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Janssen, Stefan and Giegerich, Robert The RNA shapes studio, Bioinformatics, 2015
Bjoern Voss Structural analysis of aligned RNAs., Nucleic Acids Research, 2006
Hofacker, Ivo L. and Fekete, Martin and Stadler, Peter F. Secondary structure prediction for aligned RNA sequences., Joural of Molecular Biology, 2002
Bernhart, Stephan H. and Hofacker, Ivo L. and Will, Sebastian and Gruber, Andreas R. and Stadler, Peter F. RNAalifold: improved consensus structure prediction for RNA alignments., BMC Bioinformatics, 2008
Mathews, David H. and Disney, Matthew D. and Childs, Jessica L. and Schroeder, Susan J. and Zuker, Michael and Turner, Douglas H. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proceedings of the National Academy of Sciences of the United States of America, 2004
Turner, Douglas H. and Mathews, David H. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Nucleic Acids Research, 2010
Janssen, Stefan and Schudoma, Christian and Steger, Gerhard and Giegerich, Robert Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction, BMC Bioinformatics, 2011
Janssen, Stefan and Giegerich, Robert Faster computation of exact RNA shape probabilities, Bioinformatics, 2010
Voss, Bjoern and Giegerich, Robert and Rehmsmeier, Marc Complete probabilistic analysis of RNA shapes, BMC Biology, 2006
Washietl, Stefan and Hofacker, Ivo L. and Stadler, Peter F. Fast and reliable prediction of noncoding RNAs., Proceedings of the National Academy of Sciences of the United States of America, 2004
McCaskill and S., John The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure., Biopolymers, 1990