Response to “The Reality of Pervasive Transcription”

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

(2010) Ashish Agarwal et al.   BMC GENOMICS

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

Noncoding transcripts as expression boosters

(2010) Nicole Rusk   NATURE METHODS

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay

(2009) Zhenguo Zhang et al.   BMC BIOLOGY

Exosome complex and pervasive transcription in eukaryotic genomes

(2009) Dmitry Belostotsky   CURRENT OPINION IN CELL BIOLOGY

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

A Novel Tandem Reporter Quantifies RNA Polymerase II Termination in Mammalian Cells

(2009) Ayan Banerjee et al.   PLoS One

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS