{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T02:03:29Z","timestamp":1760061809195},"publisher-location":"Berlin, Heidelberg","reference-count":26,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642316111"},{"type":"electronic","value":"9783642316128"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-642-31612-8_12","type":"book-chapter","created":{"date-parts":[[2012,6,18]],"date-time":"2012-06-18T05:14:42Z","timestamp":1339996482000},"page":"143-156","source":"Crossref","is-referenced-by-count":12,"title":["Lynx: A Programmatic SAT Solver for the RNA-Folding Problem"],"prefix":"10.1007","author":[{"given":"Vijay","family":"Ganesh","sequence":"first","affiliation":[]},{"given":"Charles W.","family":"O\u2019Donnell","sequence":"additional","affiliation":[]},{"given":"Mate","family":"Soos","sequence":"additional","affiliation":[]},{"given":"Srinivas","family":"Devadas","sequence":"additional","affiliation":[]},{"given":"Martin C.","family":"Rinard","sequence":"additional","affiliation":[]},{"given":"Armando","family":"Solar-Lezama","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"12_CR1","unstructured":"Pseudobase RNA sequence, Most widely used database for research on RNA sequences with Psuedoknots. website, \n                      \n                        http:\/\/pseudobaseplusplus.utep.edu\/"},{"key":"12_CR2","unstructured":"SMTLIB website, \n                      \n                        http:\/\/combination.cs.uiowa.edu\/smtlib\/"},{"key":"12_CR3","unstructured":"Biere, A., Heule, M.J.H., van Maaren, H., Walsh, T. (eds.): Handbook of Satisfiability. Frontiers in Artificial Intelligence and Applications, vol.\u00a0185. IOS Press (February 2009)"},{"issue":"4","key":"12_CR4","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1016\/j.jmb.2008.04.033","volume":"379","author":"M. Bon","year":"2008","unstructured":"Bon, M., Vernizzi, G., Orland, H., Zee, A.: Topological classification of RNA structures. J. Mol. Biol.\u00a0379(4), 900\u2013911 (2008)","journal-title":"J. Mol. Biol."},{"key":"12_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1007\/978-3-642-04772-5_40","volume-title":"Computer Aided Systems Theory - EUROCAST 2009","author":"R. Brummayer","year":"2009","unstructured":"Brummayer, R., Biere, A.: Effective Bit-Width and Under-Approximation. In: Moreno-D\u00edaz, R., Pichler, F., Quesada-Arencibia, A. (eds.) EUROCAST 2009. LNCS, vol.\u00a05717, pp. 304\u2013311. Springer, Heidelberg (2009)"},{"issue":"5","key":"12_CR6","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1145\/876638.876643","volume":"50","author":"E. Clarke","year":"2003","unstructured":"Clarke, E., Grumberg, O., Jha, S., Lu, Y., Veith, H.: Counterexample-guided abstraction refinement for symbolic model checking. J. ACM\u00a050(5), 752\u2013794 (2003)","journal-title":"J. ACM"},{"key":"12_CR7","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.tcs.2004.03.042","volume":"320","author":"A. Condon","year":"2004","unstructured":"Condon, A., Davy, B., Rastegari, B., Chao, S., Tarrant, F.: Classifying RNA pseudoknotted structures. Theoretical Computer Science\u00a0320, 35\u201350 (2004)","journal-title":"Theoretical Computer Science"},{"issue":"14","key":"12_CR8","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1093\/bioinformatics\/btl246","volume":"22","author":"C. Do","year":"2006","unstructured":"Do, C., Woods, D., Batzoglou, S.: CONTRAfold: RNA secondary structure prediction without energy-based models. Bioinformatics\u00a022(14), e90\u2013e98 (2006)","journal-title":"Bioinformatics"},{"key":"12_CR9","unstructured":"Een, N., Sorensson, N.: An extensible SAT-solver. In: Proc. Sixth International Conference on Theory and Applications of Satisfiability Testing, pp. 78\u201392 (May 2003)"},{"key":"12_CR10","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1007\/978-3-540-73368-3_52","volume-title":"Computer Aided Verification","author":"V. Ganesh","year":"2007","unstructured":"Ganesh, V., Dill, D.L.: A Decision Procedure for Bit-Vectors and Arrays. In: Damm, W., Hermanns, H. (eds.) CAV 2007. LNCS, vol.\u00a04590, pp. 519\u2013531. Springer, Heidelberg (2007)"},{"key":"12_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/978-3-540-27813-9_14","volume-title":"Computer Aided Verification","author":"H. Ganzinger","year":"2004","unstructured":"Ganzinger, H., Hagen, G., Nieuwenhuis, R., Oliveras, A., Tinelli, C.: DPLL(T): Fast Decision Procedures. In: Alur, R., Peled, D.A. (eds.) CAV 2004. LNCS, vol.\u00a03114, pp. 175\u2013188. Springer, Heidelberg (2004)"},{"key":"12_CR12","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1093\/bioinformatics\/15.6.446","volume":"15","author":"B. Knudsen","year":"1999","unstructured":"Knudsen, B., Hein, J.: RNA secondary structure prediction using stochasatic context-free grammars and evolutionary history. Bioinformatics\u00a015, 446\u2013454 (1999)","journal-title":"Bioinformatics"},{"key":"12_CR13","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1007\/978-3-540-27813-9_24","volume-title":"Computer Aided Verification","author":"D. Kroning","year":"2004","unstructured":"Kroning, D., Ouaknine, J., Seshia, S.A., Strichman, O.: Abstraction-Based Satisfiability Solving of Presburger Arithmetic. In: Alur, R., Peled, D.A. (eds.) CAV 2004. LNCS, vol.\u00a03114, pp. 308\u2013320. Springer, Heidelberg (2004)"},{"key":"12_CR14","doi-asserted-by":"crossref","unstructured":"Lyngs\u00f8, R.B., Pedersen, C.N.S.: Pseudoknots in RNA secondary structures. In: Proc. Computational Molecular Biology, RECOMB 2000, pp. 201\u2013209. ACM (2000)","DOI":"10.1145\/332306.332551"},{"key":"12_CR15","doi-asserted-by":"publisher","first-page":"7287","DOI":"10.1073\/pnas.0401799101","volume":"101","author":"D. Mathews","year":"2004","unstructured":"Mathews, D., Disney, M., Childs, J., Schroeder, S., Zuker, M., Turner, D.: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci.\u00a0101, 7287\u20137292 (2004)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"5","key":"12_CR16","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","volume":"288","author":"D.H. Mathews","year":"1999","unstructured":"Mathews, D.H., Sabina, J., Zuker, M., Turner, D.H.: Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology\u00a0288(5), 911\u2013940 (1999)","journal-title":"Journal of Molecular Biology"},{"key":"12_CR17","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.sbi.2006.05.010","volume":"16","author":"D.H. Mathews","year":"2006","unstructured":"Mathews, D.H., Turner, D.H.: Prediction of RNA secondary structure by free energy. Curr. Opin. Struct. Biol.\u00a016, 270\u2013278 (2006)","journal-title":"Curr. Opin. Struct. Biol."},{"key":"12_CR18","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1007\/978-3-540-74970-7_39","volume-title":"Principles and Practice of Constraint Programming \u2013 CP 2007","author":"O. Ohrimenko","year":"2007","unstructured":"Ohrimenko, O., Stuckey, P.J., Codish, M.: Propagation = Lazy Clause Generation. In: Bessi\u00e8re, C. (ed.) CP 2007. LNCS, vol.\u00a04741, pp. 544\u2013558. Springer, Heidelberg (2007)"},{"key":"12_CR19","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/nature06684","volume":"452","author":"M. Parisien","year":"2008","unstructured":"Parisien, M., Major, F.: The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature\u00a0452, 51\u201355 (2008)","journal-title":"Nature"},{"key":"12_CR20","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/1471-2105-10-S1-S38","volume":"10","author":"U. Poolsap","year":"2009","unstructured":"Poolsap, U., Kato, Y., Akutsu, T.: Prediction of RNA secondary structure with pseudoknots using integer programming. BMC Bioinformatics\u00a010, S38 (2009)","journal-title":"BMC Bioinformatics"},{"key":"12_CR21","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"},{"key":"12_CR22","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.: A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol.\u00a0285, 2053\u20132068 (1999)","journal-title":"J. Mol. Biol."},{"key":"12_CR23","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1007\/978-3-642-02777-2_24","volume-title":"Theory and Applications of Satisfiability Testing - SAT 2009","author":"M. Soos","year":"2009","unstructured":"Soos, M., Nohl, K., Castelluccia, C.: Extending SAT Solvers to Cryptographic Problems. In: Kullmann, O. (ed.) SAT 2009. LNCS, vol.\u00a05584, pp. 244\u2013257. Springer, Heidelberg (2009)"},{"issue":"6","key":"12_CR24","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1371\/journal.pbio.0030213","volume":"3","author":"D.W. Staple","year":"2005","unstructured":"Staple, D.W., Butcher, S.E.: Pseudoknots: RNA structures with diverse functions. PLoS Biol.\u00a03(6), e213 (2005)","journal-title":"PLoS Biol."},{"issue":"11","key":"12_CR25","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1038\/nbt1144","volume":"23","author":"S. Washietl","year":"2005","unstructured":"Washietl, S., Hofacker, I., Lukasser, M., H\u00fcttenhofer, A., Stadler, P.: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat. Biotechnol.\u00a023(11), 1383\u20131390 (2005)","journal-title":"Nat. Biotechnol."},{"issue":"1","key":"12_CR26","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.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research\u00a09(1), 133\u2013148 (1981)","journal-title":"Nucleic Acids Research"}],"container-title":["Lecture Notes in Computer Science","Theory and Applications of Satisfiability Testing \u2013 SAT 2012"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-31612-8_12.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T07:40:09Z","timestamp":1620114009000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-31612-8_12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783642316111","9783642316128"],"references-count":26,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-31612-8_12","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2012]]}}}