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For: Nebel ME, Scheid A. Evaluation of a sophisticated SCFG design for RNA secondary structure prediction. Theory Biosci 2011;130:313-36. [DOI: 10.1007/s12064-011-0139-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 11/07/2011] [Indexed: 10/14/2022]
Number Cited by Other Article(s)
1
Kirkpatrick A, Patton K, Tetali P, Mitchell C. Markov Chain-Based Sampling for Exploring RNA Secondary Structure under the Nearest Neighbor Thermodynamic Model and Extended Applications. MATHEMATICAL AND COMPUTATIONAL APPLICATIONS 2020;25. [PMID: 35924027 PMCID: PMC9344895 DOI: 10.3390/mca25040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
2
Lorenz R, Hofacker IL, Stadler PF. RNA folding with hard and soft constraints. Algorithms Mol Biol 2016;11:8. [PMID: 27110276 PMCID: PMC4842303 DOI: 10.1186/s13015-016-0070-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/01/2016] [Indexed: 12/21/2022]  Open
3
Combinatorial Insights into RNA Secondary Structure. DISCRETE AND TOPOLOGICAL MODELS IN MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-40193-0_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
4
Generation of RNA pseudoknot structures with topological genus filtration. Math Biosci 2013;245:216-25. [DOI: 10.1016/j.mbs.2013.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/11/2013] [Accepted: 07/12/2013] [Indexed: 11/22/2022]
5
Rivas E. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. RNA Biol 2013;10:1185-96. [PMID: 23695796 PMCID: PMC3849167 DOI: 10.4161/rna.24971] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/06/2013] [Accepted: 05/08/2013] [Indexed: 12/31/2022]  Open
6
Anderson JWJ, Haas PA, Mathieson LA, Volynkin V, Lyngsø R, Tataru P, Hein J. Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. ACTA ACUST UNITED AC 2013;29:704-10. [PMID: 23396120 DOI: 10.1093/bioinformatics/btt050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
7
Searls DB. A primer in macromolecular linguistics. Biopolymers 2012;99:203-17. [PMID: 23034580 DOI: 10.1002/bip.22101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 05/25/2012] [Indexed: 01/01/2023]
8
Scheid A, Nebel ME. Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures. BMC Bioinformatics 2012;13:159. [PMID: 22776037 PMCID: PMC3871765 DOI: 10.1186/1471-2105-13-159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 06/06/2012] [Indexed: 12/17/2022]  Open
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