RNAstructure: web servers for RNA secondary structure prediction and analysis

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

(2012) Matthew G. Seetin et al.   BIOINFORMATICS

Recent Advances in Developing Small Molecules Targeting RNA

(2011) Lirui Guan et al.   ACS Chemical Biology

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

(2011) Arif O Harmanci et al.   BMC BIOINFORMATICS

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

(2011) Chenguang Gong et al.   NATURE

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences

(2010) Zhenjiang Xu et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

On the road to reading the RNA-interference code

(2009) Haruhiko Siomi et al.   NATURE

The promises and pitfalls of RNA-interference-based therapeutics

(2009) Daniela Castanotto et al.   NATURE

A sequence similar to tRNA3 Lys gene is embedded in HIV-1 U3–R and promotes minus-strand transfer

(2009) Dorota Piekna-Przybylska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Stochastic sampling of the RNA structural alignment space

(2009) Arif Ozgun Harmanci et al.   NUCLEIC ACIDS RESEARCH

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

The impact of target site accessibility on the design of effective siRNAs

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY

Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design

(2008) Z. J. Lu et al.   NUCLEIC ACIDS RESEARCH

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

(2008) Arif Ozgun Harmanci et al.   NUCLEIC ACIDS RESEARCH

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics

(2008) Z. J. Lu 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

From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal

(2008) S. Smit et al.   RNA