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

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

(2010) Yuki Kato et al.   BIOINFORMATICS

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

(2010) Michiaki Hamada et al.   BMC BIOINFORMATICS

K-Partite RNA Secondary Structures

(2010) Minghui Jiang 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

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

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

(2009) M. Hamada et al.   BIOINFORMATICS

Prediction of RNA secondary structure with pseudoknots using integer programming

(2009) Unyanee Poolsap et al.   BMC BIOINFORMATICS

Improved free energy parameters for RNA pseudoknotted secondary structure prediction

(2009) M. S. Andronescu et al.   RNA

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space

(2008) Xiang Chen 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

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

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