Digital expression explorer 2: a repository of uniformly processed RNA sequencing data

Enabling rootless Linux Containers in multi-user environments: The udocker tool

(2018) Jorge Gomes et al.   COMPUTER PHYSICS COMMUNICATIONS

Promoter architecture determines cotranslational regulation of mRNA

(2018) Lorena Espinar et al.   GENOME RESEARCH

Massive mining of publicly available RNA-seq data from human and mouse

(2018) Alexander Lachmann et al.   Nature Communications

Context-dependent deposition and regulation of mRNAs in P-bodies

(2018) Congwei Wang et al.   eLife

Reproducible RNA-seq analysis using recount2

(2017) Leonardo Collado-Torres et al.   NATURE BIOTECHNOLOGY

Expression Atlas: gene and protein expression across multiple studies and organisms

(2017) Irene Papatheodorou et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

MEK Inhibitors Reverse Growth of Embryonal Brain Tumors Derived from Oligoneural Precursor Cells

(2016) Katarzyna Modzelewska et al.   Cell Reports

Dynamic changes in the cardiac methylome during postnatal development

(2015) Choon Boon Sim et al.   FASEB JOURNAL

Macrophage Epoxygenase Determines a Profibrotic Transcriptome Signature

(2015) Jacques Behmoaras et al.   JOURNAL OF IMMUNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Altering cancer transcriptomes using epigenomic inhibitors

(2015) Malaina Gaddis et al.   Epigenetics & Chromatin

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

The bHLH Transcription Factor HBI1 Mediates the Trade-Off between Growth and Pathogen-Associated Molecular Pattern-Triggered Immunity in Arabidopsis

(2014) M. Fan et al.   PLANT CELL

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Extension of Life Span by Impaired Glucose Metabolism in Caenorhabditis elegans Is Accompanied by Structural Rearrangements of the Transcriptomic Network

(2013) Steffen Priebe et al.   PLoS One

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

(2013) Tobias Kockmann et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

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

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

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE