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Article
Effects of dutasteride on the expression of genes related to androgen metabolism and related pathway in human prostate cancer cell lines
Androgens play an important role in controlling the growth of the normal prostate gland and in the pathogenesis of benign prostate hyperplasia, and prostate cancer. Although testosterone is the main androgen s...
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Article
Open AccessMassively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations
Virus-associated cell membrane proteins acquired by HIV-1 during budding may give information on the cellular source of circulating virions. In the present study, by applying immunosorting of the virus and of ...
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Article
Open AccessHif1α down-regulation is associated with transposition of great arteries in mice treated with a retinoic acid antagonist
Congenital heart defect (CHD) account for 25% of all human congenital abnormalities. However, very few CHD-causing genes have been identified so far. A promising approach for the identification of essential ca...
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Article
An amber compatible molecular mechanics force field for the anticancer drug topotecan
A molecular mechanics (MM) force field has been developed for the topotecan (TPT) molecule, an anticancer drug the only molecular target of which is the human topoisomerase I-DNA covalent complex. We proceeded...
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Article
Open AccessMassive screening of copy number population-scale variation in Bos taurusgenome
Copy number variations (CNVs) represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified ...
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Article
Open AccessMicroarray gene expression profiling of neural tissues in bovine spastic paresis
Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both lim...
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Article
Open AccessSignatures of selection in five Italian cattle breeds detected by a 54K SNP panel
In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmon...
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Article
Expanding the molecular diversity and phenotypic spectrum of glycerol 3-phosphate dehydrogenase 1 deficiency
Transient infantile hypertriglyceridemia (HTGT1; OMIM #614480) is a rare autosomal recessive disorder, which manifests in early infancy with transient hypertriglyceridemia, hepatomegaly, elevated liver enzymes...
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Article
Open AccessRNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk
In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo ...
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Article
A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function
The human sterile alpha motif SAM and HD domain-containing protein 1 (SAMHD1) restricts in non-cycling cells type the infection of a large range of retroviruses including HIV-1, reducing the intracellular pool...
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Chapter and Conference Paper
MXAN and Molecular Dynamics: A New Way to Look to the XANES (X-ray Absorption Near Edge Structure) Energy Region
X-ray Absorption Near Edge Structure (XANES) spectroscopy is a powerful method to obtain local structural and electronic information around a well-defined absorbing site of matter in many possible different co...
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Article
Open AccessCoVaCS: a consensus variant calling system
The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and prec...
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Article
Open AccessDROPA: DRIP-seq optimized peak annotator
R-loops are three-stranded nucleic acid structures that usually form during transcription and that may lead to gene regulation or genome instability. DRIP (DNA:RNA Immunoprecipitation)-seq techniques are widel...
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Article
Open AccessHPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis
RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversi...
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Article
Open AccessELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Mo...
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Article
Open AccessA gene expression atlas for different kinds of stress in the mouse brain
Stressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at co** with stress and maintaining homeostasis. However, repeated or intense stress can ...
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Protocol
RNA Editing Detection in HPC Infrastructures
RNA editing by A-to-I deamination is a relevant co/posttranscriptional modification carried out by ADAR enzymes. In humans, it has pivotal cellular effects and its deregulation has been linked to a variety of ...
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Chapter and Conference Paper
Using of NMR Milk Metabolomics to Evaluate Mammary Gland Health Status in Dairy Cows
Objectives. Milk of mammal origin is an important food in the diet during infancy as well as in adulthood. It contains lipids, proteins, carbohydrates, essential nutrients, bioactive compounds (immunoglobulins, o...
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Article
Open AccessDominant ARF3 variants disrupt Golgi integrity and cause a neurodevelopmental disorder recapitulated in zebrafish
Vesicle biogenesis, trafficking and signaling via Endoplasmic reticulum-Golgi network support essential developmental processes and their disruption lead to neurodevelopmental disorders and neurodegeneration. We ...
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Chapter
From Genomes to Variant Interpretations Through Protein Structures
The large amount of genetic, phenotypic, and structural data from diverse conditions and environments offers opportunities for new groundbreaking research. Today, the major scientific task is to interpret the ...
