Related papers: The Yeast Cell-Cycle Network Is Robustly Designed

A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…

Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…

Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…

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…

The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…

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…

The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…

Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…

Spin models of neural networks and genetic networks are considered elegant as they are accessible to statistical mechanics tools for spin glasses and magnetic systems. However, the conventional choice of variables in spin systems may cause…

Motivation: Since susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and…

The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…

Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the…

The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…

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…

The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological…

Network science has experienced unprecedented rapid development in the past two decades. The network perspective has also been widely applied to explore various complex systems in great depth. In the first decade, fundamental…

The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…

Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a…

Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…