miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts

DeepChrome: deep-learning for predicting gene expression from histone modifications

(2016) Ritambhara Singh et al.   BIOINFORMATICS

Pairing beyond the Seed Supports MicroRNA Targeting Specificity

(2016) James P. Broughton et al.   MOLECULAR CELL

MicroRNA Target Recognition: Insights from Transcriptome-Wide Non-Canonical Interactions

(2016)   MOLECULES AND CELLS

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

Deep learning

(2015) Yann LeCun et al.   NATURE

miRWalk2.0: a comprehensive atlas of microRNA-target interactions

(2015) Harsh Dweep et al.   NATURE METHODS

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

(2015) Miroslav Šulc et al.   NUCLEIC ACIDS RESEARCH

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G

(2015) Rafal Gumienny et al.   NUCLEIC ACIDS RESEARCH

miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

(2015) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

miRNA–target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity

(2015) Michael J. Moore et al.   Nature Communications

Learning Understandable Neural Networks With Nonnegative Weight Constraints

(2015) Jan Chorowski et al.   IEEE Transactions on Neural Networks and Learning Systems

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

(2014) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

Structural basis for microRNA targeting

(2014) N. T. Schirle et al.   SCIENCE

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

miRClassify: An advanced web server for miRNA family classification and annotation

(2013) Quan Zou et al.   COMPUTERS IN BIOLOGY AND MEDICINE

miRmap web: comprehensive microRNA target prediction online

(2013) Charles E. Vejnar et al.   NUCLEIC ACIDS RESEARCH

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

(2013) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

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

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Efficient use of accessibility in microRNA target prediction

(2010) Ray M. Marín 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

Accurate microRNA target prediction correlates with protein repression levels

(2009) Manolis Maragkakis et al.   BMC BIOINFORMATICS