miRge 2.0 for comprehensive analysis of microRNA sequencing data

Big Strides in Cellular MicroRNA Expression

(2018) Marc K. Halushka et al.   TRENDS IN GENETICS

Toward the human cellular microRNAome

(2017) Matthew N. McCall et al.   GENOME RESEARCH

Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

(2017) Yumeng Wang et al.   GENOME RESEARCH

Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types

(2017) Aristeidis G. Telonis et al.   NUCLEIC ACIDS RESEARCH

Toward the promise of microRNAs – Enhancing reproducibility and rigor in microRNA research

(2016) Kenneth W. Witwer et al.   RNA Biology

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

Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization

(2015) Mauro D. Locati et al.   NUCLEIC ACIDS RESEARCH

Prioritizing and selecting likely novel miRNAs from NGS data

(2015) Christina Backes 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

An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools

(2015) Jing Gong et al.   Database-The Journal of Biological Databases and Curation

Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing

(2015) Jing Gong et al.   RNA Biology

Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues

(2013) Leandro Castellano et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Systematic identification of edited microRNAs in the human brain

(2012) S. Alon et al.   GENOME RESEARCH

Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing

(2012) Markus Hafner et al.   METHODS

Reconstitution of an Argonaute-Dependent Small RNA Biogenesis Pathway Reveals a Handover Mechanism Involving the RNA Exosome and the Exonuclease QIP

(2012) Zhihong Xue et al.   MOLECULAR CELL

Are all the miRBase-registered microRNAs true?

(2012) Yijun Meng et al.   RNA Biology

miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay

(2012) S. Djuranovic et al.   SCIENCE

IsomiRs – the overlooked repertoire in the dynamic microRNAome

(2012) Corine T. Neilsen et al.   TRENDS IN GENETICS

ViennaRNA Package 2.0

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

The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1

(2011) Bo W. Han et al.   CURRENT BIOLOGY

Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

(2011) S. K. Wyman et al.   GENOME RESEARCH

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

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness

(2010) A. M. Burroughs et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

In-depth characterization of the microRNA transcriptome in a leukemia progression model

(2008) F. Kuchenbauer et al.   GENOME RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Small non-coding RNAs in animal development

(2008) Giovanni Stefani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY