GraphProt: modeling binding preferences of RNA-binding proteins

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

(2013) Ibrahim Avsar Ilik et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

(2013) Chaolin Zhang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity

(2013) John D. Laver et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Hilal Kazan et al.   NUCLEIC ACIDS RESEARCH

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

(2013) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

DRIMust: a web server for discovering rank imbalanced motifs using suffix trees

(2013) Limor Leibovich et al.   NUCLEIC ACIDS RESEARCH

The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability

(2013) Sachin Kumar Gupta et al.   NUCLEIC ACIDS RESEARCH

Distinct binding properties of TIAR RRMs and linker region

(2013) Henry S. Kim et al.   RNA Biology

GraphClust: alignment-free structural clustering of local RNA secondary structures

(2012) Steffen Heyne et al.   BIOINFORMATICS

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

RNA Accessibility in cubic time

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

Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

(2011) M. Schnall-Levin et al.   GENOME RESEARCH

Three RNA Recognition Motifs Participate in RNA Recognition and Structural Organization by the Pro-Apoptotic Factor TIA-1

(2011) William J. Bauer et al.   JOURNAL OF MOLECULAR BIOLOGY

U1 snRNA Directly Interacts with Polypyrimidine Tract-Binding Protein during Splicing Repression

(2011) Shalini Sharma et al.   MOLECULAR CELL

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

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

(2011) David L Corcoran et al.   GENOME BIOLOGY

TargetSpy: a supervised machine learning approach for microRNA target prediction

(2010) Martin Sturm et al.   BMC 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

Polypyrimidine Tract Binding Protein Functions as a Negative Regulator of Feline Calicivirus Translation

(2010) Ioannis Karakasiliotis et al.   PLoS One

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

(2010) Hilal Kazan et al.   PLoS Computational Biology

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

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

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

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

(2008) Donny D. Licatalosi et al.   NATURE