The Yeast search for transcriptional regulators and consensus tracking (YEASTRACT) information system (www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Last... more
Motivation: The ability to identify complex motifs, i.e. non-contiguous nucleotide sequences, is a key feature of modern motif finders. Addressing this problem is extremely important, not only because these motifs can accurately model... more
Background: Efforts using computational algorithms towards the enumeration of the full set of miRNAs of an organism have been limited by strong reliance on arguments of precursor conservation and feature similarity. However, miRNA... more
In this appendix, we present additional material concerned with the methods used and the results obtained.
In recent years, especially after the completion of genome sequencing projects for various organisms, there has been a growing interest in the study of regulation and gene expression mechanisms. The amount of data available makes it... more
The discovery of microRNAs (miRNAs), almost 10 years ago, changed dramatically our perspective on eukaryotic gene expression regulation. However, the broad and important functions of these regulators are only now becoming apparent. The... more
The computational search for novel microRNA (miRNA) precursors often involves some sort of structural analysis with the aim of identifying which type of structures are prone to being recognized and processed by the cellular... more
EpiLog, a computa.onal tool for the logical modelling of epithelial pa6ern forma.on The complexity of regulatory networks controlling cellular processes calls for the development of specific computational approaches. This complexity... more
- by Nuno Mendes
Logical models are well-suited to capture salient dynamical properties of regulatory networks. For networks controlling cell fate decisions, cell fates are associated with model attractors (stable states or cyclic attractors) whose... more
Motivation: Logical (Boolean or multi-valued) modelling is widely used to study regulatory or signalling networks. Even though these discrete models constitute a coarse, yet useful, abstraction of reality, the analysis of large networks... more