Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

DGCR8 Acts as an Adaptor for the Exosome Complex to Degrade Double-Stranded Structured RNAs

(2015) Sara Macias et al.   MOLECULAR CELL

Design and bioinformatics analysis of genome-wide CLIP experiments

(2015) T. Wang et al.   NUCLEIC ACIDS RESEARCH

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins

(2015) Martin Preusse et al.   RNA Biology

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

(2015) Heidi Theil Hansen et al.   GENOME BIOLOGY

Adaptable probabilistic mapping of short reads using position specific scoring matrices

(2014) Peter Kerpedjiev et al.   BMC BIOINFORMATICS

Contribution of natural antisense transcription to an endogenous siRNA signature in human cells

(2014) Andreas Werner et al.   BMC GENOMICS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

(2014) Je-Hyun Yoon et al.   Nature Communications

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

(2014) Matthew B Friedersdorf et al.   GENOME BIOLOGY

Global target mRNA specification and regulation by the RNA-binding protein ZFP36

(2014) Neelanjan Mukherjee et al.   GENOME BIOLOGY

Mechanisms coordinating ELAV/Hu mRNA regulons

(2013) Laura E Simone et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

(2013) Shatakshi Pandit et al.   MOLECULAR CELL

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs

(2013) Xiangyue Wu et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The interplay of HuR and miR-3134 in regulation of AU rich transcriptome

(2013) Shivani Sharma et al.   RNA Biology

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

(2013) M. Hafner et al.   RNA

Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay

(2013) Peng Jiang et al.   PLoS Computational Biology

Competition and collaboration between RNA-binding proteins and microRNAs

(2013) J. J. David Ho et al.   Wiley Interdisciplinary Reviews-RNA

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

(2013) Shivendra Kishore et al.   GENOME BIOLOGY

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

(2012) Alfredo Castello et al.   CELL

Functional Interplay between RNA-Binding Protein HuR and microRNAs

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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC

(2012) Marc R Fabian et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Polypyrimidine Tract Binding Protein (hnRNP I) Is Possibly a Conserved Modulator of miRNA-Mediated Gene Regulation

(2012) Bart Engels et al.   PLoS One

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

(2012) Yoichiro Sugimoto et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

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

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

(2011) Sonja Althammer et al.   BIOINFORMATICS

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

RNA targets of wild-type and mutant FET family proteins

(2011) Jessica I Hoell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing

(2011) J. A. Broderick et al.   RNA

MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action

(2011) J. Wen et al.   RNA

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

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

(2010) Markus Hafner et al.   CELL

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

(2010) A. Jacobsen et al.   GENOME RESEARCH

A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility

(2010) Martijn Kedde et al.   NATURE CELL BIOLOGY

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

The ribonome: a dominant force in co-ordinating gene expression

(2009) Kyle D. Mansfield et al.   BIOLOGY OF THE CELL

HuR recruits let-7/RISC to repress c-Myc expression

(2009) H. H. Kim et al.   GENES & DEVELOPMENT

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

CRD-BP Protects the Coding Region of βTrCP1 mRNA from miR-183-Mediated Degradation

(2009) Irina Elcheva et al.   MOLECULAR CELL