Predicting effective microRNA target sites in mammalian mRNAs

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

(2015) Rafal Gumienny et al.   NUCLEIC ACIDS RESEARCH

MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets

(2015) Sanghamitra Bandyopadhyay et al.   Scientific Reports

Composition of seed sequence is a major determinant of microRNA targeting patterns

(2014) X. Wang   BIOINFORMATICS

Widespread context dependency of microRNA-mediated regulation

(2014) F. Erhard et al.   GENOME RESEARCH

Global Analyses of the Effect of Different Cellular Contexts on MicroRNA Targeting

(2014) Jin-Wu Nam et al.   MOLECULAR CELL

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

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

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance

(2014) Rémy Denzler et al.   MOLECULAR CELL

mRNA Destabilization Is the Dominant Effect of Mammalian MicroRNAs by the Time Substantial Repression Ensues

(2014) Stephen W. Eichhorn et al.   MOLECULAR CELL

Identification and consequences of miRNA–target interactions — beyond repression of gene expression

(2014) Jean Hausser et al.   NATURE REVIEWS GENETICS

Structural basis for microRNA targeting

(2014) N. T. Schirle et al.   SCIENCE

Sequencing of Captive Target Transcripts Identifies the Network of Regulated Genes and Functions of Primate-Specific miR-522

(2014) Shen Mynn Tan et al.   Cell Reports

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs

(2014) Matthew B Friedersdorf et al.   GENOME BIOLOGY

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

MicroRNA target site identification by integrating sequence and binding information

(2013) William H Majoros et al.   NATURE METHODS

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

(2013) Mohsen Khorshid et al.   NATURE METHODS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Searching the coding region for microRNA targets

(2013) R. M. Marin et al.   RNA

Functional microRNA targets in protein coding sequences

(2012) Martin Reczko et al.   BIOINFORMATICS

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Argonaute CLIP – A method to identify in vivo targets of miRNAs

(2012) Lukasz Jaskiewicz et al.   METHODS

Transcriptome-wide miR-155 Binding Map Reveals Widespread Noncanonical MicroRNA Targeting

(2012) Gabriel B. Loeb et al.   MOLECULAR CELL

Structure of yeast Argonaute with guide RNA

(2012) Kotaro Nakanishi et al.   NATURE

An alternative mode of microRNA target recognition

(2012) Sung Wook Chi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRmap: Comprehensive prediction of microRNA target repression strength

(2012) Charles E. Vejnar et al.   NUCLEIC ACIDS RESEARCH

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

The Crystal Structure of Human Argonaute2

(2012) N. T. Schirle et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response

(2011) I. Lipchina et al.   GENES & DEVELOPMENT

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

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

doRiNA: a database of RNA interactions in post-transcriptional regulation

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action

(2011) J. Wen et al.   RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

TargetSpy: a supervised machine learning approach for microRNA target prediction

(2010) Martin Sturm et al.   BMC BIOINFORMATICS

Improving performance of mammalian microRNA target prediction

(2010) Hui Liu et al.   BMC BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

(2010) H. R. Chiang et al.   GENES & DEVELOPMENT

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Genome-wide Dissection of MicroRNA Functions and Cotargeting Networks Using Gene Set Signatures

(2010) John S. Tsang et al.   MOLECULAR CELL

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

Target mRNA abundance dilutes microRNA and siRNA activity

(2010) Aaron Arvey et al.   Molecular Systems Biology

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

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

(2010) Doron Betel et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets

(2009) J. Hausser et al.   GENOME RESEARCH

miR-24 Inhibits Cell Proliferation by Targeting E2F2, MYC, and Other Cell-Cycle Genes via Binding to “Seedless” 3′UTR MicroRNA Recognition Elements

(2009) Ashish Lal et al.   MOLECULAR CELL

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

(2009) Aly A Khan et al.   NATURE BIOTECHNOLOGY

Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs

(2009) Shuo Gu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alternative Processing of Primary microRNA Transcripts by Drosha Generates 5′ End Variation of Mature microRNA

(2009) Haoquan Wu et al.   PLoS One

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

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

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

Most mammalian mRNAs are conserved targets of microRNAs

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

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

The impact of target site accessibility on the design of effective siRNAs

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY

Small non-coding RNAs in animal development

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

GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay

(2008) Ana Eulalio et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing

(2008) A. Azuma-Mukai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental validation of the importance of seed complement frequency to siRNA specificity

(2008) E. M. Anderson et al.   RNA

miRDB: A microRNA target prediction and functional annotation database with a wiki interface

(2008) X. Wang   RNA

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE

Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs

(2008) Ran Elkon et al.   PLoS Computational Biology