Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Identification of a Cytoplasmic Complex That Adds a Cap onto 5'-Monophosphate RNA

(2009) Y. Otsuka et al.   MOLECULAR AND CELLULAR BIOLOGY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data

(2009) Kimberly R. Blahnik et al.   NUCLEIC ACIDS RESEARCH

Re-capping the message

(2009) Daniel R. Schoenberg et al.   TRENDS IN BIOCHEMICAL SCIENCES

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2009) Hideya Kawaji et al.   GENOME BIOLOGY

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer

(2008) Norihiro Maeda et al.   BIOTECHNIQUES

Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array

(2008) Gregory AC Singer et al.   BMC GENOMICS

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

The functional consequences of alternative promoter use in mammalian genomes

(2008) Ramana V. Davuluri et al.   TRENDS IN GENETICS

Modeling ChIP Sequencing In Silico with Applications

(2008) Zhengdong D. Zhang et al.   PLoS Computational Biology

RNA polymerase II stalling: loading at the start prepares genes for a sprint

(2008) Jia Wu et al.   GENOME BIOLOGY