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

Detection of Redundant Fusion Transcripts as Biomarkers or Disease-Specific Therapeutic Targets in Breast Cancer

(2012) Y. W. Asmann et al.   CANCER RESEARCH

Discovery of hundreds of mirtrons in mouse and human small RNA data

(2012) E. Ladewig et al.   GENOME RESEARCH

Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques

(2012) X. Liu et al.   GENOME RESEARCH

Characterization and Evolution of microRNA Genes Derived from Repetitive Elements and Duplication Events in Plants

(2012) Jie Sun et al.   PLoS One

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

Evolution of microRNA diversity and regulation in animals

(2011) Eugene Berezikov   NATURE REVIEWS GENETICS

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

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain

(2010) M. Somel et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Transcriptional regulation of mammalian miRNA genes

(2010) Brian C. Schanen et al.   GENOMICS

Introducing Knowledge into Differential Expression Analysis

(2010) Ewa Szczurek et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Structure and activity of putative intronic miRNA promoters

(2010) A. M. Monteys et al.   RNA

Towards accurate human promoter recognition: a review of currently used sequence features and classification methods

(2009) Jia Zeng et al.   BRIEFINGS IN BIOINFORMATICS

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

Functional Association of the Microprocessor Complex with the Spliceosome

(2009) N. Kataoka et al.   MOLECULAR AND CELLULAR BIOLOGY

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2009) Hideya Kawaji 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

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions

(2008) Thomas Manke et al.   PLoS Computational Biology