Search results for "Bioinformatics"

Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies

2013

High-throughput sequencing technologies produce large collections of data, mainly DNA sequences with additional information, requiring the design of efficient and effective methodologies for both their compression and storage. In this context, we first provide a classification of the main techniques that have been proposed, according to three specific research directions that have emerged from the literature and, for each, we provide an overview of the current techniques. Finally, to make this review useful to researchers and technicians applying the existing software and tools, we include a synopsis of the main characteristics of the described approaches, including details on their impleme…

Current bioinformatics tools in genomic biomedical research (Review).

2006

On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology is rapidly widening, making new approaches of high-throughput genomic analysis necessary. At present, the only effective way to keep abreast of the dramatic increase in sequence and related information is to apply biocomputational approaches. Thus, over recent years, the field of bioinformatics has r…

HepatomiRNoma: The proposal of a new network of targets for diagnosis, prognosis and therapy in hepatocellular carcinoma

2015

Abstract: The diagnosis and treatment of hepatocellular carcinoma (HCC) underwent a huge advancement in the last years. Recently, microRNAs (miRNAs) have been also studied to provide a new tool for early diagnosis of high risk patients, for prognostic classification to identify those patients who benefit cancer treatment and for predictive definition to select the right targeted drug. In this review we revised all the available data obtained to explore the role of miRNAs in HCC. This analysis led to identification of miRNAs which could gain a diagnostic, prognostic or predictive role. The results of studies on miRNAs involved in HCC are initial and far from providing scientific evidences to…

PROTEIN SECONDARY STRUCTURE PREDICTION: HOW TO IMPROVE ACCURACY BY INTEGRATION

2006

In this paper a technique to improve protein secondary structure prediction is proposed. The approach is based on the idea of combining the results of a set of prediction tools, choosing the most correct parts of each prediction. The correctness of the resulting prediction is measured referring to accuracy parameters used in several editions of CASP. Experimental evaluations validating the proposed approach are also reported.

INVESTIGATION OF BIOTIC STRESS RESPONSES IN FRUIT TREE CROPS USING META-ANALYTICAL TECHNIQUES.

2020

In recent years, RNA sequencing and analysis using Next Generation Sequencing (NGS) methods have enabled to understand the gene expression pertaining to plant biotic and abiotic stress conditions in both quantitative and qualitative manner. The large number of transcriptomic works published in plants requires more meta-analysis studies that would identify common and specific features in relation of the high number of objective studies performed at different developmental and environmental conditions. Meta-analysis of transcriptomic data will identify commonalities and differences between differentially regulated gene lists and will allow screen which genes are key players in gene-gene and p…

INVESTIGATION ON THE GENETIC BASIS OF ENVIRONMENTAL STRESS IN FRUIT TREE CROPS

2021

Plant stress can be divided into two major categories: abiotic stress and biotic stress. Abiotic stress happens when plants are exposed to the environment either physically or chemically. There is an emergency in developing crop varieties that are tolerant to abiotic stresses to ensure food security and safety in the coming years. Multiple abiotic stress like drought, heat, frost at flowering and nutrient deficiency can cause an erratic fruiting behavior or following extreme events, the death of the plants. Plants require an optimal level of nutrients and essential minerals for their growth and development that are mainly acquired from soil by their roots. Nutrient deficiency is an environm…

A high computing bioinformatic approach based on GRID for detecting recombination in whole Citrus Tristeza Virus genome

2007

Implementation of an online information system for the “Flora Critica d’Italia”

2015

Since the early 2000s, within the Italian Botanical Society was discussed the opportunity to realize collaboratively a modern Flora articulated in monographs on the model of others under construction or recently completed in several European countries (1). This initiative had a milestone in 2007 with the institution of the “Fondazione per la Flora Italiana”, with the aim of supporting the activities of study, conservation and cultural and scientific enhancement of the flora of Italy and of sensitizing the national community about the many functions that it implements, in the context of natural and semi-natural ecosystems. The “Foundation for the Italian flora” is responsible for the publica…

New insights of epithelial-to-mesenchymal transition (EMT) signature in breast cancer

2023

Genome wide survey of the Toll-like receptor family in the Mediterranean sea urchin

Toll-like receptors (TLRs) represent a conserved family of proteins widely expressed in eukaryotes. They play crucial roles in the innate immune system recognizing different pathogen-associated molecular patterns. In mammals the TLR family comprises 10-13 members, while a huge number of TLR-like genes were recovered in S.purpuratus[1-3]. The Paracentrotus lividus genome project recently generated a new highquality assembly of the genome that represents a valuable resource also for clarifying the evolutionary origin of immune system. In order to identify TLR genes in P.lividus, a genome wide survey was carried out and BLAT searches retrieved 119 TLR genes (PlivTLRs). Ab initio gene predictio…