{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T17:50:34Z","timestamp":1772041834510,"version":"3.50.1"},"publisher-location":"Berlin, Heidelberg","reference-count":31,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783642380877","type":"print"},{"value":"9783642380884","type":"electronic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013]]},"DOI":"10.1007\/978-3-642-38088-4_6","type":"book-chapter","created":{"date-parts":[[2013,5,8]],"date-time":"2013-05-08T20:38:27Z","timestamp":1368045507000},"page":"78-92","source":"Crossref","is-referenced-by-count":23,"title":["SMT-Based Analysis of Biological Computation"],"prefix":"10.1007","author":[{"given":"Boyan","family":"Yordanov","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christoph M.","family":"Wintersteiger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youssef","family":"Hamadi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hillel","family":"Kugler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"6_CR1","unstructured":"Satisfiability modulo theories competition, \n                    \n                      http:\/\/www.smtcomp.org\/2012\/"},{"key":"6_CR2","unstructured":"Z34bio at rise4fun - software engineering tools from MSR (2012), \n                    \n                      http:\/\/rise4fun.com\/z34biology"},{"issue":"5187","key":"6_CR3","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1126\/science.7973651","volume":"266","author":"L. Adleman","year":"1994","unstructured":"Adleman, L.: Molecular computation of solutions to combinatorial problems. Science\u00a0266(5187), 1021\u20131024 (1994)","journal-title":"Science"},{"issue":"6990","key":"6_CR4","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/nature02551","volume":"429","author":"Y. Benenson","year":"2004","unstructured":"Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An autonomous molecular computer for logical control of gene expression. Nature\u00a0429(6990), 423\u2013429 (2004)","journal-title":"Nature"},{"key":"6_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/3-540-49059-0_14","volume-title":"Tools and Algorithms for the Construction of Analysis of Systems","author":"A. Biere","year":"1999","unstructured":"Biere, A., Cimatti, A., Clarke, E., Zhu, Y.: Symbolic model checking without BDDs. In: Cleaveland, W.R. (ed.) TACAS 1999. LNCS, vol.\u00a01579, pp. 193\u2013207. Springer, Heidelberg (1999)"},{"issue":"1","key":"6_CR6","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.tcs.2004.03.063","volume":"325","author":"N. Chabrier-Rivier","year":"2004","unstructured":"Chabrier-Rivier, N., Chiaverini, M., Danos, V., Fages, F., Sch\u00e4chter, V.: Modeling and querying biomolecular interaction networks. Theoretical Computer Science\u00a0325(1), 25\u201344 (2004)","journal-title":"Theoretical Computer Science"},{"issue":"1","key":"6_CR7","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1089\/10665270252833208","volume":"9","author":"H. Jong de","year":"2002","unstructured":"de Jong, H.: Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology\u00a09(1), 67\u2013103 (2002)","journal-title":"Journal of Computational Biology"},{"key":"6_CR8","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1007\/978-3-540-78800-3_24","volume-title":"Tools and Algorithms for the Construction and Analysis of Systems","author":"L. Moura de","year":"2008","unstructured":"de Moura, L., Bj\u00f8rner, N.: Z3: An efficient SMT solver. In: Ramakrishnan, C.R., Rehof, J. (eds.) TACAS 2008. LNCS, vol.\u00a04963, pp. 337\u2013340. Springer, Heidelberg (2008)"},{"key":"6_CR9","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1007\/978-3-540-78929-1_13","volume-title":"Hybrid Systems: Computation and Control","author":"M. Fr\u00e4nzle","year":"2008","unstructured":"Fr\u00e4nzle, M., Hermanns, H., Teige, T.: Stochastic satisfiability modulo theory: A novel technique for the analysis of probabilistic hybrid systems. In: Egerstedt, M., Mishra, B. (eds.) HSCC 2008. LNCS, vol.\u00a04981, pp. 172\u2013186. Springer, Heidelberg (2008)"},{"key":"6_CR10","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1145\/1993316.1993506","volume":"46","author":"S. Gulwani","year":"2011","unstructured":"Gulwani, S., Jha, S., Tiwari, A., Venkatesan, R.: Synthesis of loop-free programs. SIGPLAN Not.\u00a046, 62\u201373 (2011)","journal-title":"SIGPLAN Not."},{"key":"6_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1007\/978-3-540-68894-5_7","volume-title":"Formal Methods for Computational Systems Biology","author":"M. Heiner","year":"2008","unstructured":"Heiner, M., Gilbert, D., Donaldson, R.: Petri Nets for Systems and Synthetic Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol.\u00a05016, pp. 215\u2013264. Springer, Heidelberg (2008)"},{"key":"6_CR12","doi-asserted-by":"crossref","unstructured":"Horn, F., Jackson, R.: General mass action kinetics. Archive for Rational Mechanics and Analysis 47(2) (1972)","DOI":"10.1007\/BF00251225"},{"key":"6_CR13","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1007\/978-3-642-31365-3_27","volume-title":"Automated Reasoning","author":"D. Jovanovi\u0107","year":"2012","unstructured":"Jovanovi\u0107, D., de Moura, L.: Solving Non-linear Arithmetic. In: Gramlich, B., Miller, D., Sattler, U. (eds.) IJCAR 2012. LNCS, vol.\u00a07364, pp. 339\u2013354. Springer, Heidelberg (2012)"},{"key":"6_CR14","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1007\/978-3-642-23638-9_12","volume-title":"DNA Computing and Molecular Programming","author":"M.R. Lakin","year":"2011","unstructured":"Lakin, M.R., Phillips, A.: Modelling, simulating and verifying turing-powerful strand displacement systems. In: Cardelli, L., Shih, W. (eds.) DNA 17. LNCS, vol.\u00a06937, pp. 130\u2013144. Springer, Heidelberg (2011)"},{"issue":"72","key":"6_CR15","doi-asserted-by":"publisher","first-page":"1470","DOI":"10.1098\/rsif.2011.0800","volume":"9","author":"M.R. Lakin","year":"2012","unstructured":"Lakin, M.R., Parker, D., Cardelli, L., Kwiatkowska, M., Phillips, A.: Design and analysis of DNA strand displacement devices using probabilistic model checking. Journal of the Royal Society, Interface\u00a09(72), 1470\u20131485 (2012)","journal-title":"Journal of the Royal Society, Interface"},{"issue":"22","key":"6_CR16","doi-asserted-by":"publisher","first-page":"3211","DOI":"10.1093\/bioinformatics\/btr543","volume":"27","author":"M.R. Lakin","year":"2011","unstructured":"Lakin, M.R., Youssef, S., Polo, F., Emmott, S., Phillips, A.: Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics\u00a027(22), 3211\u20133213 (2011)","journal-title":"Bioinformatics"},{"key":"6_CR17","unstructured":"Langhoff, S., Rothschild, L., Cumbers, J., Paavola, C., Worden, P.: Workshop Report on What are the Potential Roles for Synthetic Biology in NASA\u2019s Mission? Technical report (2012)"},{"key":"6_CR18","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1007\/978-3-642-20398-5_21","volume-title":"NASA Formal Methods","author":"A. Milicevic","year":"2011","unstructured":"Milicevic, A., Kugler, H.: Model checking using SMT and theory of lists. In: Bobaru, M., Havelund, K., Holzmann, G.J., Joshi, R. (eds.) NFM 2011. LNCS, vol.\u00a06617, pp. 282\u2013297. Springer, Heidelberg (2011)"},{"issue":"suppl. 4","key":"6_CR19","first-page":"S437","volume":"6","author":"M. Pedersen","year":"2009","unstructured":"Pedersen, M., Phillips, A.: Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 6(suppl. 4), S437\u2013S450 (2009)","journal-title":"J. R. Soc. Interface"},{"issue":"suppl. 4","key":"6_CR20","first-page":"S419","volume":"6","author":"A. Phillips","year":"2009","unstructured":"Phillips, A., Cardelli, L.: A programming language for composable DNA circuits. Journal of the Royal Society, Interface 6(suppl. 4), S419\u2013S436 (2009)","journal-title":"Journal of the Royal Society, Interface"},{"key":"6_CR21","doi-asserted-by":"crossref","unstructured":"Pnueli, A.: The temporal logic of programs. In: 18th Annual Symposium on Foundations of Computer Science (FOCS 1977), pp. 46\u201357. IEEE (1977)","DOI":"10.1109\/SFCS.1977.32"},{"key":"6_CR22","doi-asserted-by":"crossref","unstructured":"Purnick, P.E., Weiss, R.: The second wave of synthetic biology: from modules to systems. Nature Reviews. Molecular Cell Biology 10(6) (2009)","DOI":"10.1038\/nrm2698"},{"issue":"6034","key":"6_CR23","doi-asserted-by":"publisher","first-page":"1196","DOI":"10.1126\/science.1200520","volume":"332","author":"L. Qian","year":"2011","unstructured":"Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science\u00a0332(6034), 1196\u20131201 (2011)","journal-title":"Science"},{"issue":"1","key":"6_CR24","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/1752-0509-2-21","volume":"2","author":"A. Samal","year":"2008","unstructured":"Samal, A., Jain, S.: The regulatory network of E. coli metabolism as a boolean dynamical system exhibits both homeostasis and flexibility of response. BMC Systems Biology\u00a02(1), 21 (2008)","journal-title":"BMC Systems Biology"},{"issue":"5805","key":"6_CR25","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1126\/science.1132493","volume":"314","author":"G. Seelig","year":"2006","unstructured":"Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science\u00a0314(5805), 1585\u20131588 (2006)","journal-title":"Science"},{"key":"6_CR26","unstructured":"Soliman, S.: Finding minimal P\/T-invariants as a CSP. In: Proceedings of the fourth Workshop on Constraint Based Methods for Bioinformatics WCB, vol.\u00a08 (2008)"},{"issue":"12","key":"6_CR27","doi-asserted-by":"publisher","first-page":"5393","DOI":"10.1073\/pnas.0909380107","volume":"107","author":"D. Soloveichik","year":"2010","unstructured":"Soloveichik, D., Seelig, G., Winfree, E.: DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences of the United States of America\u00a0107(12), 5393\u20135398 (2010)","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"6_CR28","unstructured":"Wintersteiger, C., Hamadi, Y., de Moura, L.: Efficiently solving quantified bit-vector formulas. In: FMCAD, pp. 239\u2013246 (2010)"},{"issue":"8","key":"6_CR29","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1021\/sb300032y","volume":"1","author":"F. Yaman","year":"2012","unstructured":"Yaman, F., Bhatia, S., Adler, A., Densmore, D., Beal, J.: Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks. ACS Synthetic Biology\u00a01(8), 332\u2013344 (2012)","journal-title":"ACS Synthetic Biology"},{"key":"6_CR30","doi-asserted-by":"crossref","unstructured":"Yordanov, B., Belta, C.: A formal verification approach to the design of synthetic gene networks. In: IEEE Conference on Decision and Control and European Control Conference, pp. 4873\u20134878. IEEE (2011)","DOI":"10.1109\/CDC.2011.6160969"},{"issue":"6","key":"6_CR31","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1016\/j.copbio.2011.04.024","volume":"22","author":"F. Zhang","year":"2011","unstructured":"Zhang, F., Rodriguez, S., Keasling, J.D.: Metabolic engineering of microbial pathways for advanced biofuels production. Current Opinion in Biotechnology\u00a022(6), 775\u2013783 (2011)","journal-title":"Current Opinion in Biotechnology"}],"container-title":["Lecture Notes in Computer Science","NASA Formal Methods"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-38088-4_6","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,12]],"date-time":"2019-05-12T19:34:41Z","timestamp":1557689681000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-38088-4_6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"ISBN":["9783642380877","9783642380884"],"references-count":31,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-38088-4_6","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013]]}}}