{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,8]],"date-time":"2024-09-08T18:43:02Z","timestamp":1725820982337},"publisher-location":"Cham","reference-count":23,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319190471"},{"type":"electronic","value":"9783319190488"}],"license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"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":[[2015]]},"DOI":"10.1007\/978-3-319-19048-8_18","type":"book-chapter","created":{"date-parts":[[2015,4,29]],"date-time":"2015-04-29T14:57:48Z","timestamp":1430319468000},"page":"211-222","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Predicting RNA Secondary Structures: One-grammar-fits-all Solution"],"prefix":"10.1007","author":[{"given":"Menglu","family":"Li","sequence":"first","affiliation":[]},{"given":"Micheal","family":"Cheng","sequence":"additional","affiliation":[]},{"given":"Yongtao","family":"Ye","sequence":"additional","affiliation":[]},{"given":"Wk","family":"Hon","sequence":"additional","affiliation":[]},{"given":"Hf","family":"Ting","sequence":"additional","affiliation":[]},{"given":"Tw","family":"Lam","sequence":"additional","affiliation":[]},{"given":"Cy","family":"Tang","sequence":"additional","affiliation":[]},{"given":"Thomas","family":"Wong","sequence":"additional","affiliation":[]},{"given":"Sm","family":"Yiu","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"47","key":"18_CR1","doi-asserted-by":"publisher","first-page":"11665","DOI":"10.1021\/bi00162a001","volume":"31","author":"E. Dam Ten","year":"1992","unstructured":"Ten Dam, E., Pleij, K., Draper, D.: Structural and functional aspects of rna pseudoknots. Biochemistry\u00a031(47), 11665\u201311676 (1992)","journal-title":"Biochemistry"},{"issue":"5","key":"18_CR2","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1006\/jmbi.1997.1092","volume":"269","author":"K. Lee","year":"1997","unstructured":"Lee, K., Varma, S., SantaLucia Jr., J., Cunningham, P.R.: In vivo determination of rna structure-function relationships: analysis of the 790 loop in ribosomal rna. Journal of Molecular Biology\u00a0269(5), 732\u2013743 (1997)","journal-title":"Journal of Molecular Biology"},{"issue":"4","key":"18_CR3","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1016\/0092-8674(89)90124-4","volume":"57","author":"I. Brierley","year":"1989","unstructured":"Brierley, I., Digard, P., Inglis, S.C.: Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an rna pseudoknot. Cell\u00a057(4), 537\u2013547 (1989)","journal-title":"Cell"},{"key":"18_CR4","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1006\/jmbi.2000.3668","volume":"298","author":"D.P. Giedroc","year":"2000","unstructured":"Giedroc, D.P., Theimer, C.A., Nixon, P.: Structure, stability and function of rna pseudoknots involved in stimulating ribosomal frameshifting. J. Mol. Biol.\u00a0298, 167\u2013185 (2000)","journal-title":"J. Mol. Biol."},{"issue":"3-4","key":"18_CR5","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1089\/106652700750050862","volume":"7","author":"R.B. Lyngs\u00f8","year":"2004","unstructured":"Lyngs\u00f8, R.B., Pedersen, C.N.S.: RNA pseudoknot prediction in energy-based models. Journal of Computational Biology\u00a07(3-4), 409\u2013427 (2004)","journal-title":"Journal of Computational Biology"},{"key":"18_CR6","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1007\/978-3-540-27836-8_77","volume-title":"Automata, Languages and Programming","author":"R.B. Lyngs\u00f8","year":"2004","unstructured":"Lyngs\u00f8, R.B.: Complexity of pseudoknot prediction in simple models. In: D\u00edaz, J., Karhum\u00e4ki, J., Lepist\u00f6, A., Sannella, D. (eds.) ICALP 2004. LNCS, vol.\u00a03142, pp. 919\u2013931. Springer, Heidelberg (2004)"},{"issue":"8","key":"18_CR7","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, W.D., Andersen, F., Penner, J.E., Stadler, R.C., Nebel, P.F., Topology, M.E.: prediction of rna pseudoknots. Bioinformatics\u00a027(8), 1076\u20131085 (2011)","journal-title":"Bioinformatics"},{"key":"18_CR8","doi-asserted-by":"publisher","first-page":"1494","DOI":"10.1261\/rna.7284905","volume":"11","author":"J. Ren","year":"2005","unstructured":"Ren, J., Rastegari, B., Condon, A., Hoos., H.H.: Hotknots: Heuristic prediction of rna secondary structures including pseudoknots. RNA\u00a011, 1494\u20131504 (2005)","journal-title":"RNA"},{"issue":"4","key":"18_CR9","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1093\/bioinformatics\/btn601","volume":"25","author":"M. Hamada","year":"2009","unstructured":"Hamada, M., Kiryu, H., Sato, K., Mituyama, T., Asai., K.: Predictions of RNA secondary structure using generalized centroid estimators. Bioinformatics\u00a025(4), 465\u2013473 (2009)","journal-title":"Bioinformatics"},{"issue":"11","key":"18_CR10","doi-asserted-by":"publisher","first-page":"1525","DOI":"10.1089\/cmb.2011.0184","volume":"18","author":"S. Zakov","year":"2011","unstructured":"Zakov, S., Goldberg, Y., Elhadad, M., Ziv-Ukelson., M.: Rich parameterization improves rna structure prediction. Journal of Computational Biology\u00a018(11), 1525\u20131542 (2011)","journal-title":"Journal of Computational Biology"},{"key":"18_CR11","doi-asserted-by":"crossref","unstructured":"Bindewald, E., Shapiro., T.K.B.: Cylofold: secondary structure prediction including pseudoknots. Nucleic Acids Research suppl.(W), 368\u2013387 (2010)","DOI":"10.1093\/nar\/gkq432"},{"key":"18_CR12","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/S0166-218X(00)00186-4","volume":"104","author":"T. Akutsu.","year":"2000","unstructured":"Akutsu., T.: Dynamic programming algorithms for rna secondary structure prediction with pseudoknots. Discrete Applied Mathematics\u00a0104, 45\u201362 (2000)","journal-title":"Discrete Applied Mathematics"},{"issue":"6","key":"18_CR13","first-page":"803","volume":"16","author":"H. Chen","year":"2009","unstructured":"Chen, H., Condon, A., Jabbari, H.: An o(n(5)) algorithm for mfe prediction of kissing hairpins and 4-chains in nucleic acids. Discrete Applied Mathematics\u00a016(6), 803\u2013815 (2009)","journal-title":"Discrete Applied Mathematics"},{"issue":"13","key":"18_CR14","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1002\/jcc.10296","volume":"24","author":"R. Dirks","year":"2003","unstructured":"Dirks, R., Pierce, N.: A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem.\u00a024(13), 1664\u20131677 (2003)","journal-title":"J. Comput. Chem."},{"key":"18_CR15","doi-asserted-by":"publisher","first-page":"2053","DOI":"10.1006\/jmbi.1998.2436","volume":"285","author":"E. Rivas","year":"1999","unstructured":"Rivas, E., Eddy, S.R.: A dynamic programming algorithm for rna structure prediction including pseudoknots. J. Mol. Biol.\u00a0285, 2053\u20132068 (1999)","journal-title":"J. Mol. Biol."},{"issue":"1","key":"18_CR16","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1471-2105-9-33","volume":"9","author":"Y. Tabei","year":"2008","unstructured":"Tabei, Y., Kiryu, H., Kin, T., Asai, K.: A fast structural multiple alignment method for long rna sequences. BMC Bioinformatics\u00a09(1), 33 (2008)","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"18_CR17","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1186\/1471-2105-9-474","volume":"9","author":"S.H. Bernhart","year":"2008","unstructured":"Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R., Stadler, P.F.: Rnaalifold: improved consensus structure prediction for rna alignments. BMC Bioinformatics\u00a09(1), 474 (2008)","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"18_CR18","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/1471-2105-12-108","volume":"12","author":"A.O. Harmanci","year":"2011","unstructured":"Harmanci, A.O., Sharma, G., Mathews, D.H.: Turbofold: iterative probabilistic estimation of secondary structures for multiple rna sequences. BMC Bioinformatics\u00a012(1), 108 (2011)","journal-title":"BMC Bioinformatics"},{"key":"18_CR19","doi-asserted-by":"crossref","unstructured":"Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., Bateman, A.: Rfam: annotating non-coding rnas in complete genomes. Nucleic Acids Research 33(suppl. 1), D121\u2013D124 (2005)","DOI":"10.1093\/nar\/gki081"},{"key":"18_CR20","doi-asserted-by":"crossref","unstructured":"Cai, L., Malmberg, R.L., Wu, Y.: Stochastic modeling of rna pseudoknotted structures: a grammatical approach. Bioinformatics 19(suppl. 1), i66\u2013i73 (2003)","DOI":"10.1093\/bioinformatics\/btg1007"},{"key":"18_CR21","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1093\/nar\/gkm258","volume":"35","author":"J. Reeder","year":"2007","unstructured":"Reeder, J., Steffen, P., Giegerich, R.: pknotsrg: Rna pseudoknot folding including near-optimal structures and sliding windows. Nucl. Acids Res.\u00a035, 320\u2013324 (2007)","journal-title":"Nucl. Acids Res."},{"key":"18_CR22","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1002\/jcc.21596","volume":"32","author":"J.N. Zadeh","year":"2011","unstructured":"Zadeh, J.N., Steenberg, C.D., Bois, J.S., Wolfe, B.R., Pierce, M.B., Khan, A.R., Dirks, R.M., Pierce, N.A.: Nupack: Analysis and design of nucleic acid systems. Journal of Computational Chemistry\u00a032, 170\u2013173 (2011)","journal-title":"Journal of Computational Chemistry"},{"issue":"2","key":"18_CR23","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/S0304-3975(98)00090-5","volume":"210","author":"Y. Uemura","year":"1999","unstructured":"Uemura, Y., Hasegawa, A., Kobayashi, S., Yokomori, T.: Tree adjoining grammars for rna structure prediction. Theoretical Computer Science\u00a0210(2), 277\u2013303 (1999)","journal-title":"Theoretical Computer Science"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics Research and Applications"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-19048-8_18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T20:24:46Z","timestamp":1584476686000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-19048-8_18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319190471","9783319190488"],"references-count":23,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-19048-8_18","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2015]]},"assertion":[{"value":"This content has been made available to all.","name":"free","label":"Free to read"}]}}