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Synchronous versus asynchronous modeling of gene regulatory networks

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Development and application of experimental tools to elucidate the gene regulatory network underlying adipogenesis

Carine Delattre-Gubelmann

Excess fat mass in obese individuals, which is characterized by an increase of white adipocyte cell size and number, significantly raises the risk of developing metabolic syndrome symptoms as well as cancer. A detailed understanding of the transcriptional ...

EPFL2013

iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

Bart Deplancke, Sebastian Maerkl, Marcel Geertz, Sylvie Rockel

Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic ...

Oxford University Press2013

Dissecting Gene Regulatory Networks Using Targeted Quantitative Proteomics

Jovan Simicevic

Gene regulatory networks control gene expression levels, and therefore play an essential role in mammalian development and function. Regulation of gene expression is the result of a complex interplay between DNA regulatory elements and their binding partne ...

EPFL2012

Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs

Ray Marcel Marin Florez

MicroRNAs (miRNAs) comprise a large set of short noncoding RNAs that bind to messenger RNAs (mRNAs) to reduce their translation into functional proteins. Computational prediction of miRNA targets is the first stage in the discovery and validation of new re ...

EPFL2012

Transcriptome analysis of adult hematopoietic stem cells (HSCs) and their progeny has revealed mechanisms of blood differentiation and leukemogenesis, but a similar analysis of HSC development is lacking. Here, we acquired the transcriptomes of developing ...

2012

Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing

Giovanni D'Angelo

Regulation of gene expression is a carefully regulated phenomenon in the cell. “Reverse-engineering” algorithms try to reconstruct the regulatory interactions among genes from genome-scale measurements of gene expression profiles (microarrays). Mammalian c ...

2012

The determination of transcriptional regulatory networks is key to the understanding of biological systems. However, the experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while current ...

EPFL2011

The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while computational methods to infer these networks provide only modest accuracy. The latter can be attributed in part to the limi ...

Springer Verlag2011

Experimental strategies for studying transcription factor-DNA binding specificities

Sebastian Maerkl, Marcel Geertz

Specific binding of transcription factors (TFs) determines in a large part the connectivity of gene regulatory networks as well as the quantitative level of gene expression. A multiplicity of both experimental and computational methods is currently used to ...

2010

GeneNetWeaver 3.0: realistic benchmark generation and performance profiling of network inference methods

Dario Floreano, Daniel Marbach, Thomas Schaffter

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