. Bibliographie, Foundations of Systems Biology, 2002.

H. Kitano, Systems Biology: A Brief Overview, Science, vol.295, issue.5560, pp.1662-1664, 2002.
DOI : 10.1126/science.1069492

A. Funahashi, Y. Matsuoka, A. Jouraku, M. Morohashi, N. Kikushi et al., CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proceedings of the IEEE, pp.1254-1265, 2008.
DOI : 10.1109/JPROC.2008.925458

M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle et al., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003.
DOI : 10.1093/bioinformatics/btg015

G. A. Algire, M. G. Benders, L. Montague, M. M. Ma, C. Moodie et al., Creation of a bacterial cell controlled by a chemically synthesized genome, Science, vol.329, issue.5987, pp.52-56, 2010.

C. Guldberg and P. Waage, Studies concerning affinity, C. M. Forhandlinger i Videnskabs-Selskabet, p.186435, 1864.

B. Müller-hill, Repression oflacPromoter as a Function of Distance, Phase and Quality of an AuxiliarylacOperator, Journal of Molecular Biology, vol.257, issue.1, pp.21-29, 1996.
DOI : 10.1006/jmbi.1996.0143

B. Müller-hill, The function of auxiliary operators, Molecular Microbiology, vol.29, issue.1, pp.13-18, 1998.
DOI : 10.1006/jmbi.1994.0028

D. Gillespie, Exact stochastic simulation of coupled chemical reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.2340-2361, 1977.
DOI : 10.1021/j100540a008

Y. Cao, D. Gillespie, and L. Petzold, Efficient formulation of the stochastic simulation algorithm for chemically reacting systems, The Journal of Chemical Physics, vol.121, issue.9, pp.4059-4067, 2004.
DOI : 10.1063/1.1778376

H. Byrne and D. Drasdo, Individual-based and continuum models of growing cell populations: a comparison, Journal of Mathematical Biology, vol.14, issue.1, pp.4-5, 2009.
DOI : 10.1007/s00285-008-0212-0

S. S. Andrews, N. J. Addy, R. Brent, and A. P. Arkin, Detailed Simulations of Cell Biology with Smoldyn 2.1, PLoS Computational Biology, vol.174, issue.3, 2010.
DOI : 10.1371/journal.pcbi.1000705.s004

M. Klann, H. Ganguly, and A. , Hybrid spatial Gillespie and particle tracking simulation, Bioinformatics, vol.28, issue.18, 2012.
DOI : 10.1093/bioinformatics/bts384

V. Norris, T. Den-blaauwen, A. Cabin-flaman, R. Doi, R. Harshey et al., Functional Taxonomy of Bacterial Hyperstructures, Microbiology and Molecular Biology Reviews, vol.71, issue.1, pp.230-253, 2007.
DOI : 10.1128/MMBR.00035-06

R. Brown, On the general existence of active molecules in organic and inorganic bodies, Philos Mag, vol.4, 1828.

A. Einstein, Über die von der molekularkinetischen theorie der wärme geforderte bewegung von in ruhenden flüssigkeiten suspendierten teilchen. (Sur la théorie moléculaire cinétique de la chaleur requise par le mouvement des particules en suspension dans un liquide au repos, Annalen der Physik, vol.17, pp.549-560, 1905.

P. Amar and L. Paulevé, HSIM: A Hybrid Stochastic Simulation System for Systems Biology, The Third International Workshop on Static Analysis and Systems Biology, 2012.
DOI : 10.1016/j.entcs.2015.04.016

P. Amar, G. Bernot, and V. Norris, HSIM: a simulation programme to study large assemblies of proteins, Journal of Biological Physics and Chemistry, vol.4, issue.2, pp.79-84, 2004.
DOI : 10.4024/2040404.jbpc.04.02

URL : https://hal.archives-ouvertes.fr/hal-01276581

P. Amar, G. Legent, M. Thellier, C. Ripoll, G. Bernot et al., A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency, BMC Systems Biology, vol.2, issue.1, 2008.
DOI : 10.1186/1752-0509-2-27

URL : https://hal.archives-ouvertes.fr/hal-00643746

P. Tracqui, E. Promayon, P. Amar, N. Huc, V. Norris et al., Emergent features of cell structural dynamics : a review of models based on tensegrity and nonlinear oscillations, " in Proceedings of the DIEPPE spring school on Modelling and simulation of biological processes in the context of genomics Validation d'une simulation à base d'agents par l'utilisation d'un réseau de petri, Systèmes multi-agents vers la conception de systèmes artificiels socio-mimétiques, pp.161-190, 2003.

T. Moncion, G. Hutzler, and P. Amar, Verification of biochemical agent-based models using petri nets, International Symposium on Agent Based Modeling and Simulation, pp.695-700, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00340492

T. Moncion, G. Hutzler, and P. Amar, Validation of an agent based system using Petri Nets, Proceedings of the fourth international joint conference on Autonomous agents and multiagent systems , AAMAS '05, pp.1365-1366, 2005.
DOI : 10.1145/1082473.1082775

URL : https://hal.archives-ouvertes.fr/hal-00340493

T. Moncion, P. Amar, and G. Hutzler, Automatic characterization of emergent phenomena in complex systems, Journal of Biological Physics and Chemistry, vol.10, issue.1, pp.16-23, 2010.
DOI : 10.4024/07MO10A.jbpc.10.01

URL : https://hal.archives-ouvertes.fr/hal-00644627

P. Amar, G. Bernot, and V. Norris, Modelling and simulation of large assemblies of proteins, " in Proceedings of the DIEPPE spring school on Modelling and simulation of biological processes in the context of genomics, pp.41-48, 2003.

M. Thellier, G. Legent, P. Amar, V. Norris, and C. , Steady-state kinetic behaviour of functioning-dependent structures, FEBS Journal, vol.332, issue.18, pp.4287-4299, 2006.
DOI : 10.1126/science.283.5400.381

J. Deutscher, C. Francke, and P. Postma, How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria, Microbiology and Molecular Biology Reviews, vol.70, issue.4, pp.939-1031, 2006.
DOI : 10.1128/MMBR.00024-06

URL : https://hal.archives-ouvertes.fr/hal-00164056

J. Mowbray and V. Moses, The Tentative Identification in Escherichia coli of a Multienzyme Complex with Glycolytic Activity, European Journal of Biochemistry, vol.3, issue.1, pp.25-36, 1976.
DOI : 10.1016/0076-6879(55)01068-9

P. Amar, V. Norris, M. S. , and G. Bernot, Metabolons and hyperstructures in cell metabolism and signaling, Actes du colloque 4th World Congress of Cell and Molecular Biology, 2005.

F. Commichau, F. Rothe, C. Herzberg, E. Wagner, D. Hellwig et al., Novel Activities of Glycolytic Enzymes in Bacillus subtilis: INTERACTIONS WITH ESSENTIAL PROTEINS INVOLVED IN mRNA PROCESSING, Molecular & Cellular Proteomics, vol.8, issue.6, pp.1350-1360, 2009.
DOI : 10.1074/mcp.M800546-MCP200

J. Ovàdi, Experiment-based mathematical modelling of energy metabolism in diseases caused by unfolded/misfolded proteins, " in Modelling Complex Biological Systems in the Context of, Genomics, pp.47-50, 2009.

S. Chuong, A. Good, G. Taylor, M. Freeman, G. Moorhead et al., Large-scale Identification of Tubulin-binding Proteins Provides Insight on Subcellular Trafficking, Metabolic Channeling, and Signaling in Plant Cells, Molecular & Cellular Proteomics, vol.3, issue.10, pp.970-983, 2004.
DOI : 10.1074/mcp.M400053-MCP200

A. Real-hohn, P. Zancan, D. Da-silva, E. Martins, L. Salgado et al., Filamentous actin and its associated binding proteins are the stimulatory site for 6-phosphofructo-1-kinase association within the membrane of human erythrocytes, Biochimie, vol.92, issue.5, pp.538-544, 2010.
DOI : 10.1016/j.biochi.2010.01.023

V. Norris, P. Amar, G. Legent, C. Ripoll, M. Thellier et al., Sensor potency of the moonlighting enzyme-decorated cytoskeleton, BMC Biochemistry, vol.14, issue.3, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00766058

E. Rocha, J. Fralick, G. Vediyappan, A. Danchin, and V. Norris, A strand-specific model for chromosome segregation in bacteria, Molecular Microbiology, vol.21, issue.4, pp.895-903, 2003.
DOI : 10.1046/j.1365-2958.2003.03606.x

V. Norris, L. Janniere, and P. Amar, Hypothesis : Variations in the rate of dna replication determine the phenotype of daughter cells, Modelling Complex Biological Systems in the Context of Genomics, pp.71-82, 2007.

V. Norris and P. Amar, Life on the scales : initiation of replication in escherichia coli, Modelling Complex Biological Systems in the Context of Genomics, pp.55-77, 2012.

V. Norris and P. Amar, Chromosome Replication in Escherichia coli: Life on the Scales, Life, vol.2, issue.4, pp.286-312, 2012.
DOI : 10.3390/life2040286

URL : https://hal.archives-ouvertes.fr/hal-00758130

E. Bromley, K. Channon, E. Moutevelis, and D. Woolfson, Peptide and Protein Building Blocks for Synthetic Biology: From Programming Biomolecules to Self-Organized Biomolecular Systems, ACS Chemical Biology, vol.3, issue.1, pp.38-50, 2008.
DOI : 10.1021/cb700249v

S. Rialle, Méthodologie et outils bioinformatiques d'aide à la conception de systèmes biologiques synthétiques pour de nouveaux diagnostics en santé humaine, 2010.

S. Peres, S. Rialle, L. Felicori, and F. Molina, Computing biological functions using Bio??, a formal description of biological processes based on elementary bricks of actions, Bioinformatics, vol.26, issue.12, pp.1542-1547, 2010.
DOI : 10.1093/bioinformatics/btq169

S. Rialle, L. Felicori, C. Dias-lopes, S. Peres, S. E. Atia et al., BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks, Bioinformatics, vol.26, issue.18, pp.2298-2304, 2010.
DOI : 10.1093/bioinformatics/btq409

A. Norris, P. Zemirline, P. Amar, E. B. Ballet, G. Jacob et al., From bioputing to bactoputing : computing with bacteria, Modelling Complex Biological Systems in the Context of Genomics, pp.123-150, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00340470

V. Norris, A. Zemirline, P. Amar, J. N. Audinot, P. Ballet et al., Computing with bacterial constituents, cells and populations: from bioputing to bactoputing, Theory in Biosciences, vol.45, issue.3, pp.211-228, 2011.
DOI : 10.1007/s12064-010-0118-4

URL : https://hal.archives-ouvertes.fr/hal-00643738

V. Norris, A. R. Thierry, P. Amar, B. I. Holland, and F. Molina, The Mimic Chain Reaction, Journal of Molecular Microbiology and Biotechnology, vol.22, issue.5, pp.335-343, 2012.
DOI : 10.1159/000345328

URL : https://hal.archives-ouvertes.fr/hal-00761608

P. Jensen and K. Hammer, The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters, Appl Environ Microbiol, vol.64, issue.1, pp.82-87, 1998.

K. Hammer, I. Mijakovic, and P. Jensen, Synthetic promoter libraries ??? tuning of gene expression, Trends in Biotechnology, vol.24, issue.2, pp.53-55, 2006.
DOI : 10.1016/j.tibtech.2005.12.003

N. Seghezzi, P. Amar, B. Koebmann, P. R. Jensen, and M. Virolle, The construction of a library of synthetic promoters revealed some specific features of strong Streptomyces promoters, Applied Microbiology and Biotechnology, vol.203, issue.3, pp.615-623, 2011.
DOI : 10.1007/s00253-010-3018-0

URL : https://hal.archives-ouvertes.fr/hal-00591940

L. P. Kotra, J. Haddad, and S. Mobashery, Aminoglycosides: Perspectives on Mechanisms of Action and Resistance and Strategies to Counter Resistance, Antimicrobial Agents and Chemotherapy, vol.44, issue.12, pp.3249-3256, 2000.
DOI : 10.1128/AAC.44.12.3249-3256.2000

K. Shaw, P. Rather, R. Hare, and G. Miller, Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycosidemodifying enzymes, Microbiology and Molecular Biology Reviews, vol.57, issue.1, pp.138-163, 1993.

N. Seghezzi, M. Virolle, and P. Amar, Novel insights regarding the sigmoidal pattern of resistance to neomycin conferred by the aphII gene, in Streptomyces lividans, AMB Express, vol.3, issue.1, 2013.
DOI : 10.1007/BF00422072

URL : https://hal.archives-ouvertes.fr/hal-00788558