The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

Promoter proximal pausing and the control of gene expression

(2011) Jian Li et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment

(2010) O. Alder et al.   DEVELOPMENT

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Next generation software for functional trend analysis

(2009) G. F. Berriz et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Modifications of RNA polymerase II are pivotal in regulating gene expression states

(2009) Emily Brookes et al.   EMBO REPORTS

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Poised RNA Polymerase II Gives Pause for Thought

(2008) Thanasis Margaritis et al.   CELL

Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: Potential role in progression

(2008) Luigi Scotto et al.   GENES CHROMOSOMES & CANCER

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

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY