Inria / Raweb 2004
Project-Team: MODBIO

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Bibliography

Major publications by the team in recent years

[1]
E. Althaus, A. Caprara, H.-P. Lenhof, K. Reinert.
Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics., in: "Proc. European Conference on Computational Biology", Bioinformatics, October 2002, vol. 18, no Supplement 2, p. S4–S16.
[2]
E. Althaus, K. Mehlhorn.
Traveling Salesman-Based Curve Reconstruction in Polynomial Time, in: "SIAM Journal on Computing", 2001, vol. 31, no 1, p. 27–66.
[3]
E. Balas, A. Bockmayr, N. Pisaruk, L. Wolsey.
On unions and dominants of polytopes, in: "Mathematical Programming, Ser. A", 2004, vol. 299, p. 223-239.
[4]
A. Bockmayr, A. Courtois.
Using hybrid concurrent constraint programming to model dynamic biological systems, in: "18th International Conference on Logic Programming, ICLP'02, Copenhagen", Springer, LNCS 2401, 2002, p. 85-99.
[5]
A. Bockmayr, V. Weispfenning.
Solving numerical constraints, in: "Handbook of Automated Reasoning", A. Robinson, A. Voronkov (editors)., Elsevier, 2001, vol. 1, chap. 12, p. 751-842.
[6]
Y. Guermeur, A. Elisseeff, D. Zelus.
Bound on the risk for M-SVMs, in: "Statistical Learning, Theory and Applications", 2002, p. 48–52.
[7]
Y. Guermeur, C. Geourjon, P. Gallinari, G. Deléage.
Improved performance in protein secondary structure prediction by inhomogeneous score combination, in: "Bioinformatics", 1999, vol. 15, no 5, p. 413–421.
[8]
Y. Guermeur.
Combining discriminant models with new multi-class SVMs, in: "Pattern Analysis and Applications", 2002, vol. 5, no 2, p. 168–179.
[9]
Y. Guermeur, H. Paugam-Moisy.
Théorie de l'apprentissage de Vapnik et SVM, Support Vector Machines, in: "Apprentissage Automatique", M. Sebban, G. Venturini (editors)., Hermès, 1999, p. 109–138.
[10]
V. Y. Lunin, A. Urzhumtsev, A. Bockmayr.
Direct phasing by binary integer programming, in: "Acta Crystallographica Section A", 2002, vol. 58, p. 283-291.

Doctoral dissertations and Habilitation theses

[11]
D. Eveillard.
Modélisation statistique et formelle de la régulation de l'épissage alternatif, PhD Thesis, Université Henri Poincaré, Nancy 1, May 2004.

Articles in referred journals and book chapters

[12]
A. Bockmayr, J. N. Hooker.
Constraint Programming, in: "Handbook of Discrete Optimization", K. Aardal, G. Nemhauser, R. Weismantel (editors)., Handbooks in Operations Research and Management Science, To appear, Elsevier, 2004.
[13]
P. Dupont, F. Denis, Y. Esposito.
Links between Probabilistic Automata and Hidden Markov Models: probability distributions, learning models and induction algorithms, in: "Pattern Recognition Journal", to appear, 2004.
[14]
D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr.
A multi-scale constraint programming model of alternative splicing regulation, in: "Theoretical Computer Science", 2004, vol. 325, no 1, p. 3-24.
[15]
Y. Guermeur, A. Lifchitz, R. Vert.
A kernel for protein secondary structure prediction, in: "Kernel Methods in Computational Biology", B. Schölkopf, K. Tsuda, J.-P. Vert (editors)., MIT Press, 2004, p. 193–206.

Publications in Conferences and Workshops

[16]
E. Althaus, N. Karamanis, A. Koller.
Computing Locally Coherent Discourses, in: "Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics (ACL 2004), Barcelona, Spain", 2004.
[17]
A. Bockmayr, A. Courtois, D. Eveillard, M. Vezain.
Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing, in: "Computational Methods in Systems Biology, CMSB'04, Paris", To appear, Springer, LNCS, 2004.
[18]
F. Denis, Y. Esposito.
Learning classes of Probabilistic Automata, in: "COLT 2004", LNAI, 2004, no 3120, p. 124-139.
[19]
D. Eveillard, A. Larhlimi, D. Ropers, S. Billaut, S. Peyrefitte.
KOALAB: A new method for regulatory motif search, in: "5èmes Journées Ouvertes Biologie Informatique Mathématiques, JOBIM 2004, Montreal", 10 pages, 2004.

Internal Reports

[20]
S. Bonne.
Modélisation du métabolisme des monocarbones et du cycle de la méthionine, Master thesis, Univ. Bordeaux, Sep 2004.
[21]
Y. Guermeur.
Large margin multi-category discriminant models and scale-sensitive $ \Psi$-dimensions, Research Report RR-5314, INRIA, September 2004,
http://www.inria.fr/rrrt/rr-5314.html.
[22]
A. Larhlimi.
Analyse de voies métaboliques en programmation par contraintes, Stage de DEA, Université Henri Poincaré, Nancy 1, Jun 2004.
[23]
M. Vezain.
Modélisation de la régulation de l'épissage alternatif de HIV-1, Rapport de Stage, DESS EGOISt, Rouen, Université Rouen, June 2004.

Miscellaneous

[24]
E. Althaus, A. Caprara, H.-P. Lenhof, K. Reinert.
Aligning Multiple Sequences by Cutting Planes, Submitted, 2004.
[25]
Y. Guermeur, M. Maumy, F. Sur.
Model Selection for Multi-class SVMs, Submitted to ASMDA'05, 2004.

Bibliography in notes

[26]
E. Althaus, A. Bockmayr, M. Elf, T. Kasper, M. Jünger, K. Mehlhorn.
SCIL - Symbolic Constraints in Integer Linear Programming, in: "10th European Symposium on Algorithms, ESA'02, Rome", Springer, LNCS 2461, 2002, p. 75-87.
[27]
Y. Bartal.
Probabilistic approximation of metric spaces and its algorithmic applications, in: "Proceedings IEEE Symposium on Foundations of Computer Science", 1996, p. 184–193.
[28]
Y. Bartal.
On approximating arbitrary metrics by tree metrics, in: "Proceedings 30th Annual ACM Symposium on Theory of Computing", 1998, p. 161–168.
[29]
C. Burges.
A tutorial on support vector machines for pattern recognition, in: "Data Mining and Knowledge Discovery", June 1998, vol. 2, no 2, p. 121–167.
[30]
L. Cartegni, J. Wang, Z. Zhu, M. Q. Zhang, A. R. Krainer.
ESEfinder: a web resource to identify exonic splicing enhancers, in: "Nucleic Acid Research", 2003, vol. 31, no 13, p. 3568-3571.
[31]
W. J. Cook, W. H. Cunningham, W. R. Pulleyblank, A. Schrijver.
Combinatorial Optimization, Wiley, 1998.
[32]
C. Cortes, V. Vapnik.
Support-Vector Networks, in: "Machine Learning", 1995, vol. 20, p. 273–297.
[33]
F. Denis, Y. Esposito.
Residual languages and probabilistic automata, in: "Automata, Languages and Programming, 30th International Colloquium, ICALP 2003", Springer, LNCS 2719, 2003, p. 452-463.
[34]
Y. Esposito, A. Lemay, F. Denis, P. Dupont.
Learning probabilistic residual finite state automata, in: "Grammatical Inference: Algorithms and Applications, 6th International Colloquium, ICGI 2002", Springer, LNCS 2484, 2002.
[35]
J. Fakcharoenphol, S. Rao, K. Talwar.
A tight bound on approximating arbitrary metrics by tree metrics, in: "Proceedings ACM Symposium on Theory of Computing", 2003, p. 448–455.
[36]
K. Fukuda, A. Prodon.
Double Description Method Revisited., in: "Combinatorics and Computer Science", Springer, LNCS 1120, 1995, p. 91-111.
[37]
E. Gothié, Y. Guermeur, S. Muller, C. Branlant, A. Bockmayr.
Recherche des gènes de petits ARN non codants, Research Report RR-5057, INRIA, December 2003.
[38]
V. Gupta, R. Jagadeesan, V. Saraswat.
Computing with Continuous Change, in: "Science of computer programming", 1998, vol. 30, no 1-2, p. 3-49.
[39]
B. J. Hammond.
Quantitative Study of the Control of HIV-1 Gene Expression, in: "J. Theor. Biol", 1993, vol. 163, p. 199–221.
[40]
T. Kin, K. Tsuda, K. Asai.
Marginalized kernels for RNA sequence data analysis, in: "Genome Informatics 2002", Universal Academic Press, 2002, p. 112-122.
[41]
J. A. Papin, J. Stelling, N. D. Price, S. Klamt, S. Schuster, B. O. Palsson.
Comparison of Network-Based Pathway Analysis Methods, in: "Trends in Biotechnology", 2004, vol. 22, no 8, p. 400-405.
[42]
A. Patterson.
A Fourier Series Method for the Determination of the Components of Interatomic Distances in Crystals, in: "Phys. Rev.", 1934, vol. 46, p. 372–376.
[43]
M. C. Reed, H. F. Nijhout, R. Sparks, C. M. Ulrich.
A mathematical model of the methionine cycle, in: "Journal of Theoretical Biology", 2004, vol. 226, p. 33-43.
[44]
V. A. Saraswat.
Concurrent constraint programming, ACM Doctoral Dissertation Awards, MIT Press, 1993.
[45]
J. Thompson, F. Plewniak, O. Poch.
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs, in: "Bioinformatics", 1999, vol. 15, no 1, p. 87-88.
[46]
C. Tuerk, L. Gold.
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase, in: "Science", 1990, vol. 249, p. 505-510.
[47]
V. Vapnik.
Estimation of Dependences Based on Empirical Data., Springer-Verlag, N.Y., 1982.
[48]
V. Vapnik.
Statistical learning theory, John Wiley & Sons, Inc., N.Y., 1998.
[49]
E. O. Voit.
Metabolic modeling: a tool of drug discovery in the post-genomic area, in: "Drug Discovery Today", 2002, vol. 7, no 11, p. 621-628.
[50]
P. van Hentenryck, V. Saraswat.
Strategic directions in constraint programming, in: "ACM Computing Surveys", 1996, vol. 28, no 4, p. 701 – 726.

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