Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs

Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

(2013) D. M. Klass et al.   GENOME RESEARCH

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Alternative splicing: decoding an expansive regulatory layer

(2012) Manuel Irimia et al.   CURRENT OPINION IN CELL BIOLOGY

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

FMRP targets distinct mRNA sequence elements to regulate protein expression

(2012) Manuel Ascano et al.   NATURE

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

(2012) Sara Macias et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines

(2012) Rebecca L. Skalsky et al.   PLoS Pathogens

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

(2012) Yoichiro Sugimoto et al.   GENOME BIOLOGY

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

(2011) Jennifer C. Darnell et al.   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

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

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

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

Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation

(2011) Kyle D. Mansfield et al.   NUCLEIC ACIDS RESEARCH

RNA-binding protein HuR autoregulates its expression by promoting alternative polyadenylation site usage

(2011) Weijun Dai et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

RNA–protein interactions in human health and disease

(2011) Ahmad M. Khalil et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Transcriptome-wide analysis of protein–RNA interactions using high-throughput sequencing

(2011) Miha Milek et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Identification of RNA-protein interaction networks using PAR-CLIP

(2011) Manuel Ascano et al.   Wiley Interdisciplinary Reviews-RNA

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

(2011) David L Corcoran et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

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

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

A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes

(2010) Tanja Scherrer et al.   PLoS One

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Unbiased RNA-protein interaction screen by quantitative proteomics

(2009) F. Butter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic analysis of posttranscriptional gene expression

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Ribonucleoprotein complexes in neurologic diseases

(2008) Jernej Ule   CURRENT OPINION IN NEUROBIOLOGY

Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets

(2008) A. R. Morris et al.   MOLECULAR AND CELLULAR BIOLOGY

A Novel Class of mRNA-containing Cytoplasmic Granules Are Produced in Response to UV-Irradiation

(2008) Hélène Gaillard et al.   MOLECULAR BIOLOGY OF THE CELL

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System

(2008) Alessia Galgano et al.   PLoS One

RNA-binding proteins in human genetic disease

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