Related papers: Coherent organization in gene regulation: a study …
Regulatory functions are essential in both socioeconomic and biological systems, from corporate managers to regulatory genes. Regulatory functions come with substantial costs and benefits, and the balance of the two is often taken for…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
The diversity of expressed genes plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across cell types and is orchestrated by intricate,…
Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
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.…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
Power system coherency refers to the phenomenon that machines in a power network exhibit similar frequency responses after disturbances, and is foundational for model reduction and control design. Despite abundant empirical observations,…
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective,…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate…
Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…
All cells respond to changes in both their internal milieu and the environment around them through the regulation of their genes. Despite decades of effort, there remain huge gaps in our knowledge of both the function of many genes (the…
The structure of a stochastic nonlinear gene regulatory network is uncovered by studying its response to input signal generators. Four applications are studied in detail: a nonlinear connection of two linear systems, the design of a logic…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…