Design and bioinformatics analysis of genome-wide CLIP experiments

CLIPdb: a CLIP-seq database for protein-RNA interactions

(2015) Yu-Cheng T Yang et al.   BMC GENOMICS

CLIP: viewing the RNA world from an RNA-protein interactome perspective

(2015) Yin Zhang et al.   Science China-Life Sciences

HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism

(2015) Emi Sei et al.   PLoS Pathogens

Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP

(2014) Jonghyun Yun et al.   BIOMETRICS

MicroRNA Directly Enhances Mitochondrial Translation during Muscle Differentiation

(2014) Xiaorong Zhang et al.   CELL

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

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

(2014) Nicole Lambert et al.   MOLECULAR CELL

MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs

(2014) Lea H. Gregersen et al.   MOLECULAR CELL

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Transcriptome-wide Discovery of microRNA Binding Sites in Human Brain

(2014) Ryan L. Boudreau et al.   NEURON

Leveraging cross-link modification events in CLIP-seq for motif discovery

(2014) Emad Bahrami-Samani et al.   NUCLEIC ACIDS RESEARCH

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

(2014) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

7SL RNA represses p53 translation by competing with HuR

(2014) Kotb Abdelmohsen et al.   NUCLEIC ACIDS RESEARCH

A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data

(2014) Tao Wang et al.   PLoS One

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L

(2014) Oliver Rossbach et al.   RNA Biology

SR proteins control a complex network of RNA-processing events

(2014) Todd Bradley et al.   RNA

Yb Integrates piRNA Intermediates and Processing Factors into Perinuclear Bodies to Enhance piRISC Assembly

(2014) Yukiko Murota et al.   Cell Reports

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

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

(2014) Bobak Kechavarzi et al.   GENOME BIOLOGY

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

(2014) Matthew B Friedersdorf et al.   GENOME BIOLOGY

dCLIP: a computational approach for comparative CLIP-seq analyses

(2014) Tao Wang et al.   GENOME BIOLOGY

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

(2014) Tsukasa Fukunaga et al.   GENOME BIOLOGY

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

(2014) Beibei Chen et al.   GENOME BIOLOGY

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast

(2014) Shaun Webb et al.   GENOME BIOLOGY

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

The “Observer Effect” in Genome-wide Surveys of Protein-RNA Interactions

(2013) Kasandra J. Riley et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

(2013) Michael T Lovci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells

(2013) Syuzo Kaneko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

(2013) Chaolin Zhang et al.   NUCLEIC ACIDS RESEARCH

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

Finding the target sites of RNA-binding proteins

(2013) Xiao Li et al.   Wiley Interdisciplinary Reviews-RNA

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

(2013) Florian Erhard et al.   GENOME BIOLOGY

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Versatility of RNA-Binding Proteins in Cancer

(2012) Laurence Wurth   COMPARATIVE AND FUNCTIONAL GENOMICS

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain

(2012) D. D. Licatalosi et al.   GENES & DEVELOPMENT

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

Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability

(2012) Gulayse Ince-Dunn et al.   NEURON

An analysis of substitution, deletion and insertion mutations in cancer genes

(2012) Prathima Iengar   NUCLEIC ACIDS RESEARCH

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

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

(2012) C. Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models

(2012) Xinlei Wang et al.   STATISTICS IN MEDICINE

Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions

(2012) Shinsuke Ishigaki et al.   Scientific Reports

Ago HITS-CLIP Expands Understanding of Kaposi's Sarcoma-associated Herpesvirus miRNA Function in Primary Effusion Lymphomas

(2012) Irina Haecker 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

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

(2011) Sonja Althammer et al.   BIOINFORMATICS

FET proteins TAF15 and EWS are selective markers that distinguish FTLD with FUS pathology from amyotrophic lateral sclerosis with FUS mutations

(2011) Manuela Neumann et al.   BRAIN

Musashi1: an RBP with versatile functions in normal and cancer stem cells

(2011) Robert et al.   Frontiers in Bioscience-Landmark

High-Resolution Profiling and Analysis of Viral and Host Small RNAs during Human Cytomegalovirus Infection

(2011) T. J. Stark et al.   JOURNAL OF VIROLOGY

In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites

(2011) Anna-Carina Jungkamp et al.   MOLECULAR CELL

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

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

(2011) Magdalini Polymenidou et al.   NATURE NEUROSCIENCE

RNA targets of wild-type and mutant FET family proteins

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

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

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

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

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

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

MicroRNA profiling: separating signal from noise

(2010) Monya Baker   NATURE METHODS

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

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

(2010) Hilal Kazan et al.   PLoS Computational Biology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

MEME SUITE: tools for motif discovery and searching

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

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Identification of a signature motif in target mRNAs of RNA-binding protein AUF1

(2008) Krystyna Mazan-Mamczarz et al.   NUCLEIC ACIDS RESEARCH

RNA-binding proteins in human genetic disease

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