Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Z Jiang, X Zhou, R Li, JJ Michal, S Zhang… - Cellular and molecular …, 2015 - Springer
Whole transcriptome analysis plays an essential role in deciphering genome structure and
function, identifying genetic networks underlying cellular, physiological, biochemical and …

Methodologies for transcript profiling using long-read technologies

S Oikonomopoulos, A Bayega, S Fahiminiya… - Frontiers in …, 2020 - frontiersin.org
RNA sequencing using next-generation sequencing technologies (NGS) is currently the
standard approach for gene expression profiling, particularly for large-scale high-throughput …

Reviving the transcriptome studies: an insight into the emergence of single-molecule transcriptome sequencing

B Wang, V Kumar, A Olson, D Ware - Frontiers in genetics, 2019 - frontiersin.org
Advances in transcriptomics have provided an exceptional opportunity to study functional
implications of the genetic variability. Technologies such as RNA-Seq have emerged as …

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Y Hara, K Tatsumi, M Yoshida, E Kajikawa, H Kiyonari… - BMC genomics, 2015 - Springer
Background RNA-seq enables gene expression profiling in selected spatiotemporal
windows and yields massive sequence information with relatively low cost and time …

Next-generation sequencing: applications beyond genomes

S Marguerat, BT Wilhelm, J Bähler - 2008 - portlandpress.com
The development of DNA sequencing more than 30 years ago has profoundly impacted
biological research. In the last couple of years, remarkable technological innovations have …

High‐throughput sequencing for biology and medicine

WW Soon, M Hariharan, MP Snyder - Molecular systems biology, 2013 - embopress.org
Advances in genome sequencing have progressed at a rapid pace, with increased
throughput accompanied by plunging costs. But these advances go far beyond faster and …

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

FJ Pardo-Palacios, D Wang, F Reese, M Diekhans… - Nature …, 2024 - nature.com
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was
formed to evaluate the effectiveness of long-read approaches for transcriptome analysis …

Principles of transcriptome analysis and gene expression quantification: an RNA‐seq tutorial

JBW Wolf - Molecular ecology resources, 2013 - Wiley Online Library
Genome‐wide analyses and high‐throughput screening was long reserved for biomedical
applications and genetic model organisms. With the rapid development of massively parallel …

Transcriptome analysis using next-generation sequencing

KO Mutz, A Heilkenbrinker, M Lönne, JG Walter… - Current opinion in …, 2013 - Elsevier
Up to date research in biology, biotechnology, and medicine requires fast genome and
transcriptome analysis technologies for the investigation of cellular state, physiology, and …

BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data

AV Kartashov, A Barski - Genome biology, 2015 - Springer
High-throughput sequencing has revolutionized biology by enhancing our ability to perform
genome-wide studies. However, due to lack of bioinformatics expertise, modern …