Search results for " genomi"
showing 10 items of 572 documents
Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
2012
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the leng…
Interactions between dietary n-3 fatty acids and genetic variants and risk of disease
2012
Nutritional genomics has undergone rapid development and the concept is now very popular with the general public. Therefore, there is increasing demand for knowledge on adapting dietary composition to the genome. Our aim has been to undertake a systematic review so as to find out the level of evidence existing on whether the effects of n-3 fatty acids on health can be modulated by genetic variation. A systematic literature search was conducted on studies that jointly analyse the effect of one or more genetic variants in candidate genes and n-3 fatty acids. Both observational and experimental studies were included. Results are classified in accordance with whether the study was undertaken on…
Caratterizzazione di Rhynchophorous ferrugineus (Coleoptera: Curculionidae) mediante l’analisi del DNA genomico
2010
Originario dell’Asia tropicale, Rhynchophorus ferrugineus (Olivier), Coleoptera, Curculionidae, introdotto accidentalmente nel bacino del Mediterraneo nei primi anni ’90 (Salama et al, 2004), e segnalato in Sicilia nel 2005 (A.A.V.V. , 2009) è il fitofago chiave causa della moria di numerose palme. Infesta diversi generi di palme, sia giovani che adulti, quali Phoenix canariensis, P. dactylifera, Coccus nucifera, Washingtonia sp. A dispetto della pericolosità di questa specie che recentemente è stata proposta quale specie da quarantena (EPPO, 2008) non sono ancora disponibili informazioni inerenti la caratterizzazione molecolare di R. ferrugineus, utili per: i) identificazione specifica del…
A genome‐wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent …
2023
About three decades of breeding and selection in the Valle del Belìce sheep are expected to have left several genomic footprints related to milk production traits. In this study, we have assembled a dataset with 451 individuals of the Valle del Belìce sheep breed: 184 animals that underwent directional selection for milk production and 267 unselected animals, genotyped for 40,660 single-nucleotide polymorphisms (SNPs). Three different statistical approaches, both within (iHS and ROH) and between (Rsb) groups, were used to identify genomic regions potentially under selection. Population structure analyses separated all individuals according to their belonging to the two groups. A total of fo…
Sequential variation in genomic RNA patterns of human rotaviruses isolated from infantile gastroenteritis
1986
The incidence and RNA electrophoretypes of rotaviral isolates obtained from infants and young children with acute gastroenteritis were studied from October, 1985 through April, 1986. Analysis of the viral RNA was carried out by Polyacrylamide gel electrophoresis followed by silver staining. Fourteen electrophoretypes were identified. A single dominant electrophoretype was found during the first months of the rotavirus seasonal outbreak. In contrast, a large variety of RNA patterns were observed during the latter portion of the study period. Subgrouping of rotavirus isolates by a double-sandwich enzyme-linked immunosorbent assay using monoclonal-detecting antibodies showed that all strains b…
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
2019
AbstractTraditionally, the functional analysis of gene expression data has used pathway and network enrichment algorithms. These methods are usually gene rather than transcript centric and hence fall short to unravel functional roles associated to posttranscriptional regulatory mechanisms such as Alternative Splicing (AS) and Alternative PolyAdenylation (APA), jointly referred here as Alternative Transcript Processing (AltTP). Moreover, short-read RNA-seq has serious limitations to resolve full-length transcripts, further complicating the study of isoform expression. Recent advances in long-read sequencing open exciting opportunities for studying isoform biology and function. However, there…
High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs
2015
Abstract Epistasis, the interaction between genes, has become a major topic in molecular and quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex diseases. Several algorithms have been employed to detect pairwise interactions in genome-wide association studies (GWAS) but revealing higher order interactions remains a computationally challenging task. State of the art tools are not able to perform exhaustive search for all three-locus interactions in reasonable time even for relatively small input datasets. In this paper we present how a hardware-assisted design can solve this problem and provide fast, efficient and exhaus…
Next-Generation Sequencing: Application in Liver Cancer—Past, Present and Future?
2012
Hepatocellular Carcinoma (HCC) is the third most deadly malignancy worldwide characterized by phenotypic and molecular heterogeneity. In the past two decades, advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. More recently, improvements of sophisticated next-generation sequencing (NGS) technologies have enabled complete and cost-efficient analyses of cancer genomes at a single nucleotide resolution and advanced into valuable tools in translational medicine. Although the use of NGS in human liver cancer is still in its infancy, great promise rests in the systematic integration of different …
Complete karyotype characterization of the K562 cell line by combined application of G-banding, multiplex-fluorescence in situ hybridization, fluores…
2001
This study combines conventional cytogenetics, fluorescence in situ hybridization (FISH), multiplex-FISH and comparative genomic hybridization (CGH). In applying this multimodal approach on the human leukemia cell line K562, the chromosome composition was refined in detail and compared with data from the literature. A hypotriploid karyotype with a modal chromosome number of 67, and 21 unique marker chromosomes were identified. The classification of six markers was identical to published data and the composition of five further markers from the literature could be fully clarified for the first time. The composition of another five markers, which have been interpreted in divergent ways in dif…
Molecular biomarkers in glaucoma
2013
The seventh annual ARVO/Pfizer Ophthalmic Research Institute conference was held Friday and Saturday, April 29 and 30, 2011, at the Fort Lauderdale Hyatt Regency Pier 66, Fort Lauderdale, Florida. The conference, funded by The ARVO Foundation for Eye Research through a grant from Pfizer Ophthalmics, provided an opportunity to gather experts from within and outside ophthalmology to determine the state of knowledge pertaining to molecular biomarkers associated with glaucoma, as well as the methods to identify and validate them to predict (a) those who would be susceptible to development of glaucoma; (b) markers that will enable prediction of glaucoma progression; and (c) markers that will pre…