Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

The value of muscle biopsies in Pompe disease: identifying lipofuscin inclusions in juvenile- and adult-onset patients

(2014) Erin J Feeney et al.   Acta Neuropathologica Communications

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

(2013) Yuwen Liu et al.   BIOINFORMATICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing

(2012) Pengyuan Liu et al.   CARCINOGENESIS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Secondary mutations inBRCA2associated with clinical resistance to a PARP inhibitor

(2012) Louise J Barber et al.   JOURNAL OF PATHOLOGY

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

(2012) V. CAHAIS et al.   Molecular Ecology Resources

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma

(2012) Mark Sausen et al.   NATURE GENETICS

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes

(2011) J. W. Rowley et al.   BLOOD

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

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

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

(2010) B. Daines et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

(2009) Mathieu Clément-Ziza et al.   BMC GENOMICS

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

(2009) L. W. Hillier et al.   GENOME RESEARCH

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

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

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS 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