RNA–RNA interaction prediction based on multiple sequence alignments

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

(2010) Stefan E Seemann et al.   Algorithms for Molecular Biology

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

(2010) Yuki Kato et al.   BIOINFORMATICS

Partition function and base pairing probabilities for RNA–RNA interaction prediction

(2009) Fenix W. D. Huang et al.   BIOINFORMATICS

A partition function algorithm for interacting nucleic acid strands

(2009) Hamidreza Chitsaz et al.   BIOINFORMATICS

Target prediction and a statistical sampling algorithm for RNA–RNA interaction

(2009) Fenix W. D. Huang et al.   BIOINFORMATICS

On the Approximation of Optimal Structures for RNA-RNA Interaction

(2009) S. Mneimneh   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2008) Anke Busch et al.   BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

(2008) Manuela Marz et al.   JOURNAL OF MOLECULAR EVOLUTION

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

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

Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components

(2008) Marcela Dávila López et al.   NUCLEIC ACIDS RESEARCH