Global identification of functional microRNA-mRNA interactions in Drosophila

Erratum: Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling

(2018) Maria D Giraldez et al.   NATURE BIOTECHNOLOGY

Pervasive Behavioral Effects of MicroRNA Regulation in Drosophila

(2017) Joao Picao-Osorio et al.   GENETICS

Pervasive Behavioral Effects of MicroRNA Regulation in Drosophila

(2017) Joao Picao-Osorio et al.   GENETICS

Pairing beyond the Seed Supports MicroRNA Targeting Specificity

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

miR-184Regulates Pancreatic β-Cell Function According to Glucose Metabolism

(2015) Sudhir G. Tattikota et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods

(2015) Jeanette Baran-Gale et al.   Frontiers in Genetics

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

microRNA control of cell-cell signaling during development and disease

(2014) Joshua W. Hagen et al.   CELL CYCLE

Systematic Study of Drosophila MicroRNA Functions Using a Collection of Targeted Knockout Mutations

(2014) Ya-Wen Chen et al.   DEVELOPMENTAL CELL

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

(2014) J. Wen et al.   GENOME RESEARCH

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

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

miR-14 Regulates Autophagy during Developmental Cell Death by Targeting ip3-kinase 2

(2014) Charles Nelson et al.   MOLECULAR CELL

Endogenous miRNA and Target Concentrations Determine Susceptibility to Potential ceRNA Competition

(2014) Andrew D. Bosson et al.   MOLECULAR CELL

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis

(2014) Michael J Moore et al.   Nature Protocols

Regulation of microRNA biogenesis

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

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

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

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

(2014) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Target Repression Induced by Endogenous microRNAs: Large Differences, Small Effects

(2014) Ana Kozomara et al.   PLoS One

A Rapid Genome-wide MicroRNA Screen Identifies miR-14 as a Modulator of Hedgehog Signaling

(2014) Kevin Kim et al.   Cell Reports

Global target mRNA specification and regulation by the RNA-binding protein ZFP36

(2014) Neelanjan Mukherjee et al.   GENOME BIOLOGY

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell

(2013) Sudhir G. Tattikota et al.   Cell Metabolism

Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation

(2013) J. Hausser et al.   GENOME RESEARCH

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

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

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing

(2013) Zhaojie Zhang et al.   GENOME BIOLOGY

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

(2013) Florian Erhard et al.   GENOME BIOLOGY

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

An alternative mode of microRNA target recognition

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

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang 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

Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

(2012) Peter Smibert et al.   Cell Reports

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

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

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

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

(2011) Anitha D. Jayaprakash et al.   NUCLEIC ACIDS RESEARCH

Neural-specific elongation of 3' UTRs during Drosophila development

(2011) V. Hilgers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

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

(2010) Markus Hafner et al.   CELL

Drosophila miR-14 regulates insulin production and metabolism through its target, sugarbabe

(2010) J. Varghese et al.   GENES & DEVELOPMENT

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence

(2010) E. Berezikov et al.   GENOME RESEARCH

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

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

(2010) Doron Betel et al.   GENOME BIOLOGY

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

miR-184 Has Multiple Roles in Drosophila Female Germline Development

(2009) Nicola Iovino et al.   DEVELOPMENTAL CELL

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Second International Symposium on Languages in Biology and Medicine (LBM) 2007

(2008) Su Jian et al.   BMC BIOINFORMATICS

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA