Transcription factor trapping by RNA in gene regulatory elements

Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex

(2015) Lanfeng Wang et al.   NATURE

The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis

(2015) Michal Lubas et al.   Cell Reports

Rbfox2 controls autoregulation in RNA-binding protein networks

(2014) M. Jangi et al.   GENES & DEVELOPMENT

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells

(2013) N. A. Kearns et al.   DEVELOPMENT

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells

(2012) Pietro Vella et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

(2011) Filippo M. Cernilogar et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

(2011) R. A. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Use of in vivo biotinylation to study protein–protein and protein–DNA interactions in mouse embryonic stem cells

(2009) Jonghwan Kim et al.   Nature Protocols

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY