Search results for "Bioinformatic"

Simulatore a piattaforma circuitale-digitale per la riproduzione funzionale e virtuale del funzionamento di cellula umana per applicazioni di laborat…

2009

"A KNOWLEDGE-BASED EXPERT SYSTEM IN BIOINFORMATICS: AN APPLICATION TO REVERSE ENGINEERING GENE REGULATORY NETWORK"

2011

The huge amount of biological data has spread the development of plenty of bionformatics tools, databases and web services. In order to face a computational biology problem, there not exist only a way, but different methodologies and strategies, with their own pros and cons, can be applied. In this PhD thesis I present a knowledge-based expert system that aims at helping a bionformatics researcher in the choice of the proper strategy and heuristic in order to resolve a bioinformatics issue. The Knowledge Base of the system is structured by means of an ontology and codes the expertise about the application domain. KB is organized into decision-making modules that introduce a set of metareaso…

An Intelligent System for Building Bioinformatics Workflows

2012

In this paper a new intelligent system designed to support the researcher in the development of a workflow for bio informatics experiments is presented. The proposed system is capable to suggest one or more strategies in order to resolve the selected problem and to support the user in the assembly of a workflow for complex experiments, using a a Knowledge base, representing the expertise about the application domain, and a Rule-Based system for decision-making activity. Moreover, the system can represent this workflow at different abstraction layers, freeing the user from implementation details and assisting him in the correct configuration of the algorithms. A sample workflow for protein c…

An Ontology Design Methodology for Knowledge-Based Systems with Application to Bioinformatics

2012

Ontologies are formal knowledge representation models. Knowledge organization is a fundamental requirement in order to develop Knowledge-Based systems. In this paper we present Data-Problem-Solver (DPS) approach, a new ontological paradigm that allows the knowledge designer to model and represent a Knowledge Base (KB) for expert systems. Our approach clearly distinguishes among the knowledge about a problem to resolve (answering the what to do question), the solver method to resolve it (answering the how to do question) and the type of input data required (answering the what I need question). The main purpose of the proposed paradigm is to facilitate the generalization of the application do…

Normalised compression distance and evolutionary distance of genomic sequences: comparison of clustering results

2009

Genomic sequences are usually compared using evolutionary distance, a procedure that implies the alignment of the sequences. Alignment of long sequences is a time consuming procedure and the obtained dissimilarity results is not a metric. Recently, the normalised compression distance was introduced as a method to calculate the distance between two generic digital objects and it seems a suitable way to compare genomic strings. In this paper, the clustering and the non-linear mapping obtained using the evolutionary distance and the compression distance are compared, in order to understand if the two distances sets are similar.

Genetic risk factors and candidate biomarkers for Alzheimer s disease

2009

Alzheimer's disease is a multifactorial and progressive neurodegenerative disease, extremely diffused and with an increasing prevalence worldwide. There is an urgent need for biomarkers to diagnose AD early in its course. Furthermore, accurate biomarkers would be able to determine the clinical efficacy of novel neuroprotective strategies. Although the heritability of late-onset AD is high, our knowledge of the underlying putative susceptibility genes remains incomplete and the only unequivocally established late-onset AD gene is APOE. Nevertheless a number of susceptibility loci seems to influence the pathogenesis of AD, and variations in numerous genes have been considered to be important …

Prognostic significance of p16INK4a alterations and 9p21 loss of heterozigosity in locally advanced laryngeal squamous cell carcinoma

2002

The p16INK4a gene, localized within chromosome 9p21, has been identified as a cyclin-dependent kinase inhibitor and may negatively regulate the cell cycle acting as a tumor suppressor. Genetic alterations involving the 9p21 region are common in human cancers. A consecutive series of 64 untreated patients (median of follow up 53 months) undergoing surgical resection for locally advanced laryngeal squamous-cell carcinomas (LSCCs) has been studied prospectively. Our purpose was to investigate p16 alterations (9p21 allelic loss, hypermethylation and point mutations) and their possible association with clinico-pathological data and flow cytometric variables (DNA-ploidy and S-phase fraction (SPF)…

MicroRNAs in Colorectal Cancer Drug Resistance: Shooters become Targets

2013

Copyright: © 2013 Fanale D, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. MicroRNAs (MiRNAs) are involved in the regulation of several biological processes such as development, differentiation, metabolism, apoptosis and proliferation. Recently, it has been shown that deregulated expression of miRNAs are present in different human cancers, suggesting a potential role in carcinogenesis [1,2]. Recent evidence suggests that miRNAs may represent potential new therapeutic approaches in patients with dru…

Bioinformatica e database GenEnv nella gestione del rischio biologico

2004

Soft Topographic Map for Clustering and Classification of Bacteria

2007

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA…