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A large number of clustering approaches have been proposed for the analysis of gene expression data obtained from microarray experiments. However, the results from the application of standard clustering methods to genes are limited. This limitation is imposed by the existence of a number of experimental conditions where the activity of genes is(More)
We present the YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT; www.yeastract.com) database, a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. This database is a repository of 12 346 regulatory associations between transcription factors and target genes, based on experimental evidence(More)
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 updated in September 2007, this database contains over 30 990 regulatory associations between Transcription Factors (TFs)(More)
We propose a new algorithm to the problem of state reduction in incompletely specified finite state machines. This algorithm is not based on the enumeration of compatible sets, and, therefore, its performance is not dependent on the number of prime compatibles. We prove that the algorithm is exact and present results that show that, in a set of hard(More)
One of the main unresolved problems that arise during the data mining process is treating data that contains temporal information. In this case, a complete understanding of the entire phenomenon requires that the data should be viewed as a sequence of events. Temporal sequences appear in a vast range of domains, from engineering, to medicine and finance,(More)
—We present a methodology for the watermarking of synchronous sequential circuits that makes it possible to identify the authorship of designs by imposing a digital watermark on the state transition graph (STG) of the circuit. The methodology is applicable to sequential designs that are made available as firm intellectual property, the designation commonly(More)
Centroid-based models have been used in Text Categorization because, despite their computational simplicity, they show a robust behavior and good performance. In this paper we experimentally evaluate several centroid-based models on single-label text categorization tasks. We also analyze document length normalization and two different term weighting(More)
Suffix trees are by far the most important data structure in stringology, with a myriad of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require &Theta;(<i>n</i> log <i>n</i>) bits of space, for a string of size <i>n</i>. This is considerably more than the <i>n</i> log<sub>2</sub> &sigma;(More)
In this paper we propose a new algorithm for identifying cis-regulatory modules in genomic sequences. In particular, the algorithm extracts structured motifs, defined as a collection of highly conserved regions with pre-specified sizes and spacings between them. This type of motifs is extremely relevant in the research of gene regulatory mechanisms since it(More)