Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests

Re-evaluation of the roles ofDROSHA,Exportin 5, andDICERin microRNA biogenesis

(2016) Young-Kook Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Chimira: analysis of small RNA sequencing data and microRNA modifications: Fig. 1.

(2015) Dimitrios M. Vitsios et al.   BIOINFORMATICS

A Burst of miRNA Innovation in the Early Evolution of Butterflies and Moths

(2015) Shan Quah et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification and expression profiling of Helicoverpa armigera microRNAs and their possible role in the regulation of digestive protease genes

(2014) Purushottam R. Lomate et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Regulation of microRNA biogenesis

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

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray

(2014) Yoshiki Murakami et al.   PLoS One

Evidence for the biogenesis of more than 1,000 novel human microRNAs

(2014) Marc R Friedländer et al.   GENOME BIOLOGY

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

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

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

miReader: Discovering Novel miRNAs in Species without Sequenced Genome

(2013) Ashwani Jha et al.   PLoS One

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

(2013) Jinyu Wu et al.   RNA Biology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

MirPlex: A Tool for Identifying miRNAs in High-Throughput sRNA Datasets Without a Genome

(2012) Daniel Mapleson et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ViennaRNA Package 2.0

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

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

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

Deep Sequencing Reveals Novel MicroRNAs and Regulation of MicroRNA Expression during Cell Senescence

(2011) Joseph M. Dhahbi et al.   PLoS One

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

(2010) Anthony Mathelier et al.   BIOINFORMATICS

A dicer-independent miRNA biogenesis pathway that requires Ago catalysis

(2010) Sihem Cheloufi et al.   NATURE

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity

(2010) D. Cifuentes et al.   SCIENCE

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

(2010) David Hendrix et al.   GENOME BIOLOGY

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell