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Partition function and base pairing probabilities of RNA heterodimers.

Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL.

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A partition function algorithm for interacting nucleic acid strands.

Chitsaz H, Salari R, Sahinalp SC, Backofen R.

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Partition function and base pairing probabilities for RNA-RNA interaction prediction.

Huang FW, Qin J, Reidys CM, Stadler PF.

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An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.

Gaspin C, Westhof E.

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An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.

Dirks RM, Pierce NA.

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Efficient algorithms for probing the RNA mutation landscape.

Waldispühl J, Devadas S, Berger B, Clote P.

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Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model.

Waldispühl J, Clote P.

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Analysis of microRNA-target interactions by a target structure based hybridization model.

Long D, Chan CY, Ding Y.

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A statistical sampling algorithm for RNA secondary structure prediction.

Ding Y, Lawrence CE.

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Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

Wu JC, Gardner DP, Ozer S, Gutell RR, Ren P.

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A partition function algorithm for nucleic acid secondary structure including pseudoknots.

Dirks RM, Pierce NA.

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Rfold: an exact algorithm for computing local base pairing probabilities.

Kiryu H, Kin T, Asai K.

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Prediction of RNA base pairing probabilities on massively parallel computers.

Fekete M, Hofacker IL, Stadler PF.

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The equilibrium partition function and base pair binding probabilities for RNA secondary structure.

McCaskill JS.

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Assessing the reliability of RNA folding using statistical mechanics.

Huynen M, Gutell R, Konings D.

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Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications.

Rastegari B, Condon A.

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Base-pair probability profiles of RNA secondary structures.

Schmitz M, Steger G.

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Thermodynamics of RNA-RNA binding.

Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL.

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Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view.

Sponer JE, Réblova K, Mokdad A, Sychrovský V, Leszczynski J, Sponer J.

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Novel and efficient RNA secondary structure prediction using hierarchical folding.

Jabbari H, Condon A, Zhao S.

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