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Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…
We consider two mathematical dynamical models of gene regulatory networks (GRNs) and obtain results on robust synchronization on these dynamical models based on the existing theoretical results in the coupled cell network formalism. We also…
A blood cell lineage consists of several consecutive developmental stages from the pluripotent or multipotent stem cell to a particular stage of terminally differentiated cells. There is considerable interest in identifying the key…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
Generative neural networks can produce data samples according to the statistical properties of their training distribution. This feature can be used to test modern computational neuroscience hypotheses suggesting that spontaneous brain…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's…
Phenotype transition takes place in many biological processes such as differentiation, and understanding how a cell reprograms its global gene expression profile is a problem of rate theories. A cell phenotype transition accompanies with…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
Gene Regulatory Networks(GRNs) with feedback are essential components of many cellular processes and may exhibit oscillatory behavior. Analyzing such systems becomes increasingly complex as the number of components increases. Since gene…
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…
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.…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this paper we investigate these properties within an artificial genome model originally…
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…