DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition

A folding algorithm for extended RNA secondary structures

(2011) C. H. zu Siederdissen et al.   BIOINFORMATICS

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

(2011) E. Rivas et al.   RNA

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

(2010) Yuki Kato et al.   BIOINFORMATICS

A Faster Algorithm for Simultaneous Alignment and Folding of RNA

(2010) Michal Ziv-Ukelson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Improving the accuracy of predicting secondary structure for aligned RNA sequences

(2010) Michiaki Hamada et al.   NUCLEIC ACIDS RESEARCH

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Computational approaches for RNA energy parameter estimation

(2010) M. Andronescu et al.   RNA

A NON-PARAMETRIC BAYESIAN APPROACH FOR PREDICTING RNA SECONDARY STRUCTURES

(2010) KENGO SATO et al.   Journal of Bioinformatics and Computational Biology

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

(2009) M. Hamada et al.   BIOINFORMATICS

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

(2008) C. B. Do et al.   BIOINFORMATICS

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

A fast structural multiple alignment method for long RNA sequences

(2008) Yasuo Tabei et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH

Centroid estimation in discrete high-dimensional spaces with applications in biology

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