RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment von Bayegan, Amir H., Clote, Peter

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Network Properties of the Ensemble of RNA Structures von Clote, Peter, Bayegan, Amir

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Fast, approximate kinetics of RNA folding von Senter, Evan, Clote, Peter

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RNA Thermodynamic Structural Entropy von Garcia-Martin, Juan Antonio, Clote, Peter

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Integrating chemical footprinting data into RNA secondary structure prediction von Zarringhalam, Kourosh, Meyer, Michelle M, Dotu, Ivan, Chuang, Jeffrey H, Clote, Peter

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Computer Science Logic: 14th InternationalWorkshop, CSL 2000 Annual Conference of the EACSL Fischbachau, Germany, August 21 – 26, 2000 Proceedings von Clote, Peter G, Schwichtenberg, Helmut

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Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency von Clote, Peter, Ferré, Fabrizio, Kranakis, Evangelos, Krizanc, Danny

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Complete RNA inverse folding: computational design of functional hammerhead ribozymes von Dotu, Ivan, Garcia-Martin, Juan Antonio, Slinger, Betty L, Mechery, Vinodh, Meyer, Michelle M, Clote, Peter

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Using the fast fourier transform to accelerate the computational search for RNA conformational switches von Senter, Evan, Sheikh, Saad, Dotu, Ivan, Ponty, Yann, Clote, Peter

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Computing the partition function for kinetically trapped RNA secondary structures von Lorenz, William A, Clote, Peter

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RNA folding pathways and kinetics using 2D energy landscapes von Senter, Evan, Dotu, Ivan, Clote, Peter

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Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA von Dotu, Ivan, Mechery, Vinodh, Clote, Peter

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Expected distance between terminal nucleotides of RNA secondary structures von Clote, Peter, Ponty, Yann, Steyaert, Jean-Marc

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Expected degree for RNA secondary structure networks von Clote, Peter

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Computing folding pathways between RNA secondary structures von Dotu, Ivan, Lorenz, William A, Van Hentenryck, Pascal, Clote, Peter

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Maximum expected accuracy structural neighbors of an RNA secondary structure von Clote, Peter, Lou, Feng, Lorenz, William A

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Boltzmann probability of RNA structural neighbors and riboswitch detection von Freyhult, Eva, Moulton, Vincent, Clote, Peter

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Efficient algorithms for probing the RNA mutation landscape von Waldispühl, Jérôme, Devadas, Srinivas, Berger, Bonnie, Clote, Peter

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RNAmutants: a web server to explore the mutational landscape of RNA secondary structures von Waldispühl, Jerome, Devadas, Srinivas, Berger, Bonnie, Clote, Peter

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Small-World Networks and RNA Secondary Structures von Surujon, Defne, Ponty, Yann, Clote, Peter

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