Bibliography

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Bibliography

1: T. Akutsu, S. Miyano, and S. Kuhara.
Identification of genetic networks from a small number of gene expression patterns under the boolean network model.
In R. B. Altman, K. Lauderdale, A. K. Dunker, L. Hunter, and T. E. Klein, editors, Pacific Symposium on Biocomputing '99, pages 17-28, Singapore, 1999. World Scientific.
[PDF].
2: T. Akutsu, S. Miyano, and S. Kuhara.
Algorithms for inferring qualitative models of biological networks.
In R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein, editors, Pacific Symposium on Biocomputing 2000, pages 290-301, Singapore, 2000. World Scientific.
[PDF].
3: T. Akutsu, S. Miyano, and S. Kuhara.
Inferring qualitative relations in genetic networks and metabolic pathways.
Bioinformatics, 16:727-734, 2000.
[Link].
4: R. Albert and A.-L Barabási.
Statistical mechanics of complex networks.
Reviews of Modern Physics, 74:47-97, 2002.
[Link].
5: R. Albert, H. Jeong, and A.-L Barabási.
Error and attack tolerance of complex networks.
Nature, 406:378-382, 2000.
[Link].
6: B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson.
Molecular Biology of the Cell.
Garland Publishing Inc., New York, NY, 3rd edition, 1994.
7: M. Aldana, S. Coppersmith, and L. P. Kadanoff.
Boolean dynamics with random couplings.
In E. Kaplan, J. E. Marsden, and K. R. Sreenivasan, editors, Perspectives and Problems in Nonlinear Science. A celebratory volume in honor of Lawrence Sirovich, Springer Applied Mathematical Sciences Series. Springer, 2003.
[Link].
8: R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein, editors.
Pacific Symposium on Biocomputing '98, Singapore, 1998. World Scientific.
9: A. Arkin, J. Ross, and H. A. McAdams.
Stochastic kinetic analysis of developmental pathway bifurcation in phage $\lambda$ -infected Escherichia coli cells.
Genetics, 149:1633-1648, 1998.
10: M. I. Arnone and E. H. Davidson.
The hardwiring of development: organization and function of genomic regulatory systems.
Development, 124:1851-1864, 1997.
11: R. J. Bagley and L. Glass.
Counting and classifying attractors in high dimensional dynamical systems.
Journal of Theoretical Biology, 183:269-284, 1996.
[Link].
12: A.-L. Barabási and R. Albert.
Emergence of scaling in random networks.
Science, 286:509-512, 1999.
[Link].
13: A.-L. Barabási and R. Albert.
Emergence of scaling in random networks.
Science, 286:509-512, 1999.
14: N. Barkai and S. Leibler.
Robustness in simple biochemical networks.
Nature, 387:913-917, 1997.
[Link].
15: U. Bastolla and G. Parisi.
The modular structure of kauffman networks.
Physica D, 115:203-218, 1998.
[Link].
16: R. Behrevan, P. J. Bentley, and R. Carlisle.
Exploring reaction-diffusion and pattern formation.
In Proceedings of the First Australian Conference on Artificial Life (ACAL2003), pages 13-27. University of New South Wales, Australia, 2003.
17: S. Bilke and F. Sjunnesson.
Stability of the kauffman model.
Physical Review E, 65:016129, 2002.
[Link].
18: J. W. Bodnar.
Programming the Drosophila embryo.
Journal of Theoretical Biology, 188:391-445, 1997.
[Link].
19: H. Bolouri and E. H. Davidson.
Modeling dna sequence-based cis-regulatory gene networks.
Developmental Biology, 246(1):2-13, 2002.
[Link].
20: H. Bolouri and E. H. Davidson.
Modeling transcriptional regulatory networks.
BioEssays, 24:1118-1129, 2002.
[Link].
21: S. Bornholdt and K. Sneppen.
Neutral mutations and punctuated equilibrium in evolving genetic networks.
Physical Review Letters, 81(1):236-239, 1998.
[Link].
22: S. Bornholdt and K. Sneppen.
Robustness as an evolutionary principle.
Proceedings of the Royal Society of London, Series B, 267:2281-2286, 2000.
23: J. M. Bower and H. Bolouri.
Computational Modeling of Genetic and Biochemical Networks.
MITB, Cambridge, MA, 2001.
24: D. Bray.
Molecular networks: The top-down view.
Science, 301:1864-1865, 2003.
[Link].
25: K. Burrage, T. Tian, and P. Burrage.
A multi-scaled approach for simulating chemical reaction systems.
Submitted to special issue of Progress in Biophysics and Molecular Biology. Preprint available [PS], 2004.
26: S. B. Carroll, J. K. Grenier, and S. D. Weatherbee.
From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design.
Blackwell Science, Oxford, 2001.
27: E. Coen.
The Art of Genes: How Organisms Make Themselves.
Oxford University Press, Oxford, 1999.
28: E. H. Davidson.
Genomic Regulatory Systems.
Academic Press, San Diego, CA, 2001.
29: E. H. Davidson, D. R. McClay, and L. Hood.
Regulatory gene networks and the properties of the developmental process.
Proceedings of the National Academy of Science, USA, 100:1475-1480, 2003.
30: E. H. Davidson, J. P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.-H. Yuh, T. Minokawa, G. Amore, V. Hinman, C. Arenas-Mena, O. Otim, C. T. Brown, C. B. Livi, P. Y. Lee, R. Revilla, A. G. Rust, Z. Jun Pan, M. J. Schilstra, P. J. C. Clarke, M. I. Arnone, L. Rowen, R. A. Cameron, D. R. McClay, L. Hood, and H. Bolouri.
A genomic regulatory network for development.
Science, 295:1669-1678, 2002.
[Link].
31: H. de Jong.
Modeling and simulation of genetic regulatory systems: A literature review.
Journal of Computational Biology, 9(1):67-103, 2002.
[Link].
32: H. de Jong, J. Geiselmann, G. Batt, C. Hernandez, and M. Page.
Qualitative simulation of the initiation of sporulation in Bacillus subtilis.
BMB, 66:261-200, 2004.
[Link].
33: H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, and J. Geiselmann.
Qualtiative simulation of genetic regulatory networks using piecewise-linear models.
Bulletin of Mathematical Biology, 66:301-340, 2004.
[Link].
34: H. de Jong, M. Page, C. Hernandez, and J. Geiselmann.
Qualitative simulation of genetic regulatory networks: Method and application.
In Proceedings of the 17th International Joint Conference on Artificial Intelligence (IJCAI-01), pages 67-73, San Francisco, CA, 2000. Morgan Kauffman.
[Link].
35: F. Dellaert and R. D. Beer.
A developmental model for the evolution of complete autonomous agents.
In P. Maes, M. J. Mataric, J.-A. Meyer, J. Pollack, and S. W. Wilson, editors, From animals to animats 4: Proceedings of the Fourth International Conference on Simulation of Adaptive Behavior, pages 393-401, Cambridge, MA, 1996. The MIT Press/Bradford Books.
[Link].
36: P. D'haeseleer.
Reconstructing Gene Networks from Large Scale Gene Expression Data.
PhD thesis, The University of New Mexico, Albuquerque, New Mexico, 2000.
37: S. N. Dorogovtsev and J. F. F. Mendes.
Evolution of networks.
Advances in Physics, 51(4):1079-1187, 2002.
[Link].
38: L. Edelstein-Keshet.
Mathematical Models in Biology.
Random House, New York, NY, 1988.
39: R. Edwards.
Analysis of continuous-time switching networks.
Physica D, 146:165-199, 2000.
40: R. Edwards and L. Glass.
Combinatorial explosion in model gene networks.
Chaos, 10(3):691-704, 2000.
[Link].
41: M. B. Elowitz and S. Leibler.
A synthetic oscillatory network of transcriptional regulators.
Nature, 403:335-338, 2000.
[Link].
42: D. Endy and R. Brent.
Modelling cellular behaviour.
Nature, 409:391-395, 2001.
[Link].
43: J. J. Fox and C. C. Hill.
From topology to dynamics in biochemical networks.
Chaos, 11(4):809-815, 2001.
[Link].
44: S. A. Frank.
Population and quantitative genetics of regulatory networks.
Journal of Theoretical Biology, 197:281-294, 1999.
[Link].
45: T. S. Gardner, C. R. Cantor, and J. J. Collins.
Construction of a genetic toggle switch in Escherichia coli.
Nature, 403:339-342, 2000.
[Link].
46: N. Geard and J. Wiles.
Structure and dynamics of a gene network model incorporating small rnas.
In Sarker et al. [107], pages 199-206.
47: D. T. Gillespie.
Exact stochastic simulation of coupled chemical reactions.
J. Phys. Chem., 81(25), 1977.
48: D. T. Gillespie.
Approximate accelerated stochastic simulation of chemically reacting systems.
J. Chem. Phys., 115:1716-1733, 2001.
49: L. Glass and S. A. Kauffman.
The logical analysis of continuous non-linear biochemical control networks.
Journal of Theoretical Biology, 39:103-129, 1973.
50: B. D. Gomperts, P. E. R. Tatham, and I. M. Kramer.
Signal Transduction.
Academic Press, San Diego, CA, 2002.
51: P. J. E. Goss and J. Peccoud.
Quantitative modeling of stochastic systems in molecular biology by using stochastic petri nets.
Proceedings of the National Academy of Science, USA, 95:6750-6755, 1998.
[Link].
52: C. C. Guet, M. B. Elowitz, W. Hsing, and S. Leibler.
Combinatorial synthesis of genetic networks.
Science, 296:1466-1470, 2002.
[Link].
53: S. E. Harris, B. K. Sawhill, A. Wuensche, and S. A. Kauffman.
A model of transcriptional regulatory networks based on biases in the observed regulation rules.
Complexity, 7(4):23-40, 2002.
[Link].
54: L. H. Hartwell, J. J. Hopfield, S. Leibler, and A. W. Murray.
From molecular to modular cell biology.
Nature, 402:C47-C52, 1999.
55: I. Harvey and T. Bossamaier.
Time out of joint: attractors in asynchronous random boolean networks.
In P. Husbands and I. Harvey, editors, Fourth European Conference on Artificial Life, Cambridge, MA, 1997. The MIT Press/Bradford Books.
[Link].
56: J. Hasty, D. McMillen, and J. J. Collins.
Engineered gene circuits.
Nature, 420:224-230, 2002.
[Link].
57: J. Hasty, D. McMillen, F. Isaacs, and J. J. Collins.
Computational studies of gene regulatory networks: In numero molecular biology.
Nature Reviews Genetics, 2:268-279, 2001.
58: J. Hertz, A. Krogh, and R. G. Palmer.
Introduction to the Theory of Neural Computation.
Santa Fe Institute Studies in the Sciences of Complexity. Addison-Wesley, Redwood City, CA, 1990.
59: P. Hogeweg.
Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation.
Journal of Theoretical Biology, 203(4):317-333, 2000.
[Link].
60: P. Hogeweg.
Shapes in the shadow: Evolutionary dynamics of morphogenesis.
Artificial Life, 6:85-101, 2000.
[Link].
61: P. Hogeweg.
Computing an organism: on the interface between informatic and dynamic processes.
BioSystems, 64:97-109, 2002.
[Link].
62: J. Holland.
Emergence.
Addison-Wesley, Redwood City, CA, 1998.
63: S. Huang and D. E. Ingber.
Shape-dependent control of cell growth, differentiation, and apoptosis: Swtiching between attractors in cell regulatory networks.
Experimental Cell Research, 261:91-103, 2000.
[Link].
64: H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A.-L. Barabási.
The large-scale organization of metabolic networks.
Nature, 407:651-654, 2000.
[Link].
65: M. Kærn, W. J. Blake, and J. J. Collins.
The engineering of gene regulatory networks.
Annu. Rev. Biomed. Eng., 5:179-206, 2003.
[Link].
66: J. Kastner, J. Solomon, and S. Fraser.
Modeling a Hox gene network in silico using a stochastic simulation algorithm.
Developmental Biology, 246:122-131, 2002.
[Link].
67: S. A. Kauffman.
Metabolic stability and epigenesis in randomly constructed genetic nets.
Journal of Theoretical Biology, 22:437-467, 1969.
68: S. A. Kauffman.
Gene regulation networks: a theory for their global structure and behaviours.
Current Topics in Developmental Biology, 6:145-182, 1971.
69: S. A. Kauffman.
The large-scale structure and dynamics of gene control circuits: An ensemble approach.
Journal of Theoretical Biology, 44:167-190, 1974.
70: S. A. Kauffman.
The Origins of Order: Self-Organization and Selection in Evolution.
Oxford University Press, Oxford, UK, 1993.
71: S. A. Kauffman.
At Home in the Universe: The Search for Laws of Self-Organization and Complexity.
Penguin, London, UK, 1996.
72: E. F. Keller.
The Century of the Gene.
Harvard University Press, Cambridge, MA, 2000.
73: H. Kitano.
Foundations of Systems Biology.
The MIT Press/Bradford Books, Cambridge, MA, 2001.
74: H. Kitano.
Systems biology: a brief overview.
Science, 295:1662-1664, 2002.
[Link].
75: M. Ko.
A stochastic model for gene induction.
Journal of Theoretical Biology, 153:181-194, 1991.
76: J.-C. Leloup and A. Goldbeter.
Toward a detailed computational model for the mammalian circadian clock.
Proceedings of the National Academy of Science, USA, 100:7051-7056, 2003.
77: B. Lewin.
Genes VII.
Oxford University Press, Oxford, UK, 2000.
78: S. Liang, S. Fuhrman, and R. Somogyi.
REVEAL, a general reverse engineering algorithm for inference of genetic network architectures.
In Altman et al. [8], pages 18-29.
[PDF].
79: G. Marnellos and E. Mjolsness.
A gene network approach to modeling early neurogenesis in Drosophila.
In Altman et al. [8], pages 30-41.
[PDF].
80: G. Marnellos and E. D. Mjolsness.
Gene network models and neural development.
In A. van Ooyen, editor, Modeling Neural Development, pages 27-48. The MIT Press/Bradford Books, Cambridge, MA, 2003.
81: H. H. McAdams and A. Arkin.
Stochastic mechanisms in gene expression.
Proceedings of the National Academy of Science, USA, 94:814-819, 1997.
[Link].
82: H. H. McAdams and L. Shapiro.
Circuit simulation of genetic networks.
Science, 269:650-656, 1995.
83: E. Meir, G. von Dassow, and E. Munro.
Robustness, flexibility, and the role of lateral inhibition in the neurogenic network.
Current Biology, 12:778-786, 2002.
[Link].
84: L. Mendoza, D. Thieffry, and E. R. Alvarez-Buylla.
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.
Bioinformatics, 15(7):593-606, 1999.
[Link].
85: T. Mestl, E. Plahte, and S. W. Omholt.
A mathematical framework for describing and analysing gene regulatory networks.
Journal of Theoretical Biology, 176:291-300, 1995.
[Link].
86: R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon.
Network motifs: Simple building blocks of complex networks.
Science, 298:824-827, 2002.
[Link].
87: E. Mjolsness, D. H. Sharp, and J. Reinitz.
A connectionist model of development.
Journal of Theoretical Biology, 152:429-453, 1991.
88: A. Murray and T. Hunt.
The Cell Cycle: An Introduction.
Oxford University Press, New York, NY, 1993.
89: N. Le Novere and T. S. Shimizu.
STOCHSIM: modelling of stochastic biomolecular processes.
Bioinformatics, 17:575-576, 2001.
90: Z. N. Oltvai and A.-L. Barabási.
Life's complexity pyramid.
Science, 298:763-764, 2002.
[Link].
91: C. Oosawa and M. A. Savageau.
Effects of alternative connectivity on behavior of randomly constructed Boolean networks.
Physica D, 170:143-161, 2002.
[Link].
92: G. Orphanides and D. Reinberg.
A unified theory of gene expression.
Cell, 108:439-451, 2002.
[Link].
93: E. M. Ozbudak, M. Thattai, I. Kurster, A. D. Grossman, and A. van Oudenaarden.
Regulation of noise in the expression of a single gene.
Nature Genetics, 31:69-73, 2002.
94: E. A. Di Paolo.
Rhythmic and non-rhythmic attractors in asynchronous random boolean networks.
BioSystems, 59(3):185-195, 2001.
[Link].
95: M. Ptashne.
A Genetic Switch: Phage Lambda and Higher Organisms.
Blackwell Science, Oxford, UK, 1992.
96: L. Raeymaekers.
Dynamics of boolean networks controlled by biologically meaningful functions.
Journal of Theoretical Biology, 218:331-341, 2002.
[Link].
97: C. V. Rao, D. M. Wolf, and A. P. Arkin.
Control, exploitation and tolerance of intracellular noise.
Nature, 420:231-237, 2002.
[Link].
98: E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltavi, and A.-L. Barabási.
Hierarchical organization of modularity in metabolic networks.
Science, 297:1551-1555, 2002.
[Link].
99: T. Reil.
Dynamics of gene expression in an artificial genome - implications for biological and artificial ontogeny.
In D. Floreano, J.-D. Nicoud, and F. Mondada, editors, Advances in Artificial Life: 5th European Conference, ECAL '99, volume 1674 of Lecture Notes in Artificial Intelligence, pages 457-466, Berlin, 1999. Springer-Verlag.
[PS].
100: J. Reinitz, E. Mjolsness, and D. H. Sharp.
Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback.
Journal of Experimental Zoology (Mol. Dev. Evol.), 271:47-56, 1995.
101: J. Reinitz and D. H. Sharp.
Mechanism of eve stripe formation.
Mechanisms of Development, 49:133-158, 1995.
102: J. Reinitz and J. R. Vaisnys.
Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity.
Journal of Theoretical Biology, 145:295-318, 1990.
103: P. Rohlfshagen and E. A. Di Paolo.
The circular topology of rhythm in asynchronous random boolean networks.
BioSystems, 73:141-152, 2004.
[Link].
104: I. Salazar-Ciudad, J. Garcia-Fernández, and R. V. Solé.
Gene networks capable of pattern formation: From induction to reaction-diffusion.
Journal of Theoretical Biology, 205:587-603, 2000.
105: J. A. De Sales, M. L. Martins, and D. A. Stariolo.
Cellular automata model for gene networks.
Physical Review E, 55:3262-3270, 1997.
[Link].
106: L. Sánchez, J. van Helden, and D. Thieffry.
Establishment of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: A logical analysis.
Journal of Theoretical Biology, 189:377-389, 1997.
107: R. Sarker, R. Reynolds, H. Abbass, K.-C. Tan, R. McKay, D. Essam, and T. Gedeon, editors.
Proceedings of the IEEE 2003 Congress on Evolutionary Computation, Piscataway, NJ, 2003. IEEE Press.
108: C. R. Shalizi.
Methods and techniques of complex systems science: An overview.
In T. S. Deisboeck, J. Y. Kresh, and T. B. Kepler, editors, Complex Systems Science in Biomedicine. Kluwer, 2003.
[Link].
109: M. A. Shea and G. K. Ackers.
The o_r control system of bacteriophage lambda: A physical-chemical model for gene regulation.
Journal of Molecular Biology, 181:211-230, 1985.
110: C. W. Smith and J. Valcarel.
Alternative pre-mRNA splicing: the logic of combinatorial control.
Trends in Biochemical Science, 25:381-388, 2000.
[Link].
111: P. Smolen, D. A. Baxter, and J. H. Byrne.
Effects of macromolecular transport and stochastic fluctuations on the dynamics of genetic regulatory systems.
American Journal of Physiology, 274:C777-C790, 1999.
112: P. Smolen, D. A. Baxter, and J. H. Byrne.
Modeling transcriptional control in gene networks - methods, recent results, and future directions.
Bulletin of Mathematical Biology, 62:247-292, 2000.
[Link].
113: E. H. Snoussi.
Qualitative dynamics of piecewise-linear differential equations: A discrete mapping approach.
Dynamics and Stability of Systems, 4:189-207, 1989.
114: E. H. Snoussi and R. Thomas.
Logical identification of all steady states: The concept of feedback loop characteristic states.
Bulletin of Mathematical Biology, 55:973-991, 1993.
115: J. E. S. Socolar and S. A. Kauffman.
Scaling in ordered and critical random boolean networks.
Physical Review Letters, 90(6):068702, 2003.
[Link].
116: R. Solé, R. F. Cancho, J. M. Montoya, and S. Valverde.
Selection, tinkering and emergence in complex networks.
Complexity, 8(1):20-33, 2002.
[Link].
117: R. V. Solé, R. Pastor-Satorras, E. Smith, and T. B. Kepler.
A model of large-scale proteome evolution.
Advances in Complex Systems, 5(1):43-54, 2002.
118: R. V. Solé, I. Salazar-Ciudad, and J. Garcia-Fernández.
Common pattern formation, modularity and phase transitions in a gene network model of morphogenesis.
Physica A, 305:640-654, 2002.
119: R. Somogyi and C. A. Sniegoski.
Modelling the complexity of of genetic networks: Understanding multigenic and pleiotropic regulation.
Complexity, 1:45-63, 1996.
120: S. Strogatz.
Exploring complex networks.
Nature, 410:268-276, 2001.
[Link].
121: K. Struhl.
Fundamentally different logic of gene regulation in eukaryotes and prokaryotes.
Cell, 98:1-4, 1999.
[Link].
122: D. Thieffry and R. Thomas.
Dynamical behaviour of biological regulatory networks - II: Immunity control in bacteriophage lambda.
Bulletin of Mathematical Biology, 57:277-297, 1995.
123: R. Thomas.
Boolean formalization of genetic control circuits.
Journal of Theoretical Biology, 42:563-585, 1973.
124: R. Thomas.
Regulatory networks seen as asynchronous automata: A logical description.
Journal of Theoretical Biology, 153:1-23, 1991.
125: R. Thomas.
Laws for the dynamics of regulatory networks.
Int. J. Dev. Biol., 42:479-485, 1998.
[Link].
126: R. Thomas and M. Kaufman.
Dynamical behaviour of biological regulatory networks - I: Biological role of feedback loops and practical use of the concept of the loop-characteristic state.
Bulletin of Mathematical Biology, 57:247-276, 1995.
127: R. Thomas and M. Kaufman.
Multistationarity, the basis of cell differentiation and memory. I. logical analysis of regulatory networks in terms of feedback circuits.
Chaos, 11(1):180-195, 2001.
[Link].
128: R. Thomas and M. Kaufman.
Multistationarity, the basis of cell differentiation and memory. II. structural conditions of multistationarity and other nontrivial behaviour.
Chaos, 11(1):170-179, 2001.
[Link].
129: T. Tian and K. Burrage.
Stochastic neural network models for gene regulatory networks.
In Sarker et al. [107], pages 162-169.
[PDF].
130: J. J. Tyson.
Models of cell cycle control in eukaryotes.
Journal of Biotechnology, 71:239-244, 1999.
131: J. J. Tyson, K. Chen, and B. Novak.
Network dynamics and cell physiology.
Nature Reviews Molecular Cell Biology, 2:908-916, 2001.
[Link].
132: J. J. Tyson and H. Othmer.
The dynamics of feedback control circuits in biochemical pathways.
Progress in Theoretical Biology, 5:1-62, 1978.
[PDF].
133: P. van Ham.
How to deal with more than two levels.
In R. Thomas, editor, Kinetic Logic: A Boolean Approach to the Analysis of Complex Regulatory Systems, volume 29 of Lecture Notes in Biomathematics, pages 326-343. Springer-Verlage, Berlin, 1979.
134: E. P. van Someren, L. F. A. Wessels, E. Backer, and M. J. T. Reinders.
Genetic network modeling.
Pharmacogenomics, 3(4):507-525, 2002.
135: A. Vázquez, A. Flammini, A. Maritan, and A. Vespignani.
Modelling of protein interaction networks.
cond-mat/0108043, 2001.
136: J. Vohradský.
Neural model of the genetic network.
The Journal of Biological Chemistry, 276(39):36168-36173, 2001.
[Link].
137: J. Vohradský.
Neural network model of gene expression.
The FASEB Journal, 15:846-854, 2001.
[Link].
138: G. von Dassow, E. Meir, E. M. Munro, and G. M. Odell.
The segment polarity network is a robust developmental module.
Nature, 406:188-192, 2000.
[Link].
139: A. Wagner and D. A. Fell.
The small world inside large metabolic networks.
Proceedings of the Royal Society of London, Series B, 268:1803-1810, 2001.
[Link].
140: D. J. Watts.
Small Worlds: The Dynamics of Networks between Order and Randomness.
Princeton Univ. Press, Princeton, NJ, 1999.
141: D. J. Watts and S. Strogatz.
Collective dynamics of `small world' networks.
Nature, 393:440-442, 1998.
[Link].
142: L. Wolpert.
The Principles of Development.
Oxford University Press, Oxford, UK, 1998.
143: A. Wuensche.
The ghost in the machine: Basin of attraction fields of random boolean networks.
In C. G. Langton, editor, Artificial Life III, Sante Fe Institute Studies in the Sciences of Complexity. Addison-Wesley, Reading, MA, 1994.
144: A. Wuensche.
Genomic regulation modeled as a network with basins of attraction.
In Altman et al. [8], pages 89-102.
[Link].
145: C.-H. Yuh, H. Bolouri, and E. H. Davidson.
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene.
Science, 279:1896-1902, 1998.
[Link].

Nic Geard 2004-05-06