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

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins

(2013) Hilal Kazan et al.   NUCLEIC ACIDS RESEARCH

LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells

(2012) Jun Cho et al.   CELL

LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance

(2012) Melissa L. Wilbert et al.   MOLECULAR CELL

FMRP targets distinct mRNA sequence elements to regulate protein expression

(2012) Manuel Ascano et al.   NATURE

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

(2012) Raheleh Salari et al.   NUCLEIC ACIDS RESEARCH

The RCSB Protein Data Bank: new resources for research and education

(2012) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3'-end of the seed match

(2012) R. M. Marin et al.   RNA

RNA Accessibility in cubic time

(2011) Stephan H Bernhart et al.   Algorithms for Molecular Biology

ViennaRNA Package 2.0

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

A detailed investigation of accessibilities around target sites of siRNAs and miRNAs

(2011) Hisanori Kiryu et al.   BIOINFORMATICS

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

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

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

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

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

RBPDB: a database of RNA-binding specificities

(2010) K. B. Cook et al.   NUCLEIC ACIDS RESEARCH

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

(2010) X. Li et al.   RNA

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

(2008) Minghui Jiang et al.   BMC BIOINFORMATICS

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

(2008) Donny D. Licatalosi et al.   NATURE

Structure of the guide-strand-containing argonaute silencing complex

(2008) Yanli Wang et al.   NATURE

RNA-binding proteins in human genetic disease

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