microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs

ADAR mediates differential expression of polycistronic microRNAs

(2014) Geetanjali Chawla et al.   NUCLEIC ACIDS RESEARCH

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells

(2013) Gang Chang et al.   CELL RESEARCH

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

The Imprinted H19 LncRNA Antagonizes Let-7 MicroRNAs

(2013) Amanda N. Kallen et al.   MOLECULAR CELL

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

(2013) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

miRNA Biogenesis Enzyme Drosha Is Required for Vascular Smooth Muscle Cell Survival

(2013) Pei Fan et al.   PLoS One

Conditionals by inversion provide a universal method for the generation of conditional alleles

(2013) Aris N. Economides et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1

(2013) P. Monnier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

(2013) Annalisa Marsico et al.   GENOME BIOLOGY

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Divergent transcription: A new feature of active promoters

(2011) Amy C. Seila et al.   CELL CYCLE

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

(2011) T. Vergoulis et al.   NUCLEIC ACIDS RESEARCH

Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data

(2011) Chia-Hung Chien et al.   NUCLEIC ACIDS RESEARCH

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Canonical and alternate functions of the microRNA biogenesis machinery

(2010) M. M. W. Chong et al.   GENES & DEVELOPMENT

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Annotation of mammalian primary microRNAs

(2009) Harpreet K Saini et al.   BMC GENOMICS

A transcription factor affinity-based code for mammalian transcription initiation

(2009) M. Megraw et al.   GENOME RESEARCH

Chromatin poises miRNA- and protein-coding genes for expression

(2009) A. Barski et al.   GENOME RESEARCH

Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data

(2009) David L. Corcoran et al.   PLoS One

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

Chromatin structure analyses identify miRNA promoters

(2008) F. Ozsolak et al.   GENES & DEVELOPMENT

Divergent Transcription from Active Promoters

(2008) Amy C. Seila 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