A large-scale binding and functional map of human RNA-binding proteins

Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels

(2018) Julia K. Nussbacher et al.   MOLECULAR CELL

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

(2018) Jan Attig et al.   CELL

RBP-Maps enables robust generation of splicing regulatory maps

(2018) Brian A. Yee et al.   RNA

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes

(2016) Chaoliang Wei et al.   MOLECULAR CELL

Resources for the Comprehensive Discovery of Functional RNA Elements

(2016) Balaji Sundararaman et al.   MOLECULAR CELL

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes

(2016) Kristopher W. Brannan et al.   MOLECULAR CELL

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses

(2016) Katannya Kapeli et al.   Nature Communications

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival

(2016) Anne E. Conway et al.   Cell Reports

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

(2015) Shiran Naftelberg et al.   Annual Review of Biochemistry

KH–RNA interactions: back in the groove

(2015) Giuseppe Nicastro et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Generation of functionally distinct isoforms of PTBP3 by alternative splicing and translation initiation

(2015) L.-Y. Tan et al.   NUCLEIC ACIDS RESEARCH

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP

(2015) Christian Hauer et al.   Nature Communications

Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis

(2015) Hana Antonicka et al.   Cell Reports

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors

(2013) Lionel Tafforeau et al.   MOLECULAR CELL

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tumor microenvironment-associated modifications of alternative splicing

(2013) J.-P. Brosseau et al.   RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

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

(2012) Alfredo Castello et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms

(2012) S. Erkelenz et al.   RNA

Understanding splicing regulation through RNA splicing maps

(2011) Joshua T. Witten et al.   TRENDS IN GENETICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

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

(2008) Donny D. Licatalosi et al.   NATURE

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

RNA-binding proteins in human genetic disease

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