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Modeling stochasticity and robustness in gene regulatory networks

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Gene regulation is mediated by site-specific DNA-binding proteins or transcription factors (TFs), which form protein complexes at regulatory loci either to activate or repress the expression of a target gene. The study of the dynamic properties of these re ...

Royal Society of Chemistry2010

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Numerous methods have been developed for inference of gene regulatory networks from expression data, however, their strengths and weaknesses remain poorly understood. Accurate and systematic evaluation of these methods is hampered by the difficulty of cons ...

2010

Implicit methods for modeling gene regulatory networks

Abhishek Garg

Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from single-gene single-protein experimental approach to studying the behaviour of a ...

EPFL2009

The expression of genes is controlled by regulatory networks, which perform fundamental information processing and control mechanisms in a cell. Unraveling and modelling these networks will be indispensable to gain a systems-level understanding of biologic ...

EPFL2009

Face/off: Live facial puppetry

Mark Pauly, Hao Li

We present a complete integrated system for live facial puppetry that enables high-resolution real-time facial expression tracking with transfer to another person's face. The system utilizes a real-time structured light scanner that provides dense 3D data ...

2009

Synchronous versus asynchronous modeling of gene regulatory networks

Giovanni De Micheli, Abhishek Garg, 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

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

Scalable Reverse Engineering of Nonlinear Gene Networks

Dario Floreano, Claudio Mattiussi, Daniel Marbach, Thomas Schaffter

Current advanced molecular biology techniques provide gene expression (mRNA) levels of selected genes of an organism. In such aggregate, the mRNA level of one gene is mediated by the presence of specific proteins and metabolites produced by other genes. Ge ...

2008

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

A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data

Vassily Hatzimanikatis, Eleftherios Papoutsakis

Background: Proteins are the primary regulatory agents of transcription even though mRNA expression data alone, from systems like DNA microarrays, are widely used. In addition, the regulation process in genetic systems is inherently non-linear in nature, a ...

2007