Publications de l'équipe MaBioVis pour l'année 2007

Années: 2005, 2006, 2008, 2009, 2010, 2011, 2012, 2013

  1. D. Auber, Y. Chiricota, M. Delest, G. Melançon, J.-P. Domenger, and P. Mary. Visualisation de graphes avec tulip : exploration interactive de grandes masses de données en appui à la fouille de données et à l'extraction de connaissances. In G. V. Monique Noirhomme-Fraiture, editor, EGC'07: Extraction et Gestion de Connaissances, pages 147-156. Cépaduès, 2007.
  2. R. Uricaru, L. Brehelin, and E. Rivals. A new type of hidden markov models to predict complex domain architecture in protein sequences. In C. B. et G. Didier, editor, JOBIM'07 : Journées Ouvertes Biologie, Informatique et Mathématiques, pages 97-102, 2007.
  3. G. Melançon, P.-Y. Koenig, C. Bohan, and B. Gauthier. Combining dagmaps and sugiyama layout for the navigation of hierarchical data. In IV'07: 11th International Conference on Information Visualisation, pages 447-452. IEEE Computer Society, 2007.
  4. G. Melançon, D. Auber, and N. Novelli. Visually mining the datacube using a pixel-oriented technique. In IV'07: 11th International Conference on Information Visualisation. IEEE Computer Society, 2007.
  5. D. Auber and Y. Chiricota. Improved efficiency of spring embedders: taking advantage of gpu programming. In 7th IASTED International Conference on Visualization, Imaging and Image Processing, pages 169-175. ACTA Press, 2007.
  6. A. Delaherche, E. Bon, C. Miot-Sertier, L. Patrick, E. Bilhere, E. Gindreau, A. Lonvaud-Funel, and C. Le Marrec. Horizontal gene transfer in oenococcus oeni as the origin of a 7-kb island encoding dpsb, a ferritin-like protein protecting bacteria from wine stresses. In VII ème CONGRES DE LA SFM-Société Française de Microbiologie, 2007.
  7. P. Durrens, M. Nikolski, and D. J. Sherman. Gene fusion and fission events in fungus genomes. In 23rd international conference on yeast genetics and molecular biology, volume 24-S1 of Yeast. Wiley, 2007.
  8. T. Martin, P. Durrens, E. Beyne, M. Nikolski, F. Iragne, D. J. Sherman, and J.-L. Souciet. The génolevures online database. In J. Cherry and I. G. Macreadie, editors, XXIIIrd International Conference on Yeast Genetics and Molecular Biology, volume 24 of Number S1, 2007.
  9. C. Le Marrec, E. Bon, and A. Lonvaud-Funel. Evaluation de la tolérance à l'hyperosmolarité chez la bactérie lactique oenococcus oeni. In VII ème CONGRES DE LA SFM-Société Française de Microbiologie, 2007.
  10. A. Athane, E. Bilhere, E. Bon, P. Lucas, A. Lonvaud-Funel, and C. Le Marrec. Characterization of a mobile dpsa gene from the lactic acid bacterium oenocococcus oeni. In 15th Meeting of the Club des Bactéries Lactiques, 2007.
  11. P. Durrens. La comparaison de génomes de levures illustre les mécanismes d'évolution et d'adaptation. In Conférence FungEffector, 2007.
  12. D. J. Sherman. Bases de données et fouille de données chez les levures hémiascomycètes. In Conférence FungEffector, 2007.
  13. P. Durrens, M. Nikolski, and D. J. Sherman. Gene fusion and fission events in fungal genomes. In XXIIIrd International Conference on Yeast Genetics and Molecular Biology, 2007.
  14. G. Jean, D. J. Sherman, and M. Nikolski. Reconstruction and visualization of genome rearrangements within the kuyveromyces. In ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, page 44, 2007.
  15. A. Delaherche, E. Bon, C. Miot-Sertier, P. Lucas, E. Bilhere, E. Gindreau, C. Le Hénaff-Le Marrec, and A. Lonvaud-Funel. Horizontal gene transfer as the origin of a 7-kb island encoding dps, a protein protecting oenococcus oeni from wine stress. In 8th International Symposium of Enology of Bordeaux, 2007.
  16. B. Pinaud, J. Blanchard, P. Kuntz, and F. Guillet. Garviz : une plate-forme de fouille visuelle 2d-3d de règles d'association. In Actes de l'atelier visualisation et extraction de connaissances, Conf. Extraction et Gestion des Connaissances (EGC'07), 2007.
  17. B. Pinaud and P. Kuntz. On the influence of the instance structure for metaheuristic performances - application to a graph drawing problem. In IEEE Congress on Evolutionary Computation (CEC), pages 4684-4690. IEEE, 2007.
  18. A. Ouangraoua, V. Segura, E. Costes, and P. Ferraro. Plant architecture comparison methods: A review of existing algorithms and examples of application. In 5th International Workshop on Functional-Structural Plant Models, pages 47, 1-4, 2007.
  19. S. Dufour-Kowalski, C. Pradal, N. Dones, P. Barbier De Reuille, F. Boudon, J. Chopard, D. Da Silva, J.-B. Durand, P. Ferraro, C. Fournier, Y. Guédon, A. Ouangraoua, C. Smith, S. Stoma, F. Théveny, H. Sinoquet, and C. Godin. Openalea: An open-source platform for the integration of heterogeneous fspm components. In 5th International Workshop on Functional-Structural Plant Models, 2007.
  20. P. Ferraro and P. Hanna. Optimizations of local edition for evaluating similarity between monophonic musical sequences. In 8th International Conference on Information Retrieval - Large-Scale Semantic Access to Content (Text, Image, Video and Sound) RIAO07, pages 135 - 142, 2007.
  21. P. Hanna and P. Ferraro. Polyphonic music retrieval by local edition of quotiented sequences. In Proceedings of the 5th International Workshop on Content-Based Multimedia Indexing (CBMI), pages 61-68, 2007.
  22. J. Allali, P. Ferraro, P. Hanna, and C. Iliopoulos. Local transpositions in alignment of polyphonic musical sequences. In Proceedings of the 14th String Processing and Information Retrieval Symposium (SPIRE07), pages 26-38, 2007.
  23. D. Auber and Y. Chriricota. Improved efficiency of spring embedders: Taking advantage of gpu programming. In Visualization, Imaging, and Image Processing - 2007, pages 169-175. J.J. Villaneva, 2007.
  24. D. Auber, N. Novelli, and G. Melançon. Visually mining the data cube using a pixel-oriented technique. In 11th International Conference on Information Visualisation, IV 2007, pages 3-10, 2007.
  25. F. Chevalier, M. Delest, and J.-P. Domenger. A heuristic for the retrieval of objects in low resolution video. In Workshop on Content-Based Multimedia Indexing, volume 1, pages 144-151. LaBRI, 2007.
  26. F. Chevalier, D. Auber, and A. Telea. Structural analysis and visualization of c++ code evolution using syntax trees. In International Workshop on Principles of Software Evolution (IWPSE), pages 90 - 97, 2007.
  27. R. Bourqui and F. Jourdan. Comparaison visuelle de réseaux métaboliques. In 8èmes Journées Ouvertes Biologie Informatique Mathématiques, pages 285-286, 2007.
  28. R. Bourqui, D. Auber, and P. Mary. How to draw clusteredweighted graphs using a multilevel force-directed graph drawing algorithm. In 11th International Conference on Information Visualisation, IV 2007, pages 757-764, 2007.
  29. C. Godin and P. Ferraro. Self-similar analysis of plant architecture reveals hierarchical classes of meristem states. In 5th International Workshop on Functional Structural Plant Models, pages 481-484, 2007.
  30. A. Ouangraoua, V. Segura, E. Costes, and P. Ferraro. Plant architecture comparison methods: a review of existing algorithms. In 5th International Workshop on Functional Structural Plant Models, pages 471-474, 2007.
  31. D. Archambault, T. Munzner, and D. Auber. Grouse: Feature-based, steerable graph hierarchy exploration. In EuroVis07: Joint Eurographics - IEEE VGTC Symposium on Visualization, pages 67-74. Ken Museth and Torsten M"oller and Anders Ynnerman, 2007.
  32. M. Robine, P. Hanna, and P. Ferraro. Music similarity: Improvements of edit-based algorithms by considering music theory. In ACM SIGMM International Workshop on Multimedia Information Retrieval (MIR07), pages 135-141, 2007.
  33. M. Robine, P. Hanna, P. Ferraro, and J. Allali. Adaptation of string matching algorithms for identification of near-duplicate music documents. In Workshop on Plagiarism Analysis, Authorship Identification, and Near-Duplicate Detection (PAN07), pages 37-43, 2007.
  34. N. Novelli and D. Auber. Calcul et représentation efficace de cubes de données pour une visualisation orientée pixel. In EGC 2007, volume RNTI-E-9, pages 205-206. Monique Noirhomme-Fraiture and Gilles Venturini, 2007.
  35. H. Soueidan, D. J. Sherman, and M. Nikolski. Biorica: A multi model description and simulation system. In F0SBE, pages 279-287, 2007.
  36. M. Diouf, K. Musumbu, and S. Maabout. Adding semantics on models for automatic business rules generation. In International Conference on Industrial Engineering and Systems Management. Yang Shanlin, Chen Guoqing, Thomas Andre, Artiba Abdelhakim, Xu Zongwei, 2007.
  37. M. Diouf, S. Maabout, and K. Musumbu. Semantics enrichment in model driven architecture: automatic business rules generation. In International Conference on E-Business, Enterprise Information Systems and E-Government, pages 107-113, 2007.
  38. M. Diouf, S. Maabout, and K. Musumbu. Generation automatique de regles metier par enrichissement semantique de modeles. In INFORSID, pages 437-452, 2007.
  39. M. Diouf, S. Maabout, and K. Musumbu. Merging model driven architecture and semantic web for business rules generation. In International Conference on Web Reasoning and Rule Systems (RR07), pages 118-132, 2007.
  40. M. Diouf, S. Maabout, and K. Musumbu. Generating and merging business rules by weaving mda and semantic web. In International Workshop on Model-Driven Enterprise Information Systems, pages 18-29, 2007.
  41. G. Melançon and Y. Chiricota. Visually mining relational data. International Review on Computers and Software, 2(3):14, 2007.
  42. C. Le Marrec, E. Bon, and A. Lonvaud-Funel. Tolerance to high osmolality of the lactic acid bacterium oenococcus oeni and identification of potential osmoprotectants. International Journal of Food Microbiology, 115(3):335-42, 2007.
  43. J. Blanchard, B. Pinaud, P. Kuntz, and F. Guillet. A 2d-3d visualization support for human-centered rule-mining. Computer and Graphics, 31(3):350-360, 2007.
  44. G. Jean and M. Nikolski. Genome rearrangements: a correct algorithm for optimal capping. Information Processing Letters, 104(1):14-20, 2007.
  45. R. Barriot, D. J. Sherman, and I. Dutour. How to decide which are the most pertinent overly-represented features during gene set enrichment analysis. BMC Bioinformatics, 8(1), 2007.
  46. M. Nikolski and D. J. Sherman. Family relationships: should consensus reign?- consensus clustering for protein families. Bioinformatics, 23, 2007.
  47. P. Peterlongo, J. Allali, and M.-F. Sagot. Indexing gapped-factors using a tree. International Journal of Foundations of Computer Science, 2007.
  48. G. Paquin, S. Brlek, and G. Melançon. Properties of the extremal infinite smooth words. Discrete Mathematics and Theoretical Computer Science, 9(2):33-50, 2007.
  49. M. Delest, F. Chevalier, and J.-P. Domenger. A heuristic for the retrieval of objects in video in the framework of the rough indexing paradigm. Signal Processing : Image Communication, 22:622-634, 2007.
  50. V. Kovalenko, A. Zhukova, M. Rumyantseva, A. Gaskov, V. Yuschenko, I. Ivanova, and T. Pagnier. Surface chemistry of nanocrystalline sno<sub>2</sub>: effect of thermal treatment and additives. Sensors and Actuators B: Chemical, 126(1), 2007.
  51. F. Chevalier, J.-P. Domenger, J. Benois-Pineau, and M. Delest. Retrieval of objects in video by similarity based on graph matching. Pattern Recognition Letters, 28:939-949, 2007.
  52. P. Ferraro, A. Ouangraoua, L. Tichit, and S. Dulucq. Local similarity between quotiented ordered trees. Journal of Discrete Algorithms, 5(1):23-35, 2007.
  53. P. Marullo, G. Yvert, M. Bely, I. Masneuf-Pomarède, P. Durrens, and a. et. Single nucleotide resolution qtl mapping of an enological trait from derived wild saccharomyces cerevisiae strains. FEMS Yeast Research, in press:1295-1306, 2007.
  54. I. Masneuf-Pomarède, C. Lejeune, P. Durrens, M. Lollier, M. Aigle, and a. et. Molecular typing of wine yeast strains saccharomyces uvarum using microsatellite markers. Systematic and Applied Microbiology, 30:75-82, 2007.
  55. D. Archambault, T. Munzner, and D. Auber. Topolayout: Multi-level graph layout by topological features. IEEE Transactions on Visualization and Computer Graphics, 13:305-317, 2007.
  56. F. Iragne, M. Nikolski, and D. Sherman. Extrapolation of metabolic pathways as an aid to modelling completely sequenced. FEMS Yeast Research, pages 132-139, 2007.
  57. M. J. Taussing, O. Stoevesandt, C. A. K. Borrebaeck, A. R. Bradbury, D. Cahill, C. Cambillau, A. De Daruvar, S. Dübel, J. Eichler, R. Frank, T. J. Gibson, D. Gloriam, L. Gold, F. W. Herberg, H. Hermjakob, J. D. Hoheisel, T. O. Joos, O. Kallioniemi, M. Koegl, Z. Konthur, B. Korn, E. Kremmer, S. Krobitsch, U. Landegren, S. Van Der Maarel, S. Muyldermans, J. Mccafferty, P.-. Nygren, S. Palcy, A. Plückthun, B. Polic, M. Przybylski, P. Saviranta, A. Sawyer, D. J. Sherman, A. Skerra, M. Templin, M. Ueffing, and M. Uhlén. Proteomebinders: planning a european resource of affinity reagents for analysis of the human proteome. Nature Methods, 4:13-17, 2007.
  58. P. Sirand-Pugnet, 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. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genetics, 3, 2007.
  59. N. Mattiuzzo, E. Toulza, M. Galliano, N. Jonca, C. Dossat, D. Jacob, A. De Daruvar, P. Wincker, S. Serre, and M. Guerrin. Large-scale identification of human genes implicated in epidermal barrier function. Genome Biology, 8:67-74, 2007.
  60. J.-M. Schwartz, C. Gaugain, J. Nacher, A. De Daruvar, and M. Kanehisa. Observing metabolic functions at the genome scale. Genome Biology, 2007.
  61. S. Kerrien, S. Orchard, L. Montecchi-Palazzi, B. Aranda, A. Quinn, N. Vinod, G. Bader, I. Xenarios, J. Wojcik, D. Sherman, M. Tyers, J. Salama, S. Moore, A. Ceol, A. Chatr-Aryamontri, M. Oesterheld, V. Stumpflen, L. Salwinski, J. Nerothin, E. Cerami, M. Cusick, M. Vidal, M. Gilson, J. Armstrong, P. Woollard, C. Hogue, D. Eisenberg, G. Cesareni, R. Apweiler, and H. Hermjakob. Broadening the horizon - level 2.5 of the hupo-psi format for molecular. BMC Biology, 5:9;5(1):44, 2007.
  62. P. Hanna, P. Ferraro, and M. Robine. On optimizing the editing algorithms for evaluating similarity between monophonic musical sequences. Journal of New Music Research, 36:267-279, 2007.
  63. M. Dobrijevic and I. Dutour. The distribution of hydrocarbons in titan's atmosphere: An evolutionary algorithm-based model. Planetary and Space Science, 55:2128-2136, 2007.

Années: 2005, 2006, 2008, 2009, 2010, 2011, 2012, 2013

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