Related papers: Cell biology: Networks, regulation, pathways

Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the…

Many real-world complex systems are best modeled by multiplex networks of interacting network layers. The multiplex network study is one of the newest and hottest themes in the statistical physics of complex networks. Pioneering studies…

Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…

Since its first formulations almost a century ago, mathematical models for disease spreading contributed to understand, evaluate and control the epidemic processes.They promoted a dramatic change in how epidemiologists thought of the…

Endowing brain anatomy, dynamics, and function with a network structure is becoming standard in neuroscience. In its simplest form, a network is a collection of units and relationships between them. The pattern of relations among the units…

To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…

In network science complex systems are represented as a mathematical graphs consisting of a set of nodes representing the components and a set of edges representing their interactions. The framework of networks has led to significant…

Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…

This text is based on a translation of a chapter in a handbook about network analysis (published in German) where we tried to make beginners familiar with some basic notions and recent developments of network analysis applied to…

Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…

Sustainable research on computational models of neuronal networks requires published models to be understandable, reproducible, and extendable. Missing details or ambiguities about mathematical concepts and assumptions, algorithmic…

The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…

Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…

In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…

All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…

Modeling and topological analysis of networks in biological and other complex systems, must venture beyond the limited consideration of very few network metrics like degree, betweenness or assortativity. A proper identification of…

We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…

Cellular heterogeneity is an immanent property of biological systems that covers very different aspects of life ranging from genetic diversity to cell-to-cell variability driven by stochastic molecular interactions, and noise induced cell…

Network theory has unveiled the underlying structure of complex systems such as the Internet or the biological networks in the cell. It has identified universal properties of complex networks, and the interplay between their structure and…

In this paper I present some of the most representative biological models applied to robotics. In particular, this work represents a survey of some models inspired, or making use of concepts, by gene regulatory networks (GRNs): these…