{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T06:47:22Z","timestamp":1725864442355},"publisher-location":"Cham","reference-count":34,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319451763"},{"type":"electronic","value":"9783319451770"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"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":[[2016]]},"DOI":"10.1007\/978-3-319-45177-0_3","type":"book-chapter","created":{"date-parts":[[2016,9,3]],"date-time":"2016-09-03T01:42:38Z","timestamp":1472866958000},"page":"30-48","source":"Crossref","is-referenced-by-count":0,"title":["Inference of Delayed Biological Regulatory Networks from Time Series Data"],"prefix":"10.1007","author":[{"given":"Emna","family":"Ben Abdallah","sequence":"first","affiliation":[]},{"given":"Tony","family":"Ribeiro","sequence":"additional","affiliation":[]},{"given":"Morgan","family":"Magnin","sequence":"additional","affiliation":[]},{"given":"Olivier","family":"Roux","sequence":"additional","affiliation":[]},{"given":"Katsumi","family":"Inoue","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,9,4]]},"reference":[{"key":"3_CR1","doi-asserted-by":"crossref","unstructured":"Ben Abdallah, E., Folschette, M., Roux, O., Magnin, M.: Exhaustive analysis of dynamical properties of biological regulatory networks with answer set programming. In: IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 281\u2013285. IEEE (2015)","DOI":"10.1109\/BIBM.2015.7359694"},{"issue":"4","key":"3_CR2","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1159\/000110010","volume":"3","author":"J Ahmad","year":"2006","unstructured":"Ahmad, J., Bernot, G., Comet, J.-P., Lime, D., Roux, O.: Hybrid modelling and dynamical analysis of gene regulatory networks with delays. ComPlexUs 3(4), 231\u2013251 (2006)","journal-title":"ComPlexUs"},{"key":"3_CR3","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1007\/978-3-642-04414-4_14","volume-title":"Algorithmic Learning Theory","author":"T Akutsu","year":"2009","unstructured":"Akutsu, T., Tamura, T., Horimoto, K.: Completing networks using observed data. In: Gavald\u00e0, R., Lugosi, G., Zeugmann, T., Zilles, S. (eds.) ALT 2009. LNCS, vol. 5809, pp. 126\u2013140. Springer, Heidelberg (2009)"},{"key":"3_CR4","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1007\/978-3-642-40564-8_12","volume-title":"Logic Programming and Nonmonotonic Reasoning","author":"S Anwar","year":"2013","unstructured":"Anwar, S., Baral, C., Inoue, K.: Encoding higher level extensions of petri nets in answer set programming. In: Cabalar, P., Son, T.C. (eds.) LPNMR 2013. LNCS, vol. 8148, pp. 116\u2013121. Springer, Heidelberg (2013)"},{"key":"3_CR5","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511543357","volume-title":"Knowledge representation, reasoning and declarative problem solving","author":"C Baral","year":"2003","unstructured":"Baral, C.: Knowledge representation, reasoning and declarative problem solving. Cambridge University Press, New York (2003)"},{"issue":"1","key":"3_CR6","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.shpsc.2011.10.007","volume":"43","author":"W Callebaut","year":"2012","unstructured":"Callebaut, W.: Scientific perspectivism: a philosopher of sciences response to the challenge of big data biology. Stud. Hist. Philos. Sci. Part C. Stud. Hist. Philos. Biol. Biomed. Sci. 43(1), 69\u201380 (2012)","journal-title":"Stud. Hist. Philos. Sci. Part C. Stud. Hist. Philos. Biol. Biomed. Sci."},{"key":"3_CR7","series-title":"Communications in Computer and Information Science","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-3-642-16750-8_1","volume-title":"Computational Systems-Biology and Bioinformatics","author":"J-P Comet","year":"2010","unstructured":"Comet, J.-P., Fromentin, J., Bernot, G., Roux, O.: A formal model for gene regulatory networks with time delays. In: Chan, J.H., Ong, Y.-S., Cho, S.-B. (eds.) CSBio 2010. CCIS, vol. 115, pp. 1\u201313. Springer, Heidelberg (2010)"},{"issue":"2","key":"3_CR8","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1093\/nsr\/nwt032","volume":"1","author":"J Fan","year":"2014","unstructured":"Fan, J., Han, F., Liu, H.: Challenges of big data analysis. Nat. Sci. Rev. 1(2), 293\u2013314 (2014)","journal-title":"Nat. Sci. Rev."},{"key":"3_CR9","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.tcs.2014.12.002","volume":"568","author":"M Folschette","year":"2015","unstructured":"Folschette, M., Paulev\u00e9, L., Inoue, K., Magnin, M., Roux, O.: Identification of biological regulatory networks from process hitting models. Theoret. Comput. Sci. 568, 49\u201371 (2015)","journal-title":"Theoret. Comput. Sci."},{"issue":"4","key":"3_CR10","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1109\/70.86074","volume":"7","author":"P Freedman","year":"1991","unstructured":"Freedman, P.: Time, petri nets, and robotics. IEEE Trans. Robot. Autom. 7(4), 417\u2013433 (1991)","journal-title":"IEEE Trans. Robot. Autom."},{"key":"3_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/978-3-319-11737-9_11","volume-title":"Formal Methods and Software Engineering","author":"E Gallet","year":"2014","unstructured":"Gallet, E., Manceny, M., Le Gall, P., Ballarini, P.: An LTL model checking approach for biological parameter inference. In: Merz, S., Pang, J. (eds.) ICFEM 2014. LNCS, vol. 8829, pp. 155\u2013170. Springer, Heidelberg (2014)"},{"key":"3_CR12","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1007\/978-3-642-40708-6_14","volume-title":"Computational Methods in Systems Biology","author":"YAB Goldstein","year":"2013","unstructured":"Goldstein, Y.A.B., Bockmayr, A.: A lattice-theoretic framework for metabolic pathway analysis. In: Gupta, A., Henzinger, T.A. (eds.) CMSB 2013. LNCS, vol. 8130, pp. 178\u2013191. Springer, Heidelberg (2013)"},{"key":"3_CR13","unstructured":"Harvey, I., Bossomaier, T.: Time out of joint: attractors in asynchronous random boolean networks. In: Proceedings of the Fourth European Conference on Artificial Life, pp. 67\u201375. MIT Press, Cambridge (1997)"},{"issue":"3","key":"3_CR14","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1093\/bib\/4.3.228","volume":"4","author":"SY Kim","year":"2003","unstructured":"Kim, S.Y., Imoto, S., Miyano, S.: Inferring gene networks from time series microarray data using dynamic bayesian networks. Briefings Bioinf. 4(3), 228\u2013235 (2003)","journal-title":"Briefings Bioinf."},{"issue":"1","key":"3_CR15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2009\/484601","volume":"2009","author":"C Koh","year":"2009","unstructured":"Koh, C., Fang-Xiang, W., Selvaraj, G., Kusalik, A.J.: Using a state-space model and location analysis to infer time-delayed regulatory networks. EURASIP J. Bioinf. Syst. Biol. 2009(1), 1 (2009)","journal-title":"EURASIP J. Bioinf. Syst. Biol."},{"key":"3_CR16","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1145\/2480359.2429125","volume":"48","author":"AS Koksal","year":"2013","unstructured":"Koksal, A.S., Yewen, P., Srivastava, S., Bodik, R., Fisher, J., Piterman, N.: Synthesis of biological models from mutation experiments. ACM SIGPLAN Not. 48, 469\u2013482 (2013). ACM","journal-title":"ACM SIGPLAN Not."},{"key":"3_CR17","unstructured":"Liu, T.-F., Sung, W.-K., Mittal, A.: Learning multi-time delay gene network using bayesian network framework. In: 16th IEEE International Conference on Tools with Artificial Intelligence, ICTAI 2004, pp. 640\u2013645. IEEE (2004)"},{"issue":"7453","key":"3_CR18","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/498255a","volume":"498","author":"V Marx","year":"2013","unstructured":"Marx, V.: Biology: the big challenges of big data. Nature 498(7453), 255\u2013260 (2013)","journal-title":"Nature"},{"key":"3_CR19","unstructured":"Matsuno, H., doi, A., Nagasaki, M., Miyano, S.: Hybrid petri net representation of gene regulatory network. In: Pacific Symposium on Biocomputing, vol. 5, p. 87. World Scientific Press, Singapore (2000)"},{"key":"3_CR20","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1007\/978-3-319-23401-4_15","volume-title":"Computational Methods in Systems Biology","author":"M Ostrowski","year":"2015","unstructured":"Ostrowski, M., Paulev\u00e9, L., Schaub, T., Siegel, A., Guziolowski, C.: Boolean network identification from multiplex time series data. In: Roux, O., Bourdon, J. (eds.) CMSB 2015. LNCS, vol. 9308, pp. 170\u2013181. Springer, Heidelberg (2015)"},{"key":"3_CR21","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1007\/978-3-319-08867-9_23","volume-title":"Computer Aided Verification","author":"N Paoletti","year":"2014","unstructured":"Paoletti, N., Yordanov, B., Hamadi, Y., Wintersteiger, C.M., Kugler, H.: Analyzing and synthesizing genomic logic functions. In: Biere, A., Bloem, R. (eds.) CAV 2014. LNCS, vol. 8559, pp. 343\u2013357. Springer, Heidelberg (2014)"},{"key":"3_CR22","doi-asserted-by":"crossref","unstructured":"Paulev\u00e9, L.: Goal-oriented reduction of automata networks. In: CMSB 2016\u201314th Conference on Computational Methods for Systems Biology (2016)","DOI":"10.1007\/978-3-319-45177-0_16"},{"key":"3_CR23","doi-asserted-by":"crossref","unstructured":"Paulev\u00e9, L., Chancellor, C., Folschette, M., Magnin, M., Roux, O.: Logical Modeling of Biological Systems, chapter Analyzing Large Network Dynamics with Process Hitting, pp. 125\u2013166. Wiley, Hoboken (2014)","DOI":"10.1002\/9781119005223.ch4"},{"key":"3_CR24","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/978-3-642-19748-2_8","volume-title":"Transactions on Computational Systems Biology XIII","author":"L Paulev\u00e9","year":"2011","unstructured":"Paulev\u00e9, L., Magnin, M., Roux, O.: Refining dynamics of gene regulatory networks in a stochastic $$\\pi $$ -calculus framework. In: Priami, C., Back, R.-J., Petre, I., de Vink, E. (eds.) Transactions on Computational Systems Biology XIII. LNCS, vol. 6575, pp. 171\u2013191. Springer, Heidelberg (2011)"},{"issue":"189","key":"3_CR25","doi-asserted-by":"crossref","first-page":"mr7","DOI":"10.1126\/scisignal.2002212","volume":"4","author":"RJ Prill","year":"2011","unstructured":"Prill, R.J., Saez-Rodriguez, J., Alexopoulos, L.G., Sorger, P.K., Stolovitzky, G.: Crowdsourcing network inference: the dream predictive signaling network challenge. Sci. Signal. 4(189), mr7 (2011)","journal-title":"Sci. Signal."},{"issue":"1","key":"3_CR26","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/msb.2009.87","volume":"5","author":"J Saez-Rodriguez","year":"2009","unstructured":"Saez-Rodriguez, J., Alexopoulos, L.G., Epperlein, J., Samaga, R., Lauffenburger, D.A., Klamt, S., Sorger, P.K.: Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol. Syst. Biol. 5(1), 331 (2009)","journal-title":"Mol. Syst. Biol."},{"issue":"16","key":"3_CR27","doi-asserted-by":"crossref","first-page":"2263","DOI":"10.1093\/bioinformatics\/btr373","volume":"27","author":"T Schaffter","year":"2011","unstructured":"Schaffter, T., Marbach, D., Floreano, D.: Genenetweaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics 27(16), 2263\u20132270 (2011)","journal-title":"Bioinformatics"},{"issue":"3","key":"3_CR28","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.tcs.2007.11.010","volume":"391","author":"H Siebert","year":"2008","unstructured":"Siebert, H., Bockmayr, A.: Temporal constraints in the logical analysis of regulatory networks. Theoret. Comput. Sci. 391(3), 258\u2013275 (2008)","journal-title":"Theoret. Comput. Sci."},{"issue":"6","key":"3_CR29","doi-asserted-by":"crossref","first-page":"416","DOI":"10.2174\/138920209789177610","volume":"10","author":"C Sima","year":"2009","unstructured":"Sima, C., Hua, J., Jung, S.: Inference of gene regulatory networks using time-series data: a survey. Curr. Genomics 10(6), 416\u2013429 (2009)","journal-title":"Curr. Genomics"},{"key":"3_CR30","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/978-1-4939-2778-4_3","volume":"2015","author":"M Talikka","year":"2015","unstructured":"Talikka, M., Boue, S., Schlage, W.K.: Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. Comput. Syst. Toxicol. 2015, 65\u201393 (2015)","journal-title":"Comput. Syst. Toxicol."},{"issue":"1","key":"3_CR31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(05)80350-9","volume":"153","author":"R Thomas","year":"1991","unstructured":"Thomas, R.: Regulatory networks seen as asynchronous automata: a logical description. J. Theoret. Biol. 153(1), 1\u201323 (1991)","journal-title":"J. Theoret. Biol."},{"issue":"D1","key":"3_CR32","doi-asserted-by":"crossref","first-page":"D797","DOI":"10.1093\/nar\/gkr1127","volume":"40","author":"Y Namhee","year":"2012","unstructured":"Namhee, Y., Seo, J., Rho, K., Jang, Y., Park, J., Kim, W.K., Lee, S.: Hipathdb: a human-integrated pathway database with facile visualization. Nucleic Acids Res. 40(D1), D797\u2013D802 (2012)","journal-title":"Nucleic Acids Res."},{"key":"3_CR33","unstructured":"Zhang, Z.-Y., Horimoto, K., Liu, Z.: Time series segmentation for gene regulatory process with time-window-extension (2008)"},{"issue":"17","key":"3_CR34","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1093\/bioinformatics\/btl364","volume":"22","author":"W Zhao","year":"2006","unstructured":"Zhao, W., Serpedin, E., Dougherty, E.R.: Inferring gene regulatory networks from time series data using the minimum description length principle. Bioinformatics 22(17), 2129\u20132135 (2006)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-45177-0_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,13]],"date-time":"2019-09-13T01:38:41Z","timestamp":1568338721000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-45177-0_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319451763","9783319451770"],"references-count":34,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-45177-0_3","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2016]]}}}