# Bibliography

[1]

Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, and Ivo L. Hofacker. ViennaRNA package 2.0. Algorithms for Molecular Biology, 6(1):26, 2011. doi:10.1186/1748-7188-6-26.

[2]

I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly, 125(2):167–188, 1994. URL: https://www.academia.edu/download/48689421/Fast_Folding_and_Comparison_of_RNA_Secon20160908-13624-1yg70az.pdf.

[3]

I.L. Hofacker, M. Fekete, and P.F. Stadler. Secondary structure prediction for aligned RNA sequences. Journal of molecular biology, 319(5):1059–1066, 2002. doi:10.1016/S0022-2836(02)00308-X.

[4]

S.H. Bernhart, I.L. Hofacker, S. Will, A.R. Gruber, and P.F. Stadler. RNAalifold: improved consensus structure prediction for RNA alignments. BMC bioinformatics, 9(1):474, 2008. doi:10.1186/1471-2105-9-474.

[5]

Christine E Hajdin, Stanislav Bellaousov, Wayne Huggins, Christopher W Leonard, David H Mathews, and Kevin M Weeks. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proceedings of the National Academy of Sciences, 110(14):5498–5503, 2013. doi:10.1073/pnas.1219988110.

[6]

Robert D Jenison, Stanley C Gill, Arthur Pardi, and Barry Polisky. High-resolution molecular discrimination by RNA. Science, 263(5152):1425–1429, 1994. doi:10.1126/science.7510417.

[7]

Amy YQ Zhang, Anthony Bugaut, and Shankar Balasubramanian. A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology. Biochemistry, 50(33):7251–7258, 2011. doi:10.1021/bi200805j.

[8]

Robert A Forties and Ralf Bundschuh. Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure. Bioinformatics, 26(1):61–67, 2010. doi:10.1093/bioinformatics/btp627.

[9]

Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler, and Manolis Kellis. RNA folding with soft constraints: reconciliation of probing data and thermodynamics secondary structure prediction. Nucleic Acids Research, 40(10):4261–4272, 2012. doi:10.1093/nar/gks009.

[10]

S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49(2):145–165, February 1999. doi:10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G.

[11]

Ye Ding and Charles E. Lawrence. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Research, 31(24):7280–7301, 12 2003. doi:10.1093/nar/gkg938.

[12]

Christoph Flamm, Ivo L Hofacker, Sebastian Maurer-Stroh, Peter F Stadler, and Martin Zehl. Design of multistable RNA molecules. RNA, 7(02):254–265, 2001. doi:10.1017/s1355838201000863.

[13]

Ronny Lorenz, Christoph Flamm, and Ivo L. Hofacker. 2d projections of RNA folding landscapes. In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter F. Stadler, editors, German Conference on Bioinformatics 2009, volume 157 of Lecture Notes in Informatics, 11–20. Bonn, September 2009. Gesellschaft f. Informatik. URL: https://dl.gi.de/items/8f88acfe-c389-4dfe-b975-84a638900683.

[14]

Robert Giegerich, Björn Voß, and Marc Rehmsmeier. Abstract shapes of RNA. Nucleic Acids Research, 32(16):4843–4851, 2004. doi:10.1093/nar/gkh779.

[15]

W. Fontana, P.F. Stadler, E.G. Bornberg-Bauer, T. Griesmacher, I.L. Hofacker, M. Tacker, P. Tarazona, E.D. Weinberger, and P. Schuster. RNA folding and combinatory landscapes. Physical review E, 47(3):2083, 1993. doi:10.1103/PhysRevE.47.2083.

[16]

B.A. Shapiro. An algorithm for comparing multiple RNA secondary structures. Computer applications in the biosciences: CABIOS, 4(3):387–393, 1988. doi:10.1093/bioinformatics/4.3.387.

[17]

Thomas R Einert and Roland R Netz. Theory for RNA folding, stretching, and melting including loops and salt. Biophysical journal, 100(11):2745–2753, 2011. doi:10.1016/j.bpj.2011.04.038.

[18]

Ronny Lorenz, Ivo L. Hofacker, and Peter F. Stadler. RNA folding with hard and soft constraints. Algorithms for Molecular Biology, 11(1):1–13, 2016. doi:10.1186/s13015-016-0070-z.

[19]

M. Zuker and P. Stiegler. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic acids research, 9(1):133–148, 1981. doi:10.1093/nar/9.1.133.

[20]

I.L. Hofacker and P.F. Stadler. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics, 22(10):1172–1176, 2006. doi:10.1093/bioinformatics/btl023.

[21]

J.S. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29(6-7):1105–1119, 1990. doi:10.1002/bip.360290621.

[22]

Stephan H Bernhart, Ivo L Hofacker, and Peter F Stadler. Local RNA base pairing probabilities in large sequences. Bioinformatics, 22(5):614–615, 2005. doi:10.1093/bioinformatics/btk014.

[23]

Stephan H Bernhart, Ullrike Mückstein, and Ivo L Hofacker. RNA accessibility in cubic time. Algorithms for Molecular Biology, 6(1):3, 2011. doi:10.1186/1748-7188-6-3.

[24]

M. Zuker. On finding all suboptimal foldings of an RNA molecule. Science, 244(4900):48–52, April 1989. doi:10.1126/science.2468181.

[25]

G Steger, H Hofmann, J Förtsch, HJ Gross, JW Randies, HL Sänger, and D Riesner. Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data. Journal of Biomolecular Structure and Dynamics, 2(3):543–571, 1984. doi:10.1080/07391102.1984.10507591.

[26]

Juraj Michálik, Hélène Touzet, and Yann Ponty. Efficient approximations of RNA kinetics landscape using non-redundant sampling. Bioinformatics, 33(14):i283–i292, 2017. doi:10.1093/bioinformatics/btx269.

[27]

S.H. Bernhart, H. Tafer, U. Mückstein, C. Flamm, P.F. Stadler, and I.L. Hofacker. Partition function and base pairing probabilities of RNA heterodimers. Algorithms for Molecular Biology, 1(1):3, 2006. doi:10.1186/1748-7188-1-3.

[28]

Katherine E. Deigan, Tian W. Li, David H. Mathews, and Kevin M. Weeks. Accurate SHAPE-directed RNA structure determination. PNAS, 106:97–102, 2009. doi:10.1073/pnas.080692910.

[29]

Kourosh Zarringhalam, Michelle M. Meyer, Ivan Dotu, Jeffrey H. Chuang, and Peter Clote. Integrating chemical footprinting data into RNA secondary structure prediction. PLOS ONE, 2012. doi:10.1371/journal.pone.0045160.

[30]

Sean R Eddy. Computational analysis of conserved rna secondary structure in transcriptomes and genomes. Annual review of biophysics, 43:433–456, 2014. doi:10.1146/annurev-biophys-051013-022950.

[31]

Fei Deng, Mirko Ledda, Sana Vaziri, and Sharon Aviran. Data-directed RNA secondary structure prediction using probabilistic modeling. RNA, 22(8):1109–1119, 2016. doi:10.1261/rna.055756.115.

[32]

Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, and Michael T. Wolfinger. Shape directed rna folding. Bioinformatics, 32(1):145–147, 2016. doi:10.1093/bioinformatics/btv523.

[33]

Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elżbieta Purta, Małgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, and others. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Research, 50(D1):D231–D235, 2022. doi:10.1093/nar/gkab1083.

[34]

Elzbieta Kierzek, Xiaoju Zhang, Richard M Watson, Scott D Kennedy, Marta Szabat, Ryszard Kierzek, and David H Mathews. Secondary structure prediction for RNA sequences including N6-methyladenosine. Nature communications, 13(1):1–10, 2022. doi:10.1038/s41467-022-28817-4.

[35]

Graham A Hudson, Richard J Bloomingdale, and Brent M Znosko. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides. RNA, 19(11):1474–1482, 2013. doi:10.1261/rna.039610.113.

[36]

Daniel J Wright, Jamie L Rice, Dawn M Yanker, and Brent M Znosko. Nearest Neighbor Parameters for Inosine· Uridine Pairs in RNA Duplexes. Biochemistry, 46(15):4625–4634, 2007. doi:10.1021/bi0616910.

[37]

Daniel J Wright, Christopher R Force, and Brent M Znosko. Stability of RNA duplexes containing inosine· cytosine pairs. Nucleic Acids Research, 46(22):12099–12108, 2018. doi:10.1093/nar/gky907.

[38]

Katherine E Richardson and Brent M Znosko. Nearest-neighbor parameters for 7-deaza-adenosine· uridine base pairs in RNA duplexes. RNA, 22(6):934–942, 2016. doi:10.1261/rna.055277.115.

[39]

Elizabeth A Jolley and Brent M Znosko. The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide. Nucleic acids research, 45(3):1479–1487, 2017. doi:10.1093/nar/gkw830.

[40]

Eva Freyhult, Vincent Moulton, and Paul Gardner. Predicting RNA structure using mutual information. Applied bioinformatics, 4(1):53–59, 2005. doi:10.2165/00822942-200504010-00006.

[41]

Daniel Wiegreffe, Daniel Alexander, Peter F Stadler, and Dirk Zeckzer. RNApuzzler: efficient outerplanar drawing of RNA-secondary structures. Bioinformatics, 35(8):1342–1349, 2019. doi:10.1093/bioinformatics/bty817.

[42]

R.E. Bruccoleri and G. Heinrich. An improved algorithm for nucleic acid secondary structure display. Computer applications in the biosciences: CABIOS, 4(1):167–173, 1988. doi:10.1093/bioinformatics/4.1.167.

[43]

Joe Sawada. A fast algorithm to generate necklaces with fixed content. Theoretical Computer Science, 301(1):477–489, 2003. doi:10.1016/S0304-3975(03)00049-5.