{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T14:27:46Z","timestamp":1742912866104,"version":"3.40.3"},"publisher-location":"Boston","reference-count":38,"publisher":"Birkh\u00e4user Boston","isbn-type":[{"type":"print","value":"9780817647889"},{"type":"electronic","value":"9780817647896"}],"license":[{"start":{"date-parts":[[2010,9,16]],"date-time":"2010-09-16T00:00:00Z","timestamp":1284595200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2010,9,16]],"date-time":"2010-09-16T00:00:00Z","timestamp":1284595200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011]]},"DOI":"10.1007\/978-0-8176-4789-6_17","type":"book-chapter","created":{"date-parts":[[2010,10,14]],"date-time":"2010-10-14T07:42:50Z","timestamp":1287042170000},"page":"421-437","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Graph Representations and Algorithms in Computational Biology of RNA Secondary Structure"],"prefix":"10.1007","author":[{"given":"Stefan","family":"Washietl","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tanja","family":"GesellGesell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,9,16]]},"reference":[{"issue":"2","key":"17_CR1_17","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","volume":"116","author":"DP Bartel","year":"2004","unstructured":"Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2): 281\u2013297","journal-title":"Cell"},{"issue":"1\u20133","key":"17_CR2_17","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.tcs.2004.12.030","volume":"337","author":"P Bille","year":"2005","unstructured":"Bille P (2005) A survey on tree edit distance and related problems. Theor Comput Sci 337 (1\u20133):217\u2013239","journal-title":"Theor Comput Sci"},{"key":"17_CR3_17","first-page":"35","volume":"20","author":"H Bunke","year":"1983","unstructured":"Bunke H (1983) What is the distance between graphs? Bull EATCS 20:35\u201339","journal-title":"Bull EATCS"},{"issue":"5740","key":"17_CR4_17","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1126\/science.1112014","volume":"309","author":"P Carninci","year":"2005","unstructured":"Carninci P et al (2005) The transcriptional landscape of the mammalian genome. Science 309(5740):1559\u20131563","journal-title":"Science"},{"issue":"6894","key":"17_CR5_17","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/418222a","volume":"418","author":"JA Doudna","year":"2002","unstructured":"Doudna JA, Cech TR (2002) The chemical repertoire of natural ribozymes. Nature 418(6894):222\u2013228","journal-title":"Nature"},{"key":"17_CR6_17","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/1471-2105-5-71","volume":"5","author":"RD Dowell","year":"2004","unstructured":"Dowell RD, Eddy SR (2004) Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics 5:71","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"17_CR7_17","doi-asserted-by":"publisher","first-page":"2079","DOI":"10.1093\/nar\/22.11.2079","volume":"22","author":"SR Eddy","year":"1994","unstructured":"Eddy SR, Durbin R (1994) RNA sequence analysis using covariance models. Nucleic Acids Res 22(11):2079\u20132088","journal-title":"Nucleic Acids Res"},{"key":"17_CR8_17","doi-asserted-by":"publisher","first-page":"1389","DOI":"10.1002\/bip.360330909","volume":"33","author":"W Fontana","year":"1993","unstructured":"Fontana W, Konings DA, Stadler PF, Schuster P (1993) Statistics of RNA secondary structures. Biopolymers 33:1389\u20131404","journal-title":"Biopolymers"},{"key":"17_CR9_17","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/BF00818163","volume":"125","author":"IL Hofacker","year":"1994","unstructured":"Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125:167\u2013188","journal-title":"Monatsh Chem"},{"key":"17_CR10_17","first-page":"177","volume":"89","author":"IL Hofacker","year":"1998","unstructured":"Hofacker IL, Schuster P, Stadler PF (1998) Combinatorics of RNA secondary structures. Discrete Appl Math 89:177\u2013207","journal-title":"Discrete Appl Math"},{"key":"17_CR11_17","series-title":"Wiley-VCH","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1002\/9783527619368.ch14","volume-title":"Bioinformatics: from genomes to therapies","author":"IL Hofacker","year":"2007","unstructured":"Hofacker IL, Stadler PF (2007) RNA secondary structures. In: Lengauer T (ed) Bioinformatics: from genomes to therapies, vol 1. Wiley-VCH, Weinheim, Germany, pp 439\u2013489"},{"issue":"82","key":"17_CR12_17","first-page":"1","volume":"2","author":"F Kaden","year":"1982","unstructured":"Kaden F (1982) Graphmetriken und Distanzgraphen. ZKI-Informationen Akad Wiss DDR 2(82):1\u201363","journal-title":"ZKI-Informationen Akad Wiss DDR"},{"key":"17_CR13_17","doi-asserted-by":"crossref","unstructured":"Klein P (1998) Computing the edit distance between unrooted ordered trees. In: Bilardi G, Italiano GF, Pietracaprina A, Pucci G (eds) Algorithms \u2013 ESA \u201998, Proceedings of 6th annual European symposium, Venice, Italy, 24\u201326 August 1998. Lecture Notes in Computer Science, vol 1461. Springer, Heidelberg, pp 91\u2013102","DOI":"10.1007\/3-540-68530-8_8"},{"issue":"5","key":"17_CR14_17","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1016\/0010-4809(89)90039-6","volume":"22","author":"SY Le","year":"1989","unstructured":"Le SY, Nussinov R, Maizel JV (1989) Tree graphs of RNA secondary structures and their comparisons. Comput Biomed Res 22(5):461\u2013473","journal-title":"Comput Biomed Res"},{"key":"17_CR15_17","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","volume":"288","author":"DH Mathews","year":"1999","unstructured":"Mathews DH, Sabina J, Zuker M, Turner H (1999) Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J Mol Biol 288:911\u2013940","journal-title":"J Mol Biol"},{"key":"17_CR16_17","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.360290621","volume":"29","author":"JS McCaskill","year":"1990","unstructured":"McCaskill JS (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105\u20131119","journal-title":"Biopolymers"},{"key":"17_CR17_17","volume-title":"Lehninger principles of biochemistry","author":"DL Nelson","year":"2004","unstructured":"Nelson DL, Cox MM (2004) Lehninger principles of biochemistry, 4th edn. W.H. Freeman, New York","edition":"4"},{"issue":"11","key":"17_CR18_17","doi-asserted-by":"publisher","first-page":"6309","DOI":"10.1073\/pnas.77.11.6309","volume":"77","author":"R Nussinov","year":"1980","unstructured":"Nussinov R, Jacobson AB (1980) Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci USA 77(11):6309\u20136313","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"17_CR19_17","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1137\/0135006","volume":"35","author":"R Nussinov","year":"1978","unstructured":"Nussinov R, Piecznik G, Griggs JR, Kleitman DJ (1978) Algorithms for loop matching. SIAM J Appl Math 35(1):68\u201382","journal-title":"SIAM J Appl Math"},{"issue":"6","key":"17_CR20_17","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/0020-0190(77)90064-3","volume":"6","author":"SM Selkow","year":"1977","unstructured":"Selkow SM (1977) The tree-to-tree editing problem. Inf Process Lett 6(6):184\u2013186","journal-title":"Inf Process Lett"},{"key":"17_CR21_17","first-page":"387","volume":"4","author":"BA Shapiro","year":"1988","unstructured":"Shapiro BA (1988) An algorithm for comparing multiple RNA secondary stuctures. CABIOS 4:387\u2013393","journal-title":"CABIOS"},{"key":"17_CR22_17","first-page":"309","volume":"6","author":"BA Shapiro","year":"1990","unstructured":"Shapiro BA, Zhang K (1990) Comparing multiple RNA secondary structures using tree comparisons. CABIOS 6:309\u2013318","journal-title":"CABIOS"},{"issue":"82","key":"17_CR23_17","first-page":"63","volume":"2","author":"F Sobik","year":"1982","unstructured":"Sobik F (1982) Graphmetriken und Klassifikation strukturierter Objekte. ZKI-Informationen Akad Wiss DDR 2(82):63\u2013122","journal-title":"ZKI-Informationen Akad Wiss DDR"},{"key":"17_CR24_17","first-page":"104","volume":"4","author":"F Sobik","year":"1986","unstructured":"Sobik F (1986) Modellierung von Vergleichsprozessen auf der Grundlage von \u00c4hnlichkeitsma\u00dfen f\u00fcr Graphen. ZKI-Informationen Akad Wiss DDR 4:104\u2013144","journal-title":"ZKI-Informationen Akad Wiss DDR"},{"key":"17_CR25_17","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1145\/322139.322143","volume":"26","author":"K Tai","year":"1979","unstructured":"Tai K (1979) The tree-to-tree correction problem. J ACM 26:422\u2013433","journal-title":"J ACM"},{"issue":"6894","key":"17_CR26_17","doi-asserted-by":"crossref","first-page":"2","DOI":"10.4153\/CJM-1952-001-8","volume":"4","author":"J Touchard","year":"1952","unstructured":"Touchard J (1952) Sur un probl\u00e8me de configurations et sur les fractions continues. Can J Math 4(6894):2\u201325","journal-title":"Can J Math"},{"issue":"6","key":"17_CR27_17","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1101\/gr.5650707","volume":"17","author":"S Washietl","year":"2007","unstructured":"Washietl S et al (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17(6):852\u2013864","journal-title":"Genome Res"},{"key":"17_CR28_17","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1038\/nbt1144","volume":"23","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker IL, Lukasser M, H\u00fcttenhofer A, Stadler PF (2005) Mapping of conserved RNA secondary structures predicts thousands of functional non-coding RNAs in the human genome. Nat Biotechnol 23:1383\u20131390","journal-title":"Nat Biotechnol"},{"key":"17_CR29_17","unstructured":"Waterman MS (1978) Secondary structure of single-stranded nucleic acids. Studies on foundations and combinatorics. Advances in Mathematics Supplementary Studies. Academic Press, New York, 1:167\u2013212"},{"key":"17_CR30_17","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/0025-5564(78)90099-8","volume":"42","author":"MS Waterman","year":"1978","unstructured":"Waterman MS, Smith TF (1978) RNA secondary structure: a complete mathematical analysis. Math Biosci 42:257\u2013266","journal-title":"Math Biosci"},{"issue":"42","key":"17_CR31_17","doi-asserted-by":"publisher","first-page":"14719","DOI":"10.1021\/bi9809425","volume":"37","author":"T Xia","year":"1998","unstructured":"Xia T, SantaLucia J, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with watson-crick base pairs. Biochemistry 37(42):14719\u201314735","journal-title":"Biochemistry"},{"issue":"1\u20133","key":"17_CR32_17","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/0012-365X(94)00023-C","volume":"143","author":"L Yan","year":"1995","unstructured":"Yan L (1995) A family of special outerplanar graphs with only one triangle satisfying the cycle basis interpolation property. Discrete Math 143(1\u20133):293\u2013297","journal-title":"Discrete Math"},{"issue":"4","key":"17_CR33_17","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1093\/bioinformatics\/btk008","volume":"22","author":"Z Yao","year":"2006","unstructured":"Yao Z, Weinberg Z, Ruzzo WL (2006) CMfinder \u2013 a covariance model based RNA motif finding algorithm. Bioinformatics 22(4):445\u2013452","journal-title":"Bioinformatics"},{"key":"17_CR34_17","doi-asserted-by":"crossref","unstructured":"Zelinka B (1975) On a certain distance between isomorphism classes of graphs. \u010casopis pro p\u0306est Mathematiky 100:371\u2013373","DOI":"10.21136\/CPM.1975.117890"},{"key":"17_CR35_17","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.1137\/0218082","volume":"18","author":"K Zhang","year":"1989","unstructured":"Zhang K, Shasha D (1989) Simple fast algorithms for the editing distance between trees and related problems. SIAM J Comput 18:1245\u20131262","journal-title":"SIAM J Comput"},{"issue":"13","key":"17_CR36_17","doi-asserted-by":"publisher","first-page":"3406","DOI":"10.1093\/nar\/gkg595","volume":"31","author":"M Zuker","year":"2003","unstructured":"Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406\u201315","journal-title":"Nucleic Acids Res"},{"key":"17_CR37_17","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/S0092-8240(84)80062-2","volume":"46","author":"M Zuker","year":"1984","unstructured":"Zuker M, Sankoff D (1984) RNA secondary structures and their prediction. Bull Math Biol 46:591\u2013621","journal-title":"Bull Math Biol"},{"key":"17_CR38_17","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1093\/nar\/9.1.133","volume":"9","author":"M Zuker","year":"1981","unstructured":"Zuker M, Stiegler P (1981) Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133\u2013148","journal-title":"Nucleic Acids Res"}],"container-title":["Structural Analysis of Complex Networks"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-0-8176-4789-6_17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T12:03:24Z","timestamp":1675253004000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-0-8176-4789-6_17"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,9,16]]},"ISBN":["9780817647889","9780817647896"],"references-count":38,"URL":"https:\/\/doi.org\/10.1007\/978-0-8176-4789-6_17","relation":{},"subject":[],"published":{"date-parts":[[2010,9,16]]},"assertion":[{"value":"16 September 2010","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}