Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures

Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

(2013) M. Teplova et al.   GENES & DEVELOPMENT

Argonaute CLIP – A method to identify in vivo targets of miRNAs

(2012) Lukasz Jaskiewicz et al.   METHODS

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

RNA–protein interactions in vivo: global gets specific

(2012) Minna-Liisa Änkö et al.   TRENDS IN BIOCHEMICAL SCIENCES

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

(2012) Minna-Liisa Änkö et al.   GENOME BIOLOGY

AURA: Atlas of UTR Regulatory Activity

(2011) E. Dassi et al.   BIOINFORMATICS

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites

(2011) Philip J. Uren et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee 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

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

In silico characterization and prediction of global protein–mRNA interactions in yeast

(2011) Vera Pancaldi et al.   NUCLEIC ACIDS RESEARCH

The Endless Subtleties of RNA-Protein Complexes

(2011) Eric Westhof et al.   STRUCTURE

Identification of RNA-binding sites in proteins by integrating various sequence information

(2010) Cui-cui Wang et al.   AMINO ACIDS

Prediction of protein–RNA binding sites by a random forest method with combined features

(2010) Zhi-Ping Liu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

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

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS