Current and future methods for mRNA analysis: a drive toward single molecule sequencing
A Bayega, S Fahiminiya, S Oikonomopoulos… - … Analysis: Methods and …, 2018 - Springer
The transcriptome encompasses a range of species including messenger RNA, and other
noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge …
noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge …
Comparative evaluation of full-length isoform quantification from RNA-Seq
Background Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics
analyses and has been an area of active development since the beginning. The …
analyses and has been an area of active development since the beginning. The …
Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
S Oikonomopoulos, YC Wang, H Djambazian… - Scientific reports, 2016 - nature.com
To assess the performance of the Oxford Nanopore Technologies MinION sequencing
platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix …
platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix …
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Background Understanding the regulation of gene expression, including transcription start
site usage, alternative splicing, and polyadenylation, requires accurate quantification of …
site usage, alternative splicing, and polyadenylation, requires accurate quantification of …
Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data
Y Su, Z Yu, S **, Z Ai, R Yuan, X Chen, Z Xue… - Nature …, 2024 - nature.com
Abstract The advancement of Long-Read Sequencing (LRS) techniques has significantly
increased the length of sequencing to several kilobases, thereby facilitating the identification …
increased the length of sequencing to several kilobases, thereby facilitating the identification …
Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals
Transcription initiated at alternative sites can produce mRNA isoforms with different 5ʹ UTR
s, which are potentially subjected to differential translational regulation. However, the …
s, which are potentially subjected to differential translational regulation. However, the …
Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems
The availability of omic data produced from international consortia, as well as from
worldwide laboratories, is offering the possibility both to answer long-standing questions in …
worldwide laboratories, is offering the possibility both to answer long-standing questions in …
Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection
Alternative splicing (AS) contributes to diversifying and regulating cellular responses to
environmental conditions and developmental cues by differentially producing multiple …
environmental conditions and developmental cues by differentially producing multiple …
A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data
Alternative polyadenylation (APA) has been implicated to play an important role in post-
transcriptional regulation by regulating mRNA abundance, stability, localization and …
transcriptional regulation by regulating mRNA abundance, stability, localization and …
Challenges in detecting and quantifying intron retention from next generation sequencing data
L Broseus, W Ritchie - Computational and structural biotechnology journal, 2020 - Elsevier
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the
final mRNA. An increasing body of literature has demonstrated a major role for IR in …
final mRNA. An increasing body of literature has demonstrated a major role for IR in …