Inferring qualitative relations in genetic networks and metabolic pathways
TLDR
Inferring genetic network architecture from time series data of gene expression patterns is an important topic in bioinformatics and inference algorithms based on the Boolean network were proposed, but were not sufficient as a model of a genetic network.Abstract:
Motivation: Inferring genetic network architecture from time series data of gene expression patterns is an important topic in bioinformatics. Although inference algorithms based on the Boolean network were proposed, the Boolean network was not sufficient as a model of a genetic network. Results: First, a Boolean network model with noise is proposed, together with an inference algorithm for it. Next, a qualitative network model is proposed, in which regulation rules are represented as qualitative rules and embedded in the network structure. Algorithms are also presented for inferring qualitative relations from time series data. Then, an algorithm for inferring S-systems (synergistic and saturable systems) from time series data is presented, where S-systems are based on a particular kind of nonlinear differential equation and have been applied to the analysis of various biological systems. Theoretical results are shown for Boolean networks with noises and simple qualitative networks. Computational results are shown for Boolean networks with noises and S-systems, where real data are not used because the proposed models are still conceptual and the quantity and quality of currently available data are not enough for the application of the proposed methods.read more
Citations
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Modeling and simulation of genetic regulatory systems: a literature review.
TL;DR: This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equation, stochastic equations, and so on.
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Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
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Controllability and observability of Boolean control networks
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Advances to Bayesian network inference for generating causal networks from observational biological data
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References
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Johan de Kleer,John Seely Brown +1 more
TL;DR: A fairly encompassing account of qualitative physics, which introduces causality as an ontological commitment for explaining how devices behave, and presents algorithms for determining the behavior of a composite device from the generic behavior of its components.
Proceedings Article
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
TL;DR: This study investigates the possibility of completely infer a complex regulatory network architecture from input/output patterns of its variables using binary models of genetic networks, and finds the problem to be tractable within the conditions tested so far.