RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data

Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data

(2015) Ralf Eggeling et al.   BMC BIOINFORMATICS

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of YB-1-RNA interactions reveals a novel role of YB-1 in miRNA processing in glioblastoma multiforme

(2015) Shuai-Lai Wu et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The RNA shapes studio

(2014) S. Janssen et al.   BIOINFORMATICS

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

(2014) Nicole Lambert et al.   MOLECULAR CELL

Context-dependent control of alternative splicing by RNA-binding proteins

(2014) Xiang-Dong Fu et al.   NATURE REVIEWS GENETICS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

On the Value of Intra-Motif Dependencies of Human Insulator Protein CTCF

(2014) Ralf Eggeling et al.   PLoS One

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

'Oming in on RNA–protein interactions

(2014) John L Rinn et al.   GENOME BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Finding the target sites of RNA-binding proteins

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

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts

(2012) Wen-Juan Wei et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of noncoding RNAs

(2012) Stefan Washietl et al.   Wiley Interdisciplinary Reviews-RNA

Speeding up the Consensus Clustering methodology for microarray data analysis

(2011) Raffaele Giancarlo et al.   Algorithms for Molecular Biology

Regression shrinkage and selection via the lasso: a retrospective

(2011) Robert Tibshirani   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

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

(2011) Shivendra Kishore et al.   NATURE METHODS

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

(2010) X. Li 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