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Plos One|February 8, 2011
Computing the partition function for kinetically trapped RNA secondary structuresWilliam A Lorenz, Peter CloteAlgorithms for Molecular Biology : AMB|December 10, 2025
Rna triplet repeats: improved algorithms for structure prediction and interactionsKimon Boehmer, Sarah J Berkemer, Sebastian Will, et al.Methods in Molecular Biology (Clifton, N.J.)|April 9, 2021
Advanced Design of Structural RNAs Using RNARedPrintYann Ponty, Stefan Hammer, Hua-Ting Yao, et al.Journal of Mathematical Biology|March 12, 2026
Undesignable motifs in structural RNAs and combinatorial consequencesHua-Ting Yao, Cedric Chauve, Mireille Regnier, et al.Journal of Mathematical Biology|August 7, 2017
RNA folding kinetics using Monte Carlo and Gillespie algorithmsPeter Clote, Amir H BayeganPlos One|January 25, 2020
RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignmentAmir H Bayegan, Peter CloteBioinformatics (Oxford, England)|June 19, 2007
Boltzmann probability of RNA structural neighbors and riboswitch detectionEva Freyhult, Vincent Moulton, Peter CloteNucleic Acids Research|May 29, 2007
RNAbor: a web server for RNA structural neighborsEva Freyhult, Vincent Moulton, Peter ClotePlos One|March 4, 2014
Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNAIvan Dotu, Vinodh Mechery, Peter CloteNucleic Acids Research|June 11, 2013
SPARCS: a web server to analyze (un)structured regions in coding RNA sequencesYang Zhang, Yann Ponty, Mathieu Blanchette, et al.Pageof 10