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Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

Publications associées (41)

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Combining Multiple Results of a Reverse Engineering Algorithm: Application to the DREAM Five Gene Network Challenge

Dario Floreano, Claudio Mattiussi, Daniel Marbach

The output of reverse engineering methods for biological networks is often not a single network prediction, but an ensemble of networks that are consistent with the experimentally measured data. In this paper, we consider the problem of combining the infor ...

Blackwell Publishing, 9600 Garsington Rd, Oxford Ox4 2Dq, Oxen, England2009

Reducing Synchronization Cost in Weighted Dynamical Networks Using Betweenness Centrality Measures

Martin Hasler, Ali Ajdari Rad, Mahdi Jalili

In this paper we investigate optimization of synchronization cost in undirected dynamical networks. To do so, proper weights are assigned to the networks’ edges considering node and edge betweenness centrality measures. The proposed method gives near-optim ...

IEEE2008

Synchronization in dynamical networks

Mahdi Jalili

Complex dynamical networks are ubiquitous in many fields of science from engineering to biology, physics, and sociology. Collective behavior, and in particular synchronization,) is one of the most interesting consequences of interaction of dynamical system ...

EPFL2008

Enhancing synchronizability of dynamical networks using the connection graph stability method

Martin Hasler, Ali Ajdari Rad, Mahdi Jalili

Dynamical networks with diffusive couplings are investigated from the point of view of synchronizability. Arbitrary connection graphs are admitted but the coupling is symmetric. Networks with equal interaction coefficients for all edges of the interaction ...

2007

Simplifying complex networks

David Gfeller

The framework of complex networks has been shown to describe adequately a wide class of complex systems made up of a large number of interacting units. In this framework, a node is associated to each unit and two nodes are connected by an edge if the two u ...

EPFL2007

Complex network analysis of free-energy landscapes

Paolo De Los Rios, David Gfeller

The kinetics of biomolecular isomerization processes, such as protein folding, is governed by a free-energy surface of high dimensionality and complexity. As an alternative to projections into one or two dimensions, the free-energy surface can be mapped in ...

National Academy of Sciences2007

Synchronization and Graph Topology

Martin Hasler, Igor Belykh

This paper clarifies the relation between synchronization and graph topology. Applying the Connection Graph Stability method developed by Belykh et al. [2004a] to the study of synchronization in networks of coupled oscillators, we show which graph properti ...

2005

The evolution of network topology by selective removal

Marcel Salathé

The topology of large social, technical and biological networks such as the World Wide Web or protein interaction networks has caught considerable attention in the past few years (reviewed in Newman 2003), and analysis of the structure of such networks rev ...

2005

A statistical physics perspective of complex networks

Thomas Petermann

A statistical physics perspective of complex networks: from the architecture of the Internet and the brain to the spreading of an epidemic Statistical physics has revealed itself as the ideal framework to describe large networks appearing in a variety of d ...

EPFL2005

Connection Graph Stability Method for Synchronized Coupled Chaotic Systems

Martin Hasler, Igor Belykh

This paper elucidates the relation between network dynamics and graph theory. A new general method to determine global stability of total synchronization in networks with different topologies is proposed. This method combines the Lyapunov function approach ...

2004