Transcriptome software results show significant variation among different commercial pipelines

A comparison of transcriptome analysis methods with reference genome

(2022) Xu Liu et al.   BMC GENOMICS

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

(2022) Cung Nawl Thawng et al.   BMC GENOMICS

Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana

(2020) Stephanie Schaarschmidt et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing

(2020) Takehiro Matsubara et al.   Biomed Research International

The Phenotypic and Transcriptomic Response of the Caenorhabditis elegans Nematode to Background and Below-Background Radiation Levels

(2020) Wayne A. Van Voorhies et al.   Frontiers in Public Health

Current RNA-seq methodology reporting limits reproducibility

(2019) Joël Simoneau et al.   BRIEFINGS IN BIOINFORMATICS

OUP accepted manuscript

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Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation

(2018) Hugo Castillo et al.   PLoS One

Below-Background Ionizing Radiation as an Environmental Cue for Bacteria

(2017) Hugo Castillo et al.   Frontiers in Microbiology

RNA-Seq differential expression analysis: An extended review and a software tool

(2017) Juliana Costa-Silva et al.   PLoS One

Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster

(2016) Yanzhu Lin et al.   BMC GENOMICS

Simulation-based comprehensive benchmarking of RNA-seq aligners

(2016) Giacomo Baruzzo et al.   NATURE METHODS

RNA-Seq methods for transcriptome analysis

(2016) Radmila Hrdlickova et al.   Wiley Interdisciplinary Reviews-RNA

Stress induction in the bacteriaShewanella oneidensisandDeinococcus radioduransin response to below-background ionizing radiation

(2015) Hugo Castillo et al.   INTERNATIONAL JOURNAL OF RADIATION BIOLOGY

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data

(2014) Zong Hong Zhang et al.   PLoS One

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Comparison of software packages for detecting differential expression in RNA-seq studies

(2013) F. Seyednasrollah et al.   BRIEFINGS IN BIOINFORMATICS

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

(2012) José A Robles et al.   BMC GENOMICS

EXPLORING BIOLOGICAL EFFECTS OF LOW LEVEL RADIATION FROM THE OTHER SIDE OF BACKGROUND

(2011) Geoffrey Battle Smith et al.   HEALTH PHYSICS

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Uncovering the Complexity of Transcriptomes with RNA-Seq

(2010) Valerio Costa et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS