DIVINA , Federico

In this paper we propose an approach based on evolutionary computation for the prediction of secondary protein structure motifs. The prediction model consists of a set of rules that predict both the beginning and the end of the regions corresponding to a secondary structure state conformation (α-helix or β-strand). The prediction is based...

Protein structure prediction is one of the main challenges in Bioinformatics. An useful representation for protein 3D structure is the protein contact map. In this work, we propose an evolutionary approach for contact map prediction based on amino acids physicochemical properties. The evolutionary algorithm produces a set of rules...

Protein structure prediction remains one of the most important challenges in molecular biology. Contact maps have been extensively used as a simplified representation of protein structures. In this work, we propose a multi-objective evolutionary approach for contact map prediction. The proposed method bases the prediction on a set of...

La mayoría de las heurísticas utilizadas para la búsqueda de biclusters en microarrays hacen uso del residuo cuadrático medio (MSR) como medida de evaluación de las distintas soluciones generadas. El uso de MSR permite obtener biclusters importantes, sin embargo, recientemente se ha demostrado que dicha medida no es válida para reconocer...

Purpose – The purpose of this paper is to present a novel control mechanism for avoiding overlapping among biclusters in expression data. Design/methodology/approach – Biclustering is a technique used in analysis of microarray data. One of the most popular biclustering algorithms is introduced by Cheng and Church (2000) (Ch&Ch). Even if this...

Many heuristics used for finding biclusters in microarray data use the mean squared residue as a way of evaluating the quality of biclusters. This has led to the discovery of interesting biclusters. Recently it has been proven that the mean squared residue may fail to identify some interesting biclusters. This motivates us to introduce a new...

Biclustering is becoming a popular technique for the study of gene expression data. This is mainly due to the capability of biclustering to address the data using various dimensions simultaneously, as opposed to clustering, which can use only one dimension at the time. Different heuristics have been proposed in order to discover interesting...

Biclustering techniques aim at extracting significant subsets of genes and conditions from microarray gene expression data. This kind of algorithms is mainly based on two key aspects: the way in which they deal with gene similarity across the experimental conditions, that determines the quality of biclusters; and the heuristic or search...

Biclustering is a technique used in analysis of microarray data. It aims at discovering subsets of genes that presents the same tendency under a subsest of experimental conditions. Various techniques have been introduced for discovering significant biclusters. One of the most popular heuristic was introduced by Cheng and Church [6]. In the same...

Las técnicas de biclustering aplicadas a datos de expresión génica persiguen la extracción de subconjuntos de genes co-expresados frente a subconjuntos de condiciones. Una de las medidas usada más frecuentemente para cuantificar la calidad de los biclusters es el residuo cuadrático medio, la cual ha sido incorporada en diferentes métodos...

Multiple approaches have been developed in order to predict the protein secondary structure. In this paper, we propose an approach to such a problem based on evolutionary computation. The proposed ap proach considers various amino acids properties in order to predict the secondary structure of a protein. In particular, we will consider the hy...

The Protein Structure Prediction (PSP) problem consists of predicting the structure of a protein from its amino acids sequence, and have received much attention lately. In fact, being able to predict the structure of a protein, would allow to know the function of the protein. In this paper, we propose a multi-objective evolutionary algorithm...

Protein structure prediction is currently one of the main open challenges in Bioinformatics. The protein contact map is an useful, and commonly used, represen tation for protein 3D structure and represents binary proximities (contact or non-contact) between each pair of amino acids of a protein. In this work, we propose a multi objective...

This work proposes an improvement of the multi-objective evolutionary method for the protein residue-residue contact prediction called MECoMaP. This method bases its prediction on physico chemical properties of amino acids, structural features and evolutionary information of the proteins. The evolutionary algorithm produces a set of decision...

In this study, a novel residue-residue contacts prediction approach based on evolutionary computation is presented. The prediction is based on four amino acids properties. In particular, we consider the hydrophobicity, the polarity, the charge and residues size. The prediction model consists of a set of rules that identi fies contacts between...

In this study, we present a residue-residue contact prediction approach based on evolutionary computation. Some amino acid properties are employed according to their importance in the folding process: hydrophobicity, polarity, charge and residue size. Our evolutionary algorithm provides a set of rules which determine different cases where two...

Motivation: The prediction of a protein's contact map has become in recent years, a crucial stepping stone for the prediction of the com-plete 3D structure of a protein. In this article, we describe a method-ology for this problem that was shown to be successful in CASP8 and CASP9. The methodology is based on (i) the fusion of the prediction of...

We present a multi-objective evolutionary approach to predict protein contact maps. The algorithm provides a set of rules, inferring whether there is contact between a pair of residues or not. Such rules are based on a set of specific amino acid properties. These properties determine the particular features of each amino acid represented in the...