Publications

2012

Susanna-Assunta Sansone et al., Towards interoperable bioscience data, Nature Genetics, 44, 121-126 (2012) [PubMed]

Bedon F, Villar E, Vincent D, Dupuy JW, Lomenech AM, Mabialangoma A, Chaumeil P, Barré A, Plomion C,  Gion JM. Proteomic plasticity of two Eucaliplus genotypes under contrasted water regimes in the field, 35(4):790-805,2012 [PubMed]

Tardy F,et al. Emergence of Atypical Mycoplasma agalactiae Strains Harboring a New Prophage and Associated with an Alpine Wild Ungulate Mortality Episode. Appl Environ Microbiol. 2012 Jul;78(13):4659-68. [PubMed]

Amine Ghozlane, Frédéric Bringaud, Hayssam Soueidan, Isabelle Dutour, Fabien Jourdan, and Patricia Thebault. Flux analysis of the Trypanosoma brucei glycolysis based on a multi-objective criteria bioinformatic approach, Advances in Bioinfromatics, 2012, in press. International conference with published acts

Jonathan Dubois, Ludovic Cottret, Patricia Thebault, Frédéric Bringaud, Amaine ghozlane, Fabien Jourdan, David Auber and Romain Bourqui. Systrip: a visual environment for the investigation of time-series data in the context of metabolic networks. IV 2012, 16th IEEE international conference on Information Visualisation. (2012) 8-13th July 2012, Montpellier.

2011

Lemaitre C, Barré A, Citti C, Tardy F, Thiaucourt F, Sirand-Pugnet P, Thébault P. A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships. BMC Bioinformatics. 2011 Nov 24;12:457. PubMed PMID: 22115330; PubMed Central PMCID: PMC3248887. [PubMed]

D. Waltemath, R. Adams, D. Beard, F. Bergmann, U. Bhalla, R. Britten, V. Chelliah, M. Cooling, J. Cooper,E. Crampin, A. Garny, S. Hoops, M. Hucka, P. Hunter, E. Klipp, C. Laibe, A. Miller, I. Moraru, D. Nickerson, P. Nielsen, M. Nikolski, S. Sahle, H. Sauro, H. Schmidt,J. Snoep, D. Tolle, O. Wolkenhauer, N. LeNovere, Minimum Information About a Simulation Experiment (MIASE), PLoS Computational Biology, vol. 7 (4), 2011. [PLoS]

A. Sarkar and H. Soueidan and M. Nikolski, Identification of conserved gene clusters in multiple genomes based on synteny and homology, BMC Bioinformatics, vol 12 (Suppl 9), S18, 2011 [PubMed]

Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D. MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles. BMC Plant Biol. 2011 Jun 13;11:104.[PubMed]

Anasua Sarkar, Macha Nikolski, Ujjwal Maulik, "Spectral Clustering on Neighborhood Kernels with Modified Symmetry for Remote Homology Detection," eait, pp.269-272, 2011 Second International Conference on Emerging Applications of Information Technology, 2011

Aurélie Gouliemakis, Julen Bridier, Aurélien Barré, Olivier Claisse, David Sherman, Pascal Durrens, Aline Lonvaud-Funel ans Elisabeth Bon, How does Oenoccoccus oeni adapt to its environment? A pangenomic oligonucleotide microarray for analysis O. oeni gene expression under wine shock, Proc. OENO2011- 9th International Symposium of Oenology (2011), 358-363

Geraldine Jean and Macha Nikolski. 2011. SyDiG: uncovering Synteny in Distant Genomes. Int. J. Bioinformatics Res. Appl. 7, 1 (March 2011), 43-62. DOI=10.1504/IJBRA.2011.039169  [PubMed]

2010

Pereyre S, Sirand-Pugnet P, Beven L, Charron A, Renaudin H, Barré A, AvenaudP, Jacob D, Couloux A, Barbe V, de Daruvar A, Blanchard A, Bébéar C. Life onarginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas. PLoS Genet. 2009 Oct;5(10):e1000677.Epub 2009 Oct 9.[PubMed]

Garcia V, Stevens R, Gil L, Gilbert L, Gest N, Petit J, Faurobert M, Maucourt M, Deborde C, Moing A, Poessel JL, Jacob D, Bouchet JP, Giraudel JL, Gouble B,Page D, Alhagdow M, Massot C, Gautier H, Lemaire-Chamley M, de Daruvar A, Rolin D, Usadel B, Lahaye M, Causse M, Baldet P, Rothan C. An integrative genomics approach for deciphering the complex interactions between ascorbate metabolismand fruit growth and composition in tomato. C R Biol. 2009 Nov;332(11):1007-21.Epub 2009 Oct 2.[PubMed]

Biais B, Allwood JW, Deborde C, Xu Y, Maucourt M, Beauvoit B, Dunn WB, Jacob D, Goodacre R, Rolin D, Moing A. 1H NMR, GC-EI-TOFMS, and data set correlation for fruit metabolomics: application to spatial metabolite analysis in melon. Anal Chem. 2009 Apr 15;81(8):2884-94.[PubMed]

Ueno S, Le Provost G, Léger V, Klopp C, Noirot C, Frigerio J-M, Salin F, Salse J, Abrouk M, Murat F, Brendel O, Derory J, Abadie P, Léger P, Cabane C, Barré A, de Daruvar A, Couloux A, Wincker P, Reviron M-P, Kremer A, Plomion C (2010) Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11: 650 [PubMed]

Durand J, Bodénès C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herrán A, Ikaran Z, Cabané C, Ueno S, Alberto F, Dumoulin P-Y, Guichoux E, de Daruvar A, Kremer A, Plomion C (2010) A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11: 570 [PubMed]

2009

Deborde C., Maucourt M., Baldet P., Bernillon S., Biais B., Talon G., Ferrand C., Jacob D., Ferry-Dumazet H., de Daruvar A., Rolin D., Moing A. Proton NMR quantitative profiling for quality assessment of greenhouse-grown tomato fruit. Metabolomics (2009) 5 :183-198

Recordon-Pinson P, Anies G, Bruyand M, Neau D, Morlat P, Pellegrin JL, Groppi A, Thiébaut R, Dabis F, Fleury H, Masquelier B; ANRS CO3 Aquitaine Cohort. HIV type-1 transmission dynamics in recent seroconverters: relationship with transmission of drug resistance and viral diversity. Antivir Ther.2009;14(4):551-6.

Bon E, Delaherche A, Bilhère E, De Daruvar A, Lonvaud-Funel A, Le Marrec C.Oenococcus oeni genome plasticity is associated with fitness. Appl Environ Microbiol. 2009 Apr;75(7):2079-90. Epub 2009 Feb 13. [PubMed]

2008

Vincent Lacroix, Ludovic Cottret, Patricia Thébault, Marie-France Sagot: An Introduction to Metabolic Networks and Their Structural Analysis. IEEE/ACM Trans. Comput. Biology Bioinform. 5(4): 594-617 (2008) [PubMed]

2007

Schwartz JM, Gaugain C, Nacher JC, de Daruvar A, Kanehisa M. Observing metabolic functions at the genome scale. Genome Biol. 2007;8(6):R123. [PubMed]

Toulza E, Mattiuzzo NR, Galliano MF, Jonca N, Dossat C, Jacob D, de Daruvar A, Wincker P, Serre G, Guerrin M. Large-scale identification of human genes implicated in epidermal barrier function. Genome Biol. 2007;8(6) [PubMed]

Sirand-Pugnet, P, C. Citti, A. Barré and A. Blanchard. 2007. Evolution of mollicutes: down a bumpy road with twists and turns. Res. Microbiol. Oct 2 (/revue invitée/) [PubMed]

Sirand-Pugnet, P, C. Lartigue, M. Marenda, D. Jacob, A. Barré, V. Barbe, C. Schenowitz, S. Mangenot, A. Couloux, B. Segurens, A. de Daruvar, A. Blanchard and C. Citti. 2007. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet. May 18;3(5):e75. [PubMed]

Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dubel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegll M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Pluckthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlen M.  ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods. 2007 Jan;4(1):13-7. [PubMed]

Masneuf-Pomarede I, Le Jeune C, Durrens P, Lollier M, Aigle M, Dubourdieu D. Molecular typing of wine yeast strains Saccharomyces bayanus var. uvarum using microsatellite markers. Syst Appl Microbiol. 2007 Jan;30(1):75-82. Epub 2006 Apr 18. [PubMed]

2006

Plomion C, Lalanne C, Claverol S, Meddour H, Kohler A, Bogeat-Triboulot MB, Barre A, Le Provost G, Dumazet H, Jacob D, Bastien C, Dreyer E, de Daruvar A, Guehl JM, Schmitter JM, Martin F, Bonneu M. Mapping the proteome of poplar and application to the discovery of drought-stress responsive proteins. Proteomics. 2006 Dec;6(24):6509-27.[PubMed]

Delaherche A, Bon E, Dupe A, Lucas M, Arveiler B, de Daruvar A, Lonvaud-Funel A. Intraspecific diversity of Oenococcus oeni strains determined by sequence analysis of target genes. Appl Microbiol Biotechnol. 2006 Aug 16. [PubMed]

2005

Ferry-Dumazet H, Houel G, Montalent P, Moreau L, Langella O, Negroni L, Vincent D, Lalanne C, de Daruvar A, Plomion C, Zivy M, Joets J. PROTICdb: a web-based application to store, track, query, and compare plant proteome data. Proteomics. 2005 May;5(8):2069-81. [PubMed]

Gion JM, Lalanne C, Le Provost G, Ferry-Dumazet H, Paiva J, Chaumeil P, Frigerio JM, Brach J, Barre A, de Daruvar A, Claverol S, Bonneu M, Sommerer N, Negroni L, Plomion C. The proteome of maritime pine wood forming tissue. Proteomics. 2005 Sep;5(14):3731-51. [PubMed]

2004

Barre, A., A. de Daruvar, and A. Blanchard. 2004. MolliGen, a database dedicated to the comparative genomics of Mollicutes. Nucleic Acids Res 32 Database issue: D307-10.[PubMed]

Barriot, R., J. Poix, A. Groppi, A. Barre, N. Goffard, D. Sherman, I. Dutour, and A. de Daruvar. 2004. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Res 32: 3581-9. [PubMed]

Dantec, L. L., D. Chagne, D. Pot, O. Cantin, P. Garnier-Gere, F. Bedon, J. M. Frigerio, P. Chaumeil, P. Leger, V. Garcia, F. Laigret, A. De Daruvar, and C. Plomion. 2004. Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol Biol 54: 461-70.[PubMed]

Dujon, B., D. Sherman, G. Fischer, P. Durrens, S. Casaregola, I. Lafontaine, J. de Montigny, C. Marck, C. Neuveglise, E. Talla, N. Goffard, L. Frangeul, M. Aigle, V. Anthouard, A. Babour, V. Barbe, S. Barnay, S. Blanchin, J.-M. Beckerich, E. Beyne, C. Bleykasten, A. Boisrame, J. Boyer, L. Cattolico, F. Confanioleri, A. de Daruvar, L. Despons, E. Fabre, C. Fairhead, H. Ferry-Dumazet, A. Groppi, F. Hantraye, C. Hennequin, N. Jauniaux, P. Joyet, R. Kachouri, A. Kerrest, R. Koszul, M. Lemaire, I. Lesur, L. Ma, H. Muller, J.-M. Nicaud, M. Nikolski, S. Oztas, O. Ozier-Kalogeropoulos, S. Pellenz, S. Potier, G.-F. Richard, M.-L. Straub, A. Suleau, D. Swennen, F. Tekaia, M. Wesolowski-Louvel, E. Westhof, B. Wirth, M. Zeniou-Meyer, I. Zivanovic, M. Bolotin-Fukuhara, A. Thierry, C. Bouchier, B. Caudron, C. Scarpelli, C. Gaillardin, J. Weissenbach, P. Wincker, and J.-L. Souciet. 2004. Genome evolution in yeasts. Nature 430: 35-44.[PubMed]

Iragne, F., A. Barre, N. Goffard, and A. De Daruvar. 2004. AliasServer: a web server to handle multiple aliases used to refer to proteins. Bioinformatics 20: 2331-2.[PubMed]