Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

Estimation of alternative splicing isoform frequencies from RNA-Seq data

(2011) Marius Nicolae et al.   Algorithms for Molecular Biology

Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments

(2011) Bogdan Paşaniuc et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

(2011) Daniel Bottomly et al.   PLoS One

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

(2010) James R Bradford et al.   BMC GENOMICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

(2010) Qiang Gan et al.   CELL RESEARCH

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

(2010) B. Daines et al.   GENOME RESEARCH

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

(2010) N Zamudio 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

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq

(2010) Ji Wen et al.   NUCLEIC ACIDS RESEARCH

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq

(2010) Liguo Wang et al.   PLoS One

Global analysis of trans-splicing in Drosophila

(2010) C. J. McManus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis

(2009) Miguel Pérez-Enciso et al.   BMC GENOMICS

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

(2009) Joshua S Bloom et al.   BMC GENOMICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Detection of human interchromosomal trans-splicing in sequence databanks

(2009) R. H. Herai et al.   BRIEFINGS IN BIOINFORMATICS

The plasticity of the mammalian transcriptome

(2009) Johan Lindberg et al.   GENOMICS

Decreased PPARγ Expression Compromises Perigonadal-Specific Fat Deposition and Insulin Sensitivity

(2009) Yau-Sheng Tsai et al.   MOLECULAR ENDOCRINOLOGY

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Splicing of mRNA mediated by tRNA sequences in mouse cells

(2009) M. Zamboni et al.   RNA

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Many LINE1 elements contribute to the transcriptome of human somatic cells

(2009) Sanjida H Rangwala et al.   GENOME BIOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Transcriptome architecture across tissues in the pig

(2008) André LJ Ferraz et al.   BMC GENOMICS

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

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

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS