Publications related to Biological network

Implicit Methods for Probabilistic Modeling of Gene Reglatory Networks

Giovanni De Micheli, Abhishek Garg, Debasree Banerjee

In silico modeling of Gene Regulatory Networks (GRN) has recently aroused a lot of interest in the biological community for modeling and understanding complex pathways. Boolean Networks (BN) are a common modeling tool for in silico dynamic analysis of such ...

2008

The Age of Analog Networks

Dario Floreano, Claudio Mattiussi, Daniel Marbach, Peter Dürr

A large class of systems of biological and technological relevance can be described as analog networks, that is, collections of dynamical devices interconnected by links of varying strength. Some examples of analog networks are genetic regulatory networks, ...

2008

Parasites lead to evolution of robustness against gene loss in host signaling networks

Marcel Salathé

Many biological networks can maintain their function against single gene loss. However, the evolutionary mechanisms responsible for such robustness remain unclear. Here, we demonstrate that antagonistic host-parasite interactions can act as a selective pre ...

Nature / European Molecular Biology Organization2008

Representing perturbed dynamics in biological network models

Felix Naef, Jacques Rougemont

We study the dynamics of gene activities in relatively small size biological networks (up to a few tens of nodes), e.g., the activities of cell-cycle proteins during the mitotic cell-cycle progression. Using the framework of deterministic discrete dynamica ...

American Physical Society2007

Understanding the Optimal Response Properties of Tricyclic Cascade Networks through Dynamic Optimization

Dominique Bonvin, Vassily Hatzimanikatis, Benoît Chachuat

The mitogen-activated protein kinase (MAPK) cascades are ubiquitous in eukaryotic signal transduction, and these pathways are conserved in cells from yeast to mammals. They relay extracellular stimuli from the plasma membrane to targets in the cytoplasm an ...

2007

Mapping Human Whole-Brain Structural Networks with Diffusion MRI

Jean-Philippe Thiran, Patrick Thiran, Reto Meuli, Patric Hagmann, Xavier Gigandet, Maciej Kurant, Van Jay Wedeen

Understanding the large-scale structural network formed by neurons is a major challenge in system neuroscience. A detailed connectivity map covering the entire brain would therefore be of great value. Based on diffusion MRI, we propose an efficient methodo ...

2007

Modeling of Multiple Valued Gene Regulatory Networks

Giovanni De Micheli, Abhishek Garg, Ioannis Xenarios

In silico modeling of Gene Regulatory Networks has gained a lot of attention recently as it gives a very powerful tool to experimental biologists to gather the knowledge gained from different biological experiments and understand the dynamics of the overal ...

2007

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

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

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Biological network

Implicit Methods for Probabilistic Modeling of Gene Reglatory Networks

The Age of Analog Networks

Parasites lead to evolution of robustness against gene loss in host signaling networks

Representing perturbed dynamics in biological network models

Understanding the Optimal Response Properties of Tricyclic Cascade Networks through Dynamic Optimization

Mapping Human Whole-Brain Structural Networks with Diffusion MRI

Parameter identification for stochastic hybrid models of biological interaction networks

Modeling of Multiple Valued Gene Regulatory Networks

Complex network analysis of free-energy landscapes

Enhancing synchronizability of dynamical networks using the connection graph stability method

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Chat with Graph Search

The Age of Analog Networks

Representing perturbed dynamics in biological network models

Parasites lead to evolution of robustness against gene loss in host signaling networks

Implicit Methods for Probabilistic Modeling of Gene Reglatory Networks

Mapping Human Whole-Brain Structural Networks with Diffusion MRI

Understanding the Optimal Response Properties of Tricyclic Cascade Networks through Dynamic Optimization

Parameter identification for stochastic hybrid models of biological interaction networks

Enhancing synchronizability of dynamical networks using the connection graph stability method

Modeling of Multiple Valued Gene Regulatory Networks

Complex network analysis of free-energy landscapes