iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq

Deep sequencing of small RNA transcriptome reveals novel non-coding RNAs in hepatocellular carcinoma

(2013) Priscilla T.-Y. Law et al.   JOURNAL OF HEPATOLOGY

PIWI-interacting RNAs: from generation to transgenerational epigenetics

(2013) Maartje J. Luteijn et al.   NATURE REVIEWS GENETICS

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

(2013) Jinyu Wu et al.   RNA Biology

shortran: a pipeline for small RNA-seq data analysis

(2012) Vikas Gupta et al.   BIOINFORMATICS

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

(2012) M. B. Stocks et al.   BIOINFORMATICS

Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation

(2012) V. Williamson et al.   BRIEFINGS IN BIOINFORMATICS

Argonaute Divides Its RNA Guide into Domains with Distinct Functions and RNA-Binding Properties

(2012) Liang Meng Wee et al.   CELL

Altered expression of piRNAs and their relation with clinicopathologic features of breast cancer

(2012) G. Huang et al.   Clinical & Translational Oncology

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer

(2012) O Paris et al.   ONCOGENE

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

(2012) Francesca Cordero et al.   PLoS One

Evaluation of normalization methods in mammalian microRNA-Seq data

(2012) L. X. Garmire et al.   RNA

piR-823, a novel non-coding small RNA, demonstrates in vitro and in vivo tumor suppressive activity in human gastric cancer cells

(2011) Jia Cheng et al.   CANCER LETTERS

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

(2011) M. Hackenberg 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

piR_015520 Belongs to Piwi-Associated RNAs Regulates Expression of the Human Melatonin Receptor 1A Gene

(2011) Teresa Esposito et al.   PLoS One

Estrogen Receptor α Controls a Gene Network in Luminal-Like Breast Cancer Cells Comprising Multiple Transcription Factors and MicroRNAs

(2010) Luigi Cicatiello et al.   AMERICAN JOURNAL OF PATHOLOGY

DSAP: deep-sequencing small RNA analysis pipeline

(2010) Po-Jung Huang et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

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

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

(2009) Wei-Chi Wang et al.   BMC BIOINFORMATICS

miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells

(2008) Joachim Silber et al.   BMC Medicine

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis

(2008) Qihong Huang et al.   NATURE CELL BIOLOGY

Biological principles of microRNA-mediated regulation: shared themes amid diversity

(2008) Alex S. Flynt et al.   NATURE REVIEWS GENETICS

OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences

(2008) O. Croce et al.   NUCLEIC ACIDS RESEARCH

MicroRNA-134 Modulates the Differentiation of Mouse Embryonic Stem Cells, Where It Causes Post-Transcriptional Attenuation of Nanog and LRH1

(2007) Yvonne M.-S. Tay et al.   STEM CELLS