[HTML][HTML] Handling multi-mapped reads in RNA-seq

G Deschamps-Francoeur, J Simoneau… - Computational and …, 2020 - Elsevier
Many eukaryotic genomes harbour large numbers of duplicated sequences, of diverse
biotypes, resulting from several mechanisms including recombination, whole genome …

Dysregulation of MicroRNAs and target genes networks in peripheral blood of patients with sporadic amyotrophic lateral sclerosis

M Liguori, N Nuzziello, A Introna, A Consiglio… - Frontiers in molecular …, 2018 - frontiersin.org
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease.
While genetics and other factors contribute to ALS pathogenesis, critical knowledge is still …

Accurate allocation of multimapped reads enables regulatory element analysis at repeats

A Morrissey, J Shi, DQ James, S Mahony - Genome research, 2024 - genome.cshlp.org
Transposable elements (TEs) and other repetitive regions have been shown to contain gene
regulatory elements, including transcription factor binding sites. However, regulatory …

Plant miRNAs reduce cancer cell proliferation by targeting MALAT1 and NEAT1: a beneficial cross-kingdom interaction

F Marzano, MF Caratozzolo, A Consiglio… - Frontiers in …, 2020 - frontiersin.org
MicroRNAs (miRNAs) are ubiquitous regulators of gene expression, evolutionarily
conserved in plants and mammals. In recent years, although a growing number of papers …

Exogenous and endogenous dsRNAs perceived by plant Dicer-like 4 protein in the RNAi-depleted cellular context

P Leonetti, A Consiglio, D Arendt, RP Golbik… - Cellular & Molecular …, 2023 - Springer
Abstract Background In plants, RNase III Dicer-like proteins (DCLs) act as sensors of
dsRNAs and process them into short 21-to 24-nucleotide (nt)(s) RNAs. Plant DCL4 is …

Analysis of Faecal Microbiota and Small ncRNAs in Autism: Detection of miRNAs and piRNAs with Possible Implications in Host–Gut Microbiota Cross-Talk

F Chiappori, FA Cupaioli, A Consiglio, N Di Nanni… - Nutrients, 2022 - mdpi.com
Intestinal microorganisms impact health by maintaining gut homeostasis and shaping the
host immunity, while gut dysbiosis associates with many conditions, including autism, a …

Integrated analysis of microRNA and mRNA expression profiles: an attempt to disentangle the complex interaction network in attention deficit hyperactivity disorder

N Nuzziello, F Craig, M Simone, A Consiglio, F Licciulli… - Brain sciences, 2019 - mdpi.com
Attention Deficit Hyperactivity Disorder (ADHD) is a childhood-onset neurodevelopmental
disorder, whose etiology and pathogenesis are still largely unknown. In order to uncover …

Whole-exome and transcriptome sequencing expands the genotype of Majewski Osteodysplastic Primordial Dwarfism Type II

F Marzano, M Chiara, A Consiglio, G D'Amato… - International Journal of …, 2023 - mdpi.com
Microcephalic Osteodysplastic Primordial Dwarfism type II (MOPDII) represents the most
common form of primordial dwarfism. MOPD clinical features include severe prenatal and …

Explaining ovarian cancer gene expression profiles with fuzzy rules and genetic algorithms

A Consiglio, G Casalino, G Castellano, G Grillo… - Electronics, 2021 - mdpi.com
The analysis of gene expression data is a complex task, and many tools and pipelines are
available to handle big sequencing datasets for case-control (bivariate) studies. In some …

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads

RN Shah, AJ Ruthenburg - PLoS Computational Biology, 2021 - journals.plos.org
Next-generation sequencing (NGS) has transformed molecular biology and contributed to
many seminal insights into genomic regulation and function. Apart from whole-genome …