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Journal of Theoretical Biology|May 10, 2005
On realizing shapes in the theory of RNA neutral networksPeter Clote, Leszek Gasieniec, Roman Kolpakov, et al.Proteins|July 22, 2006
Predicting transmembrane beta-barrels and interstrand residue interactions from sequenceJ Waldispühl, Bonnie Berger, Peter Clote, et al.Nucleic Acids Research|January 2, 2010
Computing folding pathways between RNA secondary structuresIvan Dotu, William A Lorenz, Pascal Van Hentenryck, et al.Nucleic Acids Research|September 4, 2012
A global sampling approach to designing and reengineering RNA secondary structuresAlex Levin, Mieszko Lis, Yann Ponty, et al.Proteins|November 16, 2007
Modeling ensembles of transmembrane beta-barrel proteinsJérôme Waldispühl, Charles W O'Donnell, Srinivas Devadas, et al.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|November 13, 2009
RNA structural segmentationIvan Dotú, William A Lorenz, Pascal VAN Hentenryck, et al.BMC Bioinformatics|October 21, 2016
RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theoryJuan Antonio Garcia-Martin, Amir H Bayegan, Ivan Dotu, et al.NAR Genomics and Bioinformatics|March 26, 2025
IPANEMAP Suite: a pipeline for probing-informed RNA structure modelingPierre Hardouin, Nan Pan, Francois-Xavier Lyonnet du Moutier, et al.Plos One|October 24, 2012
Integrating chemical footprinting data into RNA secondary structure predictionKourosh Zarringhalam, Michelle M Meyer, Ivan Dotu, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|February 25, 2014
Computing the probability of RNA hairpin and multiloop formationYang Ding, William A Lorenz, Ivan Dotu, et al.Pageof 10