Ribonomic approaches to study the RNA-binding proteome

RBPmap: a web server for mapping binding sites of RNA-binding proteins

(2014) Inbal Paz et al.   NUCLEIC ACIDS RESEARCH

Dissecting the expression landscape of RNA-binding proteins in human cancers

(2014) Bobak Kechavarzi et al.   GENOME BIOLOGY

The RBPome: where the brains meet the brawn

(2014) Naomi Attar   GENOME BIOLOGY

Methods for comprehensive experimental identification of RNA-protein interactions

(2014) Colleen A McHugh et al.   GENOME BIOLOGY

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

(2013) F. Agostini et al.   BIOINFORMATICS

Roquin Promotes Constitutive mRNA Decay via a Conserved Class of Stem-Loop Recognition Motifs

(2013) Kathrin Leppek et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Identification of a long non-coding RNA-associated RNP complex regulating metastasis at the translational step

(2013) Kiranmai Gumireddy et al.   EMBO JOURNAL

Mass spectrometry-based identification of proteins interacting with nucleic acids

(2013) A. Tacheny et al.   Journal of Proteomics

System-wide identification of RNA-binding proteins by interactome capture

(2013) Alfredo Castello et al.   Nature Protocols

An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins

(2013) Kathrin Leppek et al.   NUCLEIC ACIDS RESEARCH

Identification of proteins binding coding and non-coding human RNAs using protein microarrays

(2012) Zurab Siprashvili et al.   BMC GENOMICS

From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks

(2012) S. C. Janga   Briefings in Functional Genomics

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

(2012) Alfredo Castello et al.   CELL

RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA

(2012) Hugo M. Martinez et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution

(2012) Ali Fallah-Araghi et al.   LAB ON A CHIP

MS2-TRAP (MS2-tagged RNA affinity purification): Tagging RNA to identify associated miRNAs

(2012) Je-Hyun Yoon et al.   METHODS

Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes

(2012) Chenguang Gong et al.   METHODS

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

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

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

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

A Cell-Based Method for Screening RNA-Protein Interactions: Identification of Constitutive Transport Element-Interacting Proteins

(2012) Robert L. Nakamura et al.   PLoS One

RNA–protein interactions in vivo: global gets specific

(2012) Minna-Liisa Änkö et al.   TRENDS IN BIOCHEMICAL SCIENCES

Chromatin Isolation by RNA Purification (ChIRP)

(2012) Ci Chu et al.   Jove-Journal of Visualized Experiments

Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1

(2011) Xin Wang et al.   BMC GENOMICS

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

RNA Helicase p68 (DDX5) Regulates tau Exon 10 Splicing by Modulating a Stem-Loop Structure at the 5' Splice Site

(2011) A. Kar et al.   MOLECULAR AND CELLULAR BIOLOGY

Evolution of RNA-Binding Proteins in Animals: Insights from Genome-Wide Analysis in the Sponge Amphimedon queenslandica

(2011) P. Kerner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

Efficient detection of RNA-protein interactions using tethered RNAs

(2011) H. Iioka et al.   NUCLEIC ACIDS RESEARCH

hnRNP A1 and hnRNP F Modulate the Alternative Splicing of Exon 11 of the Insulin Receptor Gene

(2011) Indrani Talukdar et al.   PLoS One

Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3’ UTR structures

(2011) Alex Michael Ward et al.   RNA Biology

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

(2010) Markus Hafner et al.   CELL

Computational approaches to 3D modeling of RNA

(2010) Christian Laing et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells

(2010) Minna-Liisa Änkö et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

(2010) H. Zhao et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Tanja Scherrer et al.   PLoS One

Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome

(2010) Linda Ly et al.   PROTEOMICS

RNase-assisted RNA chromatography

(2010) G. Michlewski et al.   RNA

A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes

(2010) B. Slobodin et al.   RNA

Identification of novel ribonucleo-protein complexes from the brain-specific snoRNA MBII-52

(2010) Y. Soeno et al.   RNA

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

(2010) Hilal Kazan et al.   PLoS Computational Biology

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution

(2009) Stefanie A Mortimer et al.   Nature Protocols

Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins

(2009) Laura Pérez-Cano et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

Regulation of class switch recombination and somatic mutation by AID phosphorylation

(2008) Kevin M. McBride et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Analysis of Cell Surface Proteome Changes via Label-free, Quantitative Mass Spectrometry

(2008) Ralph Schiess et al.   MOLECULAR & CELLULAR PROTEOMICS

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Cell-free selection of RNA-binding proteins using in vitro compartmentalization

(2008) Yu Chen et al.   NUCLEIC ACIDS RESEARCH

Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs

(2008) M. Landthaler et al.   RNA

RNA-binding proteins in human genetic disease

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

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

(2008) Daniel J Hogan et al.   PLOS BIOLOGY