RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

(2013) Mallory A Freeberg et al.   GENOME BIOLOGY

LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance

(2012) Melissa L. Wilbert et al.   MOLECULAR CELL

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

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

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

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

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

(2012) Cem Sievers et al.   NUCLEIC ACIDS RESEARCH

Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins

(2012) Stephanie C. Huelga et al.   Cell Reports

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease

(2011) Patrick Brest et al.   NATURE GENETICS

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

RNA targets of wild-type and mutant FET family proteins

(2011) Jessica I Hoell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

(2011) Jose M Muiño et al.   Plant Methods

Identification of RNA-protein interaction networks using PAR-CLIP

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

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

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

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

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

(2010) Qi Zheng et al.   PLoS Genetics

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

RNA and Disease

(2009) Thomas A. Cooper et al.   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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY