{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T00:32:41Z","timestamp":1725582761721},"publisher-location":"Berlin, Heidelberg","reference-count":41,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642208317"},{"type":"electronic","value":"9783642208324"}],"license":[{"start":{"date-parts":[[2011,1,1]],"date-time":"2011-01-01T00:00:00Z","timestamp":1293840000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2011,1,1]],"date-time":"2011-01-01T00:00:00Z","timestamp":1293840000000},"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":[[2011]]},"DOI":"10.1007\/978-3-642-20832-4_26","type":"book-chapter","created":{"date-parts":[[2011,4,28]],"date-time":"2011-04-28T02:59:49Z","timestamp":1303959589000},"page":"415-431","source":"Crossref","is-referenced-by-count":4,"title":["Applications of Answer Set Programming in Phylogenetic Systematics"],"prefix":"10.1007","author":[{"given":"Esra","family":"Erdem","sequence":"first","affiliation":[]}],"member":"297","reference":[{"key":"26_CR1","unstructured":"Bodenreider, O., \u00c7oban, Z.H., Do\u011fanay, M.C., Erdem, E., Ko\u015fucu, H.: A preliminary report on answering complex queries related to drug discovery using answer set programming. In: Proc. of ALPSWS (2008)"},{"key":"26_CR2","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1007\/3-540-55719-9_80","volume-title":"Proc. of 19th International Colloquidum on Automata Languages and Programming","author":"H.L. Bodlaender","year":"1992","unstructured":"Bodlaender, H.L., Fellows, M.R., Warnow, T.J.: Two strikes against perfect phylogeny. In: Proc. of 19th International Colloquidum on Automata Languages and Programming, pp. 273\u2013283. Springer, Heidelberg (1992)"},{"issue":"4","key":"26_CR3","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1007\/s10817-007-9082-1","volume":"39","author":"D.R. Brooks","year":"2007","unstructured":"Brooks, D.R., Erdem, E., Erdo\u011fan, S.T., Minett, J.W., Ringe, D.: Inferring phylogenetic trees using answer set programming. Journal of Automated Reasoning\u00a039(4), 471\u2013511 (2007)","journal-title":"Journal of Automated Reasoning"},{"key":"26_CR4","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1007\/978-3-540-30557-6_5","volume-title":"Practical Aspects of Declarative Languages","author":"D.R. Brooks","year":"2005","unstructured":"Brooks, D.R., Erdem, E., Minett, J.W., Ringe, D.: Character-based cladistics and answer set programming. In: Hermenegildo, M.V., Cabeza, D. (eds.) PADL 2004. LNCS, vol.\u00a03350, pp. 37\u201351. Springer, Heidelberg (2005)"},{"key":"26_CR5","unstructured":"Cakmak, D.: Reconstructing weighted phylogenetic trees and weighted phylogenetic networks using answer set programming, M.S. Thesis, Sabanc\u0131 University (2010)"},{"key":"26_CR6","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1007\/978-3-642-04238-6_36","volume-title":"Logic Programming and Nonmonotonic Reasoning","author":"D. Cakmak","year":"2009","unstructured":"Cakmak, D., Erdem, E., Erdogan, H.: Computing weighted solutions in answer set programming. In: Erdem, E., Lin, F., Schaub, T. (eds.) LPNMR 2009. LNCS, vol.\u00a05753, pp. 416\u2013422. Springer, Heidelberg (2009)"},{"key":"26_CR7","unstructured":"Cakmak, D., Erdogan, H., Erdem, E.: Computing weighted solutions in ASP: Representation-based method vs. search-based method. In: Proc. of RCRA Workshop on Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion (2010)"},{"key":"26_CR8","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1145\/368273.368557","volume":"5","author":"M. Davis","year":"1962","unstructured":"Davis, M., Logemann, G., Loveland, D.: A machine program for theorem-proving. Communications of the ACM\u00a05, 394\u2013397 (1962)","journal-title":"Communications of the ACM"},{"issue":"2","key":"26_CR9","doi-asserted-by":"publisher","first-page":"224","DOI":"10.2307\/2413432","volume":"35","author":"W.H.E. Day","year":"1986","unstructured":"Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Systematic Zoology\u00a035(2), 224\u2013229 (1986)","journal-title":"Systematic Zoology"},{"issue":"1-2","key":"26_CR10","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1007\/s10601-007-9031-y","volume":"13","author":"S. Dworschak","year":"2008","unstructured":"Dworschak, S., Grell, S., Nikiforova, V.J., Schaub, T., Selbig, J.: Modeling biological networks by action languages via answer set programming. Constraints\u00a013(1-2), 21\u201365 (2008)","journal-title":"Constraints"},{"key":"26_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1007\/978-3-642-02846-5_29","volume-title":"Logic Programming","author":"T. Eiter","year":"2009","unstructured":"Eiter, T., Erdem, E., Erdogan, H., Fink, M.: Finding similar or diverse solutions in answer set programming. In: Hill, P.M., Warren, D.S. (eds.) ICLP 2009. LNCS, vol.\u00a05649, pp. 342\u2013356. Springer, Heidelberg (2009)"},{"key":"26_CR12","unstructured":"Eiter, T., Ianni, G., Schindlauer, R., Tompits, H.: A uniform integration of higher-order reasoning and external evaluations in answer-set programming. In: Proc. of IJCAI, pp. 90\u201396 (2005)"},{"key":"26_CR13","series-title":"Lecture Notes in Computer Science","first-page":"364","volume-title":"Logic Programming and Nonmonotonic Reasoning","author":"T. Eiter","year":"1997","unstructured":"Eiter, T., Leone, N., Mateis, C., Pfeifer, G., Scarcello, F.: A deductive system for non-monotonic reasoning. In: Fuhrbach, U., Dix, J., Nerode, A. (eds.) LPNMR 1997. LNCS, vol.\u00a01265, pp. 364\u2013375. Springer, Heidelberg (1997)"},{"key":"26_CR14","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1007\/978-3-642-04238-6_60","volume-title":"Logic Programming and Nonmonotonic Reasoning","author":"E. Erdem","year":"2009","unstructured":"Erdem, E., Erdem, O., Ture, F.: HAPLO-ASP: Haplotype inference using answer set programming. In: Erdem, E., Lin, F., Schaub, T. (eds.) LPNMR 2009. LNCS, vol.\u00a05753, pp. 573\u2013578. Springer, Heidelberg (2009)"},{"key":"26_CR15","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1007\/3-540-36388-2_12","volume-title":"Practical Aspects of Declarative Languages","author":"E. Erdem","year":"2003","unstructured":"Erdem, E., Lifschitz, V., Nakhleh, L., Ringe, D.: Reconstructing the evolutionary history of indo-european languages using answer set programming. In: Dahl, V. (ed.) PADL 2003. LNCS, vol.\u00a02562, pp. 160\u2013176. Springer, Heidelberg (2003)"},{"issue":"5","key":"26_CR16","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1017\/S1471068406002729","volume":"6","author":"E. Erdem","year":"2006","unstructured":"Erdem, E., Lifschitz, V., Ringe, D.: Temporal phylogenetic networks and logic programming. Theory and Practice of Logic Programming\u00a06(5), 539\u2013558 (2006)","journal-title":"Theory and Practice of Logic Programming"},{"key":"26_CR17","unstructured":"Erdem, E., Ture, F.: Efficient haplotype inference with answer set programming. In: Proc. of AAAI, pp. 436\u2013441 (2008)"},{"key":"26_CR18","unstructured":"Erdem, E., Wang, F.: Reconstructing the evolutionary history of Chinese dialects (2006) (accepted for presentation at the 39th International Conference on Sino-Tibetan Languages and Linguistics, ICSTLL 2006)"},{"key":"26_CR19","doi-asserted-by":"crossref","unstructured":"Erdem, E., Yeniterzi, R.: Transforming controlled natural language biomedical queries into answer set programs. In: Proc. of BioNLP, pp. 117\u2013124 (2009)","DOI":"10.3115\/1572364.1572381"},{"key":"26_CR20","doi-asserted-by":"crossref","unstructured":"Erdogan, H., Bodenreider, O., Erdem, E.: Finding semantic inconsistencies in UMLS using answer set programming. In: Proc. of AAAI (2010)","DOI":"10.1609\/aaai.v24i1.7781"},{"key":"26_CR21","unstructured":"Erdogan, H., Erdem, E., Bodenreider, O.: Exploiting umls semantics for checking semantic consistency among umls concepts. In: Proc. of MedInfo (2010)"},{"key":"26_CR22","unstructured":"Gebser, M., Kaufmann, B., Neumann, A., Schaub, T.: Conflict-driven answer set solving. In: Proc. of IJCAI, pp. 386\u2013392 (2007)"},{"key":"26_CR23","unstructured":"Gebser, M., Guziolowski, C., Ivanchev, M., Schaub, T., Siegel, A., Thiele, S., Veber, P.: Repair and prediction (under inconsistency) in large biological networks with answer set programming. In: Proc. of KR (2010)"},{"key":"26_CR24","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1007\/978-3-540-89982-2_19","volume-title":"Logic Programming","author":"M. Gebser","year":"2008","unstructured":"Gebser, M., Schaub, T., Thiele, S., Usadel, B., Veber, P.: Detecting inconsistencies in large biological networks with answer set programming. In: Garcia de la Banda, M., Pontelli, E. (eds.) ICLP 2008. LNCS, vol.\u00a05366, pp. 130\u2013144. Springer, Heidelberg (2008)"},{"key":"26_CR25","unstructured":"Gelfond, M., Lifschitz, V.: The stable model semantics for logic programming. In: Kowalski, R., Bowen, K. (eds.) Logic Programming: Proceedings of the Fifth International Conference and Symposium, pp. 1070\u20131080 (1988)"},{"key":"26_CR26","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/11799573_22","volume-title":"Logic Programming","author":"S. Grell","year":"2006","unstructured":"Grell, S., Schaub, T., Selbig, J.: Modelling biological networks by action languages via answer set programming. In: Etalle, S., Truszczy\u0144ski, M. (eds.) ICLP 2006. LNCS, vol.\u00a04079, pp. 285\u2013299. Springer, Heidelberg (2006)"},{"volume-title":"Phylogenetic Systematics","year":"1966","author":"W. Hennig","key":"26_CR27","unstructured":"Hennig, W.: Phylogenetic Systematics. University of Illinois Press, Urbana (1966); translated from: Davis, D. D., Zangerl, R.: Grundzuege einer Theorie der phylogenetischen Systematik (1950)"},{"issue":"3","key":"26_CR28","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1145\/1149114.1149117","volume":"7","author":"N. Leone","year":"2006","unstructured":"Leone, N., Pfeifer, G., Faber, W., Eiter, T., Gottlob, G., Perri, S., Scarcello, F.: The dlv system for knowledge representation and reasoning. ACM Trans. Comput. Log.\u00a07(3), 499\u2013562 (2006)","journal-title":"ACM Trans. Comput. Log."},{"key":"26_CR29","series-title":"Lecture Notes in Artificial Intelligence","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1007\/978-3-540-24609-1_32","volume-title":"Logic Programming and Nonmonotonic Reasoning","author":"Y. Lierler","year":"2004","unstructured":"Lierler, Y., Maratea, M.: Cmodels-2: SAT-based answer set solver enhanced to non-tight programs. In: Lifschitz, V., Niemel\u00e4, I. (eds.) LPNMR 2004. LNCS (LNAI), vol.\u00a02923, pp. 346\u2013350. Springer, Heidelberg (2004)"},{"key":"26_CR30","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0004-3702(02)00186-8","volume":"138","author":"V. Lifschitz","year":"2002","unstructured":"Lifschitz, V.: Answer set programming and plan generation. Artificial Intelligence\u00a0138, 39\u201354 (2002)","journal-title":"Artificial Intelligence"},{"key":"26_CR31","unstructured":"Lifschitz, V.: What is answer set programming? In: Proc. of AAAI (2008)"},{"key":"26_CR32","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1007\/978-3-642-60085-2_17","volume-title":"The Logic Programming Paradigm: a 25-Year Perspective","author":"V. Marek","year":"1999","unstructured":"Marek, V., Truszczy\u0144ski, M.: Stable models and an alternative logic programming paradigm. In: The Logic Programming Paradigm: a 25-Year Perspective, pp. 375\u2013398. Springer, Heidelberg (1999)"},{"key":"26_CR33","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1109\/12.769433","volume":"5","author":"J. Marques-Silva","year":"1999","unstructured":"Marques-Silva, J., Sakallah, K.: Grasp: A search algorithm for propositional satisfiability. IEEE Trans. Computers\u00a05, 506\u2013521 (1999)","journal-title":"IEEE Trans. Computers"},{"key":"26_CR34","unstructured":"Nakhleh, L.: Phylogenetic Networks. Ph.D. thesis, The university of Texas at Austin (2004)"},{"key":"26_CR35","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1007\/3-540-63255-7_32","volume-title":"Logic Programming and Nonmonotonic Reasoning","author":"I. Niemel\u00e4","year":"1997","unstructured":"Niemel\u00e4, I., Simons, P.: Smodels - an implementation of the stable model and well-founded semantics for normal lp. In: Fuhrbach, U., Dix, J., Nerode, A. (eds.) LPNMR 1997. LNCS, vol.\u00a01265, pp. 421\u2013430. Springer, Heidelberg (1997)"},{"key":"26_CR36","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1007\/978-3-642-02846-5_27","volume-title":"Logic Programming","author":"T. Schaub","year":"2009","unstructured":"Schaub, T., Thiele, S.: Metabolic network expansion with answer set programming. In: Hill, P.M., Warren, D.S. (eds.) ICLP 2009. LNCS, vol.\u00a05649, pp. 312\u2013326. Springer, Heidelberg (2009)"},{"key":"26_CR37","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/S0004-3702(02)00187-X","volume":"138","author":"P. Simons","year":"2002","unstructured":"Simons, P., Niemel\u00e4, I., Soininen, T.: Extending and implementing the stable model semantics. Artificial Intelligence\u00a0138, 181\u2013234 (2002)","journal-title":"Artificial Intelligence"},{"key":"26_CR38","doi-asserted-by":"crossref","unstructured":"Tari, L., Anwar, S., Liang, S., Hakenberg, J., Baral, C.: Synthesis of pharmacokinetic pathways through knowledge acquisition and automated reasoning. In: Proc. of PSB, pp. 465\u2013476 (2010)","DOI":"10.1142\/9789814295291_0048"},{"key":"26_CR39","unstructured":"Tran, N., Baral, C.: Reasoning about triggered actions in ansprolog and its application to molecular interactions in cells. In: Proc. of KR, pp. 554\u2013564 (2004)"},{"issue":"3","key":"26_CR40","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.jal.2008.10.001","volume":"7","author":"N. Tran","year":"2009","unstructured":"Tran, N., Baral, C.: Hypothesizing about signaling networks. J. Applied Logic\u00a07(3), 253\u2013274 (2009)","journal-title":"J. Applied Logic"},{"key":"26_CR41","unstructured":"Ture, F., Erdem, E.: Efficient haplotype inference with answer set programming. In: Proc. of AAAI, pp. 1834\u20131835 (2008)"}],"container-title":["Lecture Notes in Computer Science","Logic Programming, Knowledge Representation, and Nonmonotonic Reasoning"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-20832-4_26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,6]],"date-time":"2023-06-06T14:10:53Z","timestamp":1686060653000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-20832-4_26"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011]]},"ISBN":["9783642208317","9783642208324"],"references-count":41,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-20832-4_26","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2011]]}}}