Ioannis Xenarios

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Related publications (26)

Modeling stochasticity and robustness in gene regulatory networks

Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios

Motivation: Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed ...

2009

Synchronous versus asynchronous modeling of gene regulatory networks

Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios

In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene–gene, ...

2008

Probabilistic base calling of Solexa sequencing data

Christian Iseli, Felix Naef, Arnaud Amzallag, Jacques Rougemont, Ioannis Xenarios

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput dat ...

BioMed Central2008

Dynamic simulation of regulatory networks using SQUAD

Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios

Background The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible t ...

2007

Modeling of Multiple Valued Gene Regulatory Networks

Abhishek Garg, Giovanni De Micheli, 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

An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments

Giovanni De Micheli, Ioannis Xenarios

With the increasing availability of experimental data on gene-gene and protein-protein interactions, modeling of gene regulatory networks has gained a special attention lately. To have a better understanding of these networks it is necessary to capture the ...

Springer2007

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