Related papers: Characteristics of Molecular-biological Systems an…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
The complexity of molecular and cellular processes forces experimental studies to focus on subsystems. To study the functioning of biological systems across levels of structural and functional organisation, we require tools to compose and…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Reliable in-silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the…
Graph theoretical approach has proved an effective tool to understand, characterize and quantify the complex brain network. However, much less attention has been paid to methods that quantitatively compare two graphs, a crucial issue in the…
We consider the population dynamics of a set of species whose network of catalytic interactions is described by a directed graph. The relationship between the attractors of this dynamics and the underlying graph theoretic structures like…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
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…
At the core of understanding dynamical systems is the ability to maintain and control the systems behavior that includes notions of robustness, heterogeneity, or regime-shift detection. Recently, to explore such functional properties, a…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
The importance of studying properties of networks is manifest in diverse fields ranging from biology, engineering, physics, chemistry, neuroscience, and medicine. The functionality of networks with regard to performance, throughput,…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
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…
Stream graphs model highly dynamic networks in which nodes and/or links arrive and/or leave over time. Strongly connected components in stream graphs were defined recently, but no algorithm was provided to compute them. We present here…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
The characterisation of quantum networks is fundamental to understanding how energy and information propagates through complex systems, with applications in control, communication, error mitigation and energy transfer. In this work, we…