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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)
Non-supervised machine learning methods have been used in the analysis of gene expression data obtained from microarray experiments. Recently, biclustering, a non-supervised approach that performs simultaneous clustering on the row and column dimensions of the data matrix, has been shown to be remarkably effective in a variety of applications. The goal of(More)
Although most biclustering formulations are NP-hard, in time series expression data analysis, it is reasonable to restrict the problem to the identification of maximal biclusters with contiguous columns, which correspond to coherent expression patterns shared by a group of genes in consecutive time points. This restriction leads to a tractable problem. We(More)
Biclustering algorithms have emerged as an important tool for the discovery of local patterns in gene expression data. For the case where the expression data corresponds to time-series, efficient algorithms that work with a discretized version of the expression matrix are known. However, these algorithms assume that the biclusters to be found are perfect,(More)
MOTIVATION Uncovering mechanisms underlying gene expression control is crucial to understand complex cellular responses. Studies in gene regulation often aim to identify regulatory players involved in a biological process of interest, either transcription factors coregulating a set of target genes or genes eventually controlled by a set of regulators. These(More)
An increasingly relevant set of tasks, such as the discovery of biclusters with order-preserving properties, can be mapped as a sequential pattern mining problem on data with item-indexable properties. An item-indexable database, typically observed in biomedical domains, does not allow item repetitions per sequence and is commonly dense. Although multiple(More)
Genes can participate in multiple biological processes at a time and thus their expression can be seen as a composition of the contributions from the active processes. Biclustering under a plaid assumption allows the modeling of interactions between transcriptional modules or biclusters (subsets of genes with coherence across subsets of conditions) by(More)