Advanced applications of RNA sequencing and challenges

Y Han, S Gao, K Muegge, W Zhang… - … and biology insights, 2015 - journals.sagepub.com
Next-generation sequencing technologies have revolutionarily advanced sequence-based
research with the advantages of high-throughput, high-sensitivity, and high-speed. RNA-seq …

From RNA-seq reads to differential expression results

A Oshlack, MD Robinson, MD Young - Genome biology, 2010 - Springer
From RNA-seq reads to differential expression results | Genome Biology Skip to main content
SpringerLink Account Menu Find a journal Publish with us Track your research Search Cart …

miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes

V Tirumalai, C Swetha, A Nair, A Pandit… - Journal of …, 2019 - academic.oup.com
MicroRNAs are a class of non-coding small RNAs involved in the negative regulation of
gene expression, which play critical roles in developmental and metabolic pathways …

Identifying RNA editing sites using RNA sequencing data alone

G Ramaswami, R Zhang, R Piskol, LP Keegan… - Nature …, 2013 - nature.com
We show that RNA editing sites can be called with high confidence using RNA sequencing
data from multiple samples across either individuals or species, without the need for …

RNA editing in the forefront of epitranscriptomics and human health

T Christofi, A Zaravinos - Journal of translational medicine, 2019 - Springer
Post-transcriptional modifications have been recently expanded with the addition of RNA
editing, which is predominantly mediated by adenosine and cytidine deaminases acting on …

RNA editing and its molecular mechanism in plant organelles

M Ichinose, M Sugita - Genes, 2016 - mdpi.com
RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria
and chloroplasts. In some plant taxa,“reverse” U-to-C editing also occurs. However, to date …

REDItools: high-throughput RNA editing detection made easy

E Picardi, G Pesole - Bioinformatics, 2013 - academic.oup.com
The reliable detection of RNA editing sites from massive sequencing data remains
challenging and, although several methodologies have been proposed, no computational …

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

JH Bahn, JH Lee, G Li, C Greer, G Peng… - Genome …, 2012 - genome.cshlp.org
RNA editing enhances the diversity of gene products at the post-transcriptional level.
Approaches for genome-wide identification of RNA editing face two main challenges …

Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

C Lo Giudice, MA Tangaro, G Pesole, E Picardi - Nature protocols, 2020 - nature.com
RNA editing is a widespread post-transcriptional mechanism able to modify transcripts
through insertions/deletions or base substitutions. It is prominent in mammals, in which …

Characterizing phage genomes for therapeutic applications

CW Philipson, LJ Voegtly, MR Lueder, KA Long… - Viruses, 2018 - mdpi.com
Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating
bacterial infections with bacteriophages alone or in combination with traditional antibiotics …