DNMT1-interacting RNAs block gene-specific DNA methylation

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

(2012) Touati Benoukraf et al.   NUCLEIC ACIDS RESEARCH

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

(2010) Maria E. Figueroa et al.   CANCER CELL

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

(2010) Andrew J Oler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Close association of RNA polymerase II and many transcription factors with Pol III genes

(2010) Debasish Raha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

(2010) J. Song et al.   SCIENCE

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

Epigenetic Modification of CCAAT/Enhancer Binding Protein   Expression in Acute Myeloid Leukemia

(2008) B. Hackanson et al.   CANCER RESEARCH

Mammalian Cytosine DNA Methyltransferase Dnmt1: Enzymatic Mechanism, Novel Mechanism-Based Inhibitors, and RNA-directed DNA Methylation

(2008) Zeljko Svedruzic   CURRENT MEDICINAL CHEMISTRY

PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element

(2008) A. K. Ebralidze et al.   GENES & DEVELOPMENT

Transcription factories are nuclear subcompartments that remain in the absence of transcription

(2008) J. A. Mitchell et al.   GENES & DEVELOPMENT

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs

(2008) Aristotelis Tsirigos et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE