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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. Among authors: penner rc. Bioinformatics. 2011 Apr 15;27(8):1076-85. doi: 10.1093/bioinformatics/btr090. Epub 2011 Feb 17. Bioinformatics. 2011. PMID: 21335320
Enumeration of RNA complexes via random matrix theory.
Andersen JE, Chekhov LO, Penner RC, Reidys CM, Sułkowski P. Andersen JE, et al. Among authors: penner rc. Biochem Soc Trans. 2013 Apr;41(2):652-5. doi: 10.1042/BST20120270. Biochem Soc Trans. 2013. PMID: 23514171 Review.
Topology of RNA-RNA interaction structures.
Andersen JE, Huang FW, Penner RC, Reidys CM. Andersen JE, et al. Among authors: penner rc. 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
Addendum: topology and prediction of RNA pseudoknots.
Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME. Reidys CM, et al. Among authors: penner rc. Bioinformatics. 2012 Jan 15;28(2):300. doi: 10.1093/bioinformatics/btr643. Epub 2011 Nov 20. Bioinformatics. 2012. PMID: 22106334 No abstract available.
Topological classification and enumeration of RNA structures by genus.
Andersen JE, Penner RC, Reidys CM, Waterman MS. Andersen JE, et al. Among authors: penner rc. J Math Biol. 2013 Nov;67(5):1261-78. doi: 10.1007/s00285-012-0594-x. Epub 2012 Oct 2. J Math Biol. 2013. PMID: 23053535
An Algebro-topological description of protein domain structure.
Penner RC, Knudsen M, Wiuf C, Andersen JE. Penner RC, et al. PLoS One. 2011;6(5):e19670. doi: 10.1371/journal.pone.0019670. Epub 2011 May 24. PLoS One. 2011. PMID: 21629687 Free PMC article.
Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture.
Penner RC, Andersen ES, Jensen JL, Kantcheva AK, Bublitz M, Nissen P, Rasmussen AM, Svane KL, Hammer B, Rezazadegan R, Nielsen NC, Nielsen JT, Andersen JE. Penner RC, et al. Nat Commun. 2014 Dec 17;5:5803. doi: 10.1038/ncomms6803. Nat Commun. 2014. PMID: 25517704
Theory of Morphogenesis.
Minarsky A, Morozova N, Penner R, Soulé C. Minarsky A, et al. Among authors: penner r. J Comput Biol. 2018 Apr;25(4):444-450. doi: 10.1089/cmb.2017.0150. Epub 2017 Nov 29. J Comput Biol. 2018. PMID: 29185804
Erratum: Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture.
Penner RC, Andersen ES, Jensen JL, Kantcheva AK, Bublitz M, Nissen P, Rasmussen AM, Svane KL, Hammer B, Rezazadegan R, Nielsen NC, Nielsen JT, Andersen JE. Penner RC, et al. Nat Commun. 2015 Feb 3;6:6209. doi: 10.1038/ncomms7209. Nat Commun. 2015. PMID: 25648452 No abstract available.
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