RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model

Fast accessibility-based prediction of RNA–RNA interactions

(2011) Hakim Tafer et al.   BIOINFORMATICS

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Lineage-specific function of the noncoding Tsix RNA for Xist repression and Xi reactivation in mice

(2011) T. Ohhata et al.   GENES & DEVELOPMENT

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

(2011) Jan Gorodkin et al.   PLoS Computational Biology

Fast prediction of RNA-RNA interaction

(2010) Raheleh Salari et al.   Algorithms for Molecular Biology

RNA–RNA interaction prediction based on multiple sequence alignments

(2010) Andrew X. Li et al.   BIOINFORMATICS

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

(2010) Yuki Kato et al.   BIOINFORMATICS

MicroRNAs: tiny targets for engineering CHO cell phenotypes?

(2010) Niall Barron et al.   BIOTECHNOLOGY LETTERS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Noncoding RNA of Glutamine Synthetase I Modulates Antibiotic Production in Streptomyces coelicolor A3(2)

(2009) D. D'Alia et al.   JOURNAL OF BACTERIOLOGY

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of structured RNAs from genomic sequences

(2009) Jan Gorodkin et al.   TRENDS IN BIOTECHNOLOGY

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster

(2008) Jonathan Houseley et al.   MOLECULAR CELL

TargetRNA: a tool for predicting targets of small RNA action in bacteria

(2008) B. Tjaden   NUCLEIC ACIDS RESEARCH

The database of experimentally supported targets: a functional update of TarBase

(2008) G. L. Papadopoulos et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

(2007) E. Torarinsson et al.   GENOME RESEARCH