Related papers: Motifs emerge from function in model gene regulato…

Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…

Signed networks, i.e., networks with positive and negative edges, commonly arise in various domains from social media to epidemiology. Modeling signed networks has many practical applications, including the creation of synthetic data sets…

Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…

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…

Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…

The study of motifs in networks can help researchers uncover links between the structure and function of networks in biology, sociology, economics, and many other areas. Empirical studies of networks have identified feedback loops,…

Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…

Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the…

Background: Networks in different domains are characterized by similar global characteristics while differing in local structures. To further extend this concept, we investigated network regularities on a fine scale in order to examine the…

Several natural and theoretical networks can be broken down into smaller portions, or subgraphs corresponding to neighborhoods. The more frequent of these neighborhoods can then be understood as motifs of the network, being therefore…

Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…

Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…

Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…

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…

Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…

Signal processing in biological systems is delicately executed by specialised networks, which are modular assemblies of network motifs. The motifs are independently functional circuits found in enormous numbers in any living cell. A very…

Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks…

How the architecture of gene regulatory networks ultimately shapes gene expression patterns is an open question, which has been approached from a multitude of angles. The dominant strategy has been to identify non-random features in these…

Logical modeling is a powerful tool in biology, offering a system-level understanding of the complex interactions that govern biological processes. A gap that hinders the scalability of logical models is the need to specify the update…

We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…