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In this paper we report an ongoing project for identifying human cytomegalovirus (HCMV) micro RNAs (miRNA) expressed in infected human cells using the new massive parallel sequencing technology with the Solexa Sequencer. We developed a data processing pipeline for analyzing such data including mapping segments to genomes, detecting highly expressed sequences and their loci, comparing sequences to...
MicroRNAs (miRNAs) are small single stranded RNAs, on average 22nt long, generated from endogenous hairpin-shaped transcripts with post-transcriptional activity. Although many computational methods are currently available for identifying miRNA genes in the genomes of various species, very few algorithms can accurately predict the functional part of the miRNA gene, namely the mature miRNA. We introduce...
Functional RNAs (fRNAs) play a key role in gene regulation, at both the transcriptional and translational levels. Identification of fRNA genes can be difficult, given that some classes of fRNAs (especially microRNAs) have short coding regions and do not use classical signals common to protein coding genes. Following on previous experiments to generate pattern recognition models for the identification...
Co-clustering has not been much exploited in biomedical informatics, despite its success in other domains. Most of the previous applications were limited to analyzing gene expression data. We performed co-clustering analysis on other types of data and obtained promising results, as summarized in this paper.
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