Direct observation of base-pair stepping by RNA polymerase, Nature, vol.60, issue.7067, pp.460-465, 2005. ,
DOI : 10.1038/nature04268
Quantitative model for gene regulation by lambda phage repressor., Proceedings of the National Academy of Sciences, vol.79, issue.4, pp.1129-1133, 1982. ,
DOI : 10.1073/pnas.79.4.1129
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks, BMC Bioinformatics, vol.5, issue.1, p.24, 2004. ,
DOI : 10.1186/1471-2105-5-24
An Introduction to Systems Biology, Mathematical and Computational Biology Series, 2006. ,
Stochastic kinetic analysis of developmental pathway bifurcation in phage ?-infected Escherichia coli cells, Genetics, vol.149, pp.1633-1648, 1998. ,
Stability puzzles in phage ??, Physical Review E, vol.65, issue.5, p.51914, 2002. ,
DOI : 10.1103/PhysRevE.65.051914
Epigenetics as a First Exit Problem, Physical Review Letters, vol.88, issue.4, pp.48101-48102, 2002. ,
DOI : 10.1103/PhysRevLett.88.048101
Transcriptional activation mechanisms of the P RM promoter of ? phage, Biophysical Chemistry, vol.11423, pp.229-234, 2005. ,
Unusual ribosome binding properties of mRNA encoding bacteriophage ?? repressor, Nucleic Acids Research, vol.20, issue.3, pp.563-571, 1992. ,
DOI : 10.1093/nar/20.3.563
A Fully Abstract Encoding of the ??-Calculus with Data Terms, Automata, Languages and Programming , 32nd International Colloquium, ICALP 2005 Proceedings, Volume 3580 of Lecture Notes in Computer Science, pp.1202-1213, 2005. ,
DOI : 10.1007/11523468_97
Rho-dependent transcription termination: More questions than answers, Journal of Microbiology, vol.44, issue.1, pp.11-22, 2006. ,
Gamma and the Chemical Reaction Model: Fifteen Years After, Multiset Programming, Volume 2235 of Lecture Notes in Computer Science, 2001. ,
DOI : 10.1007/3-540-45523-X_2
Principles of Chemical Programming, 5th International Workshop on Rule-Based Programming, pp.133-147, 2005. ,
DOI : 10.1016/j.entcs.2004.07.019
A new computational model and its discipline of programming, 1986. ,
Programming by multiset transformation, Communications of the ACM, vol.36, issue.1, pp.98-111, 1993. ,
DOI : 10.1145/151233.151242
Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes, Current Opinion in Microbiology, vol.7, issue.2, pp.102-108, 2004. ,
DOI : 10.1016/j.mib.2004.02.011
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory, Biochemistry, vol.20, issue.24, pp.6929-6948, 1981. ,
DOI : 10.1021/bi00527a028
MPA: A stochastic process algebra, 1994. ,
The chemical abstract machine, Proceedings of the ACM Symposium on Principles of Programming Languages, pp.81-94, 1990. ,
URL : https://hal.archives-ouvertes.fr/inria-00075426
A Compositional Approach to the Stochastic Dynamics of Gene Networks, Transactions on Computational Systems Biology IV LNBI vol, vol.3939, pp.99-122, 2006. ,
DOI : 10.1007/11732488_10
An Unstable Intermediate Carrying Information from Genes to Ribosomes for Protein Synthesis, Nature, vol.46, issue.4776, pp.576-581, 1961. ,
DOI : 10.1016/0042-6822(58)90101-6
The regulation of bacterial transcription initiation, Nature Reviews Microbiology, vol.57, issue.1, pp.57-65, 2004. ,
DOI : 10.1128/JB.182.15.4129-4136.2000
Independent Recruitment In Vivo by Gal4 of Two Complexes Required for Transcription, Molecular Cell, vol.11, issue.5, pp.1301-1309, 2003. ,
DOI : 10.1016/S1097-2765(03)00144-8
The Role of Dimerization in Noise Reduction of Simple Genetic Networks, Journal of Theoretical Biology, vol.220, issue.2, pp.261-269, 2003. ,
DOI : 10.1006/jtbi.2003.3164
Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA, Transactions on Computational Systems Biology, vol.4230, pp.1-23, 2006. ,
DOI : 10.1007/11905455_1
Brane Calculi, Proceedings of CMSB 2004, pp.257-278, 2005. ,
DOI : 10.1016/S0020-0190(01)00214-9
Mobile ambients, Theoretical Computer Science, vol.240, issue.1, pp.177-213, 2000. ,
DOI : 10.1016/S0304-3975(99)00231-5
URL : http://doi.org/10.1016/s0304-3975(99)00231-5
RNA degradosome: structure, function and relationship to other ribonucleolytic multienyzme complexes, Biochemical Society Transactions, vol.30, issue.2, pp.150-154, 2002. ,
DOI : 10.1042/bst0300150
Mechanistic Modeling of Prokaryotic mRNA Decay, Journal of Theoretical Biology, vol.189, issue.2, pp.195-209, 1997. ,
DOI : 10.1006/jtbi.1997.0509
Modeling and querying biomolecular interaction networks, Theoretical Computer Science, vol.325, issue.1, pp.24-44, 2004. ,
DOI : 10.1016/j.tcs.2004.03.063
URL : http://doi.org/10.1016/j.tcs.2004.03.063
The Biochemical Abstract Machine BIOCHAM, Proceedings of CMSB 2004, pp.172-191, 2005. ,
DOI : 10.1007/BF03037227
URL : https://hal.archives-ouvertes.fr/inria-00000814
PML: Toward a High-Level Formal Language for Biological Systems, 1st International Workshop on Concurrent Models in Molecular Biology, pp.15-30, 2003. ,
DOI : 10.1016/j.entcs.2004.01.039
Feedbacks and Oscillations in the Virtual Cell VICE, Computational Methods in Systems Biology (CMSB), pp.93-107, 2006. ,
DOI : 10.1007/11885191_7
On physiological multiplicity and population heterogeneity of biological systems, Chemical Engineering Science, vol.51, issue.9, pp.1509-1521, 1996. ,
DOI : 10.1016/0009-2509(95)00306-1
Biological Transactions for Quantitative Models, Proceedings of MeCBIC 2006, 2006. ,
DOI : 10.1016/j.entcs.2007.05.007
VICE: A VIrtual CEll, Proceedings of CMSB 2004, 2005. ,
Reversible Communicating Systems, In CONCUR LNCS, vol.6, issue.4, pp.292-307, 2004. ,
DOI : 10.1007/BFb0012800
URL : https://hal.archives-ouvertes.fr/hal-00784051
Transactions in RCCS, CONCUR 2005, pp.398-412, 2005. ,
DOI : 10.1007/11539452_31
URL : https://hal.archives-ouvertes.fr/hal-00164585
Formal Molecular Biology Done in CCS-R, 1st International Workshop on Concurrent Models in Molecular Biology, pp.31-49, 2003. ,
DOI : 10.1016/j.entcs.2004.01.040
Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, pp.69-110, 2004. ,
DOI : 10.1016/j.tcs.2004.03.065
URL : https://hal.archives-ouvertes.fr/hal-00164591
The Regulatory Genome: Gene Regulatory Networks In Development And Evolution, 2006. ,
Control of rRNA Synthesis in Escherichia coli: a Systems Biology Approach, Microbiology and Molecular Biology Reviews, vol.68, issue.4, pp.639-668, 2004. ,
DOI : 10.1128/MMBR.68.4.639-668.2004
Hierarchical ordering of sequential processes, Acta Informatica, vol.1, issue.2, pp.115-138, 1971. ,
DOI : 10.1007/BF00289519
Octamerization of lambda CI repressor is needed for effective repression of PRM and efficient switching from lysogeny, Genes & Development, vol.15, issue.22, pp.3013-3022, 2001. ,
DOI : 10.1101/gad.937301
Revisited gene regulation in bacteriophage ??, Current Opinion in Genetics & Development, vol.15, issue.2, pp.145-152, 2005. ,
DOI : 10.1016/j.gde.2005.02.001
Cooperativity in long-range gene regulation by the ?? CI repressor, Genes & Development, vol.18, issue.3, pp.344-354, 2004. ,
DOI : 10.1101/gad.1167904
Biomolecular Agents as Multi-behavioural Concurrent Objects, Proceedings of the First International Workshop on Methods and Tools for Coordinating Concurrent, Distributed and Mobile Systems, pp.31-49, 2005. ,
DOI : 10.1016/j.entcs.2005.12.022
URL : https://hal.archives-ouvertes.fr/hal-00460094
Handbook of Theoretical Computer Science, Volume B, Chapter Temporal and Modal Logic, pp.995-1072, 1990. ,
GENETIC NETWORKS: Small Numbers of Big Molecules, Science, vol.297, issue.5584, pp.1129-1131, 2002. ,
DOI : 10.1126/science.1075988
Computational insights into Caenorhabditis elegans vulval development, Proceedings of the National Academy of Sciences, vol.102, issue.6, pp.1951-1956, 2005. ,
DOI : 10.1073/pnas.0409433102
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548551
Boundaries and Barriers, Chapter The barrier of objects: From dynamical systems to bounded organizations, pp.56-116, 1996. ,
A ratchet-like inter-subunit reorganization of the ribosome during translocation, Nature, vol.406, issue.6793, pp.318-322, 2000. ,
DOI : 10.1038/35018597
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics, vol.22, issue.4, pp.403-434, 1976. ,
DOI : 10.1016/0021-9991(76)90041-3
Real-Time Kinetics of Gene Activity in Individual Bacteria, Cell, vol.123, issue.6, pp.1025-1036, 2005. ,
DOI : 10.1016/j.cell.2005.09.031
Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets, Proceedings of the National Academy of Sciences, vol.95, issue.12, pp.6750-6755, 1998. ,
DOI : 10.1073/pnas.95.12.6750
Bacteriophage ??: the untold story, Journal of Molecular Biology, vol.293, issue.2, pp.177-180, 1999. ,
DOI : 10.1006/jmbi.1999.3137
Little Lambda, Who Made Thee?, Microbiology and Molecular Biology Reviews, vol.68, issue.4, pp.796-813, 2004. ,
DOI : 10.1128/MMBR.68.4.796-813.2004
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539004
Why is transcription coupled to translation in bacteria?, Molecular Microbiology, vol.4, issue.3, pp.598-603, 2004. ,
DOI : 10.1111/j.1365-2958.2004.04289.x
Thinking quantitatively about transcriptional regulation, Nature Reviews Molecular Cell Biology, vol.202, issue.3, p.221, 2005. ,
DOI : 10.1038/nrm1588
Unstable Ribonucleic Acid Revealed by Pulse Labelling of Escherichia Coli, Nature, vol.46, issue.4776, pp.581-585, 1961. ,
DOI : 10.1016/0042-6822(58)90101-6
Messenger RNA Stability and Its Role in Control of Gene Expression in Bacteria and Phages, Annual Review of Genetics, vol.33, issue.1, pp.193-227, 1999. ,
DOI : 10.1146/annurev.genet.33.1.193
Combinatorial Synthesis of Genetic Networks, Science, vol.296, issue.5572, pp.1466-1470, 2002. ,
DOI : 10.1126/science.1067407
A bottom-up approach to gene regulation, Nature, vol.128, issue.7078, pp.856-860, 2006. ,
DOI : 10.1093/nar/25.6.1203
Enzyme-Mediated DNA Looping, Annual Review of Biophysics and Biomolecular Structure, vol.33, issue.1, pp.1-24, 2004. ,
DOI : 10.1146/annurev.biophys.33.110502.132711
Statecharts: a visual formalism for complex systems, Science of Computer Programming, vol.8, issue.3, pp.231-274, 1987. ,
DOI : 10.1016/0167-6423(87)90035-9
Computational studies of gene regulatory networks: In numero molecular biology, Nature Reviews Genetics, vol.2, issue.4, pp.268-279, 2001. ,
DOI : 10.1038/35066056
Functional and physical characterization of transcription initiation complexes in the bacteriophage lambda O R region, J. Biol. Chem, vol.260, issue.14, pp.8618-8626, 1985. ,
The effect of a lambda repressor mutation on the activation of transcription initiation from the lambda PRM promoter, Cell, vol.32, issue.2, pp.327-333, 1983. ,
DOI : 10.1016/0092-8674(83)90452-X
Probabilistic model checking of complex biological pathways, Computational Methods in Systems Biology (CMSB), pp.32-47, 2006. ,
Transcription termination control in bacteria, Current Opinion in Microbiology, vol.3, issue.2, pp.149-153, 2000. ,
DOI : 10.1016/S1369-5274(00)00067-9
Interactive Markov Chains: The Quest for Quantified Quality, Volume 2428 of Lecture Notes in Computer Science, 2002. ,
A Compositional Approach to Performance Modelling Distinguished Dissertations Series, 1995. ,
Two bisimilarities in new-calculus, 1992. ,
Promoter clearance and escape in prokaryotes, Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, vol.1577, issue.2, pp.191-207, 2002. ,
DOI : 10.1016/S0167-4781(02)00452-9
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, pp.524-531, 2003. ,
: Systems Biology, Annual Review of Genomics and Human Genetics, vol.2, issue.1, pp.343-72, 2001. ,
DOI : 10.1146/annurev.genom.2.1.343
Genetic regulatory mechanisms in the synthesis of proteins, Journal of Molecular Biology, vol.3, issue.3, pp.318-356, 1961. ,
DOI : 10.1016/S0022-2836(61)80072-7
Ineractions between DNAbound repressors govern regulation by the phage ? repressor, Proceedings of the National Academy of Sciences USA 76, pp.5061-5065, 1979. ,
?? Repressor and cro???components of an efficient molecular switch, Nature, vol.292, issue.5838, pp.217-223, 1981. ,
DOI : 10.1038/294217a0
Stochasticity in gene expression: from theories to phenotypes, Nature Reviews Genetics, vol.8706, issue.6, pp.451-467, 2005. ,
DOI : 10.1073/pnas.0400673101
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm, Bioinformatics, vol.18, issue.3, pp.470-481, 2002. ,
DOI : 10.1093/bioinformatics/18.3.470
The Effect of Transcription and Translation Initiation Frequencies on the Stochastic Fluctuations in Prokaryotic Gene Expression, Journal of Biological Chemistry, vol.276, issue.11, pp.8165-8172, 2001. ,
DOI : 10.1074/jbc.M006264200
Foundations of Systems Biology, 2001. ,
Quantitative kinetic analysis of the bacteriophage ?? genetic network, Proceedings of the National Academy of Sciences, vol.102, issue.12, pp.4470-4475, 2005. ,
DOI : 10.1073/pnas.0500670102
Site-specific enthalpic regulation of DNA transcription at bacteriophage .lambda. OR, Biochemistry, vol.31, issue.1, pp.57-65, 1992. ,
DOI : 10.1021/bi00116a010
Simulating bacterial transcription and translation in a stochastic pi-calculus, Transactions on Computational Systems Biology VI. A preliminary version was presented at 3rd International Workshop on Computational Methods in Systems Biology, pp.113-149, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00460081
A Stochastic Pi Calculus for Concurrent Objects, 1st International Workshop on Probabilistic Automata and Logics, 2006. ,
DOI : 10.1007/978-3-540-73433-8_17
URL : https://hal.archives-ouvertes.fr/inria-00121104
Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch, Transactions on Computational Systems Biology VII Preliminary versions presented at the 2nd International Workshop on Concurrent Models in Molecular Biology and the Dagstuhl seminar 04281, pp.24-55, 2004. ,
DOI : 10.1007/11905455_2
URL : https://hal.archives-ouvertes.fr/inria-00089218
Probabilistic symbolic model checking with PRISM: a hybrid approach, International Journal on Software Tools for Technology Transfer, vol.24, issue.2, pp.128-142, 2004. ,
DOI : 10.1007/s10009-004-0140-2
Simulation and Verification for Computational Modelling of Signalling Pathways, Proceedings of the 2006 Winter Simulation Conference, 2006. ,
DOI : 10.1109/WSC.2006.322941
A Stochastic Process Algebra Approach to Simulation of Autoreactive Lymphocyte Recruitment, SIMULATION, vol.80, issue.6, pp.273-288, 2004. ,
DOI : 10.1177/0037549704045800
Chaos and Birhythmicity in a Model for Circadian Oscillations of the PER and TIM Proteins in Drosophila, Journal of Theoretical Biology, vol.198, issue.3, pp.445-459, 1999. ,
DOI : 10.1006/jtbi.1999.0924
Genes VIII, 2003. ,
Changing the mechanism of transcriptional activation by phage ?? repressor, Proceedings of the National Academy of Sciences USA 94, pp.3691-3696, 1997. ,
DOI : 10.1073/pnas.94.8.3691
Robustness of a gene regulatory circuit, The EMBO Journal, vol.18, issue.15, pp.42999-4307, 1999. ,
DOI : 10.1093/emboj/18.15.4299
Systems-level analyses identify extensive coupling among gene expression machines, Molecular Systems Biology, vol.31, 2006. ,
DOI : 10.1038/msb4100045
URL : http://doi.org/10.1038/msb4100045
Theory of regulation by the attenuation mechanism: stochastic model for the attenuation of the Escherichia coli tryptophan operon, Journal of Theoretical Biology, vol.91, issue.4, pp.527-544, 1981. ,
DOI : 10.1016/0022-5193(81)90210-1
An extensive network of coupling among gene expression machines, Nature, vol.416, issue.6880, pp.499-506, 2002. ,
DOI : 10.1038/416499a
Stochastic mechanisms in gene expression, Proceedings of the National Academy of Sciences USA 94, pp.814-819, 1997. ,
DOI : 10.1073/pnas.94.3.814
Circuit simulation of genetic networks, Science, vol.269, issue.5224, pp.650-656, 1995. ,
DOI : 10.1126/science.7624793
Mechanism and Control of Transcription Initiation in Prokaryotes, Annual Review of Biochemistry, vol.54, issue.1, pp.171-204, 1985. ,
DOI : 10.1146/annurev.bi.54.070185.001131
The New Oxford American Dictionar, 2005. ,
Positive Autoregulation of cI Is a Dispensable Feature of the Phage ?? Gene Regulatory Circuitry, Journal of Bacteriology, vol.187, issue.18, pp.6430-6442, 2005. ,
DOI : 10.1128/JB.187.18.6430-6442.2005
A calculus of communicating systems, Lecture Notes in Computer Science, vol.92, 1980. ,
DOI : 10.1007/3-540-10235-3
Computer Systems: Theory, Technology, and Applications. A tribute to Roger Needham, Chapter What's in a name?, Monographs in Computer Science, pp.205-211, 2004. ,
A calculus of mobile processes (I and II) Information and Computation 100, pp.1-77, 1992. ,
Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control, Molecular Microbiology, vol.43, issue.1, pp.239-246, 2002. ,
DOI : 10.1093/nar/28.22.4488
Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs, Nucleic Acids Research, vol.32, issue.11, pp.3354-3363, 2004. ,
DOI : 10.1093/nar/gkh663
URL : http://doi.org/10.1093/nar/gkh663
Predicting Temporal Fluctuations in an Intracellular Signalling Pathway, Journal of Theoretical Biology, vol.192, issue.1, pp.117-128, 1998. ,
DOI : 10.1006/jtbi.1997.0651
Stochastic simulation of cell signalling pathways, 1998. ,
The Lac operon: a short history of a genetic paradigm, 1996. ,
DOI : 10.1515/9783110879476
What is life? The paradigm of DNA and protein cooperation at high local concentrations, Molecular Microbiology, vol.171, issue.2, pp.253-255, 2006. ,
DOI : 10.1016/j.gde.2005.02.005
Uniform confluence in concurrent computation, Journal of Functional Programming, vol.10, issue.5, pp.453-499, 2000. ,
DOI : 10.1017/S0956796800003762
URL : https://hal.archives-ouvertes.fr/inria-00536801
Switches in Bacteriophage Lambda Development, Annual Review of Genetics, vol.39, issue.1, pp.409-429, 2005. ,
DOI : 10.1146/annurev.genet.39.073003.113656
A Unified Theory of Gene Expression, Cell, vol.108, issue.4, pp.439-451, 2002. ,
DOI : 10.1016/S0092-8674(02)00655-4
A method for estimating stochastic noise in large genetic regulatory networks, Bioinformatics, vol.21, issue.2, pp.208-217, 2005. ,
DOI : 10.1093/bioinformatics/bth479
Regulation of noise in the expression of a single gene, Nature Genetics, vol.31, issue.1, pp.69-73, 2002. ,
DOI : 10.1038/ng869
Comparing the expressive power of the synchronous and asynchronous $pi$ -calculi, Mathematical Structures in Computer Science, vol.13, issue.5, pp.685-719, 2003. ,
DOI : 10.1017/S0960129503004043
URL : https://hal.archives-ouvertes.fr/inria-00201104
Systems Biology: Properties of Reconstructed Networks, 2006. ,
DOI : 10.1017/CBO9780511790515
Carboxy-terminal determinants of intracellular protein degradation., Genes & Development, vol.4, issue.2, pp.277-286, 1990. ,
DOI : 10.1101/gad.4.2.277
A Multi-threaded Asynchronous Language, 7th International Conference on Parallel Computing Technologies, pp.316-323, 2003. ,
DOI : 10.1007/978-3-540-45145-7_29
Models of stochastic gene expression, Physics of Life Reviews, vol.2, issue.2, pp.157-175, 2005. ,
DOI : 10.1016/j.plrev.2005.03.003
Kommunikatin mit Automaten, 1962. ,
A correct abstract machine for the stochastic pi-calculus, 2nd International Workshop on Concurrent Models in Molecular Biology, 2004. ,
Stochastic ?-calculus, Computer Journal, vol.6, pp.578-589, 1995. ,
Beta Binders for Biological Interactions, Proceedings of CMSB 2004, pp.20-33, 2005. ,
DOI : 10.1016/S0020-0190(01)00214-9
Application of a stochastic name-passing calculus to representation and simulation of molecular processes, Information Processing Letters, vol.80, issue.1, pp.25-31, 2001. ,
DOI : 10.1016/S0020-0190(01)00214-9
A Genetic Switch, 2004. ,
Regulation of transcription: from lambda to eukaryotes, Trends in Biochemical Sciences, vol.30, issue.6, pp.275-279, 2005. ,
DOI : 10.1016/j.tibs.2005.04.003
Genes and Signals, 2002. ,
Computing with membranes, Journal of Computer and System Science, vol.61, issue.1, pp.108-143, 2000. ,
R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, 2006. ,
DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS, Journal of Bioinformatics and Computational Biology, vol.03, issue.02, pp.415-436, 2005. ,
DOI : 10.1142/S0219720005001132
Noise in Gene Expression: Origins, Consequences, and Control, Noise in Gene Expression: Origins, Consequences, and Control, pp.2010-2013, 2005. ,
DOI : 10.1126/science.1105891
Typing Non-uniform Concurrent Objects, CONCUR'00, pp.474-488, 2000. ,
DOI : 10.1007/3-540-44618-4_34
Evidence for post-transcriptional control of the morphogenetic genes of bacteriophage lambda, Journal of Molecular Biology, vol.85, issue.1, pp.163-175, 1974. ,
DOI : 10.1016/0022-2836(74)90135-1
Computational Systems Biology: A Calculus for Biomolecular Knowledge, 2002. ,
BioAmbients: an abstraction for biological compartments, Theoretical Computer Science, vol.325, issue.1, pp.141-167, 2004. ,
DOI : 10.1016/j.tcs.2004.03.061
Cells as Computation, Nature, vol.419, p.343, 2002. ,
DOI : 10.1007/3-540-36481-1_1
Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach, Biochimie, vol.88, issue.2, pp.151-161, 2006. ,
DOI : 10.1016/j.biochi.2005.07.012
Multiparadigm Programming in Mozart/Oz, Second International Conference of Lecture Notes in Computer Science, 2004. ,
Four dimers of ?? repressor bound to two suitably spaced pairs of ?? operators form octamers and DNA loops over large distances, Current Biology, vol.9, issue.3, pp.151-154, 1999. ,
DOI : 10.1016/S0960-9822(99)80069-4
Stochastic dynamics of macromolecularassembly networks, Molecular Systems Biology, 2006. ,
Promoter for the establishment of repressor synthesis in bacteriophage lambda., Proceedings of the National Academy of Sciences, vol.77, issue.6, pp.3191-3195, 1980. ,
DOI : 10.1073/pnas.77.6.3191
The OR control system of bacteriophage lambda, Journal of Molecular Biology, vol.181, issue.2, pp.211-230, 1985. ,
DOI : 10.1016/0022-2836(85)90086-5
Transcriptional interference ??? a crash course, Trends in Genetics, vol.21, issue.6, pp.339-345, 2005. ,
DOI : 10.1016/j.tig.2005.04.009
Kinetics of Protein-DNA Interaction: Facilitated Target Location in Sequence-Dependent Potential, Biophysical Journal, vol.87, issue.6, pp.4021-4035, 2004. ,
DOI : 10.1529/biophysj.104.050765
The Oz Programming Model, Computer Science Today, pp.324-343, 1995. ,
DOI : 10.1007/BFb0015252
Physics in Molecular Biology, 2005. ,
DOI : 10.1017/CBO9780511755699
Emerging features of mRNA decay in bacteria, RNA, vol.6, issue.8, pp.1079-1090, 2000. ,
DOI : 10.1017/S1355838200001023
On the role of Cro in ?? prophage induction, Proceedings of the National Academy of Sciences, vol.102, issue.12, pp.4465-4469, 2005. ,
DOI : 10.1073/pnas.0409839102
System modeling in cellular biology, 2006. ,
DOI : 10.7551/mitpress/9780262195485.001.0001
Dynamical behaviour of biological networks: II. immunity control in bacteriophage lambda, Bulletin Mathematical Biology, vol.57, issue.2, pp.277-297, 1995. ,
A Complex Control Circuit. Regulation of Immunity in Temperate Bacteriophages, European Journal of Biochemistry, vol.54, issue.1, pp.211-227, 1976. ,
DOI : 10.1016/0022-5193(72)90062-8
Epstein-Barr Virus and Cancer, Clinical Cancer Research, vol.10, issue.3, pp.803-821, 2004. ,
DOI : 10.1158/1078-0432.CCR-0670-3
Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage ??, Journal of Theoretical Biology, vol.227, issue.2, pp.229-237, 2004. ,
DOI : 10.1016/j.jtbi.2003.11.003
Fundamental bacterial genetics, 2003. ,
Computer assisted biological reasoning: the simulation and analysis of fgf singalling pathway dynamics, NCRI Cancer Conference, 2006. ,
Multi-level modeling in systems biology by discrete event approaches, it ? Information Technology, vol.48, issue.3, pp.148-153, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00460088
A typing system for a calculus of objects, 1st International Symposium on Object Technologies for Advanced Software, pp.460-474, 1993. ,
DOI : 10.1007/3-540-57342-9_89
DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise, Current Opinion in Genetics & Development, vol.15, issue.2, pp.1-9, 2005. ,
DOI : 10.1016/j.gde.2005.02.005
Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists, 2000. ,
The segment polarity network is a robust developmental module, Nature, vol.406, issue.6792, pp.188-192, 2000. ,
DOI : 10.1038/35018085
Translation and messenger RNA secondary structure, Journal of Theoretical Biology, vol.68, issue.3, pp.321-329, 1977. ,
DOI : 10.1016/0022-5193(77)90063-7
Fundamentals of Transactional Information Systems, 2001. ,
Transcription Regulation in Prokaryotes, 2000. ,
Attenuation in the control of expression of bacterial operons, Nature, vol.21, issue.5800, pp.751-758, 1981. ,
DOI : 10.1038/289751a0
Epstein???Barr virus: 40 years on, Nature Reviews Cancer, vol.10, issue.10, pp.757-768, 2004. ,
DOI : 10.1038/sj.onc.1206556
Multifacetted Modelling and Discrete Event Simulation, 1984. ,
Calculating biological behaviors of epigenetic states in the phage lambda life cycle, Funct Integr Genomics, vol.4, pp.188-195, 2004. ,