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We describe a comprehensive map of putative transcription factor binding sites (TFBSs) across multiple genomes created using a search method that relies on hidden Markov models built from experimentally determined TFBSs. Using the information in the TRANSFAC and JASPAR databases, we built 1134 models for TFBSs and used them to scan regions 10 kb upstream of(More)
In the context of the EU funded Telematic Management of Insulin-Dependent Diabetes Mellitus (T-IDDM) project, we have designed, developed and evaluated a telemedicine system for insulin dependent diabetic patients management. The system relies on the integration of two modules, a Patient Unit (PU) and a Medical Unit (MU), able to communicate over the(More)
High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing(More)
Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed amplification of targeted sequences from(More)
BACKGROUND Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced(More)
MicroRNAs (miRNAs) are 19 to 23 nucleotide-long RNAs that post-transcriptionally regulate gene expression. Human cells express several hundred miRNAs which regulate important biological pathways such as development, proliferation, and apoptosis. Recently, 12 miRNA genes have been identified within the genome of Kaposi sarcoma-associated herpesvirus;(More)
This paper outlines how Temporal Abstractions can be useful to analyze and interpret longitudinal data coming from diabetic patients monitoring. We use temporal abstraction mechanisms to provide an abstract description of the patient's state useful to understand the pa-tient's response to the current protocol and, therefore, to provide proper therapeutic(More)