Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

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

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

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

Protein-RNA and Protein-Protein Recognition by Dual KH1/2 Domains of the Neuronal Splicing Factor Nova-1

(2011) Marianna Teplova et al.   STRUCTURE

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

(2010) Markus Hafner et al.   CELL

Activation of paternally expressed genes and perinatal death caused by deletion of the Gtl2 gene

(2010) Y. Zhou et al.   DEVELOPMENT

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

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

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

Maternally Expressed Gene 3 (MEG3) Noncoding Ribonucleic Acid: Isoform Structure, Expression, and Functions

(2009) Xun Zhang et al.   ENDOCRINOLOGY

The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability

(2009) Shobbir Hussain et al.   JOURNAL OF CELL BIOLOGY

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

5-methylcytosine in RNA: detection, enzymatic formation and biological functions

(2009) Yuri Motorin et al.   NUCLEIC ACIDS RESEARCH

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

(2008) A. P. Fejes et al.   BIOINFORMATICS

A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation

(2008) I. Aznarez et al.   GENOME RESEARCH

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

(2008) Donny D. Licatalosi et al.   NATURE