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

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

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies

(2012) Tina W. Han et al.   CELL

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

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

Genome-wide identification of miRNA targets by PAR-CLIP

(2012) Markus Hafner et al.   METHODS

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

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

(2012) Prathima Iengar   NUCLEIC ACIDS RESEARCH

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

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

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

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

(2011) David L Corcoran et al.   GENOME BIOLOGY

Learning transcriptional networks from the integration of ChIP–chip and expression data in a non-parametric model

(2010) Ahrim Youn et al.   BIOINFORMATICS

Discovering transcriptional modules by Bayesian data integration

(2010) Richard S. Savage 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

Phosphorylation of human Argonaute proteins affects small RNA binding

(2010) Sabine Rüdel et al.   NUCLEIC ACIDS RESEARCH

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

(2010) C. Zhang et al.   SCIENCE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

(2008) Yanli Wang et al.   NATURE

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

(2008) Donny D. Licatalosi et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY