分子网络
For practical construction of complex synthetic genetic networks able to perform elaborate functions it is important to have a pool of relatively simple "bio-bricks" with different functionality which can be compounded together. To…
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has…
The ribosome flow model with input and output (RFMIO) is a deterministic dynamical system that has been used to study the flow of ribosomes during mRNA translation. The RFMIO and its variants encapsulate important properties that are…
We study a stochastic model of biosynthesis of proteins in generic bacterial operons. The stochasticity arises from two different processes, namely from `bursting' production of either mRNA and/or protein (in the transcription/translation…
Using the formalism of information theory, we analyze the mechanism of information transduction in a simple one-step signaling cascade S$\rightarrow$X representing the gene regulatory network. Approximating the signaling channel to be…
Network-based computational approaches to predict unknown genes associated with certain diseases are of considerable significance for uncovering the molecular basis of human diseases. In this paper, we proposed a kind of new…
Many studies have shown that cells use temporal dynamics of signalling molecules to encode information. One particular class of temporal dynamics is persistent and transient signals, i.e. signals of long and short durations respectively. It…
Purpose of review: The epithelial-Mesenchymal Transition (EMT) and the generation of Cancer Stem Cells (CSC) are two fundamental aspects contributing to tumor growth, acquisition of resistance to therapy, formation of metastases, and tumor…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Stochastic fluctuations in the copy number of gene products have perceivable effects on the functioning of gene regulatory networks (GRN). The Master equation (ME) provides a theoretical basis for studying such effects. However, solving the…
Molecular variants of vitamin B12, siderophores and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
In this study, we investigated the effects of specific low frequency electromagnetic fields sequences on U937 cells, an in vitro model of human monocyte/macrophage differentiation. U937 cells were exposed to electromagnetic stimulation by…
The analysis of biological networks is characterized by the definition of precise linear constraints used to cumulatively reduce the solution space of the computed states of a multi-omic (for instance metabolic, transcriptomic and…
Parametrized polynomial ordinary differential equation systems are broadly used for modeling, specially in the study of biochemical reaction networks under the assumption of mass-action kinetics. Understanding the qualitative behavior of…
Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a…
Living cells communicate information about physiological conditions by producing signaling molecules in a specific timed manner. Different conditions can result in the same total amount of a signaling molecule, differing only in the pattern…
The formalism of partial information decomposition provides independent or non-overlapping components constituting total information content provided by a set of source variables about the target variable. These components are recognised as…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…