Detecting circular RNAs: bioinformatic and experimental challenges

L Szabo, J Salzman - Nature Reviews Genetics, 2016 - nature.com
The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of
gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect …

[PDF][PDF] A simple guide to de novo transcriptome assembly and annotation

V Raghavan, L Kraft, F Mesny… - Briefings in …, 2022 - academic.oup.com
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis

LA Corchete, EA Rojas, D Alonso-López… - Scientific reports, 2020 - nature.com
RNA-seq is currently considered the most powerful, robust and adaptable technique for
measuring gene expression and transcription activation at genome-wide level. As the …

Mettl3-mediated m6A regulates spermatogonial differentiation and meiosis initiation

K Xu, Y Yang, GH Feng, BF Sun, JQ Chen, YF Li… - Cell research, 2017 - nature.com
METTL3 catalyzes the formation of N 6-methyl-adenosine (m 6 A) which has important roles
in regulating various biological processes. However, the in vivo function of Mettl3 remains …

Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions

C Evans, J Hardin, DM Stoebel - Briefings in bioinformatics, 2018 - academic.oup.com
RNA-Seq is a widely used method for studying the behavior of genes under different
biological conditions. An essential step in an RNA-Seq study is normalization, in which raw …

HRT Atlas v1. 0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

BW Hounkpe, F Chenou, F de Lima… - Nucleic acids …, 2021 - academic.oup.com
Housekeeping (HK) genes are constitutively expressed genes that are required for the
maintenance of basic cellular functions. Despite their importance in the calibration of gene …

Circulating miRNA analysis for cancer diagnostics and therapy

L Valihrach, P Androvic, M Kubista - Molecular Aspects of Medicine, 2020 - Elsevier
Successful treatment of cancer depends on early diagnosis and effective monitoring of
patients' response to therapy. Traditional tools based on tumor biopsies lack the sensitivity …

How to do quantile normalization correctly for gene expression data analyses

Y Zhao, L Wong, WWB Goh - Scientific reports, 2020 - nature.com
Quantile normalization is an important normalization technique commonly used in high-
dimensional data analysis. However, it is susceptible to class-effect proportion effects (the …

A protocol to evaluate RNA sequencing normalization methods

ZB Abrams, TS Johnson, K Huang, PRO Payne… - BMC …, 2019 - Springer
Background RNA sequencing technologies have allowed researchers to gain a better
understanding of how the transcriptome affects disease. However, sequencing technologies …

A review of normalization and differential abundance methods for microbiome counts data

D Swift, K Cresswell, R Johnson… - Wiley …, 2023 - Wiley Online Library
The recent development of cost‐effective high‐throughput DNA sequencing technologies
has tremendously increased microbiome research. However, it has been well documented …