A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus

(2015) Sager J. Gosai et al.   MOLECULAR CELL

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

(2014) Ralph D. Hector et al.   NUCLEIC ACIDS RESEARCH

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

SAVoR: a server for sequencing annotation and visualization of RNA structures

(2012) F. Li et al.   NUCLEIC ACIDS RESEARCH

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS