Institut de Mathématiques de Luminy

PUBLICATIONS 2003-2004

Méthodes Mathématiques pour la Génomique

Brun C., Chevenet F., Martin D., Wojcik J., Guénoche Alain, Jacq B.
Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network.
Genome Biology, 2003, http ://genomebiology.com/2003/5/1/R6.

Brun C., Guénoche Alain, Jacq B.
Approach of the functional evolution of duplicated genes in Saccharomyces cerevisiae using a new classification method based on protein-protein interaction data,
Journal of Structural and Functional Genomics, 3, 213-224, 2003.

Chaouiya Claudine, Mossé Brigitte, Remy Elisabeth, Thieffry Denis.
Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework.
Positive systems, Theory and application (L. Benvenuti, A. De Santis and L. Farin eds), Lecture Notes in Control and Inform. Sci., 294, 119--126, Springer-Verlag, Berlin, 2003.

Colombo Tristan, Quentin Y., Guénoche Alain.
Recherche de zones denses dans un graphe : application aux gènes orthologues.
Colloque «Knowledge Discovery and Discrete Mathematics». Actes des Journées Informatiques de Metz (JIM 2003), 203-212, 2003.

Didier Gilles.
Common intervals of two sequences.
Workshop on Algorithms in Bioinformatics (WABI 2003). Lecture Notes in Computer Science 2812, 17-24, 2003.

Guénoche Alain.
Partitions optimisées selon différents critères: évaluation et comparaison. Recherche opérationnelle et aide à la décision.
Math. Sci. Hum. Math. Soc. Sci. No. 161, 41--58, 2003.

Jaeger Sébastien, Lima Ricardo, Mossé Brigitte.
Symbolic analysis of finite words: the complexity function.
Bull. Braz. Math. Soc. (N.S.) 34, no. 3, 457--477, 2003.

Remy Elisabeth, Mossé Brigitte, Chaouiya C., Thieffry D.
A description of dynamical graphs associated to elementary regulatory circuits. Bioinformatics 19, 172-178, 2003.

Brun C., Herrmann C., Guénoche Alain.
Clustering proteins from interaction networks for the prediction of cellular functions, BMC Bioinformatics 5 :95, 2004.

Carpentier A.S., Riva A., Tisseur Pierre, Didier Gilles, Henaut A.
The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA.
Comput. Biol. Chem.,28(1), 3-10, 2004.

Chaouiya Claudine, Mendoza Luis, Remy Élisabeth, Ruet Paul, Thieffry Denis.
From logical regulatory graphs to standard Petri nets: dynamical roles and functionality of feedback circuits.
Concurrent Models in Molecular Biology, Electronic Notes in Computer Science, Elsevier, 2004.

Chaouiya Claudine, Remy Élisabeth, Ruet Paul, Thieffry Denis.
Qualitative modelling of genetic networks: from logical regulatory graphs to standard Petri nets,
Application and Theory of Petri Nets, Lecture Notes in Computer Science 3099, pp. 137-156, Springer Verlag, 2004.

Guénoche Alain, Leclerc Bruno, Makarenkov Vladimir.
On the extension of a partial metric to a tree metric.
6th International Conference on Graph Theory. Discrete Math. 276, no. 1-3, 229--248, 2004.

Guénoche Alain.
Supersequences of masks for oligo-chips.
Journal of Bioinformatics and Computational Biology, 2, 3, 2004.

Guénoche Alain.
Clustering by vertex density in a Graph, Meeting of the International Federation of the Classification Societies.
Chicago, Classification, Clustering and Data Mining, D. Banks et al. (Eds.), Springer, 15-23, 2004.

Mathieu Pierre, Remy Elisabeth.
Isoperimetry and heat kernel decay on percolation clusters.
Ann. Probab. 32, no. 1A, 100--128, 2004.

Guénoche Alain.
About the design of oligo-chips,
Discrete Applied Maths, 147, 1, 57-67, 2005.

Charon I., Denoeud L., Guénoche Alain, Hudry O.
Classes empiétantes dans un graphe et application aux interactions entre protéines,
Actes du colloque de la «Société Française de Recherche Opérationnelle et d'Aide à la Décision» (ROADEF'05), Presses de l'Université F. Rabelais, Tours, 2005.

Denoeud L., Garreta H., Guénoche Alain.
Comparison of distance indices between partitions.
Applied Stochastic Model and Data Analysis. A paraître.

Martin D., Brun C., Remy Elisabeth, Mouren P., Thieffry D., Jacq B.
GOToolBox: Functional analysis of gene datasets based on Gene Ontology,
Genome Biology. A paraître.

Remy Elisabeth, Thieffry Denis, Chaouiya Claudine.
A Petri net formalism for multivalued logical regulatory graphs.
Journal of Discrete Algorithms. A paraître.



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