{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T10:37:01Z","timestamp":1742380621055},"publisher-location":"Berlin, Heidelberg","reference-count":29,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540884347"},{"type":"electronic","value":"9783540884361"}],"license":[{"start":{"date-parts":[[2008,1,1]],"date-time":"2008-01-01T00:00:00Z","timestamp":1199145600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008]]},"DOI":"10.1007\/978-3-540-88436-1_12","type":"book-chapter","created":{"date-parts":[[2008,10,6]],"date-time":"2008-10-06T08:56:07Z","timestamp":1223283367000},"page":"132-143","source":"Crossref","is-referenced-by-count":4,"title":["Pseudoknot Identification through Learning TAGRNA"],"prefix":"10.1007","author":[{"given":"Sahar Al","family":"Seesi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanguthevar","family":"Rajasekaran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reda","family":"Ammar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"doi-asserted-by":"crossref","unstructured":"Al Seesi, S.: Pseudoknot Identification through Learning TAG RNA , BECAT-CSE Technical Report, University of Connecticut (April 2008)","key":"12_CR1","DOI":"10.1007\/978-3-540-88436-1_12"},{"key":"12_CR2","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":"3","key":"12_CR3","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1261\/rna.2183803","volume":"9","author":"V. Ambros","year":"2003","unstructured":"Ambros, V., Bartel, B., Bartel, D.P., Burge, C.B., Carrington, J.C., Chen, X., Dreyfuss, G., Eddy, S.R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G., Tuschl, T.: A Uniform System for microRNA Annotation. RNA\u00a09(3), 277\u2013279 (2003)","journal-title":"RNA"},{"issue":"1","key":"12_CR4","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1093\/nar\/28.1.201","volume":"28","author":"F.H.D. Batenburg van","year":"2000","unstructured":"van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A., Ng, J., Oliehoek, J.: Pseudobase: a Database with RNA Pseudoknots. Nucl. Acids Res.\u00a028(1), 201\u2013204 (2000)","journal-title":"Nucl. Acids Res."},{"key":"12_CR5","series-title":"Lecture Notes in Artificial Intelligence","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1007\/BFb0054081","volume-title":"Grammatical Inference","author":"A. Brazma","year":"1998","unstructured":"Brazma, A., Jonassen, I., Vilo, J., Ukkonen, E.: Pattern Discovery in Biosequences. In: Honavar, V., Slutzki, G. (eds.) ICGI 1998. LNCS (LNAI), vol.\u00a01433, pp. 255\u2013270. Springer, Heidelberg (1998)"},{"issue":"13","key":"12_CR6","doi-asserted-by":"publisher","first-page":"4369","DOI":"10.1093\/nar\/gkm447","volume":"35","author":"E. Buratti","year":"2007","unstructured":"Buratti, E., Dhir, A., Lewandowska, M.A., Baralle, F.E.: RNA Structure is a Key Regulatory Element in Pathological ATM and CFTR Pseudoexon Inclusion Events. Nucl. Acids Res.\u00a035(13), 4369\u20134383 (2007)","journal-title":"Nucl. Acids Res."},{"issue":"supp. 1","key":"12_CR7","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1093\/bioinformatics\/btg1007","volume":"19","author":"L. Cai","year":"2003","unstructured":"Cai, L., Malmberg, R., Wu, Y.: Stochastic Modeling of RNA Pseudoknotted Structures: a Grammatical Approach. Bioinformatics\u00a019(supp. 1), 66\u201373 (2003)","journal-title":"Bioinformatics"},{"issue":"13","key":"12_CR8","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1002\/jcc.10296","volume":"24","author":"R.M. Dirks","year":"2003","unstructured":"Dirks, R.M., Pierce, N.A.: 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":"12_CR9","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/319618a0","volume":"319","author":"W. Gilbert","year":"1986","unstructured":"Gilbert, W.: The RNA World. Nature\u00a0319, 618 (1986)","journal-title":"Nature"},{"key":"12_CR10","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1093\/nar\/gki081","volume":"33","author":"S. Griffiths-Jones","year":"2005","unstructured":"Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., Bateman, A.: Rfam: Annotating Non-coding RNAs in Complete Genomes. Nucl. Acids Res.\u00a033, D121\u2013D124 (2005)","journal-title":"Nucl. Acids Res."},{"key":"12_CR11","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.sbi.2005.04.005","volume":"15","author":"S.R. Holbrook","year":"2005","unstructured":"Holbrook, S.R.: RNA Structure: the Long and the Short of it. Current Opinion in Structural Biology\u00a015, 302\u2013308 (2005)","journal-title":"Current Opinion in Structural Biology"},{"key":"12_CR12","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/S0022-0000(75)80019-5","volume":"10","author":"A.K. Joshi","year":"1975","unstructured":"Joshi, A.K., Levy, L., Takahashi, M.: Tree Adjunct Grammars. Journal of Computer and System Sciences\u00a010, 136\u2013163 (1975)","journal-title":"Journal of Computer and System Sciences"},{"unstructured":"Laxminarayana, J.A., Nagaraja, G., Balaji, P.V.: Identification of Pseudoknots in RNA Secondary Structures: A Grammatical Inference Approach. In: Mukherjee, D.P., Pal, S. (eds.) Proceedings of 5th International Conference on Advances in Pattern Recognition (2003)","key":"12_CR13"},{"unstructured":"Laxminarayana, J.A., Nagaraja, G., Balaji, P.V.: Inference of a Subclass of Even Linear Languages and its Application to Pseudoknot Identification. In: Department of Computer Science and Engineering, Indian Institute of Technology, Bombay, India (manuscript, 2003)","key":"12_CR14"},{"key":"12_CR15","doi-asserted-by":"publisher","first-page":"5995","DOI":"10.1074\/jbc.M108972200","volume":"277","author":"J.C. Paillart","year":"2002","unstructured":"Paillart, J.C., Skripkin, E., Ehresmann, B., Ehresmann, C., Marquet, R.: In vitro Evidence for a Long Range Pseudoknot in the 5\u2019-Untranslated and Matrix Coding regions of HIV-1 Genomic RNA. J. Biol. Chem.\u00a0277, 5995\u20136004 (2002)","journal-title":"J. Biol. Chem."},{"issue":"4","key":"12_CR16","first-page":"33","volume":"2","author":"J.S. Pedersen","year":"2006","unstructured":"Pedersen, J.S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E.S., Kent, J., Miller, W., Haussler, D.: Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. Public Library of Science. Computational Biology\u00a02(4), 33 (2006)","journal-title":"Public Library of Science. Computational Biology"},{"issue":"4","key":"12_CR17","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1137\/S009753979326009X","volume":"25","author":"S. Rajasekaran","year":"1996","unstructured":"Rajasekaran, S.: Tree-Adjoining Language Parsing in o(n6) Time. SIAM Journal on Computing\u00a025(4), 862\u2013873 (1996)","journal-title":"SIAM Journal on Computing"},{"key":"12_CR18","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1186\/1471-2105-5-104","volume":"5","author":"J. Reeder","year":"2004","unstructured":"Reeder, J., Giegerich, R.: Design, Implementation and Evaluation of a Practical Pseudoknot Folding Algorithm Based on Thermodynamics. BMC Bioinformatics\u00a05, 104 (2004)","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"12_CR19","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1093\/bioinformatics\/16.4.334","volume":"16","author":"E. Rivas","year":"2000","unstructured":"Rivas, E., Eddy, S.: The Language of RNA: a Formal Grammar that Includes Pseudoknots. Bioinformatics\u00a016(4), 334\u2013340 (2000)","journal-title":"Bioinformatics"},{"issue":"1","key":"12_CR20","first-page":"5","volume":"3","author":"M.P. Robertson","year":"2004","unstructured":"Robertson, M.P., Igel, H., Baertsch, R., Haussler, D., Ares Jr., M., Scott, W.G.: The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome. Public Library of Science: Biology\u00a03(1), 5 (2004)","journal-title":"Public Library of Science: Biology"},{"key":"12_CR21","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1093\/nar\/22.23.5112","volume":"22","author":"Y. Sakakibara","year":"1994","unstructured":"Sakakibara, Y., Brown, M., Hughey, R., Mian, I.S., Sjolander, K., Underwood, R.C., Haussler, D.: Stochastic Context-Free Grammars for tRNA Modeling. Nucl. Acids Res.\u00a022, 5112\u20135120 (1994)","journal-title":"Nucl. Acids Res."},{"key":"12_CR22","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1109\/TPAMI.2005.140","volume":"27","author":"Y. Sakakibara","year":"2005","unstructured":"Sakakibara, Y.: Grammatical Inference in Bioinformatics. IEEE Transactions on Pattern Analysis and Machine Intelligence\u00a027, 1051\u20131062 (2005)","journal-title":"IEEE Transactions on Pattern Analysis and Machine Intelligence"},{"key":"12_CR23","first-page":"579","volume":"80","author":"D. Searls","year":"1992","unstructured":"Searls, D.: The Linguistics of DNA. Am. Scient.\u00a080, 579\u2013591 (1992)","journal-title":"Am. Scient."},{"unstructured":"Takakura, T., Asakawa, H., Seki, S., Kobayashi, S.: Efficient Tree Grammar Modeling of RNA Secondary Structures from Alignment Data. In: Proceedings of posters of RECOMB 2005, pp. 339\u2013340 (2005)","key":"12_CR24"},{"key":"12_CR25","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1093\/nar\/30.3.766","volume":"30","author":"Y. Tanaka","year":"2002","unstructured":"Tanaka, Y., Hori, T., Tagaya, M., Sakamoto, T., Kurihara, Y., Katahira, M., Uesugi, S.: Imino Proton NMR Analysis of HDV Ribozymes: Nested Double Pseudoknot Structure and Mg2+ Ion-Binding Site Close to the Catalytic Core in Solution. Nucl. Acids Res.\u00a030, 766\u2013774 (2002)","journal-title":"Nucl. Acids Res."},{"issue":"2","key":"12_CR26","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"},{"doi-asserted-by":"crossref","unstructured":"Vijay-Shanker, K., Joshi, A.K.: Some Computational Properties of Tree Adjoining Grammars. In: 23 rd Meeting of the Association for Computational Linguistics, pp. 82\u201393 (1985)","key":"12_CR27","DOI":"10.3115\/981210.981221"},{"issue":"1","key":"12_CR28","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1093\/nar\/26.1.163","volume":"26","author":"K.P. Williams","year":"1998","unstructured":"Williams, K.P., Bartel, D.P.: The tmRNA Website. Nucl. Acids Res.\u00a026(1), 163\u2013165 (1998)","journal-title":"Nucl. Acids Res."},{"issue":"1","key":"12_CR29","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1093\/nar\/30.1.179","volume":"30","author":"K.P. Williams","year":"2002","unstructured":"Williams, K.P.: The tmRNA Website: Invasion by an Intron. Nucl. Acids Res.\u00a030(1), 179\u2013182 (2002)","journal-title":"Nucl. Acids Res."}],"container-title":["Lecture Notes in Computer Science","Pattern Recognition in Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-88436-1_12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T08:33:02Z","timestamp":1557822782000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-88436-1_12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008]]},"ISBN":["9783540884347","9783540884361"],"references-count":29,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-88436-1_12","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2008]]}}}