{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,7]],"date-time":"2024-09-07T21:31:52Z","timestamp":1725744712065},"publisher-location":"Berlin, Heidelberg","reference-count":28,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642404528"},{"type":"electronic","value":"9783642404535"}],"license":[{"start":{"date-parts":[[2013,1,1]],"date-time":"2013-01-01T00:00:00Z","timestamp":1356998400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013]]},"DOI":"10.1007\/978-3-642-40453-5_10","type":"book-chapter","created":{"date-parts":[[2013,8,15]],"date-time":"2013-08-15T23:09:49Z","timestamp":1376608189000},"page":"112-125","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures"],"prefix":"10.1007","author":[{"given":"Rolf","family":"Backofen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Fricke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Qin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"10_CR1","doi-asserted-by":"publisher","first-page":"9327","DOI":"10.1128\/MCB.23.24.9327-9337.2003","volume":"23","author":"A.P. Baraniak","year":"2003","unstructured":"Baraniak, A.P., Lasda, E.L., Wagner, E.J., Garcia-Blanco, M.A.: A stem structure in fibroblast growth factor receptor 2 transcripts mediates cell-type-specific splicing by approximating intronic control elements. Mol. Cell Biol.\u00a023, 9327\u20139337 (2003)","journal-title":"Mol. Cell Biol."},{"key":"10_CR2","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1007\/s00285-011-0467-8","volume":"65","author":"P. Clote","year":"2012","unstructured":"Clote, P., Ponty, Y., Steyaert, J.M.: Expected distance between terminal nucleotides of RNA secondary structures. J. Math. Biol.\u00a065, 581\u2013599 (2012)","journal-title":"J. Math. Biol."},{"issue":"15","key":"10_CR3","doi-asserted-by":"publisher","first-page":"1974","DOI":"10.1093\/bioinformatics\/btp250","volume":"25","author":"K. Darty","year":"2009","unstructured":"Darty, K., Denise, A.: Ponty. Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics\u00a025(15), 1974\u20131975 (2009)","journal-title":"Bioinformatics"},{"key":"10_CR4","doi-asserted-by":"publisher","first-page":"14664","DOI":"10.1073\/pnas.0703836104","volume":"104","author":"R. Das","year":"2007","unstructured":"Das, R., Baker, D.: Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. USA\u00a0104, 14664\u201314669 (2007)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"24","key":"10_CR5","doi-asserted-by":"publisher","first-page":"7280","DOI":"10.1093\/nar\/gkg938","volume":"31","author":"Y. Ding","year":"2003","unstructured":"Ding, Y., Lawrence, C.E.: A statistical sampling algorithm for RNA secondary structure prediction. Nucl. Acids Res.\u00a031(24), 7280\u20137301 (2003)","journal-title":"Nucl. Acids Res."},{"issue":"10","key":"10_CR6","doi-asserted-by":"publisher","first-page":"4963","DOI":"10.1128\/JVI.02317-10","volume":"85","author":"D. Dufour","year":"2011","unstructured":"Dufour, D., Mateos-Gomez, P.A., Enjuanes, L., Gallego, J., Sola, I.: Structure and functional relevance of a transcription-regulating sequence involved in coronavirus discontinuous RNA synthesis. J. Virol.\u00a085(10), 4963\u20134973 (2011)","journal-title":"J. Virol."},{"key":"10_CR7","doi-asserted-by":"publisher","first-page":"48103","DOI":"10.1103\/PhysRevLett.101.048103","volume":"101","author":"T.R. Einert","year":"2008","unstructured":"Einert, T.R., N\u00e4ger, P., Orland, H., Netz, R.: Impact of loop statistics on the thermodynamics of RNA folding. Phys. Rev. Lett.\u00a0101, 048103 (2008)","journal-title":"Phys. Rev. Lett."},{"key":"10_CR8","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/j.jtbi.2011.04.010","volume":"280","author":"L.T. Fang","year":"2011","unstructured":"Fang, L.T.: The end-to-end distance of RNA as a randomly self-paired polymer. J. Theor. Biol.\u00a0280, 101\u2013107 (2011)","journal-title":"J. Theor. Biol."},{"key":"10_CR9","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1093\/bioinformatics\/btp627","volume":"26","author":"R.A. Forties","year":"2010","unstructured":"Forties, R.A., Bundschuh, R.: Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure. Bioinformatics\u00a026, 61\u201367 (2010)","journal-title":"Bioinformatics"},{"key":"10_CR10","doi-asserted-by":"publisher","first-page":"1324","DOI":"10.1016\/S0006-3495(01)75789-X","volume":"81","author":"U. Gerland","year":"2001","unstructured":"Gerland, U., Bundschuh, R., Hwa, T.: Force-induced denaturation of RNA. Biophys. J.\u00a081, 1324\u20131332 (2001)","journal-title":"Biophys. J."},{"key":"10_CR11","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1088\/1478-3967\/1\/1\/002","volume":"1","author":"U. Gerland","year":"2004","unstructured":"Gerland, U., Bundschuh, R., Hwa, T.: Translocation of structured polynucleotides through nanopores. Phys. Biol.\u00a01, 19\u201326 (2004)","journal-title":"Phys. Biol."},{"key":"10_CR12","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1007\/3-540-45719-4_24","volume-title":"Algebraic Methodology and Software Technology","author":"R. Giegerich","year":"2002","unstructured":"Giegerich, R., Meyer, C.: Algebraic dynamic programming. In: Kirchner, H., Ringeissen, C. (eds.) AMAST 2002. LNCS, vol.\u00a02422, pp. 349\u2013364. Springer, Heidelberg (2002)"},{"key":"10_CR13","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1089\/cmb.2011.0301","volume":"19","author":"H.S. Han","year":"2012","unstructured":"Han, H.S., Reidys, C.M.: The 5\u2019-3\u2019 distance of RNA secondary structures. J. Comput. Biol.\u00a019, 867\u2013878 (2012)","journal-title":"J. Comput. Biol."},{"issue":"6","key":"10_CR14","doi-asserted-by":"publisher","first-page":"2047","DOI":"10.1093\/nar\/gkm072","volume":"35","author":"A. Kobitski","year":"2007","unstructured":"Kobitski, A., Nierth, A., Helm, M., Jaschke, A., Nienhaus, U.G.: Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis. Nucleic Acids Res.\u00a035(6), 2047\u20132059 (2007)","journal-title":"Nucleic Acids Res."},{"key":"10_CR15","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1016\/S0076-6879(09)69021-2","volume":"469","author":"D. Leipply","year":"2009","unstructured":"Leipply, D., Lambert, D., Draper, D.E.: Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria. Methods Enzymol.\u00a0469, 433\u2013463 (2009)","journal-title":"Methods Enzymol."},{"issue":"4","key":"10_CR16","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1093\/bioinformatics\/btq659","volume":"27","author":"A.X. Li","year":"2011","unstructured":"Li, A.X., Marz, M., Qin, J., Reidys, C.M.: RNA-RNA interaction prediction based on multiple sequence alignments. Bioinformatics\u00a027(4), 456\u2013463 (2011)","journal-title":"Bioinformatics"},{"key":"10_CR17","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1748-7188-6-26","volume":"6","author":"R. Lorenz","year":"2011","unstructured":"Lorenz, R., Bernhart, S.H., H\u00f6ner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P.F., Hofacker, I.L.: ViennaRNA Package 2.0. Alg. Mol. Biol.\u00a06, 26 (2011)","journal-title":"Alg. Mol. Biol."},{"issue":"PrePrints","key":"10_CR18","first-page":"1","volume":"99","author":"R. Lorenz","year":"2013","unstructured":"Lorenz, R., Bernhart, S.H., Qin, J., Honer zu Siederdissen, C., Tanzer, A., Amman, F., Hofacker, I.L.: 2d meets 4g: G-quadruplexes in rna secondary structure prediction. IEEE\/ACM Transactions on Computational Biology and Bioinformatics\u00a099(PrePrints), 1 (2013)","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"10_CR19","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","volume":"288","author":"D. Mathews","year":"1999","unstructured":"Mathews, D., Sabina, J., Zuker, M., Turner, D.H.: Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol.\u00a0288, 911\u2013940 (1999)","journal-title":"J. Mol. Biol."},{"key":"10_CR20","doi-asserted-by":"publisher","first-page":"7287","DOI":"10.1073\/pnas.0401799101","volume":"101","author":"D.H. Mathews","year":"2004","unstructured":"Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M., Turner, D.H.: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA\u00a0101, 7287\u20137292 (2004)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"6-7","key":"10_CR21","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.360290621","volume":"29","author":"J.S. McCaskill","year":"1990","unstructured":"McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers\u00a029(6-7), 1105\u20131119 (1990)","journal-title":"Biopolymers"},{"key":"10_CR22","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/j.gde.2011.04.001","volume":"21","author":"C.J. McManus","year":"2011","unstructured":"McManus, C.J., Graveley, B.R.: RNA structure and the mechanisms of alternative splicing. Curr. Opin. Genet. Dev.\u00a021, 373\u2013379 (2011)","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10_CR23","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1140\/epje\/i2002-10057-5","volume":"9","author":"M. M\u00fcller","year":"2002","unstructured":"M\u00fcller, M., Krzakala, F., M\u00e9zard, M.: The secondary structure of RNA under tension. Eur. Phys. J. E\u00a09, 67\u201377 (2002)","journal-title":"Eur. Phys. J. E"},{"issue":"8","key":"10_CR24","doi-asserted-by":"publisher","first-page":"1076","DOI":"10.1093\/bioinformatics\/btr090","volume":"27","author":"C.M. Reidys","year":"2011","unstructured":"Reidys, C.M., Huang, F.W.D., Andersen, J.E., Penner, R.C., Stadler, P.F., Nebel, M.E.: Topology and prediction of RNA pseudoknots. Bioinformatics\u00a027(8), 1076\u20131085 (2011)","journal-title":"Bioinformatics"},{"key":"10_CR25","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1038\/nmeth.1208","volume":"5","author":"R. Roy","year":"2008","unstructured":"Roy, R., Hohng, S., Ha, T.: A practical guide to single-molecule FRET. Nature Methods\u00a05, 507\u2013516 (2008)","journal-title":"Nature Methods"},{"issue":"1344","key":"10_CR26","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1098\/rspb.1994.0040","volume":"255","author":"P. Schuster","year":"1994","unstructured":"Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L.: From sequences to shapes and back: a case study in RNA secondary structures. Proc. Royal Society London B\u00a0255(1344), 279\u2013284 (1994)","journal-title":"Proc. Royal Society London B"},{"key":"10_CR27","doi-asserted-by":"crossref","unstructured":"Senter, E., Sheikh, S., Dotu, I., Ponty, Y., Clote, P.: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. PLoS ONE\u00a07(12), e50506 (2012)","DOI":"10.1371\/journal.pone.0050506"},{"key":"10_CR28","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1093\/nar\/gkq642","volume":"39","author":"A.M. Yoffe","year":"2011","unstructured":"Yoffe, A.M., Prinsen, P., Gelbart, W.M., Ben-Shaul, A.: The ends of a large RNA molecule are necessarily close. Nucl. Acids Res.\u00a039, 292\u2013299 (2011)","journal-title":"Nucl. Acids Res."}],"container-title":["Lecture Notes in Computer Science","Algorithms in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-40453-5_10","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T16:27:10Z","timestamp":1584462430000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-40453-5_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"ISBN":["9783642404528","9783642404535"],"references-count":28,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-40453-5_10","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2013]]},"assertion":[{"value":"This content has been made available to all.","name":"free","label":"Free to read"}]}}