A5035923960- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Lung Cancer Treatments and Mutations
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Cancer-related gene regulation
- RNA and protein synthesis mechanisms
- Biotechnology and Related Fields
- Ferroptosis and cancer prognosis
- Genomic variations and chromosomal abnormalities
- RNA regulation and disease
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- Plant Pathogens and Resistance
- RNA Research and Splicing
- Plant Pathogens and Fungal Diseases
- Molecular Biology Techniques and Applications
- Genetic diversity and population structure
IFOM
2019-2024
Cineca
2017
RNA editing is a widespread co-/post-transcriptional mechanism that alters primary sequences through the modification of specific nucleotides and it can increase both transcriptome proteome diversity. The automatic detection RNA-editing from RNA-seq data computational intensive limited to small sets, thus preventing reliable genome-wide characterisation such process.In this work we introduce HPC-REDItools, an upgraded tool for accurate events discovery large dataset...
Abstract Chromatin three-dimensional (3D) organization inside the cell nucleus determines separation of euchromatin and heterochromatin domains. Their segregation results in definition active inactive chromatin compartments, whereby local concentration associated proteins, RNA DNA formation distinct subnuclear structures. Thus, domains spatially confined a specific 3D nuclear compartment are expected to share similar epigenetic features biochemical properties, terms accessibility solubility....
Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential accelerate understanding and exploration genetic resources. The storage, availability maintenance huge quantities NGS-generated data remains a major challenge. PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog variants present in peach (Prunus persica L. Batsch) wild-related Prunus genera, annotated from 146 samples publicly released...
A growing amount of evidence in literature suggests that germline sequence variants and somatic mutations non-coding distal regulatory elements may be crucial for defining disease risk prognostic stratification patients, genetic disorders as well cancer. Their functional interpretation is challenging because genome-wide enhancer-target gene (ETG) pairing an open problem genomics. The solutions proposed so far do not account the hierarchy structural domains which define chromatin...
<div>Abstract<p>Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with genomic sequence. Enhancer alterations have been associated various pathological conditions, including cancer. However, identification and characterization somatic mutations in a functional effect on tumorigenesis prognosis remain major challenge. Here, we present strategy for detecting characterizing enhancer genome-wide analysis...
ABSTRACT Chromatin three-dimensional (3D) organization inside the cell nucleus determines separation of euchromatin and heterochromatin domains. Their segregation results in definition active inactive chromatin compartments, whereby local concentration associated proteins, RNA DNA formation distinct subnuclear structures. Thus, domains spatially confined a specific 3D nuclear compartment are expected to share similar epigenetic features biochemical properties, terms accessibility solubility....
Abstract Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with genomic sequence. Enhancer alterations have been associated various pathological conditions, including cancer. However, identification and characterization somatic mutations in a functional effect on tumorigenesis prognosis remain major challenge. Here, we present strategy for detecting characterizing enhancer genome-wide analysis patient cohorts,...
Genome-wide chromosome conformation capture based on high-throughput sequencing (Hi-C) has been widely adopted to study chromatin architecture by generating datasets of ever-increasing complexity and size. HiCBricks offers user-friendly efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks build more complex data analysis pipelines algorithms. already incorporates functions calling domain boundaries high quality...
Abstract Background RNA editing is a widespread co-/post-transcriptional mechanism that alters primary sequences through the modification of specific nucleotides and it can increase both transcriptome proteome diversity. The automatic detection RNA-editing from RNA-seq data computational intensive limited to small sets, thus preventing reliable genome-wide characterisation such process. Results In this work we introduce HPC-REDItools, an upgraded tool for accurate events discovery large...
<div>Abstract<p>Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with genomic sequence. Enhancer alterations have been associated various pathological conditions, including cancer. However, identification and characterization somatic mutations in a functional effect on tumorigenesis prognosis remain major challenge. Here, we present strategy for detecting characterizing enhancer genome-wide analysis...
<p>Supplementary Figures S1-S7</p>
<p>Supplementary Figures S1-S7</p>