Related papers: Cell biology: Networks, regulation, pathways
Network theory provides tools which are particularly appropriate for assessing the complex interdependencies that characterise our modern connected world. This article presents an introduction to network theory, in a way that doesn't…
This work presents the current collection of mathematical models related to neural networks and proposes a new family of such with extended structure and dynamics in order to attain a selection of cognitive capabilities. It starts by…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
Cell formation problem is among the first obstacles the designer of cellular production systems must overcome. This paper presents a critical analysis of the various criteria and constraints considered in the literature. The objective is to…
Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers…
This article reviews and presents various solved and open problems in the development, analysis, and control of epidemic models. We are interested in presenting a relatively concise report for new engineers looking to enter the field of…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…
Networked structure emerged from a wide range of fields such as biological systems, World Wide Web and technological infrastructure. A deeply insight into the topological complexity of these networks has been gained. Some works start to pay…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
The brain is immensely complex, with diverse components and dynamic interactions building upon one another to orchestrate a wide range of functions and behaviors. Understanding patterns of these complex interactions and how they are…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
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…
First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
Systems engineering has developed a mature knowledge on how to design, integrate and manage complex industrial systems, whereas disciplines studying complex systems in nature or society also propose numerous tools for their understanding.…