An integrated expression atlas of miRNAs and their promoters in human and mouse

Distribution of miRNA expression across human tissues

(2016) Nicole Ludwig et al.   NUCLEIC ACIDS RESEARCH

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

(2016) Imad Abugessaisa et al.   Database-The Journal of Biological Databases and Curation

A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome

(2015) Bastian Fromm et al.   Annual Review of Genetics

MicroRNA-345 induces apoptosis in pancreatic cancer cells through potentiation of caspase-dependent and -independent pathways

(2015) Sanjeev K Srivastava et al.   BRITISH JOURNAL OF CANCER

Data Normalization Strategies for MicroRNA Quantification

(2015) H. Schwarzenbach et al.   CLINICAL CHEMISTRY

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

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

Trbp regulates heart function through microRNA-mediated Sox6 repression

(2015) Jian Ding et al.   NATURE GENETICS

Towards a molecular understanding of microRNA-mediated gene silencing

(2015) Stefanie Jonas et al.   NATURE REVIEWS GENETICS

Roles for noncoding RNAs in cell-fate determination and regeneration

(2015) Mo Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators

(2015) Georgios Georgakilas et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Chirag Nepal et al.   NUCLEIC ACIDS RESEARCH

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

(2015) Eric Londin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Roles for noncoding RNAs in cell-fate determination and regeneration

(2015) Mo Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

miR-206 controls LXRα expression and promotes LXR-mediated cholesterol efflux in macrophages

(2014) Manjula Vinod et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

A tool for design of primers for microRNA-specific quantitative RT-qPCR

(2014) Peter K Busk   BMC BIOINFORMATICS

Aberrant Regulation and Function of MicroRNAs in Cancer

(2014) Brian D. Adams et al.   CURRENT BIOLOGY

miR-15a/16 Regulates Macrophage Phagocytosis after Bacterial Infection

(2014) Hyung-Geun Moon et al.   JOURNAL OF IMMUNOLOGY

A promoter-level mammalian expression atlas

(2014)   NATURE

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

(2014) Alexandre Fort et al.   NATURE GENETICS

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulation of microRNA function in somatic stem cell proliferation and differentiation

(2014) Archana Shenoy et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues

(2014) Zhiyun Guo et al.   Scientific Reports

miR-191: an emerging player in disease biology

(2014) Neha Nagpal et al.   Frontiers in Genetics

miR-153 Supports Colorectal Cancer Progression via Pleiotropic Effects That Enhance Invasion and Chemotherapeutic Resistance

(2013) L. Zhang et al.   CANCER RESEARCH

Adult-specific functions of animal microRNAs

(2013) Kailiang Sun et al.   NATURE REVIEWS GENETICS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

MiR-200b and miR-429 Function in Mouse Ovulation and Are Essential for Female Fertility

(2013) H. Hasuwa et al.   SCIENCE

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences

(2012) Phil Arnold et al.   BIOINFORMATICS

MicroRNAs in Stress Signaling and Human Disease

(2012) Joshua T. Mendell et al.   CELL

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

Birth and expression evolution of mammalian microRNA genes

(2012) J. Meunier et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Mincle polarizes human monocyte and neutrophil responses to Candida albicans

(2012) Dipti Vijayan et al.   IMMUNOLOGY AND CELL BIOLOGY

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Site-specific DICER and DROSHA RNA products control the DNA-damage response

(2012) Sofia Francia et al.   NATURE

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

MicroRNA profiling: approaches and considerations

(2012) Colin C. Pritchard et al.   NATURE REVIEWS GENETICS

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Mirtrons: microRNA biogenesis via splicing

(2011) Jakub O. Westholm et al.   BIOCHIMIE

Logical Development of the Cell Ontology

(2011) Terrence F Meehan et al.   BMC BIOINFORMATICS

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

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

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

(2011) Eivind Valen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

(2010) M. J.L. de Hoon et al.   GENOME RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS