Long non-coding RNAs: definitions, functions, challenges and recommendations

JS Mattick, PP Amaral, P Carninci… - … reviews Molecular cell …, 2023 - nature.com
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes
of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II …

Current challenges and best-practice protocols for microbiome analysis

R Bharti, DG Grimm - Briefings in bioinformatics, 2021 - academic.oup.com
Analyzing the microbiome of diverse species and environments using next-generation
sequencing techniques has significantly enhanced our understanding on metabolic …

Non-coding RNAs as drug targets

M Matsui, DR Corey - Nature reviews Drug discovery, 2017 - nature.com
Most of the human genome encodes RNAs that do not code for proteins. These non-coding
RNAs (ncRNAs) may affect normal gene expression and disease progression, making them …

The rise of regulatory RNA

KV Morris, JS Mattick - Nature Reviews Genetics, 2014 - nature.com
Discoveries over the past decade portend a paradigm shift in molecular biology. Evidence
suggests that RNA is not only functional as a messenger between DNA and protein but also …

[HTML][HTML] lincRNAs: genomics, evolution, and mechanisms

I Ulitsky, DP Bartel - Cell, 2013 - cell.com
Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in
mammalian genomes and might play widespread roles in gene regulation and other cellular …

On the classification of long non-coding RNAs

L Ma, VB Bajic, Z Zhang - RNA biology, 2013 - Taylor & Francis
Long non-coding RNAs (lncRNAs) have been found to perform various functions in a wide
variety of important biological processes. To make easier interpretation of lncRNA …

Genome regulation by long noncoding RNAs

JL Rinn, HY Chang - Annual review of biochemistry, 2012 - annualreviews.org
The central dogma of gene expression is that DNA is transcribed into messenger RNAs,
which in turn serve as the template for protein synthesis. The discovery of extensive …

Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs

MJ Hangauer, IW Vaughn, MT McManus - PLoS genetics, 2013 - journals.plos.org
Known protein coding gene exons compose less than 3% of the human genome. The
remaining 97% is largely uncharted territory, with only a small fraction characterized. The …

ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq

AD Fernandes, JM Macklaim, TG Linn, G Reid… - PloS one, 2013 - journals.plos.org
Experimental variance is a major challenge when dealing with high-throughput sequencing
data. This variance has several sources: sampling replication, technical replication …

lncRNAdb v2. 0: expanding the reference database for functional long noncoding RNAs

XC Quek, DW Thomson, JLV Maag… - Nucleic acids …, 2015 - academic.oup.com
Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes,
only a small proportion have been examined for biological function. lncRNAdb, available at …