Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

MicroRNA functions in insects

(2012) Sassan Asgari   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

A fast ab-initio method for predicting miRNA precursors in genomes

(2012) Sébastien Tempel et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

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

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

(2011) Yonggan Wu et al.   BMC BIOINFORMATICS

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

(2010) Anthony Mathelier et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)

(2010) Sumeet Agarwal et al.   BMC BIOINFORMATICS

miRBase: integrating microRNA annotation and deep-sequencing data

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

miR-9a prevents apoptosis during wing development by repressing Drosophila LIM-only

(2009) Fernando Bejarano et al.   DEVELOPMENTAL BIOLOGY

Computational approaches for microRNA studies: a review

(2009) Li Li et al.   MAMMALIAN GENOME

Current tools for the identification of miRNA genes and their targets

(2009) N. D. Mendes et al.   NUCLEIC ACIDS RESEARCH

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY