Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinkingin vivo

(2016) Erik Holmqvist et al.   EMBO JOURNAL

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

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

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells

(2016) Matthew J. Smola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput analyses of hnRNP H1 dissects its multi-functional aspect

(2016) Philip J. Uren et al.   RNA Biology

The PUF binding landscape in metazoan germ cells

(2016) Aman Prasad et al.   RNA

RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence

(2016) A. Galloway et al.   SCIENCE

IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC

(2016) Hanane Ennajdaoui et al.   Cell Reports

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

BackCLIP: a tool to identify common background presence in PAR-CLIP datasets

(2015) P. H. Reyes-Herrera et al.   BIOINFORMATICS

A multiprotein occupancy map of the mRNP on the 3′ end of histone mRNAs

(2015) Lionel Brooks et al.   RNA

Probing RNA–protein networks: biochemistry meets genomics

(2015) Zachary T. Campbell et al.   TRENDS IN BIOCHEMICAL SCIENCES

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

(2015) Heidi Theil Hansen et al.   GENOME BIOLOGY

Rbfox2 controls autoregulation in RNA-binding protein networks

(2014) M. Jangi et al.   GENES & DEVELOPMENT

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

(2014) Nicole Lambert et al.   MOLECULAR CELL

ELAVL1 Modulates Transcriptome-wide miRNA Binding in Murine Macrophages

(2014) Yi-Chien Lu et al.   Cell Reports

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

(2014) Matthew B Friedersdorf et al.   GENOME BIOLOGY

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq

(2013) A. Kucukural et al.   BIOINFORMATICS

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

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

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

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Functional Interplay between RNA-Binding Protein HuR and microRNAs

(2012) Subramanya Srikantan et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

The RNA-Binding Protein Human Antigen R Controls Global Changes in Gene Expression during Schwann Cell Development

(2012) M. Iruarrizaga-Lejarreta et al.   JOURNAL OF NEUROSCIENCE

Regulation of CUG-binding Protein 1 (CUGBP1) Binding to Target Transcripts upon T Cell Activation

(2011) Daniel Beisang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

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

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

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan 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

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

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

Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator

(2010) Aaron M. Kershner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

Posttranscriptional regulation of cancer traits by HuR

(2010) Kotb Abdelmohsen et al.   Wiley Interdisciplinary Reviews-RNA

Coordinated posttranscriptional mRNA population dynamics during T-cell activation

(2009) Neelanjan Mukherjee et al.   Molecular Systems Biology

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

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

Identification of Transformation-Related Pathways in a Breast Epithelial Cell Model Using a Ribonomics Approach

(2008) K. Mazan-Mamczarz et al.   CANCER RESEARCH

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets

(2008) A. R. Morris et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2008) Donny D. Licatalosi et al.   NATURE

RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways

(2008) M. P. van der Brug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing

(2007) Markus Hafner et al.   METHODS