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A new parallel programming framework for DNA sequence alignment in homogeneous multi-core processor architectures is proposed. Contrasting with traditional coarse-grained parallel approaches, that divide the considered database in several smaller subsets of complete sequences to be aligned with the query sequence, the presented methodology is based on a slicing procedure of both the query and the...
Regulatory cascades consisting of stress-induced gene modules and their transcriptional regulators were recently identified and quantitatively modeled using Artificial Neural Networks (ANNs). Here, we extent our approach to account for regulators that consist of transcription factor dimers. The latter are frequently missed by module-finding tools since the expression profile of one of the dimers is...
Gene regulation is one of the most important processes in the molecular biology, in the last years the microRNA molecule, one of the non-coding RNAs involved in the process, has been the focus of attention for several studies. The computational research on this area has gained a notable importance, considering the low amount of experimental information available and the lack of understanding of the...
Discovery biological organisation of the cell in modules network is a challenging task. Currently, approaches based on a controlled vocabulary, as Gene Ontology, to identify the function similarity among a pair of genes have developed. We present RGO: a rewriting of the GO aiming at obtaining a more compact and informative ontology, leading to closer biological regulated GO terms. The RGO will help...
The main objective of this work is to analyze metabolic networks evolution in terms of their robustness and fault tolerance capabilities. In metabolic networks, errors can be seen as random removal of network nodes, while attacks are high-connectivity-degree node deletion aimed at compromising network activity. This paper proposes a software framework, namely BioAnalysis, used to test the robustness...
Clinical practice shows that, despite the frequent use of major computer-assisted diagnostic equipment, the obtained visualisations of the spatial reconstructions of specific body parts, later undergo only a rough qualitative assessment by the physician diagnostician, with no in-depth semantic analysis. Moreover, often a new method of medical visualisation does present the essence of a medical problem,...
Repetitive substructures within a protein play an important role in understanding protein folding and stability, biological function, and genome evolution. About 25% of all proteins contain repeat structures for eukaryote species and most of them do not have the resolved structural information yet. Therefore, this study aimed to design a comprehensive system for identifying internal repeats either...
Ribonuclease 3 (RNase3) is a member of the human RNaseA superfamily. It is led by a 27-residue signal peptide and secreted into body fluid to eliminate the infection of microbial pathogens in innate immune systems. The signal peptide of RNase3 (RNase3sp) not only directs protein secretion via endoplasmic reticulum (ER) and Golgi apparatus, but also its N-terminal 17 amino acid residues (RNase3sp1-17)...
Every function in a living cell is accomplished by proteins interactions. The capability of predicting such interactions gives greater insight in the study of many diseases and provides valuable information in the study of active small molecules. Here, we formulate the problem as a binary task on information extracted only from amino acid sequences. We apply a k-Nearest Neighbors classification technique...
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