Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia

(2016) Susanna Teppo et al.   GENOME RESEARCH

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis

(2016) Dimitrios M. Vitsios et al.   NUCLEIC ACIDS RESEARCH

A let-7-to-miR-125 MicroRNA Switch Regulates Neuronal Integrity and Lifespan in Drosophila

(2016) Geetanjali Chawla et al.   PLoS Genetics

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

(2015) Tsung-Cheng Chang et al.   GENOME RESEARCH

The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes

(2015) Wenwen Fang et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

(2015) Chirag Nepal et al.   NUCLEIC ACIDS RESEARCH

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Primary microRNA processing is functionally coupled to RNAP II transcription in vitro

(2015) Shanye Yin et al.   Scientific Reports

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization

(2014) Minna U. Kaikkonen et al.   NUCLEIC ACIDS RESEARCH

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

(2014) C.-L. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis

(2014) Maria Bouvy-Liivrand et al.   RNA Biology

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

(2013) Warren A. Whyte et al.   CELL

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

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Diversifying microRNA sequence and function

(2013) Stefan L. Ameres et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

(2013) Oskar Marín-Béjar et al.   GENOME BIOLOGY

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Non-coding RNAs as regulators of gene expression and epigenetics

(2011) M. U. Kaikkonen et al.   CARDIOVASCULAR RESEARCH

miR221/222 in Cancer: Their Role in Tumor Progression and Response to Therapy

(2011) M. Garofalo et al.   CURRENT MOLECULAR MEDICINE

Small RNA-mediated regulation of iPS cell generation

(2011) Zhonghan Li et al.   EMBO JOURNAL

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling

(2011) Felix Krueger et al.   PLoS One

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

MicroRNA-125b is a novel negative regulator of p53

(2009) M. T.N. Le et al.   GENES & DEVELOPMENT

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Primary microRNA transcripts are processed co-transcriptionally

(2008) Mariangela Morlando et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miR-29 miRNAs activate p53 by targeting p85α and CDC42

(2008) Seong-Yeon Park et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2008) Leighton J. Core et al.   SCIENCE