ABSTRACT
Recent work has presented logical models and showed the benefits of applying logical approaches to studying the dynamics of biological networks. In this work, we develop a methodology for automating the design of such models by utilizing methods and algorithms from the field of electronic design automation. We anticipate that automated discrete model development will greatly improve the efficiency of qualitative analysis of biological networks.
- R. Zhang, et al., "Network model of survival signaling in large granular lymphocyte leukemia," Proc Natl Acad Sci U S A, vol. 105, pp. 16308--13, Oct 21 2008.Google ScholarCross Ref
- L. Mendoza, "A network model for the control of the differentiation process in Th cells," Biosystems, vol. 84, pp. 101--14, May 2006.Google ScholarCross Ref
- M. I. Davidich and S. Bornholdt, "Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast," PLoS One, vol. 3, pp. -, Feb 27 2008.Google ScholarCross Ref
- J. Saez-Rodriguez, et al., "Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction," Molecular Systems Biology, vol. 5, pp. -, Dec 2009.Google Scholar
- S. Bornholdt, "Boolean network models of cellular regulation: prospects and limitations," J R Soc Interface, vol. 5 Suppl 1, pp. S85--94, Aug 6 2008.Google Scholar
- N. Miskov-Zivanov, et al., "Boolean Modeling and Analysis of Peripheral T Cell Differentiation of Work," personal communication, 2013.Google Scholar
- N. Miskov-Zivanov, et al., "Emulation of Biological Networks in Reconfigurable Hardware," in Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), 2011, pp. 536--540. Google ScholarDigital Library
- N. Miskov-Zivanov, et al., "Regulatory network analysis acceleration with reconfigurable hardware," Conf Proc IEEE Eng Med Biol Soc, vol. 2011, pp. 149--52, 2011.Google Scholar
- D. T. Gillespie, "Exact stochastic simulation of coupled chemical reactions," The Journal of Physical Chemistry, vol. 81, pp. 2340--2361, 1977.Google ScholarCross Ref
- J. J. Tyson, et al., "The dynamics of cell cycle regulation," Bioessays, vol. 24, pp. 1095--1109, Dec 2002.Google ScholarCross Ref
- M. Novak and J. J. Tyson, "A model for restriction point control of the mammalian cell cycle," Journal of Theoretical Biology, vol. 230, pp. 563--579, Oct 21 2004.Google ScholarCross Ref
- M. L. Blinov, et al., "BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains," Bioinformatics, vol. 20, pp. 3289--91, Nov 22 2004. Google ScholarDigital Library
- J. R. Faeder, et al., "Rule-based modeling of biochemical systems with BioNetGen," Methods Mol Biol, vol. 500, pp. 113--67, 2009.Google ScholarCross Ref
- I. Albert, et al., "Boolean network simulations for life scientists," Source Code Biol Med, vol. 3, p. 16, 2008.Google ScholarCross Ref
- M. Chaves, et al., "Robustness and fragility of Boolean models for genetic regulatory networks," J Theor Biol, vol. 235, pp. 431--49, Aug 7 2005.Google ScholarCross Ref
- J. R. Faeder, et al., "Investigation of early events in Fc epsilon RI- mediated signaling using a detailed mathematical model," J Immunol, vol. 170, pp. 3769--81, Apr 1 2003.Google ScholarCross Ref
- The Systems Biology Markup Language (SBML). Available: http://sbml.org/Main_PageGoogle Scholar
- K. Sachs, et al., "Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data," Science, vol. 308, pp. 523--529, April 22, 2005 2005.Google ScholarCross Ref
- T. S. Gardner, et al., "Inferring genetic networks and identifying compound mode of action via expression profiling," Science, vol. 301, pp. 102--5, Jul 4 2003.Google ScholarCross Ref
- J. Saez-Rodriguez, et al., "Flexible informatics for linking experimental data to mathematical models via DataRail," Bioinformatics, vol. 24, pp. 840--7, Mar 15 2008. Google ScholarDigital Library
- G. D. Hachtel and F. Somenzi, Logic synthesis and verification algorithms. Boston: Kluwer Academic Publishers, 1996. Google ScholarDigital Library
- R. K. Brayton, Logic minimization algorithms for VLSI synthesis. Boston: Kluwer Academic Publishers, 1984. Google ScholarDigital Library
- Y. Vodovotz, et al., "Modeling Host-Vector-Pathogen Immuno-inflammatory Interactions in Malaria," in Complex Systems and Computational Biology Approaches to Acute Inflammation, ed: Springer Science+Business Media, LLC., 2013.Google Scholar
- ModelSim - Advanced Simulation and Debugging. Available: http://model.com/Google Scholar
Index Terms
- Dynamic behavior of cell signaling networks: model design and analysis automation
Recommendations
An algorithm for modularization of MAPK and calcium signaling pathways: Comparative analysis among different species
Signaling pathways are large complex biochemical networks. It is difficult to analyze the underlying mechanism of such networks as a whole. In the present article, we have proposed an algorithm for modularization of signal transduction pathways. Unlike ...
Synthetic biology of cell signaling
Synthetic biology often takes cues from complex natural networks and pathways to create novel biological systems. The design modalities used in synthetic systems generally follow the different classes of gene regulation in cells such as transcriptional, ...
Evidence for the relationship between the regulatory effects of microRNAs and attack robustness of biological networks
It has been previously suggested that microRNAs (miRNAs) have a tendency to regulate the important components of biological networks. The goal of the present study was to systematically test if one can establish a relationship between miRNA targets and ...
Comments