Publication

Revealing strengths and weaknesses of methods for gene network inference

Related publications (32)

Structural Identification of Unate-Like Genetic Network Models from Time-Lapse Protein Concentration Measurements

We consider the problem of learning dynamical models of genetic regulatory networks from time-lapse measurements of gene expression. In our previous work [Porreca et al,Bioinformatics,2010], we described a method for the structural and parametric identific ...

2010

Gene expression profiling in cells with enhanced gamma-secretase activity

Alexandra Marie-Isabelle Karoline Brigitte Magold, Patrick Fraering

BACKGROUND: Processing by gamma-secretase of many type-I membrane protein substrates triggers signaling cascades by releasing intracellular domains (ICDs) that, following nuclear translocation, modulate the transcription of different genes regulating a div ...

Public Library of Science2009

Evolutionary reverse engineering of gene networks

Daniel Marbach

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

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

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

Differential gene expression as a toxicant-sensitive endpoint in zebrafish embryos and larvae

Kristin Schirmer

The zebrafish (Danio rerio) embryo toxicity test (DarT) is under consideration as an alternative to the acute fish toxicity test. Microscopically visible developmental disorders or death are the endpoints used to report on toxicity in DarT. These endpoints ...

2007

Exploiting Binary Abstractions in Deciphering Gene Interactions

Giovanni De Micheli, Abhishek Garg

We consider computationally reconstructing gene regulatory networks on top of the binary abstraction of gene expression state information. Unlike previous Boolean network approaches, the proposed method does not handle noisy gene expression values directly ...

2006

Prediction and Analysis of Human MicroRNA Regulatory Modules

Giovanni De Micheli

MicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner. We propose a computational method to predict miRNA regulatory modules or groups of miRNAs and target genes that are believed to participate cooper ...

2005

Microarray analysis of VEGF-C responsive genes in human lymphatic endothelial cells

Melody Swartz, Carolyn Yong Pullin

Vascular endothelial growth factor-C (VEGF-C) is considered one of the most important factors influencing lymphatic endothelial cell biology. The goal of this work was to characterize the gene expression response by lymphatic endothelial cells (LECs) to VE ...

2005

Prediction of regulatory modules comprising microRNAs and target genes

Giovanni De Micheli

Motivation: MicroRNAs (miRNAs) are small endogenous RNAs that can play important regulatory roles via the RNA-interference pathway by targeting mRNAs for cleavage or translational repression. We propose a computational method to predict mi ...

Oxford University Press2005

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