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Gene regulatory network inference is crucial for understanding the complex molecular interactions in various genetic and environmental conditions. The rapid development of single-cell RNA sequencing (scRNA-seq) technologies unprecedentedly…
The past decade has seen great advances in our understanding of the role of noise in gene regulation and the physical limits to signaling in biological networks. Here we introduce the spectral method for computation of the joint probability…
Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
In recent years, the study of biological transportation networks has attracted significant interest, focusing on their self-regulating, demand-driven nature. This paper examines a mathematical model for these networks, featuring nonlinear…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
Self-regulation of living tissue as an example of self-organization phenomena in active fractal systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
The reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions.…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
Regulatory networks (RNs) are a well-accepted modelling formalism in computational systems biology. The control of RNs is currently receiving a lot of attention because it provides a computational basis for cell reprogramming -- an…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Dynamical properties of the transcriptional regulatory network of {\it Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…