Genomic limitations to RNA sequencing expression profiling

CD Hirsch, NM Springer, CN Hirsch - The Plant Journal, 2015 - Wiley Online Library
The field of genomics has grown rapidly with the advent of massively parallel sequencing
technologies, allowing for novel biological insights with regards to genomic, transcriptomic …

The 'TranSeq'3′‐end sequencing method for high‐throughput transcriptomics and gene space refinement in plant genomes

O Tzfadia, S Bocobza, J Defoort… - The Plant …, 2018 - Wiley Online Library
High‐throughput RNA sequencing has proven invaluable not only to explore gene
expression but also for both gene prediction and genome annotation. However, RNA …

Discovering new biology through sequencing of RNA

APM Weber - Plant physiology, 2015 - academic.oup.com
Abstract Sequencing of RNA (RNA-Seq) was invented approximately 1 decade ago and has
since revolutionized biological research. This update provides a brief historic perspective on …

Design, execution, and interpretation of plant RNA-seq analyses

RN Upton, FH Correr, J Lile, GL Reynolds… - Frontiers in Plant …, 2023 - frontiersin.org
Genomics has transformed our understanding of the genetic architecture of traits and the
genetic variation present in plants. Here, we present a review of how RNA-seq can be …

Analysis of RNA-Seq data using TopHat and Cufflinks

S Ghosh, CKK Chan - Plant Bioinformatics: Methods and Protocols, 2016 - Springer
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge
amounts of data in a very short span of time for a single sample. These data have required …

An 'eFP‐Seq Browser'for visualizing and exploring RNA sequencing data

A Sullivan, PK Purohit, NH Freese, A Pasha… - The Plant …, 2019 - Wiley Online Library
Improvements in next‐generation sequencing technologies have resulted in dramatically
reduced sequencing costs. This has led to an explosion of '‐seq'‐based methods, of which …

RNA-Seq: revelation of the messengers

MC Van Verk, R Hickman, CMJ Pieterse… - Trends in plant …, 2013 - cell.com
Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the
technology of choice for whole-transcriptome studies. However, the bioinformatics skills …

Short-read sequencing technologies for transcriptional analyses

SA Simon, J Zhai, RS Nandety… - Annual Review of …, 2009 - annualreviews.org
The technological advances in DNA sequencing over the past five years have changed our
approaches to gene expression analysis, fundamentally altering the basic methods used …

[HTML][HTML] Tools for building de novo transcriptome assembly

M Geniza, P Jaiswal - Current Plant Biology, 2017 - Elsevier
The availability of RNA-Seq method allows researchers to capture the spatial or temporal
profile of transcriptomes from various types of biological samples. The transcriptome data …

Plant Transcriptome Analysis with HISAT–StringTie–Ballgown and TopHat–Cufflinks Pipelines

X Rao - Transcriptome Data Analysis, 2024 - Springer
The development of next-generation sequencing technology has led to a burst of data in a
single assay. Management of a large dataset requires high demands on bioinformatic skills …