Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

Quantitative visualization of alternative exon expression from RNA-seq data

(2015) Yarden Katz et al.   BIOINFORMATICS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Alternative mRNA transcription, processing, and translation: insights from RNA sequencing

(2015) Eleonora de Klerk et al.   TRENDS IN GENETICS

Chimera: a Bioconductor package for secondary analysis of fusion products

(2014) Marco Beccuti et al.   BIOINFORMATICS

SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing

(2014) Xi Wang et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

(2014) Krishna R Kalari et al.   BMC BIOINFORMATICS

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

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage

(2014) Stuart K Archer et al.   BMC GENOMICS

Open-access synthetic spike-in mRNA-seq data for cancer gene fusions

(2014) Waibhav D Tembe et al.   BMC GENOMICS

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing

(2014) T Okeyo-Owuor et al.   LEUKEMIA

Bringing RNA-seq closer to the clinic

(2014) Kendall Van Keuren-Jensen et al.   NATURE BIOTECHNOLOGY

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

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

(2014) Zong Hong Zhang et al.   PLoS One

Detection of a Recurrent DNAJB1-PRKACA Chimeric Transcript in Fibrolamellar Hepatocellular Carcinoma

(2014) J. N. Honeyman et al.   SCIENCE

GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data

(2014) Qing Xiong et al.   Scientific Reports

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

populacDNA normalization by hydroxyapatite chromatography to enrich transcriptome diversity in RNA-seq applications

(2013) Victoria A. VanderNoot et al.   BIOTECHNIQUES

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

(2013) Matteo Carrara et al.   BMC BIOINFORMATICS

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Assessing De Novo transcriptome assembly metrics for consistency and utility

(2013) Shawn T O’Neil et al.   BMC GENOMICS

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

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

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

(2013) J. D. Khoury et al.   JOURNAL OF VIROLOGY

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

(2013) Emma M. Quinn et al.   PLoS One

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity

(2013) Matteo Carrara et al.   Biomed Research International

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Next-generation sequencing technology in clinical virology

(2012) M.R. Capobianchi et al.   CLINICAL MICROBIOLOGY AND INFECTION

Exome versus transcriptome sequencing in identifying coding region variants

(2012) Chee-Seng Ku et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

RNA editing in the human ENCODE RNA-seq data

(2012) E. Park et al.   GENOME RESEARCH

Application of next-generation sequencing technologies in virology

(2012) A. D. Radford et al.   JOURNAL OF GENERAL VIROLOGY

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Savant Genome Browser 2: visualization and analysis for population-scale genomics

(2012) M. Fiume et al.   NUCLEIC ACIDS RESEARCH

Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma

(2012) D. Singh et al.   SCIENCE

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

(2011) Laurence D. Parnell et al.   PLoS Computational Biology

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Correlations between RNA and protein expression profiles in 23 human cell lines

(2009) Marcus Gry et al.   BMC GENOMICS

The completion of the Mammalian Gene Collection (MGC)

(2009) et al.   GENOME RESEARCH

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Genetics of human gene expression: mapping DNA variants that influence gene expression

(2009) Vivian G. Cheung et al.   NATURE REVIEWS GENETICS

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY