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In order to cope with the large amounts of data that have become available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory networks, based on a class of piecewise-linear (PL) differential(More)
MOTIVATION The study of genetic regulatory networks has received a major impetus from the recent development of experimental techniques allowing the measurement of patterns of gene expression in a massively parallel way. This experimental progress calls for the development of appropriate computer tools for the modeling and simulation of gene regulation(More)
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in(More)
Computer modeling and simulation are indispensable for understanding the functioning of an organism on a molecular level. We present an implemented method for the qualitative simulation of large and complex genetic regulatory networks. The method allows a broad range of regulatory interactions between genes to be represented and has been applied to the(More)
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics(More)
Methods developed for the qualitative simulation of dy-namical systems have turned out to be powerful tools for studying genetic regulatory networks. We present a generalization of a simulation method based on piecewise-linear differential equation models that is able to deal with discontinuities. The method is sound and has been implemented in a computer(More)
The identification and characterization of peptides from tandem mass spectrometry (MS/MS) data represents a critical aspect of proteomics. Today, tandem MS analysis is often performed by only using a single identification program achieving identification rates between 10-50% (Elias and Gygi, 2007). Beside the development of new analysis tools, recent(More)
  • J Barnat, L Brim, I ˇ Cerná, S Dražan, D ˇ Safránek, H De Jong +6 others
  • 2007
Studies of cells in silico can greatly reduce the need for expensive and prolonged laboratory experimentation. The use of model checking for the analysis of biological networks has attracted much attention [2, 6]. The individual approaches differ in reduction methods used for discretization of biological models and model-checking tools employed for the(More)
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