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SYNASC
2007
IEEE
119views Algorithms» more  SYNASC 2007»
13 years 11 months ago
Graph Rewriting and Strategies for Modeling Biochemical Networks
In this paper, we present a rewriting framework for modeling molecular complexes, biochemical reaction rules, and generation of biochemical networks based on the representation of...
Oana Andrei, Hélène Kirchner
CSB
2005
IEEE
163views Bioinformatics» more  CSB 2005»
13 years 10 months ago
A symbolic approach to the simulation of biochemical models: application to circadian rhythms
Symbolic rewriting systems are gaining interest as tools for simulating biochemical dynamics. Compared to traditional methods based on differential equations, the symbolic approac...
Federico Fontana, Luca Bianco, Vincenzo Manca
CEC
2010
IEEE
13 years 6 days ago
Parameter estimation with term-wise decomposition in biochemical network GMA models by hybrid regularized Least Squares-Particle
High-throughput analytical techniques such as nuclear magnetic resonance, protein kinase phosphorylation, and mass spectroscopic methods generate time dense profiles of metabolites...
Prospero C. Naval, Luis G. Sison, Eduardo R. Mendo...
HYBRID
2007
Springer
13 years 9 months ago
Qualitative Analysis of Nonlinear Biochemical Networks with Piecewise-Affine Functions
Abstract. Nonlinearities and the lack of accurate quantitative information considerably hamper modeling and system analysis of biochemical networks. Here we propose a procedure for...
M. W. J. M. Musters, Hidde de Jong, P. P. J. van d...
EVOW
2008
Springer
13 years 7 months ago
Enhancing Parameter Estimation of Biochemical Networks by Exponentially Scaled Search Steps
A fundamental problem of modelling in Systems Biology is to precisely characterise quantitative parameters, which are hard to measure experimentally. For this reason, it is common ...
Hendrik Rohn, Bashar Ibrahim, Thorsten Lenser, Tho...