Моделовање биолошких система

Моделовање биолошких система је значајан задатак системске биологије и математичке биологије. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks), to both analyze and visualize the complex connections of these cellular processes.

Вештачки живот или virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.

Литература

• Antmann, S. S.; Marsden, J. E.; Sirovich, L., ур. (2009). Mathematical Physiology (2nd изд.). New York, New York: Springer. ISBN 978-0-387-75846-6. 
• Barnes, D.J.; Chu, D. (2010), Introduction to Modelling for Biosciences, Springer Verlag 
• An Introduction to Infectious Disease Modelling by Emilia Vynnycky and Richard G White. An introductory book on infectious disease modelling and its applications.
• Barab, A. -L.; Oltvai, Z. (2004). „Network biology* understanding the cell's functional organization”. Nature Reviews Genetics. 5 (2): 101—113. PMID 14735121. doi:10.1038/nrg1272. 
• Covert; Schilling, C.; Palsson, B. (2001). „Regulation of gene expression in flux balance models of metabolism”. Journal of Theoretical Biology. 213 (1): 73—88. CiteSeerX 10.1.1.110.1647 . PMID 11708855. doi:10.1006/jtbi.2001.2405. 
• Covert, M. W.; Palsson, B. . (2002). „Transcriptional regulation in constraints-based metabolic models of Escherichia coli”. The Journal of Biological Chemistry. 277 (31): 28058—28064. PMID 12006566. doi:10.1074/jbc.M201691200. 
• Edwards; Palsson, B. (2000). „The Escherichia coli MG1655 in silico metabolic genotype* its definition, characteristics, and capabilities”. Proceedings of the National Academy of Sciences of the United States of America. 97 (10): 5528—5533. Bibcode:2000PNAS...97.5528E. PMC 25862 . PMID 10805808. doi:10.1073/pnas.97.10.5528. 
• Bonneau, R. (2008). „Learning biological networks* from modules to dynamics”. Nature Chemical Biology. 4 (11): 658—664. PMID 18936750. doi:10.1038/nchembio.122. 
• Edwards, J. S.; Ibarra, R. U.; Palsson, B. O. (2001). „In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data”. Nature Biotechnology. 19 (2): 125—130. PMID 11175725. doi:10.1038/84379. 
• Fell, D. A. (1998). „Increasing the flux in metabolic pathways* A metabolic control analysis perspective”. Biotechnology and Bioengineering. 58 (2–3): 121—124. PMID 10191380. doi:10.1002/(SICI)1097-0290(19980420)58:2/3<121::AID-BIT2>3.0.CO;2-N. 
• Hartwell, L. H.; Hopfield, J. J.; Leibler, S.; Murray, A. W. (1999). „From molecular to modular cell biology”. Nature. 402 (6761 Suppl): C47—C52. PMID 10591225. doi:10.1038/35011540. 
• Ideker; Galitski, T.; Hood, L. (2001). „A new approach to decoding life* systems biology”. Annual Review of Genomics and Human Genetics. 2 (1): 343—372. PMID 11701654. doi:10.1146/annurev.genom.2.1.343. 
• Kitano, H. (2002). „Computational systems biology”. Nature. 420 (6912): 206—210. Bibcode:2002Natur.420..206K. PMID 12432404. doi:10.1038/nature01254. 
• Kitano, H. (2002). „Systems biology* a brief overview”. Science. 295 (5560): 1662—1664. Bibcode:2002Sci...295.1662K. CiteSeerX 10.1.1.473.8389 . PMID 11872829. doi:10.1126/science.1069492. 
• Kitano (2002). „Looking beyond the details* a rise in system-oriented approaches in genetics and molecular biology”. Current Genetics. 41 (1): 1—10. PMID 12073094. doi:10.1007/s00294-002-0285-z. 
• Gilman, A. G.; Simon, M. I.; Bourne, H. R.; Harris, B. A.; Long, R.; Ross, E. M.; Stull, J. T.; Taussig, R.; Bourne, H. R.; Arkin, A. P.; Cobb, M. H.; Cyster, J. G.; Devreotes, P. N.; Ferrell, J. E.; Fruman, D.; Gold, M.; Weiss, A.; Stull, J. T.; Berridge, M. J.; Cantley, L. C.; Catterall, W. A.; Coughlin, S. R.; Olson, E. N.; Smith, T. F.; Brugge, J. S.; Botstein, D.; Dixon, J. E.; Hunter, T.; Lefkowitz, R. J.; Pawson, A. J. (2002). „Overview of the Alliance for Cellular Signaling”. Nature. 420 (6916): 703—706. Bibcode:2002Natur.420..703G. PMID 12478301. doi:10.1038/nature01304. 
• Palsson, Bernhard (2006). Systems biology* properties of reconstructed networks. Cambridge: Cambridge University Press. ISBN 978-0-521-85903-5. 
• Kauffman; Prakash, P.; Edwards, J. S. (2003). „Advances in flux balance analysis”. Current Opinion in Biotechnology. 14 (5): 491—496. PMID 14580578. doi:10.1016/j.copbio.2003.08.001. 
• Segrè, D.; Vitkup, D.; Church, G. M. (2002). „Analysis of optimality in natural and perturbed metabolic networks”. Proceedings of the National Academy of Sciences of the United States of America. 99 (23): 15112—15117. Bibcode:2002PNAS...9915112S. PMC 137552 . PMID 12415116. doi:10.1073/pnas.232349399. 
• Wildermuth, MC (2000). „Metabolic control analysis* biological applications and insights.”. Genome Biology. 1 (6): REVIEWS1031. PMC 138895 . PMID 11178271. doi:10.1186/gb-2000-1-6-reviews1031. 

Спољашње везе

• The Center for Modeling Immunity to Enteric Pathogens (MIEP)