Publications
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Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information. Flanders Institute for Biotechnology
A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks KU Leuven
Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic quantitative and a limited time resolution to a discrete (Boolean) framework. Quantitative resolution is improved through the employ of normalized variables in unison with an additive approach. Increased time resolution stems from the introduction ...
Multistability equivalence between gene regulatory networks of different dimensionality with application to a differentiation network KU Leuven
Copyright © 2016 John Wiley & Sons, Ltd. This paper formulates and addresses the problem of equivalence in terms of multistability properties between nonlinear models of gene regulatory systems of different dimensionality. Given a nonlinear dynamical model of a gene regulatory network and the structure of another higher-dimensional gene regulatory network, the aim is to find a dynamical model for the latter that has the same equilibria and ...
Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant Flanders Institute for Biotechnology Ghent University
Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation KU Leuven
Perhaps the most fundamental aspect of development is the acquisition by a cell of a terminal and stable fate because it marks the usually irreversible commitment to a specific morphology and function. Understanding the molecular mechanisms that control this process has profound implications for stem cell biology and cancer research. Because cell fate commitment is regulated by transcription factors acting as master switches, a mechanistic ...
Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation KU Leuven
Perhaps the most fundamental aspect of development is the acquisition by a cell of a terminal and stable fate because it marks the usually irreversible commitment to a specific morphology and function. Understanding the molecular mechanisms that control this process has profound implications for stem cell biology and cancer research. Because cell fate commitment is regulated by transcription factors acting as master switches, a mechanistic ...
Repairing inconsistent answer set programs using rules of thumb : a gene regulatory networks case study Ghent University
Modeling Gene and Protein Regulatory Networks with ASP Vrije Universiteit Brussel
Recently, many approaches to model regulatory networks have been proposed in the systems biology domain. However, the task is far from being solved. In this paper, we propose an Answer Set Programming (ASP)-based approach to model interaction networks. We build a general ASP framework that describes the network semantics and allows modelling specific networks with little effort. ASP provides a rich and flexible toolbox that allows expanding the ...