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

Deinococcus radiodurans UWO298 Dependence on Background Radiation for Optimal Growth

(2021) Hugo Castillo et al.   Frontiers in Genetics

Chinese hamster V79 cells’ dependence on background ionizing radiation for optimal growth

(2021) Hugo Castillo et al.   RADIATION AND ENVIRONMENTAL BIOPHYSICS

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

Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

(2020) Shanrong Zhao et al.   RNA

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

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods

(2018) Thomas P. Quinn et al.   BMC BIOINFORMATICS

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

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

(2018) Hugo Castillo et al.   PLoS One

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

Differential Gene Expression of Three Mastitis-Causing Escherichia coli Strains Grown under Planktonic, Swimming, and Swarming Culture Conditions

(2016) John D. Lippolis et al.   mSystems

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

(2015) Peipei Li et al.   BMC BIOINFORMATICS

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

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

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug-resistant Salmonella enterica serovar Typhimurium

(2015) Brian W. Brunelle et al.   Frontiers in Microbiology

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

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

A record-based case–control study of natural background radiation and the incidence of childhood leukaemia and other cancers in Great Britain during 1980–2006

(2012) G M Kendall et al.   LEUKEMIA

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS