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Topology and prediction of RNA pseudoknots.
Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME. Reidys CM, et al. Bioinformatics. 2011 Apr 15;27(8):1076-85. doi: 10.1093/bioinformatics/btr090. Epub 2011 Feb 17. Bioinformatics. 2011. PMID: 21335320
Degeneracy and genetic assimilation in RNA evolution.
Rezazadegan R, Reidys C. Rezazadegan R, et al. BMC Bioinformatics. 2018 Dec 27;19(1):543. doi: 10.1186/s12859-018-2497-3. BMC Bioinformatics. 2018. PMID: 30587112 Free PMC article.
The block spectrum of RNA pseudoknot structures.
Li TJX, Burris CS, Reidys CM. Li TJX, et al. Among authors: reidys cm. J Math Biol. 2019 Aug;79(3):791-822. doi: 10.1007/s00285-019-01379-8. Epub 2019 Jun 6. J Math Biol. 2019. PMID: 31172257
Sequence-structure relations of biopolymers.
Barrett C, Huang FW, Reidys CM. Barrett C, et al. Among authors: reidys cm. Bioinformatics. 2017 Feb 1;33(3):382-389. doi: 10.1093/bioinformatics/btw621. Bioinformatics. 2017. PMID: 28171628
The Rainbow Spectrum of RNA Secondary Structures.
Li TJX, Reidys CM. Li TJX, et al. Among authors: reidys cm. Bull Math Biol. 2018 Jun;80(6):1514-1538. doi: 10.1007/s11538-018-0411-9. Epub 2018 Mar 14. Bull Math Biol. 2018. PMID: 29541998
Topological language for RNA.
Huang FW, Reidys CM. Huang FW, et al. Among authors: reidys cm. Math Biosci. 2016 Dec;282:109-120. doi: 10.1016/j.mbs.2016.10.006. Epub 2016 Oct 20. Math Biosci. 2016. PMID: 27773681
On the combinatorics of sparsification.
Huang FW, Reidys CM. Huang FW, et al. Algorithms Mol Biol. 2012 Oct 22;7(1):28. doi: 10.1186/1748-7188-7-28. Algorithms Mol Biol. 2012. PMID: 23088372 Free PMC article.
Generation of RNA pseudoknot structures with topological genus filtration.
Huang FW, Nebel ME, Reidys CM. Huang FW, et al. Math Biosci. 2013 Oct;245(2):216-25. doi: 10.1016/j.mbs.2013.07.014. Epub 2013 Jul 27. Math Biosci. 2013. PMID: 23900061
Addendum: topology and prediction of RNA pseudoknots.
Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME. Reidys CM, et al. Bioinformatics. 2012 Jan 15;28(2):300. doi: 10.1093/bioinformatics/btr643. Epub 2011 Nov 20. Bioinformatics. 2012. PMID: 22106334 No abstract available.
Topology of RNA-RNA interaction structures.
Andersen JE, Huang FW, Penner RC, Reidys CM. Andersen JE, et al. J Comput Biol. 2012 Jul;19(7):928-43. doi: 10.1089/cmb.2011.0308. Epub 2012 Jun 25. J Comput Biol. 2012. PMID: 22731621
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