ViennaRNA Package 2.0

Fast accessibility-based prediction of RNA–RNA interactions

(2011) Hakim Tafer et al.   BIOINFORMATICS

BioXSD: the common data-exchange format for everyday bioinformatics web services

(2010) M. Kalas et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Nucleic acid sequence design via efficient ensemble defect optimization

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

RNAsnoop: efficient target prediction for H/ACA snoRNAs

(2009) Hakim Tafer et al.   BIOINFORMATICS

Lightweight comparison of RNAs based on exact sequence–structure matches

(2009) Steffen Heyne et al.   BIOINFORMATICS

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

(2009) Roman R. Stocsits et al.   NUCLEIC ACIDS RESEARCH

Improved free energy parameters for RNA pseudoknotted secondary structure prediction

(2009) M. S. Andronescu et al.   RNA

Structural profiles of human miRNA families from pairwise clustering

(2008) B. Kaczkowski et al.   BIOINFORMATICS

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

(2008) Mirela Andronescu et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

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

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY