Related papers: Networking genetic regulation and neural computati…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
The understanding of neural activity patterns is fundamentally linked to an understanding of how the brain's network architecture shapes dynamical processes. Established approaches rely mostly on deviations of a given network from certain…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of…
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…
We investigate to what extent the degree sequence of a directed network constrains the number of driver nodes. We develop a pair of algorithms that take a directed degree sequence as input and aim to output a network with the maximum or…
We present and analyze a topologically induced transition from ordered, synchronized to disordered dynamics in directed networks of oscillators. The analysis reveals where in the space of networks this transition occurs and its underlying…
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…
Knowing which nodes are influential in a complex network and whether the network can be influenced by a small subset of nodes is a key part of network analysis. However, many traditional measures of importance focus on node level…
Previous work on undirected small-world networks established the paradigm that locally structured networks tend to have high density of short loops. On the other hand, many realistic networks are directed. Here we investigate the local…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
Discrete-time regulatory networks are dynamical systems on directed graphs, with a structure inspired on natural systems of interacting units. There is a natural notion of determination amongst vertices, which we use to classify the nodes…
Inferring the network topology from the dynamics is a fundamental problem with wide applications in geology, biology and even counter-terrorism. Based on the propagation process, we present a simple method to uncover the network topology.…
This thesis is a compendium of research which brings together ideas from the fields of Complex Networks and Computational Neuroscience to address two questions regarding neural systems: 1) How the activity of neurons, via synaptic changes,…
Many complex networks are described by directed links; in such networks, a link represents, for example, the control of one node over the other node or unidirectional information flows. Some centrality measures are used to determine the…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
Controlling a complex network is of great importance in many applications. The network can be controlled by inputting external control signals through some selected nodes, which are called input nodes. Previous works found that the majority…