|
ABSTRACT
The convergence of CS and biology will serve both disciplines, providing each with greater power and relevance.
REFERENCES
Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.
| |
1
|
Alon, U. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall, 2006.
|
| |
2
|
R. Alur , C. Courcoubetis , N. Halbwachs , T. A. Henzinger , P.-H. Ho , X. Nicollin , A. Olivero , J. Sifakis , S. Yovine, The algorithmic analysis of hybrid systems, Theoretical Computer Science, v.138 n.1, p.3-34, Feb. 6, 1995
[doi> 10.1016/0304-3975(94)00202-T]
|
| |
3
|
Auffray, C. and Nottale, L. Scale relativity theory and integrative systems biology: Founding principles and scale laws. Progress in Biophysics and Molecular Biology 97 (2008), 79--114.
|
| |
4
|
Benner, S.A. and Sismour, A.M. Synthetic biology. Nature Reviews Genetics 6 (2005), 533--544.
|
| |
5
|
|
| |
6
|
Bernardo, M., Degano, P., and Zavattaro, G. Formal Methods for Computational Systems Biology. LNCS 5016, Springer, 2008.
|
| |
7
|
Boogerd, F. et al. Systems Biology: Philosophical Foundations. Elsevier, 2007.
|
| |
8
|
Breckling, B. Individual-based modelling: Potentials and limitations. Scientific World Journal 2 (April 19,2002). 1044--1062.
|
| |
9
|
Cassman, M., Arkin, A., Doyle, F., Katagiri, F., Lauffenburg, D., and Stokes, C. International Research and Development in Systems Biology, WTEC Panel on Systems Biology final report (Oct. 2005).
|
| |
10
|
Chiarugi, D., Degano, P., and Marangoni, R. A computational approach to the functional screening of genomes. PLoS Comput Biol 3, 9 (Sept. 3, 2007), 1801--1806.
|
| |
11
|
Ciocchetta, F. and Hillston, J. Process algebras in systems biology. In Formal Methods for Computational Systems Biology, LNCS 5016. Springer, 2008, 313--365.
|
 |
12
|
|
| |
13
|
|
| |
14
|
|
| |
15
|
Dematté, L., Priami, C., and Romanel, A. The BlenX language: A tutorial. In Formal Methods for Computational Systems Biology, LNCS 5016. Springer, 2008. 313--365.
|
| |
16
|
Dematté, L., Priami, C., Romanel, A. The Beta Workbench: A tool to study the dynamics of biological systems. Briefings in Bioinformatics, 2008.
|
 |
17
|
|
 |
18
|
|
 |
19
|
|
 |
20
|
|
| |
21
|
Dijstra, E.W. Programming as a discipline of mathematical nature. American Mathematical Monthly 81 (1974), 608--612.
|
| |
22
|
Fisher, J. and Henzinger, T. Executable cell biology. Nature Biotechnology 25 (2007), 1239--1249.
|
| |
23
|
Forrest, S. and Beauchemin, C. Imm. Reviews 216 (2007), 176--197.
|
| |
24
|
Foster, A.C., Church, G.M. Towards synthesis of a minimal cell. Molecular Systems Biology (2006).
|
| |
25
|
Gillespie, D.T. Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81 (1977), 2340--2361.
|
| |
26
|
Goldbeter, A. Computational approaches to cellular rhythms. Nature 420 (2002), 238--245.
|
| |
27
|
Gutowitz, H. Introduction (to cellular automata). Physica D 45, 1990.
|
 |
28
|
|
 |
29
|
|
| |
30
|
Hood, L., Galas, D. The digital code of DNA. Nature 421 (2003), 444--448.
|
| |
31
|
Kitano, H. Systems biology: A brief overview. Science 295 (2002), 1662--1664.
|
 |
32
|
|
| |
33
|
Knuth, D. Computer science and its relation to mathematics. American Mathematical Monthly 81 (1974), 323--343.
|
| |
34
|
Kuwahara, H. and Mura, I. An efficient and exact stochastic simulation method to analyze rare events in biological systems. Journal of Chemical Physics 129. 2008.
|
| |
35
|
Ludtke, N., Panzeri, S., Brown, M., Broornhead, D.S., Knowles, J., Montemurro M.A., and Kell, D.B. Information-theoretic sensitivity analysis: A general method for credit assignment in complex networks. J. R. Soc Interface 5 (2008), 223--235.
|
 |
36
|
|
| |
37
|
Nature insight: Computational biology. Nature 420 (2002), 206--251.
|
| |
38
|
Nurse, P. Life, logic and information. Nature 454 (2008), 424--426.
|
 |
39
|
|
| |
40
|
O'Malley, M. and Dupré, J. Fundamental issues in systems biology. BioEssays, 27 (2005), 1270--1276.
|
| |
41
|
|
| |
42
|
Priami, C. and Quaglia, P. Modeling the dynamics of biosystems. Briefings in Bioinformatics 5 (2004), 259--269.
|
| |
43
|
|
| |
44
|
Rao, C.V., Wolf, D.M., and Arkin, A.P. Control, exploitation and tolerance of intracellular noise. Nature 420 (2002), 231--237.
|
| |
45
|
Rapin, N., Kesmir, C., Frankild, S., Nielsen, M., Lundegaard, C., Brunak, S., and Lund, O. Modeling the human immune system by combining bioinformatics and systems biology approaches. Journal Biol. Phys. 32 (2006), 335--353.
|
| |
46
|
Regev, A. and Shapiro, E. Cells as computation. Nature 419 (2002), 343.
|
| |
47
|
Roos, D. Bioinformatics--- Trying to swim in a sea of data. Science 291 (2001), 260--1261.
|
| |
48
|
Searls, D. The language of genes. Nature 420 (2002), 211--217.
|
| |
49
|
Spengler, S.J. Bioinformatics in the information age. Science 287 (2000), 1221--1223.
|
 |
50
|
|
| |
51
|
Volterra, V. Fluctuations in the abundance of species considered mathematically. Nature 118 (1926). 558--560.
|
| |
52
|
Welch, P.H. and Barnes, F.R.M. Communicating mobile processes: Introducing occam-pi. In CSP25, LNCS 3525. Springer, 2005, 175--210.
|
 |
53
|
|
|