., & others. (2013). Genome sequence of the obligate gammaproteobacterial methanotroph methylomicrobium album strain bg8. Genome announcements, 1(2), e00170–13.
    [BibTeX]
    @article{kits2013genome,
    title={Genome sequence of the obligate gammaproteobacterial methanotroph Methylomicrobium album strain BG8},
    author={Kits, K Dimitri and Kalyuzhnaya, Marina G and Klotz, Martin G and Jetten, Mike SM and den Camp, Huub JM Op and Vuilleumier, St{\'e}phane and Bringel, Fran{\c{c}}oise and DiSpirito, Alan A and Murrell, J Colin and Bruce, David and others},
    journal={Genome announcements},
    volume={1},
    number={2},
    pages={e00170--13},
    year={2013},
    publisher={Am Soc Microbiol}
    }

  • Belda, E., Sekowska, A., Le Fèvre, F., Morgat, A., Mornico, D., Ouzounis, C., Vallenet, D., Médigue, C., & Danchin, A.. (2013). An updated metabolic view of the bacillus subtilis 168 genome. Microbiology, 159(4), 757–770.
    [BibTeX]
    @article{belda2013updated,
    title={An updated metabolic view of the Bacillus subtilis 168 genome},
    author={Belda, Eugeni and Sekowska, Agnieszka and Le F{\`e}vre, Fran{\c{c}}ois and Morgat, Anne and Mornico, Damien and Ouzounis, Christos and Vallenet, David and M{\'e}digue, Claudine and Danchin, Antoine},
    journal={Microbiology},
    volume={159},
    number={4},
    pages={757--770},
    year={2013},
    publisher={Microbiology Society}
    }

  • Zoropogui, A., Pujic, P., Normand, P., Barbe, V., Belli, P., Graindorge, A., Roche, D., Vallenet, D., Mangenot, S., Boiron, P., & others. (2013). The nocardia cyriacigeorgica guh-2 genome shows ongoing adaptation of an environmental actinobacteria to a pathogen’s lifestyle. Bmc genomics, 14(1), 286.
    [BibTeX]
    @article{zoropogui2013nocardia,
    title={The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen’s lifestyle},
    author={Zoropogui, Anthony and Pujic, Petar and Normand, Philippe and Barbe, Val{\'e}rie and Belli, Patrick and Graindorge, Arnault and Roche, David and Vallenet, David and Mangenot, Sophie and Boiron, Patrick and others},
    journal={BMC genomics},
    volume={14},
    number={1},
    pages={286},
    year={2013},
    publisher={BioMed Central}
    }

  • Wielgoss, S., Barrick, J. E., Tenaillon, O., Wiser, M. J., Dittmar, J. W., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R. E., & Schneider, D.. (2013). Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proceedings of the national academy of sciences, 110(1), 222–227.
    [BibTeX]
    @article{wielgoss2013mutation,
    title={Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load},
    author={Wielgoss, S{\'e}bastien and Barrick, Jeffrey E and Tenaillon, Olivier and Wiser, Michael J and Dittmar, W James and Cruveiller, St{\'e}phane and Chane-Woon-Ming, B{\'e}atrice and M{\'e}digue, Claudine and Lenski, Richard E and Schneider, Dominique},
    journal={Proceedings of the National Academy of Sciences},
    volume={110},
    number={1},
    pages={222--227},
    year={2013},
    publisher={National Acad Sciences}
    }

  • Ji, B., Gimenez, G., Barbe, V., Vacherie, B., Rouy, Z., Amrani, A., Fardeau, M., Bertin, P., Alazard, D., Leroy, S., & others. (2013). Complete genome sequence of the piezophilic, mesophilic, sulfate-reducing bacterium desulfovibrio hydrothermalis am13t. Genome announcements, 1(1), e00226–12.
    [BibTeX]
    @article{ji2013complete,
    title={Complete genome sequence of the piezophilic, mesophilic, sulfate-reducing bacterium Desulfovibrio hydrothermalis AM13T},
    author={Ji, Boyang and Gimenez, Gregory and Barbe, Val{\'e}rie and Vacherie, Beno{\^\i}t and Rouy, Zo{\'e} and Amrani, Amira and Fardeau, Marie-Laure and Bertin, Philippe and Alazard, Didier and Leroy, Sabine and others},
    journal={Genome announcements},
    volume={1},
    number={1},
    pages={e00226--12},
    year={2013},
    publisher={Am Soc Microbiol}
    }

  • Guan, S. H., Gris, C., Cruveiller, S., Pouzet, C., Tasse, L., Leru, A., Maillard, A., Médigue, C., Batut, J., Masson-Boivin, C., & others. (2013). Experimental evolution of nodule intracellular infection in legume symbionts. The isme journal, 7(7), 1367–1377.
    [BibTeX]
    @article{guan2013experimental,
    title={Experimental evolution of nodule intracellular infection in legume symbionts},
    author={Guan, Su Hua and Gris, Carine and Cruveiller, St{\'e}phane and Pouzet, C{\'e}cile and Tasse, Lena and Leru, Aur{\'e}lie and Maillard, Aline and M{\'e}digue, Claudine and Batut, Jacques and Masson-Boivin, Catherine and others},
    journal={The ISME journal},
    volume={7},
    number={7},
    pages={1367--1377},
    year={2013},
    publisher={Nature Publishing Group}
    }

  • Leikoski, N., Liu, L., Jokela, J., Wahlsten, M., Gugger, M., Calteau, A., Permi, P., Kerfeld, C. A., Sivonen, K., & Fewer, D. P.. (2013). Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides. Chemistry & biology, 20(8), 1033–1043.
    [BibTeX]
    @article{leikoski2013genome,
    title={Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides},
    author={Leikoski, Niina and Liu, Liwei and Jokela, Jouni and Wahlsten, Matti and Gugger, Muriel and Calteau, Alexandra and Permi, Perttu and Kerfeld, Cheryl A and Sivonen, Kaarina and Fewer, David P},
    journal={Chemistry \& biology},
    volume={20},
    number={8},
    pages={1033--1043},
    year={2013},
    publisher={Elsevier}
    }

  • Lanois, A., Ogier, J., Gouzy, J., Laroui, C., Rouy, Z., Givaudan, A., & Gaudriault, S.. (2013). Draft genome sequence and annotation of the entomopathogenic bacterium xenorhabdus nematophila strain f1. Genome announcements, 1(3), e00342–13.
    [BibTeX]
    @article{lanois2013draft,
    title={Draft genome sequence and annotation of the entomopathogenic bacterium Xenorhabdus nematophila strain F1},
    author={Lanois, Anne and Ogier, Jean-Claude and Gouzy, J{\'e}rome and Laroui, Christine and Rouy, Zo{\'e} and Givaudan, Alain and Gaudriault, Sophie},
    journal={Genome announcements},
    volume={1},
    number={3},
    pages={e00342--13},
    year={2013},
    publisher={Am Soc Microbiol}
    }

  • Sugawara, M., Epstein, B., Badgley, B. D., Unno, T., Xu, L., Reese, J., Gyaneshwar, P., Denny, R., Mudge, J., Bharti, A. K., & others. (2013). Comparative genomics of the core and accessory genomes of 48 sinorhizobium strains comprising five genospecies. Genome biology, 14(2), R17.
    [BibTeX]
    @article{sugawara2013comparative,
    title={Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies},
    author={Sugawara, Masayuki and Epstein, Brendan and Badgley, Brian D and Unno, Tatsuya and Xu, Lei and Reese, Jennifer and Gyaneshwar, Prasad and Denny, Roxanne and Mudge, Joann and Bharti, Arvind K and others},
    journal={Genome biology},
    volume={14},
    number={2},
    pages={R17},
    year={2013},
    publisher={BioMed Central}
    }

  • Gac, M., Cooper, T. F., Cruveiller, S., Médigue, C., & Schneider, D.. (2013). Evolutionary history and genetic parallelism affect correlated responses to evolution. Molecular ecology, 22(12), 3292–3303.
    [BibTeX]
    @article{gac2013evolutionary,
    title={Evolutionary history and genetic parallelism affect correlated responses to evolution},
    author={Gac, Mickael and Cooper, Tim F and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Schneider, Dominique},
    journal={Molecular ecology},
    volume={22},
    number={12},
    pages={3292--3303},
    year={2013},
    publisher={Wiley Online Library}
    }

  • Goudenège, D., Labreuche, Y., Krin, E., Ansquer, D., Mangenot, S., Calteau, A., Médigue, C., Mazel, D., Polz, M. F., & Le Roux, F.. (2013). Comparative genomics of pathogenic lineages of vibrio nigripulchritudo identifies virulence-associated traits. The isme journal, 7(10), 1985–1996.
    [BibTeX]
    @article{goudenege2013comparative,
    title={Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits},
    author={Gouden{\`e}ge, David and Labreuche, Yannick and Krin, Evelyne and Ansquer, Dominique and Mangenot, Sophie and Calteau, Alexandra and M{\'e}digue, Claudine and Mazel, Didier and Polz, Martin F and Le Roux, Fr{\'e}d{\'e}rique},
    journal={The ISME journal},
    volume={7},
    number={10},
    pages={1985--1996},
    year={2013},
    publisher={Nature Publishing Group}
    }

  • Andres, J., Arsene-Ploetze, F., Barbe, V., Brochier-Armanet, C., Cleiss-Arnold, J., Coppee, J., Dillies, M., Geist, L., Joublin, A., Koechler, S., & others. (2013). Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. nt-26. Genome biology and evolution, 5(5), 934–953.
    [BibTeX]
    @article{andres2013life,
    title={Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium Rhizobium sp. NT-26},
    author={Andres, J{\'e}r{\'e}my and Arsene-Ploetze, Florence and Barbe, Valerie and Brochier-Armanet, Celine and Cleiss-Arnold, Jessica and Coppee, Jean-Yves and Dillies, Marie-Agn{\`e}s and Geist, Lucie and Joublin, Aur{\'e}lie and Koechler, Sandrine and others},
    journal={Genome biology and evolution},
    volume={5},
    number={5},
    pages={934--953},
    year={2013},
    publisher={Oxford University Press}
    }

  • Amin, O., Fardeau, M., Valette, O., Hirschler-Réa, A., Barbe, V., Médigue, C., Vacherie, B., Ollivier, B., Bertin, P. N., & Dolla, A.. (2013). Genome sequence of the sulfate-reducing bacterium desulfotomaculum hydrothermale lam5t. Genome announcements, 1(1), e00114–12.
    [BibTeX]
    @article{amin2013genome,
    title={Genome sequence of the sulfate-reducing bacterium Desulfotomaculum hydrothermale LAM5T},
    author={Amin, Oulfat and Fardeau, Marie-Laure and Valette, Odile and Hirschler-R{\'e}a, Agn{\`e}s and Barbe, Val{\'e}rie and M{\'e}digue, Claudine and Vacherie, Benoit and Ollivier, Bernard and Bertin, Philippe N and Dolla, Alain},
    journal={Genome announcements},
    volume={1},
    number={1},
    pages={e00114--12},
    year={2013},
    publisher={Am Soc Microbiol}
    }

  • Humbert, J., Barbe, V., Latifi, A., Gugger, M., Calteau, A., Coursin, T., Lajus, A., Castelli, V., Oztas, S., Samson, G., & others. (2013). A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium microcystis aeruginosa. Plos one, 8(8), e70747.
    [BibTeX]
    @article{humbert2013tribute,
    title={A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa},
    author={Humbert, Jean-Fran{\c{c}}ois and Barbe, Val{\'e}rie and Latifi, Amel and Gugger, Muriel and Calteau, Alexandra and Coursin, Therese and Lajus, Aur{\'e}lie and Castelli, Vanina and Oztas, Sophie and Samson, Ga{\"e}lle and others},
    journal={PLoS One},
    volume={8},
    number={8},
    pages={e70747},
    year={2013},
    publisher={Public Library of Science}
    }

  • Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., De Marsac, N. T., Rippka, R., & others. (2013). Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the national academy of sciences, 110(3), 1053–1058.
    [BibTeX]
    @article{shih2013improving,
    title={Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing},
    author={Shih, Patrick M and Wu, Dongying and Latifi, Amel and Axen, Seth D and Fewer, David P and Talla, Emmanuel and Calteau, Alexandra and Cai, Fei and De Marsac, Nicole Tandeau and Rippka, Rosmarie and others},
    journal={Proceedings of the National Academy of Sciences},
    volume={110},
    number={3},
    pages={1053--1058},
    year={2013},
    publisher={National Acad Sciences}
    }

  • Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Le Fèvre, F., Longin, C., Mornico, D., Roche, D., & others. (2013). Microscope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic acids research, 41(D1), D636–D647.
    [BibTeX]
    @article{vallenet2013microscope,
    title={MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data},
    author={Vallenet, David and Belda, Eugeni and Calteau, Alexandra and Cruveiller, St{\'e}phane and Engelen, Stefan and Lajus, Aur{\'e}lie and Le F{\`e}vre, Fran{\c{c}}ois and Longin, Cyrille and Mornico, Damien and Roche, David and others},
    journal={Nucleic acids research},
    volume={41},
    number={D1},
    pages={D636--D647},
    year={2013},
    publisher={Oxford University Press}
    }

  • Ailloud, F., Cellier, G., Roche, D., Allen, C., & Prior, P.. (2013). Glancing at host adaptation in\# ralstonia solanacearum\# through comparative genomics of highly host-adapted lineages. Phytopathology, 103(6), S2.
    [BibTeX]
    @article{ailloud2013glancing,
    title={Glancing at host adaptation in\# Ralstonia solanacearum\# through comparative genomics of highly host-adapted lineages},
    author={Ailloud, Florent and Cellier, Gilles and Roche, David and Allen, Caitilyn and Prior, Philippe},
    journal={Phytopathology},
    volume={103},
    number={6},
    pages={S2},
    year={2013}
    }

  • Maynaud, G., Brunel, B., Mornico, D., Durot, M., Severac, D., Dubois, E., Navarro, E., Cleyet-Marel, J., & Le Quéré, A.. (2013). Genome-wide transcriptional responses of two metal-tolerant symbiotic mesorhizobium isolates to zinc and cadmium exposure. Bmc genomics, 14(1), 292.
    [BibTeX]
    @article{maynaud2013genome,
    title={Genome-wide transcriptional responses of two metal-tolerant symbiotic Mesorhizobium isolates to zinc and cadmium exposure},
    author={Maynaud, G{\'e}raldine and Brunel, Brigitte and Mornico, Damien and Durot, Maxime and Severac, Dany and Dubois, Emeric and Navarro, Elisabeth and Cleyet-Marel, Jean-Claude and Le Qu{\'e}r{\'e}, Antoine},
    journal={BMC genomics},
    volume={14},
    number={1},
    pages={292},
    year={2013},
    publisher={BioMed Central}
    }

  • Supply, P., Marceau, M., Mangenot, S., Roche, D., Rouanet, C., Khanna, V., Majlessi, L., Criscuolo, A., Tap, J., Pawlik, A., & others. (2013). Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of mycobacterium tuberculosis. Nature genetics, 45(2), 172–179.
    [BibTeX]
    @article{supply2013genomic,
    title={Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis},
    author={Supply, Philip and Marceau, Michael and Mangenot, Sophie and Roche, David and Rouanet, Carine and Khanna, Varun and Majlessi, Laleh and Criscuolo, Alexis and Tap, Julien and Pawlik, Alexandre and others},
    journal={Nature genetics},
    volume={45},
    number={2},
    pages={172--179},
    year={2013},
    publisher={Nature Publishing Group}
    }

2012

  • Marx, C. J., Bringel, F., Chistoserdova, L., Moulin, L., Haque, M. F. U., Fleischman, D. E., Gruffaz, C., Jourand, P., Knief, C., Lee, M., & others. (2012). Complete genome sequences of six strains of the genus methylobacterium. Journal of bacteriology, 194(17), 4746.
    [BibTeX]
    @article{marx2012complete,
    title={Complete genome sequences of six strains of the genus Methylobacterium},
    author={Marx, Christopher J and Bringel, Fran{\c{c}}oise and Chistoserdova, Ludmila and Moulin, Lionel and Haque, Muhammad Farhan Ul and Fleischman, Darrell E and Gruffaz, Christelle and Jourand, Philippe and Knief, Claudia and Lee, Ming-Chun and others},
    journal={Journal of bacteriology},
    volume={194},
    number={17},
    pages={4746},
    year={2012},
    publisher={American Society for Microbiology (ASM)}
    }

  • Bustos, P., Lozano, L., Barbe, V., Minard, V., Tran, F., Voronin, D., Rouy, Z., Wisniewski-Dyé, F., Raquin, V., Mavingui, G. P., & others. (2012). Whole-genome sequence of wolbachia. J. bacteriol, 194(7), 1840.
    [BibTeX]
    @article{bustos2012whole,
    title={Whole-Genome Sequence of Wolbachia},
    author={Bustos, Patricia and Lozano, Luis and Barbe, Val{\'e}rie and Minard, V{\'\i}ctor and Tran, Florence-H{\'e}l{\`e}ne and Voronin, Denis and Rouy, Zo{\'e} and Wisniewski-Dy{\'e}, Florence and Raquin, Vincent and Mavingui, Guillaume Patrick and others},
    journal={J. Bacteriol},
    volume={194},
    number={7},
    pages={1840},
    year={2012}
    }

  • Chouaia, B., Crotti, E., Brusetti, L., Daffonchio, D., Essoussi, I., Nouioui, I., Sbissi, I., Ghodhbane-Gtari, F., Gtari, M., Vacherie, B., & others. (2012). Genome sequence of blastococcus saxobsidens dd2, a stone-inhabiting bacterium. Journal of bacteriology, 194(10), 2752–2753.
    [BibTeX]
    @article{chouaia2012genome,
    title={Genome sequence of Blastococcus saxobsidens DD2, a stone-inhabiting bacterium},
    author={Chouaia, Bessem and Crotti, Elena and Brusetti, Lorenzo and Daffonchio, Daniele and Essoussi, Imen and Nouioui, Imen and Sbissi, Imed and Ghodhbane-Gtari, Faten and Gtari, Maher and Vacherie, Benoit and others},
    journal={Journal of bacteriology},
    volume={194},
    number={10},
    pages={2752--2753},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Khadem, A. F., Wieczorek, A. S., Pol, A., Vuilleumier, S., Harhangi, H. R., Dunfield, P. F., Kalyuzhnaya, M. G., Murrell, C. J., Francoijs, K., Stunnenberg, H. G., & others. (2012). Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph methylacidiphilum fumariolicum strain solv. Journal of bacteriology, 194(14), 3729–3730.
    [BibTeX]
    @article{khadem2012draft,
    title={Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph Methylacidiphilum fumariolicum strain SolV},
    author={Khadem, Ahmad F and Wieczorek, Adam S and Pol, Arjan and Vuilleumier, St{\'e}phane and Harhangi, Harry R and Dunfield, Peter F and Kalyuzhnaya, Marina G and Murrell, J Colin and Francoijs, Kees-Jan and Stunnenberg, Henk G and others},
    journal={Journal of bacteriology},
    volume={194},
    number={14},
    pages={3729--3730},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Engelen, S., Vallenet, D., Médigue, C., & Danchin, A.. (2012). Distinct co-evolution patterns of genes associated to dna polymerase iii dnae and polc. Bmc genomics, 13(1), 69.
    [BibTeX]
    @article{engelen2012distinct,
    title={Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC},
    author={Engelen, Stefan and Vallenet, David and M{\'e}digue, Claudine and Danchin, Antoine},
    journal={BMC genomics},
    volume={13},
    number={1},
    pages={69},
    year={2012},
    publisher={BioMed Central}
    }

  • Grimaud, R., Ghiglione, J., Cagnon, C., Lauga, B., Vaysse, P., Rodriguez-Blanco, A., Mangenot, S., Cruveiller, S., Barbe, V., Duran, R., & others. (2012). Genome sequence of the marine bacterium marinobacter hydrocarbonoclasticus sp17, which forms biofilms on hydrophobic organic compounds. Journal of bacteriology, 194(13), 3539–3540.
    [BibTeX]
    @article{grimaud2012genome,
    title={Genome sequence of the marine bacterium Marinobacter hydrocarbonoclasticus SP17, which forms biofilms on hydrophobic organic compounds},
    author={Grimaud, Regis and Ghiglione, Jean-Fran{\c{c}}ois and Cagnon, Christine and Lauga, B{\'e}atrice and Vaysse, Pierre-Joseph and Rodriguez-Blanco, Arturo and Mangenot, Sophie and Cruveiller, Stephane and Barbe, Val{\'e}rie and Duran, Robert and others},
    journal={Journal of bacteriology},
    volume={194},
    number={13},
    pages={3539--3540},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Zoropogui, A., Pujic, P., Normand, P., Barbe, V., Beaman, B., Beaman, L., Boiron, P., Colinon, C., Deredjian, A., Graindorge, A., & others. (2012). Genome sequence of the human-and animal-pathogenic strain nocardia cyriacigeorgica guh-2. Journal of bacteriology, 194(8), 2098–2099.
    [BibTeX]
    @article{zoropogui2012genome,
    title={Genome sequence of the human-and animal-pathogenic strain Nocardia cyriacigeorgica GUH-2},
    author={Zoropogui, Anthony and Pujic, Petar and Normand, Philippe and Barbe, Val{\'e}rie and Beaman, Blaine and Beaman, LoVelle and Boiron, Patrick and Colinon, C{\'e}line and Deredjian, Am{\'e}lie and Graindorge, Arnault and others},
    journal={Journal of bacteriology},
    volume={194},
    number={8},
    pages={2098--2099},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Wisniewski-Dyé, F., Lozano, L., Acosta-Cruz, E., Borland, S., Drogue, B., Prigent-Combaret, C., Rouy, Z., Barbe, V., Herrera, A. M., González, V., & others. (2012). Genome sequence of cbg497 and azospirillum brasilense comparative analyses of core and accessory azospirillum genomes provide insight into niche adaptation.. Genes, 3(4).
    [BibTeX]
    @article{wisniewski2012genome,
    title={Genome Sequence of CBG497 and Azospirillum brasilense Comparative Analyses of Core and Accessory Azospirillum Genomes provide Insight into Niche Adaptation.},
    author={Wisniewski-Dy{\'e}, Florence and Lozano, Luis and Acosta-Cruz, Erika and Borland, St{\'e}phanie and Drogue, Beno{\^\i}t and Prigent-Combaret, Claire and Rouy, Zo{\'e} and Barbe, Val{\'e}rie and Herrera, Alberto Mendoza and Gonz{\'a}lez, Victor and others},
    journal={Genes},
    volume={3},
    number={4},
    year={2012}
    }

  • Vuilleumier, S., Khmelenina, V. N., Bringel, F., Reshetnikov, A. S., Lajus, A., Mangenot, S., Rouy, Z., den Camp, H. J. O., Jetten, M. S., Dispirito, A. A., & others. (2012). Genome sequence of the haloalkaliphilic methanotrophic bacterium methylomicrobium alcaliphilum 20z. Journal of bacteriology, 194(2), 551–552.
    [BibTeX]
    @article{vuilleumier2012genome,
    title={Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z},
    author={Vuilleumier, St{\'e}phane and Khmelenina, Valentina N and Bringel, Fran{\c{c}}oise and Reshetnikov, Alexandr S and Lajus, Aur{\'e}lie and Mangenot, Sophie and Rouy, Zo{\'e} and den Camp, Huub JM Op and Jetten, Mike SM and Dispirito, Alan A and others},
    journal={Journal of bacteriology},
    volume={194},
    number={2},
    pages={551--552},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Normand, P., Gury, J., Pujic, P., Chouaia, B., Crotti, E., Brusetti, L., Daffonchio, D., Vacherie, B., Barbe, V., Médigue, C., & others. (2012). Genome sequence of radiation-resistant modestobacter marinus strain bc501, a representative actinobacterium that thrives on calcareous stone surfaces. Journal of bacteriology, 194(17), 4773–4774.
    [BibTeX]
    @article{normand2012genome,
    title={Genome sequence of radiation-resistant Modestobacter marinus strain BC501, a representative actinobacterium that thrives on calcareous stone surfaces},
    author={Normand, Philippe and Gury, J{\'e}r{\^o}me and Pujic, Petar and Chouaia, Bessem and Crotti, Elena and Brusetti, Lorenzo and Daffonchio, Daniele and Vacherie, Benoit and Barbe, Val{\'e}rie and M{\'e}digue, Claudine and others},
    journal={Journal of bacteriology},
    volume={194},
    number={17},
    pages={4773--4774},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Le Fevre, F., Mornico, D., Belda, E., Vallenet, D., & Médigue, C.. (2012). From automatic and expert annotation to the reconstruction of genome-scale metabolic networks and models. Modellingcomplex biologicalsystems.
    [BibTeX]
    @article{le2012automatic,
    title={From automatic and expert annotation to the reconstruction of genome-scale metabolic networks and models},
    author={Le Fevre, Fran{\c{c}}ois and Mornico, Damien and Belda, Eugeni and Vallenet, David and M{\'e}digue, Claudine},
    journal={ModellingComplex BiologicalSystems},
    year={2012},
    publisher={Citeseer}
    }

  • Smith, A. A. T., Belda, E., Viari, A., Medigue, C., & Vallenet, D.. (2012). The canoe strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. Plos computational biology, 8(5), e1002540.
    [BibTeX]
    @article{smith2012canoe,
    title={The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes},
    author={Smith, Adam Alexander Thil and Belda, Eugeni and Viari, Alain and Medigue, Claudine and Vallenet, David},
    journal={PLoS computational biology},
    volume={8},
    number={5},
    pages={e1002540},
    year={2012},
    publisher={Public Library of Science}
    }

  • Alonso-Vega, P., Normand, P., Bacigalupe, R., Pujic, P., Lajus, A., Vallenet, D., Carro, L., Coll, P., & Trujillo, M. E.. (2012). Genome sequence of micromonospora lupini lupac 08, isolated from root nodules of lupinus angustifolius. Journal of bacteriology, 194(15), 4135–4135.
    [BibTeX]
    @article{alonso2012genome,
    title={Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius},
    author={Alonso-Vega, Pablo and Normand, Philippe and Bacigalupe, Rodrigo and Pujic, Petar and Lajus, Aurelie and Vallenet, David and Carro, Lorena and Coll, Pedro and Trujillo, Martha E},
    journal={Journal of bacteriology},
    volume={194},
    number={15},
    pages={4135--4135},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Remenant, B., Babujee, L., Lajus, A., Médigue, C., Prior, P., & Allen, C.. (2012). Sequencing of k60, type strain of the major plant pathogen ralstonia solanacearum. Journal of bacteriology, 194(10), 2742–2743.
    [BibTeX]
    @article{remenant2012sequencing,
    title={Sequencing of K60, type strain of the major plant pathogen Ralstonia solanacearum},
    author={Remenant, Beno{\^\i}t and Babujee, Lavanya and Lajus, Aur{\'e}lie and M{\'e}digue, Claudine and Prior, Philippe and Allen, Caitilyn},
    journal={Journal of bacteriology},
    volume={194},
    number={10},
    pages={2742--2743},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Wisniewski-Dyé, F., Lozano, L., Acosta-Cruz, E., Borland, S., Drogue, B., Prigent-Combaret, C., Rouy, Z., Barbe, V., Herrera, A. M., González, V., & others. (2012). Genome sequence of azospirillum brasilense cbg497 and comparative analyses of azospirillum core and accessory genomes provide insight into niche adaptation. Genes, 3(4), 576–602.
    [BibTeX]
    @article{wisniewski2012genome,
    title={Genome sequence of Azospirillum brasilense CBG497 and comparative analyses of Azospirillum core and accessory genomes provide insight into niche adaptation},
    author={Wisniewski-Dy{\'e}, Florence and Lozano, Luis and Acosta-Cruz, Erika and Borland, St{\'e}phanie and Drogue, Beno{\^\i}t and Prigent-Combaret, Claire and Rouy, Zo{\'e} and Barbe, Val{\'e}rie and Herrera, Alberto Mendoza and Gonz{\'a}lez, Victor and others},
    journal={Genes},
    volume={3},
    number={4},
    pages={576--602},
    year={2012},
    publisher={Molecular Diversity Preservation International}
    }

  • Kristiansen, R., Nguyen, H. T. T., Saunders, A. M., Nielsen, J. L., Wimmer, R., Le, V., Petrovski, S., McIlroy, S. J., Seviour, R., Calteau, A., & others. (2012). Metabolic model for an unusual and versatile tetrasphaera involved in enhanced biological phosphorus removal based on whole genome sequencing. Paper presented at the 14th international symposium on microbial ecology.
    [BibTeX]
    @inproceedings{kristiansen2012metabolic,
    title={Metabolic model for an unusual and versatile Tetrasphaera involved in enhanced biological phosphorus removal based on whole genome sequencing},
    author={Kristiansen, Rikke and Nguyen, Hien Thi Thu and Saunders, Aaron Marc and Nielsen, Jeppe Lund and Wimmer, Reinhard and Le, Vang and Petrovski, Steve and McIlroy, Simon Jon and Seviour, Robert and Calteau, Alexandra and others},
    booktitle={14th International Symposium on Microbial Ecology},
    year={2012}
    }

  • Fournier, P., El Karkouri, K., Robert, C., Médigue, C., & Raoult, D.. (2012). Complete genome sequence of rickettsia slovaca, the agent of tick-borne lymphadenitis. Journal of bacteriology, 194(6), 1612–1612.
    [BibTeX]
    @article{fournier2012complete,
    title={Complete genome sequence of Rickettsia slovaca, the agent of tick-borne lymphadenitis},
    author={Fournier, Pierre-Edouard and El Karkouri, Khalid and Robert, Catherine and M{\'e}digue, Claudine and Raoult, Didier},
    journal={Journal of bacteriology},
    volume={194},
    number={6},
    pages={1612--1612},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Smith, A., Belda, E., Viari, A., Medigue, C., & Vallenet, D.. (2012). The canoe strategy: integrating genomic and metabolic contexts across multiple prokaryote. .
    [BibTeX]
    @article{smith2012canoe,
    title={The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote},
    author={Smith, AAT and Belda, E and Viari, A and Medigue, C and Vallenet, D},
    year={2012}
    }

  • Ghignone, S., Salvioli, A., Anca, I., Lumini, E., Ortu, G., Petiti, L., Cruveiller, S., Bianciotto, V., Piffanelli, P., Lanfranco, L., & others. (2012). The genome of the obligate endobacterium of an am fungus reveals an interphylum network of nutritional interactions. The isme journal, 6(1), 136–145.
    [BibTeX]
    @article{ghignone2012genome,
    title={The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions},
    author={Ghignone, Stefano and Salvioli, Alessandra and Anca, Iulia and Lumini, Erica and Ortu, Giuseppe and Petiti, Luca and Cruveiller, St{\'e}phane and Bianciotto, Valeria and Piffanelli, Pietro and Lanfranco, Luisa and others},
    journal={The ISME journal},
    volume={6},
    number={1},
    pages={136--145},
    year={2012},
    publisher={Nature Publishing Group}
    }

  • Mavingui, P., Moro, C. V., Tran-Van, V., Wisniewski-Dyé, F., Raquin, V., Minard, G., Tran, F., Voronin, D., Rouy, Z., Bustos, P., & others. (2012). Whole-genome sequence of wolbachia strain walbb, an endosymbiont of tiger mosquito vector aedes albopictus. Journal of bacteriology, 194(7), 1840–1840.
    [BibTeX]
    @article{mavingui2012whole,
    title={Whole-genome sequence of Wolbachia strain wAlbB, an endosymbiont of tiger mosquito vector Aedes albopictus},
    author={Mavingui, Patrick and Moro, Claire Valiente and Tran-Van, Van and Wisniewski-Dy{\'e}, Florence and Raquin, Vincent and Minard, Guillaume and Tran, Florence-H{\'e}l{\`e}ne and Voronin, Denis and Rouy, Zo{\'e} and Bustos, Patricia and others},
    journal={Journal of bacteriology},
    volume={194},
    number={7},
    pages={1840--1840},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Duquesne, K., Prima, V., Ji, B., Rouy, Z., Médigue, C., Talla, E., & Sturgis, J.. (2012). Draft genome sequence of the purple photosynthetic bacterium phaeospirillum molischianum dsm120, a particularly versatile bacterium. Journal of bacteriology, 194(13), 3559–3560.
    [BibTeX]
    @article{duquesne2012draft,
    title={Draft genome sequence of the purple photosynthetic bacterium Phaeospirillum molischianum DSM120, a particularly versatile bacterium},
    author={Duquesne, K and Prima, Val{\'e}rie and Ji, B and Rouy, Z and M{\'e}digue, C and Talla, E and Sturgis, JN},
    journal={Journal of bacteriology},
    volume={194},
    number={13},
    pages={3559--3560},
    year={2012},
    publisher={Am Soc Microbiol}
    }

  • Acosta-Cruz, E., Wisniewski-Dyé, F., Rouy, Z., Barbe, V., Valdés, M., & Mavingui, P.. (2012). Insights into the 1.59-mbp largest plasmid of azospirillum brasilense cbg497. Archives of microbiology, 194(9), 725–736.
    [BibTeX]
    @article{acosta2012insights,
    title={Insights into the 1.59-Mbp largest plasmid of Azospirillum brasilense CBG497},
    author={Acosta-Cruz, Erika and Wisniewski-Dy{\'e}, Florence and Rouy, Zo{\'e} and Barbe, Val{\'e}rie and Vald{\'e}s, Mar{\'\i}a and Mavingui, Patrick},
    journal={Archives of microbiology},
    volume={194},
    number={9},
    pages={725--736},
    year={2012},
    publisher={Springer}
    }

  • Alcántara, R., Axelsen, K. B., Morgat, A., Belda, E., Coudert, E., Bridge, A., Cao, H., De Matos, P., Ennis, M., Turner, S., & others. (2012). Rhea—a manually curated resource of biochemical reactions. Nucleic acids research, 40(D1), D754–D760.
    [BibTeX]
    @article{alcantara2012rhea,
    title={Rhea—a manually curated resource of biochemical reactions},
    author={Alc{\'a}ntara, Rafael and Axelsen, Kristian B and Morgat, Anne and Belda, Eugeni and Coudert, Elisabeth and Bridge, Alan and Cao, Hong and De Matos, Paula and Ennis, Marcus and Turner, Steve and others},
    journal={Nucleic acids research},
    volume={40},
    number={D1},
    pages={D754--D760},
    year={2012},
    publisher={Oxford University Press}
    }

2011

  • Kittichotirat, W., Good, N. M., Hall, R., Bringel, F., Lajus, A., Médigue, C., Smalley, N. E., Beck, D., Bumgarner, R., Vuilleumier, S., & others. (2011). Genome sequence of methyloversatilis universalisfam5t, a methylotrophic representative of the order rhodocyclales. Journal of bacteriology, 193(17), 4541–4542.
    [BibTeX]
    @article{kittichotirat2011genome,
    title={Genome Sequence of Methyloversatilis universalisFAM5T, a Methylotrophic Representative of the Order Rhodocyclales},
    author={Kittichotirat, Weerayuth and Good, Nathan M and Hall, Rob and Bringel, Fran{\c{c}}oise and Lajus, Aur{\'e}lie and M{\'e}digue, Claudine and Smalley, Nicole E and Beck, David and Bumgarner, Roger and Vuilleumier, St{\'e}phane and others},
    journal={Journal of bacteriology},
    volume={193},
    number={17},
    pages={4541--4542},
    year={2011},
    publisher={Am Soc Microbiol}
    }

  • Monot, M., Boursaux-Eude, C., Thibonnier, M., Vallenet, D., Moszer, I., Medigue, C., Martin-Verstraete, I., & Dupuy, B.. (2011). Reannotation of the genome sequence of clostridium difficile strain 630. Journal of medical microbiology, 60(8), 1193–1199.
    [BibTeX]
    @article{monot2011reannotation,
    title={Reannotation of the genome sequence of Clostridium difficile strain 630},
    author={Monot, Marc and Boursaux-Eude, Caroline and Thibonnier, Marie and Vallenet, David and Moszer, Ivan and Medigue, Claudine and Martin-Verstraete, Isabelle and Dupuy, Bruno},
    journal={Journal of medical microbiology},
    volume={60},
    number={8},
    pages={1193--1199},
    year={2011},
    publisher={Microbiology Society}
    }

  • Wisniewski-Dyé, F., Borziak, K., Khalsa-Moyers, G., Alexandre, G., Sukharnikov, L. O., Wuichet, K., Hurst, G. B., McDonald, H. W., Robertson, J. S., Barbe, V., & others. (2011). Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. Plos genetics, 7(12), e1002430.
    [BibTeX]
    @article{wisniewski2011azospirillum,
    title={Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments},
    author={Wisniewski-Dy{\'e}, Florence and Borziak, Kirill and Khalsa-Moyers, Gurusahai and Alexandre, Gladys and Sukharnikov, Leonid O and Wuichet, Kristin and Hurst, Gregory B and McDonald, W Hayes and Robertson, Jon S and Barbe, Val{\'e}rie and others},
    journal={PLoS genetics},
    volume={7},
    number={12},
    pages={e1002430},
    year={2011},
    publisher={Public Library of Science}
    }

  • Bertin, P. N., Heinrich-Salmeron, A., Pelletier, E., Goulhen-Chollet, F., Arsène-Ploetze, F., Gallien, S., Lauga, B., Casiot, C., Calteau, A., Vallenet, D., & others. (2011). Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics. The isme journal, 5(11), 1735–1747.
    [BibTeX]
    @article{bertin2011metabolic,
    title={Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics},
    author={Bertin, Philippe N and Heinrich-Salmeron, Audrey and Pelletier, Eric and Goulhen-Chollet, Florence and Ars{\`e}ne-Ploetze, Florence and Gallien, S{\'e}bastien and Lauga, B{\'e}atrice and Casiot, Corinne and Calteau, Alexandra and Vallenet, David and others},
    journal={The ISME journal},
    volume={5},
    number={11},
    pages={1735--1747},
    year={2011},
    publisher={Nature Publishing Group}
    }

  • Gomez-Valero, L., Rusniok, C., Jarraud, S., Vacherie, B., Rouy, Z., Barbe, V., Medigue, C., Etienne, J., & Buchrieser, C.. (2011). Extensive recombination events and horizontal gene transfer shaped the legionella pneumophila genomes. Bmc genomics, 12(1), 536.
    [BibTeX]
    @article{gomez2011extensive,
    title={Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes},
    author={Gomez-Valero, Laura and Rusniok, Christophe and Jarraud, Sophie and Vacherie, Benoit and Rouy, Zo{\'e} and Barbe, Valerie and Medigue, Claudine and Etienne, Jerome and Buchrieser, Carmen},
    journal={BMC genomics},
    volume={12},
    number={1},
    pages={536},
    year={2011},
    publisher={BioMed Central}
    }

  • Perret, A., Lechaplais, C., Tricot, S., Perchat, N., Vergne, C., Pellé, C., Bastard, K., Kreimeyer, A., Vallenet, D., Zaparucha, A., & others. (2011). A novel acyl-coa beta-transaminase characterized from a metagenome. Plos one, 6(8), e22918.
    [BibTeX]
    @article{perret2011novel,
    title={A novel acyl-CoA beta-transaminase characterized from a metagenome},
    author={Perret, Alain and Lechaplais, Christophe and Tricot, Sabine and Perchat, Nadia and Vergne, Carine and Pell{\'e}, Christine and Bastard, Karine and Kreimeyer, Annett and Vallenet, David and Zaparucha, Anne and others},
    journal={PloS one},
    volume={6},
    number={8},
    pages={e22918},
    year={2011},
    publisher={Public Library of Science}
    }

  • Pujol, A., Crost, E. H., Simon, G., Barbe, V., Vallenet, D., Gomez, A., & Fons, M.. (2011). Characterization and distribution of the gene cluster encoding rumc, an anti-c lostridium perfringens bacteriocin produced in the gut. Fems microbiology ecology, 78(2), 405–415.
    [BibTeX]
    @article{pujol2011characterization,
    title={Characterization and distribution of the gene cluster encoding RumC, an anti-C lostridium perfringens bacteriocin produced in the gut},
    author={Pujol, Ange and Crost, Emmanuelle H and Simon, Gwenola and Barbe, Valerie and Vallenet, David and Gomez, Ana and Fons, Michel},
    journal={FEMS microbiology ecology},
    volume={78},
    number={2},
    pages={405--415},
    year={2011},
    publisher={Blackwell Publishing Ltd Oxford, UK}
    }

  • Mornico, D., Miché, L., Béna, G., Nouwen, N., Verméglio, A., Vallenet, D., Smith, A. A., Giraud, E., Médigue, C., & Moulin, L.. (2011). Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. Genes, 3(1), 35–61.
    [BibTeX]
    @article{mornico2011comparative,
    title={Comparative genomics of Aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia},
    author={Mornico, Damien and Mich{\'e}, Lucie and B{\'e}na, Gilles and Nouwen, Nico and Verm{\'e}glio, Andr{\'e} and Vallenet, David and Smith, Alexander AT and Giraud, Eric and M{\'e}digue, Claudine and Moulin, Lionel},
    journal={Genes},
    volume={3},
    number={1},
    pages={35--61},
    year={2011},
    publisher={Molecular Diversity Preservation International}
    }

  • Remenant, B., de Cambiaire, J., Cellier, G., Jacobs, J. M., Mangenot, S., Barbe, V., Lajus, A., Vallenet, D., Medigue, C., Fegan, M., & others. (2011). Ralstonia syzygii, the blood disease bacterium and some asian r. solanacearum strains form a single genomic species despite divergent lifestyles. Plos one, 6(9), e24356.
    [BibTeX]
    @article{remenant2011ralstonia,
    title={Ralstonia syzygii, the blood disease bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles},
    author={Remenant, Beno{\^\i}t and de Cambiaire, Jean-Charles and Cellier, Gilles and Jacobs, Jonathan M and Mangenot, Sophie and Barbe, Valerie and Lajus, Aurelie and Vallenet, David and Medigue, Claudine and Fegan, Mark and others},
    journal={PLoS One},
    volume={6},
    number={9},
    pages={e24356},
    year={2011},
    publisher={Public Library of Science}
    }

  • Vieira, G., Sabarly, V., Bourguignon, P., Durot, M., Le Fèvre, F., Mornico, D., Vallenet, D., Bouvet, O., Denamur, E., Schachter, V., & others. (2011). Core and panmetabolism in escherichia coli. Journal of bacteriology, 193(6), 1461–1472.
    [BibTeX]
    @article{vieira2011core,
    title={Core and panmetabolism in Escherichia coli},
    author={Vieira, Gilles and Sabarly, Victor and Bourguignon, Pierre-Yves and Durot, Maxime and Le F{\`e}vre, Fran{\c{c}}ois and Mornico, Damien and Vallenet, David and Bouvet, Odile and Denamur, Erick and Schachter, Vincent and others},
    journal={Journal of bacteriology},
    volume={193},
    number={6},
    pages={1461--1472},
    year={2011},
    publisher={Am Soc Microbiol}
    }

  • Wielgoss, S., Barrick, J. E., Tenaillon, O., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R. E., & Schneider, D.. (2011). Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with escherichia coli. G3: genes, genomes, genetics, 1(3), 183–186.
    [BibTeX]
    @article{wielgoss2011mutation,
    title={Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli},
    author={Wielgoss, S{\'e}bastien and Barrick, Jeffrey E and Tenaillon, Olivier and Cruveiller, St{\'e}phane and Chane-Woon-Ming, B{\'e}atrice and M{\'e}digue, Claudine and Lenski, Richard E and Schneider, Dominique},
    journal={G3: Genes, Genomes, Genetics},
    volume={1},
    number={3},
    pages={183--186},
    year={2011},
    publisher={G3: Genes, Genomes, Genetics}
    }

  • Vuilleumier, S., Nadalig, T., Haque, M. F. U., Magdelenat, G., Lajus, A., Roselli, S., Muller, E. E., Gruffaz, C., Barbe, V., Médigue, C., & others. (2011). Complete genome sequence of the chloromethane-degrading hyphomicrobium sp. strain mc1. Journal of bacteriology, 193(18), 5035–5036.
    [BibTeX]
    @article{vuilleumier2011complete,
    title={Complete genome sequence of the chloromethane-degrading Hyphomicrobium sp. strain MC1},
    author={Vuilleumier, St{\'e}phane and Nadalig, Thierry and Haque, Muhammad Farhan Ul and Magdelenat, Ghislaine and Lajus, Aur{\'e}lie and Roselli, Sandro and Muller, Emilie EL and Gruffaz, Christelle and Barbe, Val{\'e}rie and M{\'e}digue, Claudine and others},
    journal={Journal of bacteriology},
    volume={193},
    number={18},
    pages={5035--5036},
    year={2011},
    publisher={Am Soc Microbiol}
    }

  • Billard-Pomares, T., Tenaillon, O., Le Nagard, H., Rouy, Z., Cruveiller, S., Médigue, C., Arlet, G., Denamur, E., & Branger, C.. (2011). Complete nucleotide sequence of plasmid ptn48, encoding the ctx-m-14 extended-spectrum $\beta$-lactamase from an escherichia coli o102-st405 strain. Antimicrobial agents and chemotherapy, 55(3), 1270–1273.
    [BibTeX]
    @article{billard2011complete,
    title={Complete nucleotide sequence of plasmid pTN48, encoding the CTX-M-14 extended-spectrum $\beta$-lactamase from an Escherichia coli O102-ST405 strain},
    author={Billard-Pomares, Typhaine and Tenaillon, Olivier and Le Nagard, Herv{\'e} and Rouy, Zo{\'e} and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine and Arlet, Guillaume and Denamur, Erick and Branger, Catherine},
    journal={Antimicrobial agents and chemotherapy},
    volume={55},
    number={3},
    pages={1270--1273},
    year={2011},
    publisher={Am Soc Microbiol}
    }

  • Stein, L. Y., Bringel, F., DiSpirito, A. A., Han, S., Jetten, M. S., Kalyuzhnaya, M. G., Kits, D. K., Klotz, M. G., den Camp, H. J. O., Semrau, J. D., & others. (2011). Genome sequence of the methanotrophic alphaproteobacterium, methylocystis sp. rockwell (atcc 49242). Journal of bacteriology.
    [BibTeX]
    @article{stein2011genome,
    title={Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242)},
    author={Stein, Lisa Y and Bringel, Fran{\c{c}}oise and DiSpirito, Alan A and Han, Sukkyun and Jetten, Mike SM and Kalyuzhnaya, Marina G and Kits, K Dimitri and Klotz, Martin G and den Camp, Huub JM Op and Semrau, Jeremy D and others},
    journal={Journal of bacteriology},
    year={2011},
    publisher={Am Soc Microbiol}
    }

  • Engel, P., Salzburger, W., Liesch, M., Chang, C., Maruyama, S., Lanz, C., Calteau, A., Lajus, A., Médigue, C., Schuster, S. C., & others. (2011). Parallel evolution of a type iv secretion system in radiating lineages of the host-restricted bacterial pathogen bartonella. Plos genetics, 7(2), e1001296.
    [BibTeX]
    @article{engel2011parallel,
    title={Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella},
    author={Engel, Philipp and Salzburger, Walter and Liesch, Marius and Chang, Chao-Chin and Maruyama, Soichi and Lanz, Christa and Calteau, Alexandra and Lajus, Aur{\'e}lie and M{\'e}digue, Claudine and Schuster, Stephan C and others},
    journal={PLoS genetics},
    volume={7},
    number={2},
    pages={e1001296},
    year={2011},
    publisher={Public Library of Science}
    }

  • Svenning, M. M., Hestnes, A. G., Wartiainen, I., Stein, L. Y., Klotz, M. G., Kalyuzhnaya, M. G., Spang, A., Bringel, F., Vuilleumier, S., Lajus, A., & others. (2011). Genome sequence of the arctic methanotroph methylobacter tundripaludum sv96. Journal of bacteriology, 193(22), 6418–6419.
    [BibTeX]
    @article{svenning2011genome,
    title={Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96},
    author={Svenning, Mette M and Hestnes, Anne Grethe and Wartiainen, Ingvild and Stein, Lisa Y and Klotz, Martin G and Kalyuzhnaya, Marina G and Spang, Anja and Bringel, Fran{\c{c}}oise and Vuilleumier, St{\'e}phane and Lajus, Aur{\'e}lie and others},
    journal={Journal of bacteriology},
    volume={193},
    number={22},
    pages={6418--6419},
    year={2011},
    publisher={Am Soc Microbiol}
    }

  • Barbe, V., Bouzon, M., Mangenot, S., Badet, B., Poulain, J., Segurens, B., Vallenet, D., Marlière, P., & Weissenbach, J.. (2011). Complete genome sequence of streptomyces cattleya nrrl 8057, a producer of antibiotics and fluorometabolites. Journal of bacteriology, 193(18), 5055–5056.
    [BibTeX]
    @article{barbe2011complete,
    title={Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites},
    author={Barbe, Val{\'e}rie and Bouzon, Madeleine and Mangenot, Sophie and Badet, Bernard and Poulain, Julie and Segurens, B{\'e}atrice and Vallenet, David and Marli{\`e}re, Philippe and Weissenbach, Jean},
    journal={Journal of bacteriology},
    volume={193},
    number={18},
    pages={5055--5056},
    year={2011},
    publisher={Am Soc Microbiol}
    }

  • Marlière, P., Patrouix, J., Döring, V., Herdewijn, P., Tricot, S., Cruveiller, S., Bouzon, M., & Mutzel, R.. (2011). Chemical evolution of a bacterium’s genome. Angewandte chemie international edition, 50(31), 7109–7114.
    [BibTeX]
    @article{marliere2011chemical,
    title={Chemical evolution of a bacterium’s genome},
    author={Marli{\`e}re, Philippe and Patrouix, Julien and D{\"o}ring, Volker and Herdewijn, Piet and Tricot, Sabine and Cruveiller, St{\'e}phane and Bouzon, Madeleine and Mutzel, Rupert},
    journal={Angewandte Chemie International Edition},
    volume={50},
    number={31},
    pages={7109--7114},
    year={2011},
    publisher={Wiley Online Library}
    }

  • Chaston, J. M., Suen, G., Tucker, S. L., Andersen, A. W., Bhasin, A., Bode, E., Bode, H. B., Brachmann, A. O., Cowles, C. E., Cowles, K. N., & others. (2011). The entomopathogenic bacterial endosymbionts xenorhabdus and photorhabdus: convergent lifestyles from divergent genomes. Plos one, 6(11), e27909.
    [BibTeX]
    @article{chaston2011entomopathogenic,
    title={The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes},
    author={Chaston, John M and Suen, Garret and Tucker, Sarah L and Andersen, Aaron W and Bhasin, Archna and Bode, Edna and Bode, Helge B and Brachmann, Alexander O and Cowles, Charles E and Cowles, Kimberly N and others},
    journal={PloS one},
    volume={6},
    number={11},
    pages={e27909},
    year={2011},
    publisher={Public Library of Science}
    }

  • Bellinzoni, M., Bastard, K., Perret, A., Zaparucha, A., Perchat, N., Vergne, C., Wagner, T., de Melo-Minardi, R. C., Artiguenave, F., Cohen, G. N., & others. (2011). 3-keto-5-aminohexanoate cleavage enzyme a common fold for an uncommon claisen-type condensation. Journal of biological chemistry, 286(31), 27399–27405.
    [BibTeX]
    @article{bellinzoni20113,
    title={3-Keto-5-aminohexanoate Cleavage Enzyme A COMMON FOLD FOR AN UNCOMMON CLAISEN-TYPE CONDENSATION},
    author={Bellinzoni, Marco and Bastard, Karine and Perret, Alain and Zaparucha, Anne and Perchat, Nadia and Vergne, Carine and Wagner, Tristan and de Melo-Minardi, Raquel C and Artiguenave, Fran{\c{c}}ois and Cohen, Georges N and others},
    journal={Journal of Biological Chemistry},
    volume={286},
    number={31},
    pages={27399--27405},
    year={2011},
    publisher={ASBMB}
    }

  • Remenant, B., De Cambiaire, J., Cellier, G., Jacobs, J., Mangenot, S., Barbe, V., Lajus, A., Vallenet, D., Medigue, C., Fegan, M., & others. (2011). The genomes of the insect-transmitted plant pathogens ralstonia syzygii and blood disease bacterium reveal a recent evolutionary origin within the r. solanacearum species. Plos one, 6(9), e24356.
    [BibTeX]
    @article{remenant2011genomes,
    title={The genomes of the insect-transmitted plant pathogens Ralstonia syzygii and Blood Disease Bacterium reveal a recent evolutionary origin within the R. solanacearum species},
    author={Remenant, B and De Cambiaire, JC and Cellier, G and Jacobs, JM and Mangenot, S and Barbe, V and Lajus, A and Vallenet, D and Medigue, C and Fegan, M and others},
    journal={PLoS One},
    volume={6},
    number={9},
    pages={e24356},
    year={2011}
    }

2010

  • Roche, D., Fléchard, M., Lallier, N., Répérant, M., Brée, A., Pascal, G., Schouler, C., & Germon, P.. (2010). Iceec2, a new integrative and conjugative element belonging to the pklc102/pagi-2 family, identified in escherichia coli strain ben374. Journal of bacteriology, 192(19), 5026–5036.
    [BibTeX]
    @article{roche2010iceec2,
    title={ICEEc2, a new integrative and conjugative element belonging to the pKLC102/PAGI-2 family, identified in Escherichia coli strain BEN374},
    author={Roche, David and Fl{\'e}chard, Maud and Lallier, Nathalie and R{\'e}p{\'e}rant, Maryline and Br{\'e}e, Annie and Pascal, G{\'e}raldine and Schouler, Catherine and Germon, Pierre},
    journal={Journal of bacteriology},
    volume={192},
    number={19},
    pages={5026--5036},
    year={2010},
    publisher={Am Soc Microbiol}
    }

  • Touzain, F., Denamur, E., Médigue, C., Barbe, V., El Karoui, M., & Petit, M.. (2010). Research small variable segments constitute a major type of diversity of bacterial genomes at the species level. .
    [BibTeX]
    @article{touzain2010research,
    title={Research Small variable segments constitute a major type of diversity of bacterial genomes at the species level},
    author={Touzain, Fabrice and Denamur, Erick and M{\'e}digue, Claudine and Barbe, Val{\'e}rie and El Karoui, Meriem and Petit, Marie-Agn{\`e}s},
    year={2010},
    publisher={Citeseer}
    }

  • Touzain, F., Denamur, E., Médigue, C., Barbe, V., El Karoui, M., & Petit, M.. (2010). Small variable segments constitute a major type of diversity of bacterial genomes at the species level. Genome biology, 11(4), R45.
    [BibTeX]
    @article{touzain2010small,
    title={Small variable segments constitute a major type of diversity of bacterial genomes at the species level},
    author={Touzain, Fabrice and Denamur, Erick and M{\'e}digue, Claudine and Barbe, Val{\'e}rie and El Karoui, Meriem and Petit, Marie-Agn{\`e}s},
    journal={Genome biology},
    volume={11},
    number={4},
    pages={R45},
    year={2010},
    publisher={BioMed Central}
    }

  • Remenant, B., Coupat-Goutaland, B., Guidot, A., Cellier, G., Wicker, E., Allen, C., Fegan, M., Pruvost, O., Elbaz, M., Calteau, A., & others. (2010). Genomes of three tomato pathogens within the ralstonia solanacearum species complex reveal significant evolutionary divergence. Bmc genomics, 11(1), 379.
    [BibTeX]
    @article{remenant2010genomes,
    title={Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence},
    author={Remenant, Beno{\^\i}t and Coupat-Goutaland, B{\'e}n{\'e}dicte and Guidot, Alice and Cellier, Gilles and Wicker, Emmanuel and Allen, Caitilyn and Fegan, Mark and Pruvost, Olivier and Elbaz, Mounira and Calteau, Alexandra and others},
    journal={BMC genomics},
    volume={11},
    number={1},
    pages={379},
    year={2010},
    publisher={BioMed Central}
    }

  • Méjean, A., Mazmouz, R., Mann, S., Calteau, A., Médigue, C., & Ploux, O.. (2010). The genome sequence of the cyanobacterium oscillatoria sp. pcc 6506 reveals several gene clusters responsible for the biosynthesis of toxins and secondary metabolites. Journal of bacteriology, 192(19), 5264–5265.
    [BibTeX]
    @article{mejean2010genome,
    title={The genome sequence of the cyanobacterium Oscillatoria sp. PCC 6506 reveals several gene clusters responsible for the biosynthesis of toxins and secondary metabolites},
    author={M{\'e}jean, Annick and Mazmouz, Rabia and Mann, St{\'e}phane and Calteau, Alexandra and M{\'e}digue, Claudine and Ploux, Olivier},
    journal={Journal of bacteriology},
    volume={192},
    number={19},
    pages={5264--5265},
    year={2010},
    publisher={Am Soc Microbiol}
    }

  • Miquel, S., Peyretaillade, E., Claret, L., De Vallée, A., Dossat, C., Vacherie, B., Segurens, B., Barbe, V., Sauvanet, P., Neut, C., & others. (2010). Complete genome sequence of crohn’s disease-associated adherent-invasive e. coli strain lf82. Plos one, 5(9), e12714.
    [BibTeX]
    @article{miquel2010complete,
    title={Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82},
    author={Miquel, Sylvie and Peyretaillade, Eric and Claret, Laurent and De Vall{\'e}e, Am{\'e}lie and Dossat, Carole and Vacherie, Benoit and Segurens, Beatrice and Barbe, Valerie and Sauvanet, Pierre and Neut, Christel and others},
    journal={PloS one},
    volume={5},
    number={9},
    pages={e12714},
    year={2010},
    publisher={Public Library of Science}
    }

  • Janssen, P. J., Van Houdt, R., Moors, H., Monsieurs, P., Morin, N., Michaux, A., Benotmane, M. A., Leys, N., Vallaeys, T., Lapidus, A., & others. (2010). The complete genome sequence of cupriavidus metallidurans strain ch34, a master survivalist in harsh and anthropogenic environments. Plos one, 5(5), e10433.
    [BibTeX]
    @article{janssen2010complete,
    title={The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments},
    author={Janssen, Paul J and Van Houdt, Rob and Moors, Hugo and Monsieurs, Pieter and Morin, Nicolas and Michaux, Arlette and Benotmane, Mohammed A and Leys, Natalie and Vallaeys, Tatiana and Lapidus, Alla and others},
    journal={PLoS One},
    volume={5},
    number={5},
    pages={e10433},
    year={2010},
    publisher={Public Library of Science}
    }

  • Marchetti, M., Capela, D., Glew, M., Cruveiller, S., Chane-Woon-Ming, B., Gris, C., Timmers, T., Poinsot, V., Gilbert, L. B., Heeb, P., & others. (2010). Experimental evolution of a plant pathogen into a legume symbiont. Plos biology, 8(1), e1000280.
    [BibTeX]
    @article{marchetti2010experimental,
    title={Experimental evolution of a plant pathogen into a legume symbiont},
    author={Marchetti, Marta and Capela, Delphine and Glew, Michelle and Cruveiller, St{\'e}phane and Chane-Woon-Ming, B{\'e}atrice and Gris, Carine and Timmers, Ton and Poinsot, V{\'e}r{\'e}na and Gilbert, Luz B and Heeb, Philipp and others},
    journal={PLoS biology},
    volume={8},
    number={1},
    pages={e1000280},
    year={2010},
    publisher={Public Library of Science}
    }

  • Bonaldi, K., Gourion, B., Fardoux, J., Hannibal, L., Cartieaux, F., Boursot, M., Vallenet, D., Chaintreuil, C., Prin, Y., Nouwen, N., & others. (2010). Large-scale transposon mutagenesis of photosynthetic bradyrhizobium sp. strain ors278 reveals new genetic loci putatively important for nod-independent symbiosis with aeschynomene indica. Molecular plant-microbe interactions, 23(6), 760–770.
    [BibTeX]
    @article{bonaldi2010large,
    title={Large-scale transposon mutagenesis of photosynthetic Bradyrhizobium sp. strain ORS278 reveals new genetic loci putatively important for nod-independent symbiosis with Aeschynomene indica},
    author={Bonaldi, Katia and Gourion, Benjamin and Fardoux, Joel and Hannibal, Laure and Cartieaux, Fabienne and Boursot, Marc and Vallenet, David and Chaintreuil, Cl{\'e}mence and Prin, Yves and Nouwen, Nico and others},
    journal={Molecular plant-microbe interactions},
    volume={23},
    number={6},
    pages={760--770},
    year={2010},
    publisher={Am Phytopath Society}
    }

  • Bechah, Y., El Karkouri, K., Mediannikov, O., Leroy, Q., Pelletier, N., Robert, C., Médigue, C., Mege, J., & Raoult, D.. (2010). Genomic, proteomic, and transcriptomic analysis of virulent and avirulent rickettsia prowazekii reveals its adaptive mutation capabilities. Genome research, 20(5), 655–663.
    [BibTeX]
    @article{bechah2010genomic,
    title={Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities},
    author={Bechah, Yassina and El Karkouri, Khalid and Mediannikov, Oleg and Leroy, Quentin and Pelletier, Nicolas and Robert, Catherine and M{\'e}digue, Claudine and Mege, Jean-Louis and Raoult, Didier},
    journal={Genome research},
    volume={20},
    number={5},
    pages={655--663},
    year={2010},
    publisher={Cold Spring Harbor Lab}
    }

  • Stein, L. Y., Yoon, S., Semrau, J. D., DiSpirito, A. A., Crombie, A., Murrell, C. J., Vuilleumier, S., Kalyuzhnaya, M. G., Den Camp, H. J. O., Bringel, F., & others. (2010). Genome sequence of the obligate methanotroph methylosinus trichosporium strain ob3b. Journal of bacteriology, 192(24), 6497–6498.
    [BibTeX]
    @article{stein2010genome,
    title={Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b},
    author={Stein, Lisa Y and Yoon, Sukhwan and Semrau, Jeremy D and DiSpirito, Alan A and Crombie, Andrew and Murrell, J Colin and Vuilleumier, St{\'e}phane and Kalyuzhnaya, Marina G and Den Camp, Huub JM Op and Bringel, Fran{\c{c}}oise and others},
    journal={Journal of bacteriology},
    volume={192},
    number={24},
    pages={6497--6498},
    year={2010},
    publisher={Am Soc Microbiol}
    }

  • Ogier, J., Calteau, A., Forst, S., Goodrich-Blair, H., Roche, D., Rouy, Z., Suen, G., Zumbihl, R., Givaudan, A., Tailliez, P., & others. (2010). Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, photorhabdus and xenorhabdus. Bmc genomics, 11(1), 568.
    [BibTeX]
    @article{ogier2010units,
    title={Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus},
    author={Ogier, Jean-Claude and Calteau, Alexandra and Forst, Steve and Goodrich-Blair, Heidi and Roche, David and Rouy, Zo{\'e} and Suen, Garret and Zumbihl, Robert and Givaudan, Alain and Tailliez, Patrick and others},
    journal={BMC genomics},
    volume={11},
    number={1},
    pages={568},
    year={2010},
    publisher={BioMed Central}
    }

  • Alloisio, N., Queiroux, C., Fournier, P., Pujic, P., Normand, P., Vallenet, D., Médigue, C., Yamaura, M., Kakoi, K., & Kucho, K.. (2010). The frankia alni symbiotic transcriptome. Molecular plant-microbe interactions, 23(5), 593–607.
    [BibTeX]
    @article{alloisio2010frankia,
    title={The Frankia alni symbiotic transcriptome},
    author={Alloisio, Nicole and Queiroux, Clothilde and Fournier, Pascale and Pujic, Petar and Normand, Philippe and Vallenet, David and M{\'e}digue, Claudine and Yamaura, Masatoshi and Kakoi, Kentaro and Kucho, Ken-ichi},
    journal={Molecular Plant-Microbe Interactions},
    volume={23},
    number={5},
    pages={593--607},
    year={2010},
    publisher={Am Phytopath Society}
    }

  • Fonknechten, N., Chaussonnerie, S., Tricot, S., Lajus, A., Andreesen, J. R., Perchat, N., Pelletier, E., Gouyvenoux, M., Barbe, V., Salanoubat, M., & others. (2010). Clostridium sticklandii, a specialist in amino acid degradation: revisiting its metabolism through its genome sequence. Bmc genomics, 11(1), 555.
    [BibTeX]
    @article{fonknechten2010clostridium,
    title={Clostridium sticklandii, a specialist in amino acid degradation: revisiting its metabolism through its genome sequence},
    author={Fonknechten, Nuria and Chaussonnerie, S{\'e}bastien and Tricot, Sabine and Lajus, Aur{\'e}lie and Andreesen, Jan R and Perchat, Nadia and Pelletier, Eric and Gouyvenoux, Michel and Barbe, Val{\'e}rie and Salanoubat, Marcel and others},
    journal={Bmc Genomics},
    volume={11},
    number={1},
    pages={555},
    year={2010},
    publisher={BioMed Central}
    }

  • Thiberge, J., Boursaux-Eude, C., Lehours, P., Dillies, M., Creno, S., Coppée, J., Rouy, Z., Lajus, A., Ma, L., Burucoa, C., & others. (2010). From array-based hybridization of helicobacter pylori isolates to the complete genome sequence of an isolate associated with malt lymphoma. Bmc genomics, 11(1), 368.
    [BibTeX]
    @article{thiberge2010array,
    title={From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma},
    author={Thiberge, Jean-Michel and Boursaux-Eude, Caroline and Lehours, Philippe and Dillies, Marie-Agn{\`e}s and Creno, Sophie and Copp{\'e}e, Jean-Yves and Rouy, Zo{\'e} and Lajus, Aur{\'e}lie and Ma, Laurence and Burucoa, Christophe and others},
    journal={BMC genomics},
    volume={11},
    number={1},
    pages={368},
    year={2010},
    publisher={BioMed Central}
    }

  • Derbise, A., Chenal-Francisque, V., Huon, C., Fayolle, C., Demeure, C. E., Chane-Woon-Ming, B., Médigue, C., Hinnebusch, J. B., & Carniel, E.. (2010). Delineation and analysis of chromosomal regions specifying yersinia pestis. Infection and immunity, 78(9), 3930–3941.
    [BibTeX]
    @article{derbise2010delineation,
    title={Delineation and analysis of chromosomal regions specifying Yersinia pestis},
    author={Derbise, Anne and Chenal-Francisque, Viviane and Huon, Christ{\`e}le and Fayolle, Corinne and Demeure, Christian E and Chane-Woon-Ming, B{\'e}atrice and M{\'e}digue, Claudine and Hinnebusch, B Joseph and Carniel, Elisabeth},
    journal={Infection and immunity},
    volume={78},
    number={9},
    pages={3930--3941},
    year={2010},
    publisher={Am Soc Microbiol}
    }

  • de Melo-Minardi, R. C., Bastard, K., & Artiguenave, F.. (2010). Identification of subfamily-specific sites based on active sites modeling and clustering. Bioinformatics, 26(24), 3075–3082.
    [BibTeX]
    @article{de2010identification,
    title={Identification of subfamily-specific sites based on active sites modeling and clustering},
    author={de Melo-Minardi, Raquel C and Bastard, Karine and Artiguenave, Fran{\c{c}}ois},
    journal={Bioinformatics},
    volume={26},
    number={24},
    pages={3075--3082},
    year={2010},
    publisher={Oxford University Press}
    }

  • Arsène-Ploetze, F., Koechler, S., Marchal, M., Coppée, J., Chandler, M., Bonnefoy, V., Brochier-Armanet, C., Barakat, M., Barbe, V., Battaglia-Brunet, F., & others. (2010). Structure, function, and evolution of the thiomonas spp. genome. Plos genetics, 6(2), e1000859.
    [BibTeX]
    @article{arsene2010structure,
    title={Structure, function, and evolution of the Thiomonas spp. genome},
    author={Ars{\`e}ne-Ploetze, Florence and Koechler, Sandrine and Marchal, Marie and Copp{\'e}e, Jean-Yves and Chandler, Michael and Bonnefoy, Violaine and Brochier-Armanet, C{\'e}line and Barakat, Mohamed and Barbe, Val{\'e}rie and Battaglia-Brunet, Fabienne and others},
    journal={PLoS genetics},
    volume={6},
    number={2},
    pages={e1000859},
    year={2010},
    publisher={Public Library of Science}
    }

2009

  • Peigne, C., Bidet, P., Mahjoub-Messai, F., Plainvert, C., Barbe, V., Médigue, C., Frapy, E., Nassif, X., Denamur, E., Bingen, E., & others. (2009). The plasmid of escherichia coli strain s88 (o45: k1: h7) that causes neonatal meningitis is closely related to avian pathogenic e. coli plasmids and is associated with high-level bacteremia in a neonatal rat meningitis model. Infection and immunity, 77(6), 2272–2284.
    [BibTeX]
    @article{peigne2009plasmid,
    title={The plasmid of Escherichia coli strain S88 (O45: K1: H7) that causes neonatal meningitis is closely related to avian pathogenic E. coli plasmids and is associated with high-level bacteremia in a neonatal rat meningitis model},
    author={Peigne, Chantal and Bidet, Philippe and Mahjoub-Messai, Farah and Plainvert, C{\'e}line and Barbe, Val{\'e}rie and M{\'e}digue, Claudine and Frapy, Eric and Nassif, Xavier and Denamur, Erick and Bingen, Edouard and others},
    journal={Infection and immunity},
    volume={77},
    number={6},
    pages={2272--2284},
    year={2009},
    publisher={Am Soc Microbiol}
    }

  • Peigne, C., Bidet, P., Mahjoub-Messai, F., Plainvert, C., Barbe, V., Médigue, C., Frapy, E., Nassif, X., Denamur, E., Bingen, E., & others. (2009). The plasmid of neonatal meningitis escherichia coli strain s88 (o45: k1: h7) is closely related to avian pathogenic e. coli plasmids and is associated with high level bacteremia in neonatal rat meningitis model. Infection and immunity.
    [BibTeX]
    @article{peigne2009plasmid,
    title={The plasmid of neonatal meningitis Escherichia coli strain S88 (O45: K1: H7) is closely related to avian pathogenic E. coli plasmids and is associated with high level bacteremia in neonatal rat meningitis model},
    author={Peigne, Chantal and Bidet, Philippe and Mahjoub-Messai, Farah and Plainvert, C{\'e}line and Barbe, Val{\'e}rie and M{\'e}digue, Claudine and Frapy, Eric and Nassif, Xavier and Denamur, Erick and Bingen, Edouard and others},
    journal={Infection and Immunity},
    year={2009},
    publisher={American Society for Microbiology}
    }

  • Barbe, V., Cruveiller, S., Kunst, F., Lenoble, P., Meurice, G., Sekowska, A., Vallenet, D., Wang, T., Moszer, I., Médigue, C., & others. (2009). From a consortium sequence to a unified sequence: the bacillus subtilis 168 reference genome a decade later. Microbiology, 155(6), 1758–1775.
    [BibTeX]
    @article{barbe2009consortium,
    title={From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later},
    author={Barbe, Valerie and Cruveiller, Stephane and Kunst, Frank and Lenoble, Patricia and Meurice, Guillaume and Sekowska, Agnieszka and Vallenet, David and Wang, Tingzhang and Moszer, Ivan and M{\'e}digue, Claudine and others},
    journal={Microbiology},
    volume={155},
    number={6},
    pages={1758--1775},
    year={2009},
    publisher={Microbiology Society}
    }

  • Jeong, H., Barbe, V., Lee, C. H., Vallenet, D., Yu, D. S., Choi, S., Couloux, A., Lee, S., Yoon, S. H., Cattolico, L., & others. (2009). Genome sequences of escherichia coli b strains rel606 and bl21 (de3). Journal of molecular biology, 394(4), 644–652.
    [BibTeX]
    @article{jeong2009genome,
    title={Genome sequences of Escherichia coli B strains REL606 and BL21 (DE3)},
    author={Jeong, Haeyoung and Barbe, Val{\'e}rie and Lee, Choong Hoon and Vallenet, David and Yu, Dong Su and Choi, Sang-Haeng and Couloux, Arnaud and Lee, Seung-Won and Yoon, Sung Ho and Cattolico, Laurence and others},
    journal={Journal of molecular biology},
    volume={394},
    number={4},
    pages={644--652},
    year={2009},
    publisher={Elsevier}
    }

  • Barabote, R. D., Xie, G., Leu, D. H., Normand, P., Necsulea, A., Daubin, V., Médigue, C., Adney, W. S., Xu, X. C., Lapidus, A., & others. (2009). Complete genome of the cellulolytic thermophile acidothermus cellulolyticus 11b provides insights into its ecophysiological and evolutionary adaptations. Genome research, 19(6), 1033–1043.
    [BibTeX]
    @article{barabote2009complete,
    title={Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations},
    author={Barabote, Ravi D and Xie, Gary and Leu, David H and Normand, Philippe and Necsulea, Anamaria and Daubin, Vincent and M{\'e}digue, Claudine and Adney, William S and Xu, Xin Clare and Lapidus, Alla and others},
    journal={Genome research},
    volume={19},
    number={6},
    pages={1033--1043},
    year={2009},
    publisher={Cold Spring Harbor Lab}
    }

  • Weiss, S., Carapito, C., Cleiss, J., Koechler, S., Turlin, E., Coppee, J., Heymann, M., Kugler, V., Stauffert, M., Cruveiller, S., & others. (2009). Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain herminiimonas arsenicoxydans by proteomics data. Biochimie, 91(2), 192–203.
    [BibTeX]
    @article{weiss2009enhanced,
    title={Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data},
    author={Weiss, St{\'e}phanie and Carapito, Christine and Cleiss, Jessica and Koechler, Sandrine and Turlin, Evelyne and Coppee, Jean-Yves and Heymann, Micha{\"e}l and Kugler, Val{\'e}rie and Stauffert, Magalie and Cruveiller, St{\'e}phane and others},
    journal={Biochimie},
    volume={91},
    number={2},
    pages={192--203},
    year={2009},
    publisher={Elsevier}
    }

  • Berglund, E. C., Frank, C. A., Calteau, A., Pettersson, O. V., Granberg, F., Eriksson, A., Näslund, K., Holmberg, M., Lindroos, H., & Andersson, S. G.. (2009). Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting bartonella grahamii. Plos genetics, 5(7), e1000546.
    [BibTeX]
    @article{berglund2009run,
    title={Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii},
    author={Berglund, Eva C and Frank, A Carolin and Calteau, Alexandra and Pettersson, Olga Vinnere and Granberg, Fredrik and Eriksson, Ann-Sofie and N{\"a}slund, Kristina and Holmberg, Martin and Lindroos, Hillevi and Andersson, Siv GE},
    journal={PLoS genetics},
    volume={5},
    number={7},
    pages={e1000546},
    year={2009},
    publisher={Public Library of Science}
    }

  • Rusniok, C., Vallenet, D., Floquet, S., Ewles, H., Mouzé-Soulama, C., Brown, D., Lajus, A., Buchrieser, C., Médigue, C., Glaser, P., & others. (2009). Nemesys: a biological resource for narrowing the gap between sequence and function in the human pathogen neisseria meningitidis. Genome biology, 10(10), R110.
    [BibTeX]
    @article{rusniok2009nemesys,
    title={NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis},
    author={Rusniok, Christophe and Vallenet, David and Floquet, St{\'e}phanie and Ewles, Helen and Mouz{\'e}-Soulama, Coralie and Brown, Daniel and Lajus, Aur{\'e}lie and Buchrieser, Carmen and M{\'e}digue, Claudine and Glaser, Philippe and others},
    journal={Genome biology},
    volume={10},
    number={10},
    pages={R110},
    year={2009},
    publisher={BioMed Central}
    }

  • Le Roux, F., Zouine, M., Chakroun, N., Binesse, J., Saulnier, D., Bouchier, C., Zidane, N., Ma, L., Rusniok, C., Lajus, A., & others. (2009). Genome sequence of vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Environmental microbiology, 11(8), 1959–1970.
    [BibTeX]
    @article{le2009genome,
    title={Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity},
    author={Le Roux, Fr{\'e}d{\'e}rique and Zouine, Mohamed and Chakroun, Nesrine and Binesse, Johan and Saulnier, Denis and Bouchier, Christiane and Zidane, Nora and Ma, Laurence and Rusniok, Christophe and Lajus, Aur{\'e}lie and others},
    journal={Environmental microbiology},
    volume={11},
    number={8},
    pages={1959--1970},
    year={2009},
    publisher={Wiley Online Library}
    }

  • Fonknechten, N., Perret, A., Perchat, N., Tricot, S., Lechaplais, C., Vallenet, D., Vergne, C., Zaparucha, A., Le Paslier, D., Weissenbach, J., & others. (2009). A conserved gene cluster rules anaerobic oxidative degradation of l-ornithine. Journal of bacteriology, 191(9), 3162–3167.
    [BibTeX]
    @article{fonknechten2009conserved,
    title={A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine},
    author={Fonknechten, Nuria and Perret, Alain and Perchat, Nadia and Tricot, Sabine and Lechaplais, Christophe and Vallenet, David and Vergne, Carine and Zaparucha, Anne and Le Paslier, Denis and Weissenbach, Jean and others},
    journal={Journal of bacteriology},
    volume={191},
    number={9},
    pages={3162--3167},
    year={2009},
    publisher={Am Soc Microbiol}
    }

  • Lescat, M., Calteau, A., Hoede, C., Barbe, V., Touchon, M., Rocha, E., Tenaillon, O., Médigue, C., Johnson, J. R., & Denamur, E.. (2009). A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from escherichia coli clonal group a. Antimicrobial agents and chemotherapy, 53(6), 2283–2288.
    [BibTeX]
    @article{lescat2009module,
    title={A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from Escherichia coli clonal group A},
    author={Lescat, Mathilde and Calteau, Alexandra and Hoede, Claire and Barbe, Val{\'e}rie and Touchon, Marie and Rocha, Eduardo and Tenaillon, Olivier and M{\'e}digue, Claudine and Johnson, James R and Denamur, Erick},
    journal={Antimicrobial agents and chemotherapy},
    volume={53},
    number={6},
    pages={2283--2288},
    year={2009},
    publisher={Am Soc Microbiol}
    }

  • Vaysse, P., Prat, L., Mangenot, S., Cruveiller, S., Goulas, P., & Grimaud, R.. (2009). Proteomic analysis of marinobacter hydrocarbonoclasticus sp17 biofilm formation at the alkane-water interface reveals novel proteins and cellular processes involved in hexadecane assimilation. Research in microbiology, 160(10), 829–837.
    [BibTeX]
    @article{vaysse2009proteomic,
    title={Proteomic analysis of Marinobacter hydrocarbonoclasticus SP17 biofilm formation at the alkane-water interface reveals novel proteins and cellular processes involved in hexadecane assimilation},
    author={Vaysse, Pierre-Joseph and Prat, Laure and Mangenot, Sophie and Cruveiller, St{\'e}phane and Goulas, Philippe and Grimaud, R{\'e}gis},
    journal={Research in microbiology},
    volume={160},
    number={10},
    pages={829--837},
    year={2009},
    publisher={Elsevier}
    }

  • Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., Bingen, E., Bonacorsi, S., Bouchier, C., Bouvet, O., & others. (2009). Organised genome dynamics in the escherichia coli species results in highly diverse adaptive paths. Plos genetics, 5(1), e1000344.
    [BibTeX]
    @article{touchon2009organised,
    title={Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths},
    author={Touchon, Marie and Hoede, Claire and Tenaillon, Olivier and Barbe, Val{\'e}rie and Baeriswyl, Simon and Bidet, Philippe and Bingen, Edouard and Bonacorsi, St{\'e}phane and Bouchier, Christiane and Bouvet, Odile and others},
    journal={PLoS genetics},
    volume={5},
    number={1},
    pages={e1000344},
    year={2009},
    publisher={Public Library of Science}
    }

  • Le Fèvre, F., Smidtas, S., Combe, C., Durot, M., d’Alché-Buc , F., & Schachter, V.. (2009). Cycsim—an online tool for exploring and experimenting with genome-scale metabolic models. Bioinformatics, 25(15), 1987–1988.
    [BibTeX]
    @article{le2009cycsim,
    title={CycSim—an online tool for exploring and experimenting with genome-scale metabolic models},
    author={Le F{\`e}vre, Fran{\c{c}}ois and Smidtas, Serge and Combe, Cyril and Durot, Maxime and d'Alch{\'e}-Buc, Florence and Schachter, V},
    journal={Bioinformatics},
    volume={25},
    number={15},
    pages={1987--1988},
    year={2009},
    publisher={Oxford University Press}
    }

  • de Berardinis, V., Durot, M., Weissenbach, J., & Salanoubat, M.. (2009). Acinetobacter baylyi adp1 as a model for metabolic system biology. Current opinion in microbiology, 12(5), 568–576.
    [BibTeX]
    @article{de2009acinetobacter,
    title={Acinetobacter baylyi ADP1 as a model for metabolic system biology},
    author={de Berardinis, V{\'e}ronique and Durot, Maxime and Weissenbach, Jean and Salanoubat, Marcel},
    journal={Current opinion in microbiology},
    volume={12},
    number={5},
    pages={568--576},
    year={2009},
    publisher={Elsevier}
    }

  • Vuilleumier, S., Chistoserdova, L., Lee, M., Bringel, F., Lajus, A., Zhou, Y., Gourion, B., Barbe, V., Chang, J., Cruveiller, S., & others. (2009). Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of c1 compounds from natural and industrial sources. Plos one, 4(5), e5584.
    [BibTeX]
    @article{vuilleumier2009methylobacterium,
    title={Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources},
    author={Vuilleumier, St{\'e}phane and Chistoserdova, Ludmila and Lee, Ming-Chun and Bringel, Fran{\c{c}}oise and Lajus, Aur{\'e}lie and Zhou, Yang and Gourion, Benjamin and Barbe, Val{\'e}rie and Chang, Jean and Cruveiller, St{\'e}phane and others},
    journal={PloS one},
    volume={4},
    number={5},
    pages={e5584},
    year={2009},
    publisher={Public Library of Science}
    }

  • Vallenet, D., Engelen, S., Mornico, D., Cruveiller, S., Fleury, L., Lajus, A., Rouy, Z., Roche, D., Salvignol, G., Scarpelli, C., & others. (2009). Microscope: a platform for microbial genome annotation and comparative genomics. Database, 2009.
    [BibTeX]
    @article{vallenet2009microscope,
    title={MicroScope: a platform for microbial genome annotation and comparative genomics},
    author={Vallenet, David and Engelen, Stefan and Mornico, Damien and Cruveiller, St{\'e}phane and Fleury, Ludovic and Lajus, Aur{\'e}lie and Rouy, Zo{\'e} and Roche, David and Salvignol, Gregory and Scarpelli, Claude and others},
    journal={Database},
    volume={2009},
    year={2009},
    publisher={Oxford University Press}
    }

2008

  • Médigue, C., & Danchin, A.. (2008). Annotating bacterial genomes. In Modern genome annotation (pp. 165–190). Springer.
    [BibTeX]
    @incollection{medigue2008annotating,
    title={Annotating bacterial genomes},
    author={M{\'e}digue, C and Danchin, A},
    booktitle={Modern Genome Annotation},
    pages={165--190},
    year={2008},
    publisher={Springer}
    }

  • Xie, G., Detter, C., Bruce, D., Challacome, J. F., Brettin, T. S., Barabote, R. D., Leu, D., Normand, P., Necsula, A., Daubin, V., & others. (2008). Complete genome of the cellulolytic thermophile acidothermus cellulolyticus 11b provides insights into its ecophysiological and evolutionary adaptations Los Alamos National Laboratory (LANL).
    [BibTeX]
    @techreport{xie2008complete,
    title={Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations},
    author={Xie, Gary and Detter, Chris and Bruce, David and Challacome, Jean F and Brettin, Thomas S and Barabote, Ravi D and Leu, David and Normand, Philippe and Necsula, Anamaria and Daubin, Vincent and others},
    year={2008},
    institution={Los Alamos National Laboratory (LANL)}
    }

  • De Berardinis, V., Vallenet, D., Castelli, V., Besnard, M., Pinet, A., Cruaud, C., Samair, S., Lechaplais, C., Gyapay, G., Richez, C., & others. (2008). A complete collection of single-gene deletion mutants of acinetobacter baylyi adp1. Molecular systems biology, 4(1), 174.
    [BibTeX]
    @article{de2008complete,
    title={A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1},
    author={De Berardinis, V{\'e}ronique and Vallenet, David and Castelli, Vanina and Besnard, Marielle and Pinet, Agnes and Cruaud, Corinne and Samair, Sumitta and Lechaplais, Christophe and Gyapay, Gabor and Richez, C{\'e}line and others},
    journal={Molecular systems biology},
    volume={4},
    number={1},
    pages={174},
    year={2008},
    publisher={EMBO Press}
    }

  • Amadou, C., Pascal, G., Mangenot, S., Glew, M., Bontemps, C., Capela, D., Carrère, S., Cruveiller, S., Dossat, C., Lajus, A., & others. (2008). Genome sequence of the $\beta$-rhizobium cupriavidus taiwanensis and comparative genomics of rhizobia. Genome research, 18(9), 1472–1483.
    [BibTeX]
    @article{amadou2008genome,
    title={Genome sequence of the $\beta$-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia},
    author={Amadou, Claire and Pascal, G{\'e}raldine and Mangenot, Sophie and Glew, Michelle and Bontemps, Cyril and Capela, Delphine and Carr{\`e}re, S{\'e}bastien and Cruveiller, St{\'e}phane and Dossat, Carole and Lajus, Aur{\'e}lie and others},
    journal={Genome Research},
    volume={18},
    number={9},
    pages={1472--1483},
    year={2008},
    publisher={Cold Spring Harbor Lab}
    }

  • Bertin, P. N., Médigue, C., & Normand, P.. (2008). Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems. Microbiology, 154(2), 347–359.
    [BibTeX]
    @article{bertin2008advances,
    title={Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems},
    author={Bertin, Philippe N and M{\'e}digue, Claudine and Normand, Philippe},
    journal={Microbiology},
    volume={154},
    number={2},
    pages={347--359},
    year={2008},
    publisher={Microbiology Society}
    }

  • Marais, G. A., Calteau, A., & Tenaillon, O.. (2008). Mutation rate and genome reduction in endosymbiotic and free-living bacteria. Genetica, 134(2), 205–210.
    [BibTeX]
    @article{marais2008mutation,
    title={Mutation rate and genome reduction in endosymbiotic and free-living bacteria},
    author={Marais, Gabriel AB and Calteau, Alexandra and Tenaillon, Olivier},
    journal={Genetica},
    volume={134},
    number={2},
    pages={205--210},
    year={2008},
    publisher={Springer}
    }

  • Rosso, M., Chauvaux, S., Dessein, R., Laurans, C., Frangeul, L., Lacroix, C., Schiavo, A., Dillies, M., Foulon, J., Coppée, J., & others. (2008). Growth of yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression. Bmc microbiology, 8(1), 211.
    [BibTeX]
    @article{rosso2008growth,
    title={Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression},
    author={Rosso, Marie-Laure and Chauvaux, Sylvie and Dessein, Rodrigue and Laurans, Caroline and Frangeul, Lionel and Lacroix, C{\'e}line and Schiavo, Ang{\`e}le and Dillies, Marie-Agn{\`e}s and Foulon, Jeannine and Copp{\'e}e, Jean-Yves and others},
    journal={BMC microbiology},
    volume={8},
    number={1},
    pages={211},
    year={2008},
    publisher={BioMed Central}
    }

  • Pelletier, E., Kreimeyer, A., Bocs, S., Rouy, Z., Gyapay, G., Chouari, R., Rivière, D., Ganesan, A., Daegelen, P., Sghir, A., & others. (2008). “candidatus cloacamonas acidaminovorans”: genome sequence reconstruction provides a first glimpse of a new bacterial division. Journal of bacteriology, 190(7), 2572–2579.
    [BibTeX]
    @article{pelletier2008candidatus,
    title={“Candidatus Cloacamonas acidaminovorans”: genome sequence reconstruction provides a first glimpse of a new bacterial division},
    author={Pelletier, Eric and Kreimeyer, Annett and Bocs, St{\'e}phanie and Rouy, Zo{\'e} and Gyapay, G{\'a}bor and Chouari, Rakia and Rivi{\`e}re, Delphine and Ganesan, Akila and Daegelen, Patrick and Sghir, Abdelghani and others},
    journal={Journal of Bacteriology},
    volume={190},
    number={7},
    pages={2572--2579},
    year={2008},
    publisher={Am Soc Microbiol}
    }

  • Durot, M., Le Fèvre, F., de Berardinis, V., Kreimeyer, A., Vallenet, D., Combe, C., Smidtas, S., Salanoubat, M., Weissenbach, J., & Schachter, V.. (2008). Iterative reconstruction of a global metabolic model of acinetobacter baylyi adp1 using high-throughput growth phenotype and gene essentiality data. Bmc systems biology, 2(1), 85.
    [BibTeX]
    @article{durot2008iterative,
    title={Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data},
    author={Durot, Maxime and Le F{\`e}vre, Fran{\c{c}}ois and de Berardinis, V{\'e}ronique and Kreimeyer, Annett and Vallenet, David and Combe, Cyril and Smidtas, Serge and Salanoubat, Marcel and Weissenbach, Jean and Schachter, Vincent},
    journal={BMC systems biology},
    volume={2},
    number={1},
    pages={85},
    year={2008},
    publisher={BioMed Central}
    }

  • Giraud, E., Moulin, L., Avarre, J., Jaubert, M., Barbe, V., Béna, G., Cartiaux, F., De Lajudie, P., Dreyfus, B., Elmerich, D., & others. (2008). The mosaic genomes of two phtosynthetic\# bradyrhizobium\# strains do not contain canonical nodulation genes. .
    [BibTeX]
    @article{giraud2008mosaic,
    title={The mosaic genomes of two phtosynthetic\# Bradyrhizobium\# strains do not contain canonical nodulation genes},
    author={Giraud, Eric and Moulin, Lionel and Avarre, Jean-Christophe and Jaubert, Marianne and Barbe, Val{\'e}rie and B{\'e}na, Gilles and Cartiaux, F and De Lajudie, Philippe and Dreyfus, Bernard and Elmerich, D and others},
    year={2008}
    }

  • Vallenet, D., Nordmann, P., Barbe, V., Poirel, L., Mangenot, S., Bataille, E., Dossat, C., Gas, S., Kreimeyer, A., Lenoble, P., & others. (2008). Comparative analysis of acinetobacters: three genomes for three lifestyles. Plos one, 3(3), e1805.
    [BibTeX]
    @article{vallenet2008comparative,
    title={Comparative analysis of Acinetobacters: three genomes for three lifestyles},
    author={Vallenet, David and Nordmann, Patrice and Barbe, Val{\'e}rie and Poirel, Laurent and Mangenot, Sophie and Bataille, Elodie and Dossat, Carole and Gas, Shahinaz and Kreimeyer, Annett and Lenoble, Patricia and others},
    journal={PloS one},
    volume={3},
    number={3},
    pages={e1805},
    year={2008},
    publisher={Public Library of Science}
    }

  • Picardeau, M., Bulach, D. M., Bouchier, C., Zuerner, R. L., Zidane, N., Wilson, P. J., Creno, S., Kuczek, E. S., Bommezzadri, S., Davis, J. C., & others. (2008). Genome sequence of the saprophyte leptospira biflexa provides insights into the evolution of leptospira and the pathogenesis of leptospirosis. Plos one, 3(2), e1607.
    [BibTeX]
    @article{picardeau2008genome,
    title={Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis},
    author={Picardeau, Mathieu and Bulach, Dieter M and Bouchier, Christiane and Zuerner, Richard L and Zidane, Nora and Wilson, Peter J and Creno, Sophie and Kuczek, Elizabeth S and Bommezzadri, Simona and Davis, John C and others},
    journal={PloS one},
    volume={3},
    number={2},
    pages={e1607},
    year={2008},
    publisher={Public Library of Science}
    }

  • Durot, M., Bourguignon, P., & Schachter, V.. (2008). Genome-scale models of bacterial metabolism: reconstruction and applications. Fems microbiology reviews, 33(1), 164–190.
    [BibTeX]
    @article{durot2008genome,
    title={Genome-scale models of bacterial metabolism: reconstruction and applications},
    author={Durot, Maxime and Bourguignon, Pierre-Yves and Schachter, Vincent},
    journal={FEMS microbiology reviews},
    volume={33},
    number={1},
    pages={164--190},
    year={2008},
    publisher={Federation of European Microbiological Societies}
    }

2007

  • Chauvaux, S., Rosso, M., Frangeul, L., Lacroix, C., Labarre, L., Schiavo, A., Marceau, M., Dillies, M., Foulon, J., Coppée, J., & others. (2007). Transcriptome analysis of yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague. Microbiology, 153(9), 3112–3124.
    [BibTeX]
    @article{chauvaux2007transcriptome,
    title={Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague},
    author={Chauvaux, Sylvie and Rosso, Marie-Laure and Frangeul, Lionel and Lacroix, Celine and Labarre, Laurent and Schiavo, Angele and Marceau, Michael and Dillies, Marie-Agn{\`e}s and Foulon, Jeannine and Copp{\'e}e, Jean-Yves and others},
    journal={Microbiology},
    volume={153},
    number={9},
    pages={3112--3124},
    year={2007},
    publisher={Microbiology Society}
    }

  • Bourhy, P., Salaün, L., Lajus, A., Médigue, C., Boursaux-Eude, C., & Picardeau, M.. (2007). A genomic island of the pathogen leptospira interrogans serovar lai can excise from its chromosome. Infection and immunity, 75(2), 677–683.
    [BibTeX]
    @article{bourhy2007genomic,
    title={A genomic island of the pathogen Leptospira interrogans serovar Lai can excise from its chromosome},
    author={Bourhy, Pascale and Sala{\"u}n, Laurence and Lajus, Aur{\'e}lie and M{\'e}digue, Claudine and Boursaux-Eude, Caroline and Picardeau, Mathieu},
    journal={Infection and immunity},
    volume={75},
    number={2},
    pages={677--683},
    year={2007},
    publisher={Am Soc Microbiol}
    }

  • Giraud, E., Moulin, L., Vallenet, D., Barbe, V., Cytryn, E., Avarre, J., Jaubert, M., Simon, D., Cartieaux, F., Prin, Y., & others. (2007). Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia. Science, 316(5829), 1307–1312.
    [BibTeX]
    @article{giraud2007legumes,
    title={Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia},
    author={Giraud, Eric and Moulin, Lionel and Vallenet, David and Barbe, Val{\'e}rie and Cytryn, Eddie and Avarre, Jean-Christophe and Jaubert, Marianne and Simon, Damien and Cartieaux, Fabienne and Prin, Yves and others},
    journal={Science},
    volume={316},
    number={5829},
    pages={1307--1312},
    year={2007},
    publisher={American Association for the Advancement of Science}
    }

  • Médigue, C., & Moszer, I.. (2007). Annotation, comparison and databases for hundreds of bacterial genomes. Research in microbiology, 158(10), 724–736.
    [BibTeX]
    @article{medigue2007annotation,
    title={Annotation, comparison and databases for hundreds of bacterial genomes},
    author={M{\'e}digue, Claudine and Moszer, Ivan},
    journal={Research in microbiology},
    volume={158},
    number={10},
    pages={724--736},
    year={2007},
    publisher={Elsevier}
    }

  • Normand, P., Queiroux, C., Tisa, L. S., Benson, D. R., Rouy, Z., Cruveiller, S., & Médigue, C.. (2007). Exploring the genomes of frankia. Physiologia plantarum, 130(3), 331–343.
    [BibTeX]
    @article{normand2007exploring,
    title={Exploring the genomes of Frankia},
    author={Normand, Philippe and Queiroux, Clothilde and Tisa, Louis S and Benson, David R and Rouy, Zo{\'e} and Cruveiller, St{\'e}phane and M{\'e}digue, Claudine},
    journal={Physiologia Plantarum},
    volume={130},
    number={3},
    pages={331--343},
    year={2007},
    publisher={Wiley Online Library}
    }

  • Plainvert, C., Bidet, P., Peigne, C., Barbe, V., Médigue, C., Denamur, E., Bingen, E., & Bonacorsi, S.. (2007). A new o-antigen gene cluster has a key role in the virulence of the escherichia coli meningitis clone o45: k1: h7. Journal of bacteriology, 189(23), 8528–8536.
    [BibTeX]
    @article{plainvert2007new,
    title={A new O-antigen gene cluster has a key role in the virulence of the Escherichia coli meningitis clone O45: K1: H7},
    author={Plainvert, C{\'e}line and Bidet, Philippe and Peigne, Chantal and Barbe, Val{\'e}rie and M{\'e}digue, Claudine and Denamur, Erick and Bingen, Edouard and Bonacorsi, St{\'e}phane},
    journal={Journal of bacteriology},
    volume={189},
    number={23},
    pages={8528--8536},
    year={2007},
    publisher={Am Soc Microbiol}
    }

  • Vallenet, D.. ((2007). La plateforme microscope pour l’annotation de génomes microbiens: application à l’analyse de trois bactéries du genre acinetobacter.). PhD Thesis.
    [BibTeX]
    @phdthesis{vallenet2007plateforme,
    title={La plateforme microscope pour l'annotation de g{\'e}nomes microbiens: application {\`a} l'analyse de trois bact{\'e}ries du genre acinetobacter},
    author={Vallenet, David},
    year={2007},
    school={Evry-Val d'Essonne}
    }

  • Derbise, A., Chenal-Francisque, V., Pouillot, F., Fayolle, C., Prévost, M., Médigue, C., Hinnebusch, B. J., & Carniel, E.. (2007). A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus. Molecular microbiology, 63(4), 1145–1157.
    [BibTeX]
    @article{derbise2007horizontally,
    title={A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus},
    author={Derbise, Anne and Chenal-Francisque, Viviane and Pouillot, Flavie and Fayolle, Corinne and Pr{\'e}vost, Marie-Christine and M{\'e}digue, Claudine and Hinnebusch, Bernard Joseph and Carniel, Elisabeth},
    journal={Molecular microbiology},
    volume={63},
    number={4},
    pages={1145--1157},
    year={2007},
    publisher={Wiley Online Library}
    }

  • Muller, D., Médigue, C., Koechler, S., Barbe, V., Barakat, M., Talla, E., Bonnefoy, V., Krin, E., Arsene-Ploetze, F., Carapito, C., & others. (2007). A tale of two oxidation states: bacterial colonization of arsenic-rich environments. Plos genetics, 3(4), e53.
    [BibTeX]
    @article{muller2007tale,
    title={A tale of two oxidation states: bacterial colonization of arsenic-rich environments},
    author={Muller, Daniel and M{\'e}digue, Claudine and Koechler, Sandrine and Barbe, Val{\'e}rie and Barakat, Mohamed and Talla, Emmanuel and Bonnefoy, Violaine and Krin, Evelyne and Arsene-Ploetze, Florence and Carapito, Christine and others},
    journal={PLoS genetics},
    volume={3},
    number={4},
    pages={e53},
    year={2007},
    publisher={Public Library of Science}
    }

  • Normand, P., Lapierre, P., Tisa, L. S., Gogarten, J. P., Alloisio, N., Bagnarol, E., Bassi, C. A., Berry, A. M., Bickhart, D. M., Choisne, N., & others. (2007). Genome characteristics of facultatively symbiotic frankia sp. strains reflect host range and host plant biogeography. Genome research, 17(1), 7–15.
    [BibTeX]
    @article{normand2007genome,
    title={Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography},
    author={Normand, Philippe and Lapierre, Pascal and Tisa, Louis S and Gogarten, Johann Peter and Alloisio, Nicole and Bagnarol, Emilie and Bassi, Carla A and Berry, Alison M and Bickhart, Derek M and Choisne, Nathalie and others},
    journal={Genome research},
    volume={17},
    number={1},
    pages={7--15},
    year={2007},
    publisher={Cold Spring Harbor Lab}
    }

  • Cruveiller, S., Clay, O., Jabbari, K., & Bernardi, G.. (2007). Simple proteomic checks for detecting noncoding rna. Proteomics, 7(3), 361–363.
    [BibTeX]
    @article{cruveiller2007simple,
    title={Simple proteomic checks for detecting noncoding RNA},
    author={Cruveiller, St{\'e}phane and Clay, Oliver and Jabbari, Kamel and Bernardi, Giorgio},
    journal={Proteomics},
    volume={7},
    number={3},
    pages={361--363},
    year={2007},
    publisher={Wiley Online Library}
    }

  • Kreimeyer, A., Perret, A., Lechaplais, C., Vallenet, D., Médigue, C., Salanoubat, M., & Weissenbach, J.. (2007). Identification of the last unknown genes in the fermentation pathway of lysine. Journal of biological chemistry, 282(10), 7191–7197.
    [BibTeX]
    @article{kreimeyer2007identification,
    title={Identification of the last unknown genes in the fermentation pathway of lysine},
    author={Kreimeyer, Annett and Perret, Alain and Lechaplais, Christophe and Vallenet, David and M{\'e}digue, Claudine and Salanoubat, Marcel and Weissenbach, Jean},
    journal={Journal of Biological Chemistry},
    volume={282},
    number={10},
    pages={7191--7197},
    year={2007},
    publisher={ASBMB}
    }

  • Germon, P., Roche, D., Melo, S., Mignon-Grasteau, S., Dobrindt, U., Hacker, J., Schouler, C., & Moulin-Schouleur, M.. (2007). Tdna locus polymorphism and ecto-chromosomal dna insertion hot-spots are related to the phylogenetic group of escherichia coli strains. Microbiology, 153(3), 826–837.
    [BibTeX]
    @article{germon2007tdna,
    title={tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains},
    author={Germon, Pierre and Roche, David and Melo, Sandrine and Mignon-Grasteau, Sandrine and Dobrindt, Ulrich and Hacker, J{\"o}rg and Schouler, Catherine and Moulin-Schouleur, Maryvonne},
    journal={Microbiology},
    volume={153},
    number={3},
    pages={826--837},
    year={2007},
    publisher={Microbiology Society}
    }

  • Fall, S., Mercier, A., Bertolla, F., Calteau, A., Gueguen, L., Perriere, G., Vogel, T. M., & Simonet, P.. (2007). Horizontal gene transfer regulation in bacteria as a “spandrel” of dna repair mechanisms. Plos one, 2(10), e1055.
    [BibTeX]
    @article{fall2007horizontal,
    title={Horizontal gene transfer regulation in bacteria as a “spandrel” of DNA repair mechanisms},
    author={Fall, Saliou and Mercier, Anne and Bertolla, Franck and Calteau, Alexandra and Gueguen, Laurent and Perriere, Guy and Vogel, Timothy M and Simonet, Pascal},
    journal={PLoS One},
    volume={2},
    number={10},
    pages={e1055},
    year={2007},
    publisher={Public Library of Science}
    }

  • Alloisio, N., Félix, S., Maréchal, J., Pujic, P., Rouy, Z., Vallenet, D., Medigue, C., & Normand, P.. (2007). Frankia alni proteome under nitrogen-fixing and nitrogen-replete conditions. Physiologia plantarum, 130(3), 440–453.
    [BibTeX]
    @article{alloisio2007frankia,
    title={Frankia alni proteome under nitrogen-fixing and nitrogen-replete conditions},
    author={Alloisio, Nicole and F{\'e}lix, Servane and Mar{\'e}chal, Jo{\"e}lle and Pujic, Petar and Rouy, Zo{\'e} and Vallenet, David and Medigue, Claudine and Normand, Philippe},
    journal={Physiologia plantarum},
    volume={130},
    number={3},
    pages={440--453},
    year={2007},
    publisher={Wiley Online Library}
    }

2006

  • Vodovar, N., Vallenet, D., Cruveiller, S., Rouy, Z., Barbe, V., Acosta, C., Cattolico, L., Jubin, C., Lajus, A., Segurens, B., & others. (2006). Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium pseudomonas entomophila. Nature biotechnology, 24(6), 673–679.
    [BibTeX]
    @article{vodovar2006complete,
    title={Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila},
    author={Vodovar, Nicolas and Vallenet, David and Cruveiller, St{\'e}phane and Rouy, Zo{\'e} and Barbe, Val{\'e}rie and Acosta, Carlos and Cattolico, Laurence and Jubin, Claire and Lajus, Aur{\'e}lie and Segurens, B{\'e}atrice and others},
    journal={Nature biotechnology},
    volume={24},
    number={6},
    pages={673--679},
    year={2006},
    publisher={Nature Publishing Group}
    }

  • Pascal, G., Médigue, C., & Danchin, A.. (2006). Persistent biases in the amino acid composition of prokaryotic proteins. Bioessays, 28(7), 726–738.
    [BibTeX]
    @article{pascal2006persistent,
    title={Persistent biases in the amino acid composition of prokaryotic proteins},
    author={Pascal, G{\'e}raldine and M{\'e}digue, Claudine and Danchin, Antoine},
    journal={Bioessays},
    volume={28},
    number={7},
    pages={726--738},
    year={2006},
    publisher={Wiley Online Library}
    }

  • Louvel, H., Bommezzadri, S., Zidane, N., Boursaux-Eude, C., Creno, S., Magnier, A., Rouy, Z., Medigue, C., Saint Girons, I., Bouchier, C., & others. (2006). Comparative and functional genomic analyses of iron transport and regulation in leptospira spp.. Journal of bacteriology, 188(22), 7893–7904.
    [BibTeX]
    @article{louvel2006comparative,
    title={Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp.},
    author={Louvel, H and Bommezzadri, S and Zidane, N and Boursaux-Eude, C and Creno, S and Magnier, A and Rouy, Z and Medigue, C and Saint Girons, I and Bouchier, C and others},
    journal={Journal of bacteriology},
    volume={188},
    number={22},
    pages={7893--7904},
    year={2006},
    publisher={Am Soc Microbiol}
    }

  • Thiberge, J., Lehours, P., Bouchier, C., Ma, L., Creno, S., Medigue, C., Vallenet, D., Ecobichon, C., Boursaux-Eude, C., & Labigne, A.. (2006). Molecular genetics and genomics-sequence of the first helicobacter pylori strains involved in low-grade gastric mucosa-associated lymphoid tissue (malt) lymphoma. Paper presented at the Helicobacter.
    [BibTeX]
    @inproceedings{thiberge2006molecular,
    title={Molecular genetics and genomics-Sequence of the first Helicobacter pylori strains involved in low-grade gastric mucosa-associated lymphoid tissue (MALT) lymphoma},
    author={Thiberge, JM and Lehours, P and Bouchier, C and Ma, L and Creno, S and Medigue, C and Vallenet, D and Ecobichon, C and Boursaux-Eude, C and Labigne, A},
    booktitle={HELICOBACTER},
    volume={11},
    number={4},
    pages={324--324},
    year={2006},
    organization={BLACKWELL PUBLISHING 9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}
    }

  • Vallenet, D., Labarre, L., Rouy, Z., Barbe, V., Bocs, S., Cruveiller, S., Lajus, A., Pascal, G., Scarpelli, C., & Medigue, C.. (2006). Mage: a microbial genome annotation system supported by synteny results. Nucleic acids research, 34(1), 53–65.
    [BibTeX]
    @article{vallenet2006mage,
    title={MaGe: a microbial genome annotation system supported by synteny results},
    author={Vallenet, David and Labarre, Laurent and Rouy, Zoe and Barbe, Valerie and Bocs, Stephanie and Cruveiller, Stephane and Lajus, Aurelie and Pascal, Geraldine and Scarpelli, Claude and Medigue, Claudine},
    journal={Nucleic acids research},
    volume={34},
    number={1},
    pages={53--65},
    year={2006},
    publisher={Oxford University Press}
    }

  • Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M. W., Horn, M., Daims, H., Bartol-Mavel, D., Wincker, P., & others. (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature, 440(7085), 790–794.
    [BibTeX]
    @article{strous2006deciphering,
    title={Deciphering the evolution and metabolism of an anammox bacterium from a community genome},
    author={Strous, Marc and Pelletier, Eric and Mangenot, Sophie and Rattei, Thomas and Lehner, Angelika and Taylor, Michael W and Horn, Matthias and Daims, Holger and Bartol-Mavel, Delphine and Wincker, Patrick and others},
    journal={Nature},
    volume={440},
    number={7085},
    pages={790--794},
    year={2006},
    publisher={Nature Publishing Group}
    }

  • Siroy, A., Cosette, P., Seyer, D., Lema{^i}tre-Guillier, C., Vallenet, D., Van Dorsselaer, A., Boyer-Mariotte, S., Jouenne, T., & Dé, E.. (2006). Global comparison of the membrane subproteomes between a multidrug-resistant acinetobacter baumannii strain and a reference strain. Journal of proteome research, 5(12), 3385–3398.
    [BibTeX]
    @article{siroy2006global,
    title={Global comparison of the membrane subproteomes between a multidrug-resistant Acinetobacter baumannii strain and a reference strain},
    author={Siroy, Axel and Cosette, Pascal and Seyer, Damien and Lema{\^\i}tre-Guillier, Christelle and Vallenet, David and Van Dorsselaer, Alain and Boyer-Mariotte, Sophie and Jouenne, Thierry and D{\'e}, Emmanuelle},
    journal={Journal of proteome research},
    volume={5},
    number={12},
    pages={3385--3398},
    year={2006},
    publisher={ACS Publications}
    }

  • Moulin, L., Avarre, J., Jaubert, M., Barbe, V., Béna, G., Cartiaux, F., Delajudie, P., Dreyfus, B., Elmerich, D., Fardoux, J., & others. (2006). Abscence de gènes nod chez certaines souches de\# bradyrhizobium\# photosynthétiques révélée par l’analyse de la séquence de leurs génomes. .
    [BibTeX]
    @article{moulin2006abscence,
    title={Abscence de g{\`e}nes nod chez certaines souches de\# Bradyrhizobium\# photosynth{\'e}tiques r{\'e}v{\'e}l{\'e}e par l'analyse de la s{\'e}quence de leurs g{\'e}nomes},
    author={Moulin, L and Avarre, Jean-Christophe and Jaubert, Marianne and Barbe, Val{\'e}rie and B{\'e}na, Gilles and Cartiaux, F and Delajudie, P and Dreyfus, Bernard and Elmerich, D and Fardoux, Jo{\"e}l and others},
    year={2006},
    publisher={INRA}
    }

  • Thiberge, J., Lehours, P., Bouchier, C., Ma, L., Creno, S., Medigue, C., Vallenet, D., Ecobichon, C., Boursaux-eude, C., & Labigne, A.. (2006). Sequence of the first helicobacter pylori strains involved in low-grade gastric mucosa-associated lymphoid tissue (malt) lymphoma. Helicobacter, 11(4), 324.
    [BibTeX]
    @article{thiberge2006sequence,
    title={Sequence of the First Helicobacter pylori Strains Involved in Low-grade Gastric Mucosa-associated Lymphoid Tissue (malt) Lymphoma},
    author={Thiberge, JM and Lehours, P and Bouchier, C and Ma, L and Creno, S and Medigue, C and Vallenet, D and Ecobichon, C and Boursaux-eude, C and Labigne, A},
    journal={Helicobacter},
    volume={11},
    number={4},
    pages={324},
    year={2006}
    }

  • Fournier, P., Vallenet, D., Barbe, V., Audic, S., Ogata, H., Poirel, L., Richet, H., Robert, C., Mangenot, S., Abergel, C., & others. (2006). Comparative genomics of multidrug resistance in acinetobacter baumannii. Plos genetics, 2(1), e7.
    [BibTeX]
    @article{fournier2006comparative,
    title={Comparative genomics of multidrug resistance in Acinetobacter baumannii},
    author={Fournier, Pierre-Edouard and Vallenet, David and Barbe, Val{\'e}rie and Audic, St{\'e}phane and Ogata, Hiroyuki and Poirel, Laurent and Richet, Herv{\'e} and Robert, Catherine and Mangenot, Sophie and Abergel, Chantal and others},
    journal={PLoS genetics},
    volume={2},
    number={1},
    pages={e7},
    year={2006},
    publisher={Public Library of Science}
    }

2005

  • Siroy, A., Molle, V., Lema{^i}tre-Guillier, C., Vallenet, D., Pestel-Caron, M., Cozzone, A. J., Jouenne, T., & Dé, E.. (2005). Channel formation by caro, the carbapenem resistance-associated outer membrane protein of acinetobacter baumannii. Antimicrobial agents and chemotherapy, 49(12), 4876–4883.
    [BibTeX]
    @article{siroy2005channel,
    title={Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii},
    author={Siroy, Axel and Molle, Virginie and Lema{\^\i}tre-Guillier, Christelle and Vallenet, David and Pestel-Caron, Martine and Cozzone, Alain J and Jouenne, Thierry and D{\'e}, Emmanuelle},
    journal={Antimicrobial agents and chemotherapy},
    volume={49},
    number={12},
    pages={4876--4883},
    year={2005},
    publisher={Am Soc Microbiol}
    }

  • Médigue, C., Krin, E., Pascal, G., Barbe, V., Bernsel, A., Bertin, P. N., Cheung, F., Cruveiller, S., D’Amico, S., Duilio, A., & others. (2005). Coping with cold: the genome of the versatile marine antarctica bacterium pseudoalteromonas haloplanktis tac125. Genome research, 15(10), 1325–1335.
    [BibTeX]
    @article{medigue2005coping,
    title={Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125},
    author={M{\'e}digue, Claudine and Krin, Evelyne and Pascal, G{\'e}raldine and Barbe, Val{\'e}rie and Bernsel, Andreas and Bertin, Philippe N and Cheung, Frankie and Cruveiller, St{\'e}phane and D'Amico, Salvino and Duilio, Angela and others},
    journal={Genome research},
    volume={15},
    number={10},
    pages={1325--1335},
    year={2005},
    publisher={Cold Spring Harbor Lab}
    }

  • Calteau, A., Gouy, M., & Perrière, G.. (2005). Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea. Journal of molecular evolution, 60(5), 557–565.
    [BibTeX]
    @article{calteau2005horizontal,
    title={Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea},
    author={Calteau, Alexandra and Gouy, Manolo and Perri{\`e}re, Guy},
    journal={Journal of molecular evolution},
    volume={60},
    number={5},
    pages={557--565},
    year={2005},
    publisher={Springer}
    }

  • MEDIGUE, C.. (2005). L’annotation des génomes bactériens: bioinformatique et génome. Biofutur, 251, 23–27.
    [BibTeX]
    @article{medigue2005annotation,
    title={L'annotation des g{\'e}nomes bact{\'e}riens: Bioinformatique et g{\'e}nome},
    author={MEDIGUE, Claudine},
    journal={Biofutur},
    volume={251},
    pages={23--27},
    year={2005},
    publisher={Lavoisier}
    }

  • Pascal, G., Médigue, C., & Danchin, A.. (2005). Universal biases in protein composition of model prokaryotes. Proteins: structure, function, and bioinformatics, 60(1), 27–35.
    [BibTeX]
    @article{pascal2005universal,
    title={Universal biases in protein composition of model prokaryotes},
    author={Pascal, G{\'e}raldine and M{\'e}digue, Claudine and Danchin, Antoine},
    journal={Proteins: Structure, Function, and Bioinformatics},
    volume={60},
    number={1},
    pages={27--35},
    year={2005},
    publisher={Wiley Online Library}
    }

  • Medigue, C.. (2005). Bioinformatique et genome-l’annotation des genomes bacteriens. Biofutur(251), 19.
    [BibTeX]
    @article{medigue2005bioinformatique,
    title={Bioinformatique et genome-L'annotation des genomes bacteriens},
    author={Medigue, C},
    journal={Biofutur},
    number={251},
    pages={19},
    year={2005},
    publisher={Paris: Biofutur, 1982-}
    }

  • Cruveiller, S., Le Saux, J., Vallenet, D., Lajus, A., Bocs, S., & Medigue, C.. (2005). Micheck: a web tool for fast checking of syntactic annotations of bacterial genomes. Nucleic acids research, 33(suppl_2), W471–W479.
    [BibTeX]
    @article{cruveiller2005micheck,
    title={MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes},
    author={Cruveiller, Stephane and Le Saux, Jeroˆme and Vallenet, David and Lajus, Aurelie and Bocs, Stephanie and Medigue, Claudine},
    journal={Nucleic acids research},
    volume={33},
    number={suppl\_2},
    pages={W471--W479},
    year={2005},
    publisher={Oxford University Press}
    }

2004

  • Chain, P. S., Carniel, E., Larimer, F. W., Lamerdin, J., Stoutland, P., Regala, W., Georgescu, A., Vergez, L., Land, M., Motin, V., & others. (2004). Insights into the evolution of yersinia pestis through whole-genome comparison with yersinia pseudotuberculosis. Proceedings of the national academy of sciences, 101(38), 13826–13831.
    [BibTeX]
    @article{chain2004insights,
    title={Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis},
    author={Chain, Patrick SG and Carniel, E and Larimer, Frank W and Lamerdin, Jane and Stoutland, PO and Regala, WM and Georgescu, AM and Vergez, LM and Land, ML and Motin, VL and others},
    journal={Proceedings of the National Academy of Sciences},
    volume={101},
    number={38},
    pages={13826--13831},
    year={2004},
    publisher={National Academy of Sciences}
    }

  • Jabbari, K., Cruveiller, S., Clay, O., Le Saux, J., & Bernardi, G.. (2004). The new genes of rice: a closer look. Trends in plant science, 9(6), 281–285.
    [BibTeX]
    @article{jabbari2004new,
    title={The new genes of rice: a closer look},
    author={Jabbari, Kamel and Cruveiller, Stephane and Clay, Oliver and Le Saux, J{\'e}r{\^o}me and Bernardi, Giorgio},
    journal={Trends in plant science},
    volume={9},
    number={6},
    pages={281--285},
    year={2004},
    publisher={Elsevier}
    }

  • Cruveiller, S., Jabbari, K., Clay, O., & Bernardi, G.. (2004). Compositional gene landscapes in vertebrates. Genome research, 14(5), 886–892.
    [BibTeX]
    @article{cruveiller2004compositional,
    title={Compositional gene landscapes in vertebrates},
    author={Cruveiller, St{\'e}phane and Jabbari, Kamel and Clay, Oliver and Bernardi, Giorgio},
    journal={Genome research},
    volume={14},
    number={5},
    pages={886--892},
    year={2004},
    publisher={Cold Spring Harbor Lab}
    }

  • Calteau, A., Daubin, V., & Perrieère, G.. (2004). Super-tree approach for studying the phylogeny of prokaryotes: new results on completely sequenced genomes. Paper presented at the International conference on computational science.
    [BibTeX]
    @inproceedings{calteau2004super,
    title={Super-tree approach for studying the phylogeny of prokaryotes: New results on completely sequenced genomes},
    author={Calteau, Alexandra and Daubin, Vincent and Perrie{\`e}re, Guy},
    booktitle={International Conference on Computational Science},
    pages={700--708},
    year={2004},
    organization={Springer}
    }

  • Alvarez-Valin, F., Clay, O., Cruveiller, S., & Bernardi, G.. (2004). Inaccurate reconstruction of ancestral gc levels creates a “vanishing isochores” effect. Molecular phylogenetics and evolution, 31(2), 788–793.
    [BibTeX]
    @article{alvarez2004inaccurate,
    title={Inaccurate reconstruction of ancestral GC levels creates a “vanishing isochores” effect},
    author={Alvarez-Valin, Fernando and Clay, Oliver and Cruveiller, St{\'e}phane and Bernardi, Giorgio},
    journal={Molecular phylogenetics and evolution},
    volume={31},
    number={2},
    pages={788--793},
    year={2004},
    publisher={Elsevier}
    }

  • Barbe, V., Vallenet, D., Fonknechten, N., Kreimeyer, A., Oztas, S., Labarre, L., Cruveiller, S., Robert, C., Duprat, S., Wincker, P., & others. (2004). Unique features revealed by the genome sequence of acinetobacter sp. adp1, a versatile and naturally transformation competent bacterium. Nucleic acids research, 32(19), 5766–5779.
    [BibTeX]
    @article{barbe2004unique,
    title={Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium},
    author={Barbe, Valerie and Vallenet, David and Fonknechten, Nuria and Kreimeyer, Annett and Oztas, Sophie and Labarre, Laurent and Cruveiller, Stephane and Robert, Catherine and Duprat, Simone and Wincker, Patrick and others},
    journal={Nucleic Acids Research},
    volume={32},
    number={19},
    pages={5766--5779},
    year={2004},
    publisher={Oxford University Press}
    }

  • Cruveiller, S., Jabbari, K., Clay, O., & Bernardi, G.. (2004). Incorrectly predicted genes in rice?. Gene, 333, 187–188.
    [BibTeX]
    @article{cruveiller2004incorrectly,
    title={Incorrectly predicted genes in rice?},
    author={Cruveiller, St{\'e}phane and Jabbari, Kamel and Clay, Oliver and Bernardi, Giorgio},
    journal={Gene},
    volume={333},
    pages={187--188},
    year={2004},
    publisher={Elsevier}
    }

  • Calteau, A., Daubin, V., & Perrieere, G.. (2004). Part iv-workshop on gene, genome, and population evolution-super-tree approach for studying the phylogeny of prokaryotes: new results on completely sequenced genomes. Lecture notes in computer science, 3036, 700–700.
    [BibTeX]
    @article{calteau2004part,
    title={Part IV-Workshop on Gene, Genome, and Population Evolution-Super-tree Approach for Studying the Phylogeny of Prokaryotes: New Results on Completely Sequenced Genomes},
    author={Calteau, A and Daubin, V and Perrieere, G},
    journal={Lecture Notes in Computer Science},
    volume={3036},
    pages={700--700},
    year={2004},
    publisher={Berlin: Springer-Verlag, 1973-}
    }

2003

  • Bénit, L., Calteau, A., & Heidmann, T.. (2003). Characterization of the low-copy herv-fc family: evidence for recent integrations in primates of elements with coding envelope genes. Virology, 312(1), 159–168.
    [BibTeX]
    @article{benit2003characterization,
    title={Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes},
    author={B{\'e}nit, Laurence and Calteau, Alexandra and Heidmann, Thierry},
    journal={Virology},
    volume={312},
    number={1},
    pages={159--168},
    year={2003},
    publisher={Elsevier}
    }

  • Duchaud, E., Rusniok, C., Frangeul, L., Buchrieser, C., Givaudan, A., Taourit, S., Bocs, S., Boursaux-Eude, C., Chandler, M., Charles, J., & others. (2003). The genome sequence of the entomopathogenic bacterium photorhabdus luminescens. Nature biotechnology, 21(11), 1307–1313.
    [BibTeX]
    @article{duchaud2003genome,
    title={The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens},
    author={Duchaud, Eric and Rusniok, Christophe and Frangeul, Lionel and Buchrieser, Carmen and Givaudan, Alain and Taourit, S{\'e}ad and Bocs, St{\'e}phanie and Boursaux-Eude, Caroline and Chandler, Michael and Charles, Jean-Fran{\c{c}}ois and others},
    journal={Nature biotechnology},
    volume={21},
    number={11},
    pages={1307--1313},
    year={2003},
    publisher={Nature Publishing Group}
    }

  • Cruveiller, S., Jabbari, K., Clay, O., & Bernardi, G.. (2003). Compositional features of eukaryotic genomes for checking predicted genes. Briefings in bioinformatics, 4(1), 43–52.
    [BibTeX]
    @article{cruveiller2003compositional,
    title={Compositional features of eukaryotic genomes for checking predicted genes},
    author={Cruveiller, St{\'e}phane and Jabbari, Kamel and Clay, Oliver and Bernardi, Giorgio},
    journal={Briefings in bioinformatics},
    volume={4},
    number={1},
    pages={43--52},
    year={2003},
    publisher={Henry Stewart Publications}
    }

  • Jabbari, K., Cruveiller, S., Clay, O., & Bernardi, G.. (2003). The correlation between gc 3 and hydropathy in human genes. Gene, 317, 137–140.
    [BibTeX]
    @article{jabbari2003correlation,
    title={The correlation between GC 3 and hydropathy in human genes},
    author={Jabbari, Kamel and Cruveiller, St{\'e}phane and Clay, Oliver and Bernardi, Giorgio},
    journal={Gene},
    volume={317},
    pages={137--140},
    year={2003},
    publisher={Elsevier}
    }

  • Durand, P., Médigue, C., Morgat, A., Vandenbrouck, Y., Viari, A., & Rechenmann, F.. (2003). Integration of data and methods for genome analysis.. Current opinion in drug discovery & development, 6(3), 346–352.
    [BibTeX]
    @article{durand2003integration,
    title={Integration of data and methods for genome analysis.},
    author={Durand, Patrick and M{\'e}digue, Claudine and Morgat, Anne and Vandenbrouck, Yves and Viari, Alain and Rechenmann, Fran{\c{c}}ois},
    journal={Current opinion in drug discovery \& development},
    volume={6},
    number={3},
    pages={346--352},
    year={2003}
    }

  • Yuen, K., Pascal, G., Wong, S. S., Glaser, P., Woo, P. C., Kunst, F., Cai, J. J., Cheung, E. Y., Médigue, C., & Danchin, A.. (2003). Exploring the penicillium marneffei genome. Archives of microbiology, 179(5), 339–353.
    [BibTeX]
    @article{yuen2003exploring,
    title={Exploring the Penicillium marneffei genome},
    author={Yuen, Kwok-yung and Pascal, G{\'e}raldine and Wong, Samson SY and Glaser, Philippe and Woo, Patrick CY and Kunst, Frank and Cai, James J and Cheung, Elim YL and M{\'e}digue, Claudine and Danchin, Antoine},
    journal={Archives of microbiology},
    volume={179},
    number={5},
    pages={339--353},
    year={2003},
    publisher={Springer}
    }

  • Bocs, S., Cruveiller, S., Vallenet, D., Nuel, G., & Medigue, C.. (2003). Amigene: annotation of microbial genes. Nucleic acids research, 31(13), 3723–3726.
    [BibTeX]
    @article{bocs2003amigene,
    title={AMIGene: annotation of microbial genes},
    author={Bocs, Stephanie and Cruveiller, Stephane and Vallenet, David and Nuel, Gregory and Medigue, Claudine},
    journal={Nucleic Acids Research},
    volume={31},
    number={13},
    pages={3723--3726},
    year={2003},
    publisher={Oxford University Press}
    }

2002

  • Camus, J., Pryor, M. J., Médigue, C., & Cole, S. T.. (2002). Re-annotation of the genome sequence of mycobacterium tuberculosis h37rv. Microbiology, 148(10), 2967–2973.
    [BibTeX]
    @article{camus2002re,
    title={Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv},
    author={Camus, Jean-Christophe and Pryor, Melinda J and M{\'e}digue, Claudine and Cole, Stewart T},
    journal={Microbiology},
    volume={148},
    number={10},
    pages={2967--2973},
    year={2002},
    publisher={Microbiology Society}
    }

  • Médigue, C., Bocs, S., Labarre, L., Mathé, C., & Vallenet, D.. (2002). L’annotation in silico des séquences génomiques-bio-informatique (1). Médecine/sciences, 18(2), 237–250.
    [BibTeX]
    @article{medigue2002annotation,
    title={L’annotation in silico des s{\'e}quences g{\'e}nomiques-Bio-informatique (1)},
    author={M{\'e}digue, Claudine and Bocs, St{\'e}phanie and Labarre, Laurent and Math{\'e}, Catherine and Vallenet, David},
    journal={m{\'e}decine/sciences},
    volume={18},
    number={2},
    pages={237--250},
    year={2002},
    publisher={EDK}
    }

  • Medigue, C., Bocs, S., Labarre, L., Mathe, C., & Vallenet, D.. (2002). Bio-informatics (1)-in silico annotation of genomic sequences. M s-medecine sciences, 18(2), 237–250.
    [BibTeX]
    @article{medigue2002bio,
    title={Bio-informatics (1)-In silico annotation of genomic sequences},
    author={Medigue, Claudine and Bocs, Stephane and Labarre, Laurent and Mathe, Catherine and Vallenet, David},
    journal={M S-MEDECINE SCIENCES},
    volume={18},
    number={2},
    pages={237--250},
    year={2002},
    publisher={EDP SCIENCES SA 17, AVE DU HOGGAR, PA COURTABOEUF, BP 112, F-91944 LES ULIS~…}
    }

  • Bocs, S., Danchin, A., & Médigue, C.. (2002). Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes. Bmc bioinformatics, 3(1), 5.
    [BibTeX]
    @article{bocs2002re,
    title={Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes},
    author={Bocs, St{\'e}phanie and Danchin, Antoine and M{\'e}digue, Claudine},
    journal={BMC bioinformatics},
    volume={3},
    number={1},
    pages={5},
    year={2002},
    publisher={BioMed Central}
    }

  • Médigue, C., Wong, B. C., Lin, M. C., Bocs, S., & Danchin, A.. (2002). The sece gene of helicobacter pylori. Journal of bacteriology, 184(10), 2837–2840.
    [BibTeX]
    @article{medigue2002sece,
    title={The secE gene of Helicobacter pylori},
    author={M{\'e}digue, Claudine and Wong, Benjamin Chun-Yu and Lin, Marie Chia-Mi and Bocs, St{\'e}phanie and Danchin, Antoine},
    journal={Journal of bacteriology},
    volume={184},
    number={10},
    pages={2837--2840},
    year={2002},
    publisher={Am Soc Microbiol}
    }

2001

  • Musto, H., Cruveiller, S., D’Onofrio, G., Romero, H., & Bernardi, G.. (2001). Translational selection on codon usage in xenopus laevis. Molecular biology and evolution, 18(9), 1703–1707.
    [BibTeX]
    @article{musto2001translational,
    title={Translational selection on codon usage in Xenopus laevis},
    author={Musto, H{\'e}ctor and Cruveiller, St{\'e}phane and D'Onofrio, Giuseppe and Romero, H{\'e}ctor and Bernardi, Giorgio},
    journal={Molecular biology and evolution},
    volume={18},
    number={9},
    pages={1703--1707},
    year={2001},
    publisher={Oxford University Press}
    }

2000

  • Cruveiller, S., D’Onofrio, G., & Bernardi, G.. (2000). The compositional transition between the genomes of cold-and warm-blooded vertebrates: codon frequencies in orthologous genes. Gene, 261(1), 71–83.
    [BibTeX]
    @article{cruveiller2000compositional,
    title={The compositional transition between the genomes of cold-and warm-blooded vertebrates: codon frequencies in orthologous genes},
    author={Cruveiller, St{\'e}phane and D'Onofrio, Giuseppe and Bernardi, Giorgio},
    journal={Gene},
    volume={261},
    number={1},
    pages={71--83},
    year={2000},
    publisher={Elsevier}
    }

1999

  • Cruveiller, S., Jabbari, K., D’Onofrio, G., & Bernardi, G.. (1999). Different hydrophobicities of orthologous proteins from xenopus and human. Gene, 238(1), 15–21.
    [BibTeX]
    @article{cruveiller1999different,
    title={Different hydrophobicities of orthologous proteins from Xenopus and human},
    author={Cruveiller, S and Jabbari, K and D'Onofrio, G and Bernardi, G},
    journal={Gene},
    volume={238},
    number={1},
    pages={15--21},
    year={1999},
    publisher={Elsevier}
    }

  • Médigue, C., Rose, M., Viari, A., & Danchin, A.. (1999). Detecting and analyzing dna sequencing errors: toward a higher quality of the bacillus subtilis genome sequence. Genome research, 9(11), 1116–1127.
    [BibTeX]
    @article{medigue1999detecting,
    title={Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence},
    author={M{\'e}digue, Claudine and Rose, Matthias and Viari, Alain and Danchin, Antoine},
    journal={Genome research},
    volume={9},
    number={11},
    pages={1116--1127},
    year={1999},
    publisher={Cold Spring Harbor Lab}
    }

  • D’onofrio, G., Jabbari, K., Musto, H., ALVAREZ-VALIN, F., Cruveiller, S., & Bernardi, G.. (1999). Evolutionary genomics of vertebrates and its implications. Annals of the new york academy of sciences, 870(1), 81–94.
    [BibTeX]
    @article{d1999evolutionary,
    title={Evolutionary genomics of vertebrates and its implications},
    author={D'onofrio, Giuseppe and Jabbari, Kamel and Musto, Hector and ALVAREZ-VALIN, FERNANDO and Cruveiller, Stephane and Bernardi, Giorgio},
    journal={Annals of the New York Academy of Sciences},
    volume={870},
    number={1},
    pages={81--94},
    year={1999},
    publisher={Wiley Online Library}
    }

  • Médigue, C., Rechenmann, F., Danchin, A., & Viari, A.. (1999). Imagene: an integrated computer environment for sequence annotation and analysis.. Bioinformatics (oxford, england), 15(1), 2–15.
    [BibTeX]
    @article{medigue1999imagene,
    title={Imagene: an integrated computer environment for sequence annotation and analysis.},
    author={M{\'e}digue, C and Rechenmann, Fran{\c{c}}ois and Danchin, Antoine and Viari, Alain},
    journal={Bioinformatics (Oxford, England)},
    volume={15},
    number={1},
    pages={2--15},
    year={1999}
    }

1998

  • Danchin, A., Médigue, C., & Rechenmann, F.. (1998). Integrated genome informatics. In Bacterial genomes (pp. 567–582). Springer.
    [BibTeX]
    @incollection{danchin1998integrated,
    title={Integrated Genome Informatics},
    author={Danchin, Antoine and M{\'e}digue, Claudine and Rechenmann, Fran{\c{c}}ois},
    booktitle={Bacterial Genomes},
    pages={567--582},
    year={1998},
    publisher={Springer}
    }

1997

  • Kunst, F., Ogasawara, N., Moszer, I., Albertini, A., Alloni, G., Azevedo, V., Bertero, M., Bessieres, P., Bolotin, A., Borchert, S., & others. (1997). The complete genome sequence of the gram-positive bacterium bacillus subtilis. Nature, 390(6657), 249.
    [BibTeX]
    @article{kunst1997complete,
    title={The complete genome sequence of the gram-positive bacterium Bacillus subtilis},
    author={Kunst, F and Ogasawara, N and Moszer, I and Albertini, AM and Alloni, GO and Azevedo, V and Bertero, MG and Bessieres, P and Bolotin, A and Borchert, Sea and others},
    journal={Nature},
    volume={390},
    number={6657},
    pages={249},
    year={1997},
    publisher={Nature Publishing Group}
    }

1995

  • Médigue, C., Moszer, I., Viari, A., & Danchin, A.. (1995). Analysis of a bacillus subtilis genome fragment using a co-operative computer system prototype. Gene, 165(1), GC37–GC51.
    [BibTeX]
    @article{medigue1995analysis,
    title={Analysis of a Bacillus subtilis genome fragment using a co-operative computer system prototype},
    author={M{\'e}digue, C and Moszer, I and Viari, A and Danchin, A},
    journal={Gene},
    volume={165},
    number={1},
    pages={GC37--GC51},
    year={1995},
    publisher={Elsevier}
    }

  • Medigue, C., Vermat, T., Bisson, G., Viari, A., & Danchin, A.. (1995). Cooperative computer system for genome sequence analysis.. Paper presented at the Ismb.
    [BibTeX]
    @inproceedings{medigue1995cooperative,
    title={Cooperative computer system for genome sequence analysis.},
    author={Medigue, Claudine and Vermat, Thierry and Bisson, Gilles and Viari, Alain and Danchin, Antoine},
    booktitle={ISMB},
    pages={249--258},
    year={1995}
    }

  • Borodovsky, M., Mclninch, J. D., Koonin, E. V., Rudd, K. E., Médigue, C., & Danchin, A.. (1995). Detection of new genes in a bacterial genome using markov models for three gene classes. Nucleic acids research, 23(17), 3554–3562.
    [BibTeX]
    @article{borodovsky1995detection,
    title={Detection of new genes in a bacterial genome using Markov models for three gene classes},
    author={Borodovsky, Mark and Mclninch, James D and Koonin, Eugene V and Rudd, Kenneth E and M{\'e}digue, Claudine and Danchin, Antoine},
    journal={Nucleic acids research},
    volume={23},
    number={17},
    pages={3554--3562},
    year={1995},
    publisher={Oxford University Press}
    }

1993

  • Schmeltzer, O., Médigue, C., Uvietta, P., Rechenmann, F., Dorkeld, F., Perrière, G., & Gautier, C.. (1993). Building large knowledge bases in molecular biology.. Paper presented at the Ismb.
    [BibTeX]
    @inproceedings{schmeltzer1993building,
    title={Building large knowledge bases in molecular biology.},
    author={Schmeltzer, Olivier and M{\'e}digue, Claudine and Uvietta, P and Rechenmann, Fran{\c{c}}ois and Dorkeld, Frank and Perri{\`e}re, Guy and Gautier, Christian},
    booktitle={ISMB},
    pages={345--353},
    year={1993}
    }

  • Médigue, C., Viari, A., Henaut, A., & Danchin, A.. (1993). Colibri: a functional data base for the escherichia coli genome.. Microbiology and molecular biology reviews, 57(3), 623–654.
    [BibTeX]
    @article{medigue1993colibri,
    title={Colibri: a functional data base for the Escherichia coli genome.},
    author={M{\'e}digue, CLAUDINE and Viari, ALIIN and Henaut, A and Danchin, ANTOINE},
    journal={Microbiology and Molecular Biology Reviews},
    volume={57},
    number={3},
    pages={623--654},
    year={1993},
    publisher={American Society for Microbiology Journals}
    }

1991

  • Danchin, A., Médigue, C., Gascuel, O., Soldano, H., & Hénaut, A.. (1991). From data banks to data bases. Research in microbiology, 142(7-8), 913–916.
    [BibTeX]
    @article{danchin1991data,
    title={From data banks to data bases},
    author={Danchin, A and M{\'e}digue, C and Gascuel, O and Soldano, H and H{\'e}naut, A},
    journal={Research in microbiology},
    volume={142},
    number={7-8},
    pages={913--916},
    year={1991},
    publisher={Elsevier}
    }

  • Médigue, C., Viari, A., Hénaut, A., & Danchin, A.. (1991). Escherichia coli molecular genetic map (1500 kbp): update ii. Molecular microbiology, 5(11), 2629–2640.
    [BibTeX]
    @article{medigue1991escherichia,
    title={Escherichia coli molecular genetic map (1500 kbp): update II},
    author={M{\'e}digue, C and Viari, A and H{\'e}naut, A and Danchin, A},
    journal={Molecular microbiology},
    volume={5},
    number={11},
    pages={2629--2640},
    year={1991},
    publisher={Wiley Online Library}
    }

  • Médigue, C.. ((1991). Conception et exploitation d’une base de donnees specialisee dediee a l’analyse du genome d’escherichia coli.). PhD Thesis.
    [BibTeX]
    @phdthesis{medigue1991conception,
    title={Conception et exploitation d'une base de donnees specialisee dediee a l'analyse du genome d'escherichia coli},
    author={M{\'e}digue, Claudine},
    year={1991},
    school={Paris 6}
    }

  • Médigue, C., Rouxel, T., Vigier, P., Hénaut, A., & Danchin, A.. (1991). Evidence for horizontal gene transfer in escherichia coli speciation. Journal of molecular biology, 222(4), 851–856.
    [BibTeX]
    @article{medigue1991evidence,
    title={Evidence for horizontal gene transfer in Escherichia coli speciation},
    author={M{\'e}digue, Claudine and Rouxel, Thierry and Vigier, Ph and H{\'e}naut, Alain and Danchin, Antoine},
    journal={Journal of molecular biology},
    volume={222},
    number={4},
    pages={851--856},
    year={1991},
    publisher={Elsevier}
    }

1990

  • Médigue, C., Bouché, J., Hénaut, A., & Danchin, A.. (1990). Mapping of sequenced genes (700 kbp) in the restriction map of the escherichia coli chromosome. Molecular microbiology, 4(2), 169–187.
    [BibTeX]
    @article{medigue1990mapping,
    title={Mapping of sequenced genes (700 kbp) in the restriction map of the Escherichia coli chromosome},
    author={M{\'e}digue, C and Bouch{\'e}, JP and H{\'e}naut, A and Danchin, A},
    journal={Molecular microbiology},
    volume={4},
    number={2},
    pages={169--187},
    year={1990},
    publisher={Wiley Online Library}
    }

  • Médigue, C., Hénaut, A., & Danchin, A.. (1990). Escherichia coli molecular genetic map (1000kbp): update. Molecular microbiology, 4(9), 1443–1454.
    [BibTeX]
    @article{medigue1990escherichia,
    title={Escherichia coli molecular genetic map (1000Kbp): update},
    author={M{\'e}digue, C and H{\'e}naut, A and Danchin, A},
    journal={Molecular microbiology},
    volume={4},
    number={9},
    pages={1443--1454},
    year={1990},
    publisher={Wiley Online Library}
    }