Site identification in high-throughput RNA–protein interaction data

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites

(2011) Philip J. Uren et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-β1

(2011) Antoine Cléry 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

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

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

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

(2011) David L Corcoran et al.   GENOME BIOLOGY

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

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

(2010) Markus Hafner et al.   CELL

Musashi1 regulates breast tumor cell proliferation and is a prognostic indicator of poor survival

(2010) Xiao-Yang Wang et al.   Molecular Cancer

A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility

(2010) Martijn Kedde et al.   NATURE CELL BIOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

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

Structural basis for the dual RNA-recognition modes of human Tra2-β RRM

(2010) Kengo Tsuda et al.   NUCLEIC ACIDS RESEARCH

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

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

(2010) C. Zhang et al.   SCIENCE

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

Alternative Splicing of Cyr61 Is Regulated by Hypoxia and Significantly Changed in Breast Cancer

(2009) M. Hirschfeld et al.   CANCER RESEARCH

The Centrality of RNA

(2009) Phillip A. Sharp   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

On the road to reading the RNA-interference code

(2009) Haruhiko Siomi et al.   NATURE

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

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

Significance of nuclear hTra2-beta1 expression in cervical cancer

(2008) Boris Gabriel et al.   ACTA OBSTETRICIA ET GYNECOLOGICA SCANDINAVICA

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

(2008) Donny D. Licatalosi et al.   NATURE

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS

New implications for the QUAKING RNA binding protein in human disease

(2007) Carol Anne Chénard et al.   JOURNAL OF NEUROSCIENCE RESEARCH