Protein–RNA interactions: new genomic technologies and perspectives

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

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

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

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

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

Understanding splicing regulation through RNA splicing maps

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

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

(2011) David L Corcoran et al.   GENOME BIOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

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

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

(2010) Robert B. Darnell   Wiley Interdisciplinary Reviews-RNA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs

(2009) Julian König et al.   EMBO JOURNAL

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey 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

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Donny D. Licatalosi et al.   NATURE