Related papers: Cell biology: Networks, regulation, pathways
This paper provides the analysis for structural and functional approaches of complex network systems research. In order to study the behavior of these systems the flow adjacency matrices were introduced, and local and global dynamic…
Several complexity metrics are described which are related to logic structure, data structure and size of spreadsheet models. They primarily concentrate on the dispersion of cell references and cell paths. Most metrics are newly defined,…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in…
The origin and early evolution of eukaryotes are one of the major transitions in the evolution of life on earth. One of its most interesting aspects is the emergence of cellular organelles, their dynamics, their functions, and their…
The emergence and popularization of online social networks suddenly made available a large amount of data from social organization, interaction and human behavior. All this information opens new perspectives and challenges to the study of…
We review measures of street network structure proposed in the recent literature, establish their relevance to practice, and identify open challenges facing researchers. These measures' empirical values vary substantially across world…
Despite their widespread utility across domains, basic network models face fundamental limitations when applied to complex biological systems, particularly in neuroscience. This paper critically examines these limitations and explores…
A coupled map is suggested to investigate various spatial or temporal designs in biology: Several cells (or tissues) in an organ are considered as connected to each other in terms of some molecular diffusions or electrical potential…
With the tremendous increase in the amount of biological literature, developing automated methods for extracting big data from papers, building models and explaining big mechanisms becomes a necessity. We describe here our approach to…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Over the past decade network theory has turned out to be a powerful methodology to investigate complex systems of various sorts. Through data analysis, modeling, and simulation quite an unparalleled insight into their structure, function,…
Network-based approaches have become increasingly prominent in science education research as tools for analysing relational structures in learning, teaching, and knowledge production. This review presents a PRISMA-informed scoping analysis…
Cell complexes (CCs) are a higher-order network model deeply rooted in algebraic topology that has gained interest in signal processing and network science recently. However, while the processing of signals supported on CCs can be described…
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…
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Networks are pervasive in the real world. Nature, society, economy, and technology are supported by ostensibly different networks that in fact share an amazing number of interesting structural properties. Network thinking exploded in the…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…