Understanding principles of miRNA target recognition and function through integrated biological and bioinformatics approaches

Design and interpretation of microRNA–reporter gene activity

(2013) Adam P. Carroll et al.   ANALYTICAL BIOCHEMISTRY

Fine-tuning of microRNA-mediated repression of mRNA by splicing-regulated and highly repressive microRNA recognition element

(2013) Cheng-Tao Wu et al.   BMC GENOMICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Epigenetic modulation of the miR-200 family is associated with transition to a breast cancer stem-cell-like state

(2013) Y.-Y. Lim et al.   JOURNAL OF CELL SCIENCE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

MicroRNA target site identification by integrating sequence and binding information

(2013) William H Majoros et al.   NATURE METHODS

CLIP-based prediction of mammalian microRNA binding sites

(2013) Chaochun Liu et al.   NUCLEIC ACIDS RESEARCH

The interplay of HuR and miR-3134 in regulation of AU rich transcriptome

(2013) Shivani Sharma et al.   RNA Biology

Context-specific microRNA function in developmental complexity

(2013) A. P. Carroll et al.   Journal of Molecular Cell Biology

Alternative mRNA fates identified in microRNA-associated transcriptome analysis

(2012) Adam P Carroll et al.   BMC GENOMICS

MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship

(2012) Amy E. Pasquinelli   NATURE REVIEWS GENETICS

miRmap: Comprehensive prediction of microRNA target repression strength

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

Association of Argonaute proteins and microRNAs can occur after cell lysis

(2012) K. J. Riley et al.   RNA

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

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

GW182 Proteins Directly Recruit Cytoplasmic Deadenylase Complexes to miRNA Targets

(2011) Joerg E. Braun et al.   MOLECULAR CELL

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

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

(2011) Shivendra Kishore et al.   NATURE METHODS

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4–NOT

(2011) Marc R Fabian et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

(2011) Anthony K L Leung et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRNA repression involves GW182-mediated recruitment of CCR4–NOT through conserved W-containing motifs

(2011) Marina Chekulaeva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Experimental strategies for microRNA target identification

(2011) D. W. Thomson 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

Posttranscriptional Upregulation by MicroRNAs

(2011) Shobha Vasudevan   Wiley Interdisciplinary Reviews-RNA

Identifying functional miRNA–mRNA regulatory modules with correspondence latent dirichlet allocation

(2010) Bing Liu et al.   BIOINFORMATICS

WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit

(2010) Dexter Duncan et al.   BMC BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2

(2010) Filipp Frank et al.   NATURE

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Small RNA sorting: matchmaking for Argonautes

(2010) Benjamin Czech et al.   NATURE REVIEWS GENETICS

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Towards computational prediction of microRNA function and activity

(2010) Igor Ulitsky et al.   NUCLEIC ACIDS RESEARCH

MAGIA, a web-based tool for miRNA and Genes Integrated Analysis

(2010) G. Sales et al.   NUCLEIC ACIDS RESEARCH

Joint Genome-Wide Profiling of miRNA and mRNA Expression in Alzheimer's Disease Cortex Reveals Altered miRNA Regulation

(2010) Juan Nunez-Iglesias et al.   PLoS One

Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules

(2010) Eric Bonnet et al.   PLoS One

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

(2010) Doron Betel et al.   GENOME BIOLOGY

Lost in translation: an assessment and perspective for computational microRNA target identification

(2009) Panagiotis Alexiou et al.   BIOINFORMATICS

Accurate microRNA target prediction correlates with protein repression levels

(2009) Manolis Maragkakis et al.   BMC BIOINFORMATICS

Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy

(2009) Bing Liu et al.   BMC BIOINFORMATICS

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers

(2009) Xinxia Peng et al.   BMC GENOMICS

Importin 8 Is a Gene Silencing Factor that Targets Argonaute Proteins to Distinct mRNAs

(2009) Lasse Weinmann et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

HuR recruits let-7/RISC to repress c-Myc expression

(2009) H. H. Kim et al.   GENES & DEVELOPMENT

Discovery of functional miRNA–mRNA regulatory modules with computational methods

(2009) Bing Liu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Schizophrenia is associated with an increase in cortical microRNA biogenesis

(2009) N J Beveridge et al.   MOLECULAR PSYCHIATRY

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

Predicting microRNA targets and functions: traps for the unwary

(2009) William Ritchie et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Revisiting the principles of microRNA target recognition and mode of action

(2009) Peter Brodersen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

miRo: a miRNA knowledge base

(2009) A. Lagana et al.   Database-The Journal of Biological Databases and Curation

Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model

(2008) Je-Gun Joung et al.   BIOINFORMATICS

Finding microRNA regulatory modules in human genome using rule induction

(2008) Dang Tran et al.   BMC BIOINFORMATICS

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

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH

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

(2008) X. Wang   RNA