Related papers: Structural characteristics in network control of m…
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…
Recently, the structural controllability theory has been introduced to analyze the Protein-Protein Interaction (PPI) network. The indispensable nodes, which their removal increase the number of driver nodes to control the network, are found…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Networked systems display complex patterns of interactions between a large number of components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology,…
The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death.…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
Two different types of directed networks are investigated, transcriptional regulation networks and neural networks. The directed network structure are studied and also shown to reflect the different processes taking place on the networks.…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
The controllability of a network is a theoretical problem of relevance in a variety of contexts ranging from financial markets to the brain. Until now, network controllability has been characterized only on isolated networks, while the vast…
Predicting how the brain can be driven to specific states by means of internal or external control requires a fundamental understanding of the relationship between neural connectivity and activity. Network control theory is a powerful tool…
Despite the significant advances in identifying the driver nodes and energy requiring in network control, a framework that incorporates more complicated dynamics remains challenging. Here, we consider the conformity behavior into network…
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly understood. Here we analyze distinct cellular networks…
The paradigm of layered networks is used to describe many real-world systems -- from biological networks, to social organizations and transportation systems. Recently there has been much progress in understanding the general properties of…
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…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
A reflection of our ultimate understanding of a complex system is our ability to control its behavior. Typically, control has multiple prerequisites: It requires an accurate map of the network that governs the interactions between the…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…