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Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
Networks are a powerful abstraction with applicability to a variety of scientific fields. Models explaining their morphology and growth processes permit a wide range of phenomena to be more systematically analysed and understood. At the…
We introduce a new methodology to analyze the evolution of epidemic time series, which is based on the construction of epidemic networks. First, we translate the time series into ordinal patterns containing information about local…
The possibility to use Neural Networks for reconstruction of the energy deposited in the calorimetry system of the CMS detector is investigated. It is shown that using feed - forward neural network, good linearity, Gaussian energy…
The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…
Temporal gene expression data (Wen, et. al.) was analyzed using the recently introduced inverse modeling technique of Embedded Complex Logistic Maps (ECLM). Preliminary results indicate scale-free structure in the gene regulatory network…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
A model of cellular metabolism due to S. Kauffman is analyzed. It consists of a network of Boolean gates randomly assembled according to a probability distribution. It is shown that the behavior of the network depends very critically on…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
We study the network reconstruction problem for an epidemic reaction-diffusion. These models are an extension of deterministic, compartmental models to a graph setting, where the reactions within the nodes are coupled by a diffusion. We…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
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…
Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational…