Related papers: A Taxonomy of Causality-Based Biological Propertie…
Causal Bayesian networks are 'causal' models since they make predictions about interventional distributions. To connect such causal model predictions to real-world outcomes, we must determine which actions in the world correspond to which…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Metabolic networks have two properties that are generally regarded as unrelated: One, they have metabolic reactions whose single knockout is lethal for the organism, and two, they have correlated sets of reactions forming functional…
Provenance, or information about the sources, derivation, custody or history of data, has been studied recently in a number of contexts, including databases, scientific workflows and the Semantic Web. Many provenance mechanisms have been…
Provenance, or information about the sources, derivation, custody or history of data, has been studied recently in a number of contexts, including databases, scientific workflows and the Semantic Web. Many provenance mechanisms have been…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
A new method is developed to represent probabilistic relations on multiple random events. Where previously knowledge bases containing probabilistic rules were used for this purpose, here a probability distribution over the relations is…
This paper analyzes the notion of causality in a conceptual model, mainly as applied in software engineering. Conceptual system modeling can be considered a three-level process that begins with building a static structural description to…
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…