ARC Calculs de Processus et Biologie des Réseaux Moléculaires

Action de Recherche Coopérative INRIA 2002-2003

 

Bibliographie 


R. Alur, C. Belta, F. Ivancic, V. Kumar, M. Mintz, G. J. Pappas, H. Rubin et J. Schug.
Hybrid modeling and simulation of biomolecular networks.
Hybrid Systems: Computation and Control, 4th International Workshop, HSCC 2001, Rome, Italy, pages 19--32. Springer, LNCS 2034, 2001.

A. Bockmayr et A. Courtois
Modeling biological systems in hybrid concurrent constraint programming (Poster).
2nd Int. Conf. Systems Biology, ICSB'01, Pasadena, CA, 2001.

A. Bockmayr, N. Pisaru et A. Aggoun.
Network flow problems in constraint programming.
Principles and Practice of Constraint Programming, CP'2001, Paphos, Cyprus. Springer, LNCS, 2001.

J. M. Bower and H. Bolouri.
Computational modeling of genetic and biochemical networks.
MIT Press, 2001.

L. Cardelli.
Mobility and Security.
Lecture notes for Marktoberdorf Summer School. 1999.

A. Courtois.
Modélisation de systèmes biologiques en programmation par contraintes.
Rapport de DEA, Univ. Henri Poincaré,  LORIA, Juillet 2001.

V. Danos, J.-L. Krivine.
Disjunctive Tautologies and Synchronisation Schemes.
Proceedings of CSL'00, Springer Verlag, LNCS 1862, pp. 292--301. 2000.

H. de Jong.
Modeling and simulation of genetic regulatory systems: a literature review.
INRIA,  RR-4032, Septembre 2000.

F.  Fages.
Concurrent constraint programming and linear logic.
Invited talk at the ACM conference on Principles and Practice of Declarative Programming, PPDP'2000, Montreal.

F. Fages, P. Ruet et S. Soliman.
Linear concurrent constraint programming: operational and phase semantics.
Journal of Information and Computation 165(1). Février 2001.

W. Fontana, L. Buss.
The barrier of objects: From dynamical systems to bounded organizations.
In Boundaries and Barriers, J. Casti and A. Karlqvist (eds.), pp. 56-116, Addison-Wesley, 1996.

C. Fournet, G. Gonthier.
The Reflexive CHAM and the Join Calculus.
In Proceedings of POPL'96. 1996.

C. Fournet, G. Gonthier.
The Join Calculus: a language for distributed mobile programming.
Applied Semantics Summer School; Caminha, September 2000.

R. Ghosh, C. Tomlin.
Lateral inhibition through Delta-Notch signaling: A piecewise affine hybrid model.
Hybrid Systems: Computation and Control, 4th International  Workshop, HSCC 2001, Rome, Italy, pp. 232--246, Springer, LNCS 2034, 2001.

D. Gilbert et C. Palamidessi.
Concurrent constraint programming with process mobility.
In Proceedings CL'2000. 2000.

V. Gupta, R. Jagadeesan et P. Panangaden.
Stochastic processes as Concurrent Constraint Programs.
In Proceedings POPL'99. 1999.

V. Gupta, R. Jagadeesan, et V. Saraswat.
Computing with continuous change.
Science of computer programming, 30(1-2):3--49, 1998.

V. Gupta, R. Jagadeesan, V. Saraswat, et D. G. Bobrow.
Programming in hybrid constraint languages.
Hybrid Systems II, Springer, LNCS 999,  1995.

P. van Hentenryck et V. Saraswat
Strategic directions in constraint programming.
ACM Computing Surveys, 28(4):701 -- 726, 1996.

O. Herescu et C. Palamidessi
Probabilistic asynchronous Pi-calculus.
In Proceedings FOSSACS'2000. 2000.

P. Legrain J.-L. Jestin., et V. Schachter
From the analysis of protein complexes to proteome-wide linkage maps.
Current Opinions in Biotechnology Vol. 11, 402-407. 2000.

H. Matsuno, A. Doi, M. Nagasaki et S. Miyano.
Hybrid Petri Net Representation of Gene Regulatory Network.
Pacific Symposium on Biocomputing (5), pp. 338-349, 2000.

R. Milner.
Communicating and mobile systems; the pi-calculus.
Cambridge University Press. 1999.

C. Priami,  A. Regev, W. Silverman et E. Shapiro,
Application of a stochastic name passing calculus to representation and simulation of molecular processes.
Information Processing Letters 80: 25-31. 2001

A. Regev, W. Silverman, E. Shapiro.
Representation and simulation of biochemical processes using the $\pi$-calculus process algebra.
In Proceedings of PSB'01, 6: 459--470. 2001.

M. Roux-Rouquié, M.L. Chauvet, A. Munnich, J. Frézal.
Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the genatlas database.
Molecular Genet. and Metabol. 67, 261-277. 1999

M. Roux-Rouquié, M. Marilley.
Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.
Nucleic Acids Res., 28, 3433-3441. 2000.

M. Roux-Rouquié.
Genetic and epigenetic regulation schemes: Need for an alternative paradigm,
Mol. Genet. Metabol. 71, 1-9. 2000.

M. Roux-Rouquié.
Systemic modeling of biological functions : Application to the development of the  GENINTER software dedicated to the compilation of interrelationships between genes and/or gene products.  In : Advanced Studies in Plant Biology - Integrating Plant Systems, Edited by H. Greppin, University of Geneva, 2000, pp 33- 53.

M. Roux-Rouquié.
The  Relevance of the Systemic Paradigm to the Modeling of  Biological Processes and Systems : Experimentation with the Unified Modeling Language (UML).  TRANSCRIPTOME 2002:  From Functional Genomics to Systems Biology, March 10-13, 2002 Seattle, Washington, USA

V. Schachter.
The bioinformatics of protein interaction maps.
Biotechniques, Special Issue on Computational Proteomics, March 2002.

V. Schachter et A. Regev.
A framework proposal for the evaluation of pathways representation formalisms.
BioPathways Consortium Formalisms Workgroup draft proposal, presented at PSB'01. 2001.

N. Tapon, K.H. Moberg et I.K. Hariharan.
The coupling of cell growth to the cell cycle.
Curr Opin Cell Biol 2001 Dec;13(6):731-7. 2001.

J. Wojcik et V. Schachter.
Protein-protein interaction map inference using Interacting Domain Profile Pairs.
Bioinformatics 2001 Vol 17 Supp. 1(Proceedings of ISMB'2001),S296-305. 2001.