Identification of RNA-protein interaction networks using PAR-CLIP

Reversible Inhibition of PSD-95 mRNA Translation by miR-125a, FMRP Phosphorylation, and mGluR Signaling

(2011) Ravi S. Muddashetty 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

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva 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

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

(2011) Magdalini Polymenidou et al.   NATURE NEUROSCIENCE

RNA targets of wild-type and mutant FET family proteins

(2011) Jessica I Hoell 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

The prospects for designer single-stranded RNA-binding proteins

(2011) Joel P Mackay et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Impact of miRNA Target Sites in Coding Sequences and in 3′UTRs

(2011) Zhuo Fang et al.   PLoS One

Genome-Wide Studies Reveal That Lin28 Enhances the Translation of Genes Important for Growth and Survival of Human Embryonic Stem Cells

(2011) Shuping Peng et al.   STEM CELLS

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

(2010) Markus Hafner et al.   CELL

TDP-43 regulates its mRNA levels through a negative feedback loop

(2010) Youhna M Ayala et al.   EMBO JOURNAL

Feed-Forward Regulation of a Cell Fate Determinant by an RNA-Binding Protein Generates Asymmetry in Yeast

(2010) J. J. Wolf et al.   GENETICS

Identification of Neuronal RNA Targets of TDP-43-containing Ribonucleoprotein Complexes

(2010) Chantelle F. Sephton et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

A role for a bacterial ortholog of the Ro autoantigen in starvation-induced rRNA degradation

(2010) E. J. Wurtmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Prp43 Bound at Different Sites on the Pre-rRNA Performs Distinct Functions in Ribosome Synthesis

(2009) Markus T. Bohnsack et al.   MOLECULAR CELL

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

Zcchc11-dependent uridylation of microRNA directs cytokine expression

(2009) Matthew R. Jones et al.   NATURE CELL BIOLOGY

TU-tagging: cell type–specific RNA isolation from intact complex tissues

(2009) Michael R Miller et al.   NATURE METHODS

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

(2009) Gene W Yeo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

MIWI-independent small RNAs (MSY-RNAs) bind to the RNA-binding protein, MSY2, in male germ cells

(2009) M. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

(2009) S. Granneman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Systematic analysis of posttranscriptional gene expression

(2009) Adam R. Morris et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

(2009) Randy S. Daughters et al.   PLoS Genetics

GIMSAN: a Gibbs motif finder with significance analysis

(2008) P. Ng et al.   BIOINFORMATICS

Targeted Deletion Reveals Essential and Overlapping Functions of the miR-17∼92 Family of miRNA Clusters

(2008) Andrea Ventura et al.   CELL

RNA under attack: Cellular handling of RNA damage

(2008) Elisabeth J. Wurtmann et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Identification of Nuclear and Cytoplasmic mRNA Targets for the Shuttling Protein SF2/ASF

(2008) Jeremy R. Sanford et al.   PLoS One

Site-specific crosslinking of human microRNPs to RNA targets

(2008) Y. Kirino et al.   RNA

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

(2008) L. Dolken et al.   RNA

Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs

(2008) M. Landthaler et al.   RNA