{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T18:48:49Z","timestamp":1761677329891,"version":"3.40.3"},"publisher-location":"Cham","reference-count":32,"publisher":"Springer Nature Switzerland","isbn-type":[{"type":"print","value":"9783031716706"},{"type":"electronic","value":"9783031716713"}],"license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024]]},"DOI":"10.1007\/978-3-031-71671-3_5","type":"book-chapter","created":{"date-parts":[[2024,9,19]],"date-time":"2024-09-19T22:45:48Z","timestamp":1726785948000},"page":"62-70","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Bio-Stark: A Tool for\u00a0the\u00a0Time-Point Robustness Analysis of\u00a0Biological Systems"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8112-6523","authenticated-orcid":false,"given":"Valentina","family":"Castiglioni","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3061-863X","authenticated-orcid":false,"given":"Michele","family":"Loreti","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3991-5123","authenticated-orcid":false,"given":"Simone","family":"Tini","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,9,19]]},"reference":[{"key":"5_CR1","series-title":"LNCS","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-031-42697-1_1","volume-title":"CMSB 2023","author":"P Ballarini","year":"2023","unstructured":"Ballarini, P., Bentriou, M., Courn\u00e8de, P.: A formal approach for tuning stochastic oscillators. In: Pang, J., Niehren, J. (eds.) CMSB 2023. LNCS, vol. 14137, pp. 1\u201317. Springer, Cham (2023). https:\/\/doi.org\/10.1007\/978-3-031-42697-1_1"},{"key":"5_CR2","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1038\/43199","volume":"387","author":"N Barkai","year":"1997","unstructured":"Barkai, N., Leibler, S.: Robustness in simple biochemical networks. Nature 387, 913\u2013917 (1997). https:\/\/doi.org\/10.1038\/43199","journal-title":"Nature"},{"key":"5_CR3","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1387\/ijdb.051973jc","volume":"49","author":"JJ Casal","year":"2005","unstructured":"Casal, J.J., Yanossky, M.J.: Regulation of gene expression by light. Int. J. Dev. Biol. 49, 501\u2013511 (2005). https:\/\/doi.org\/10.1387\/ijdb.051973jc","journal-title":"Int. J. Dev. Biol."},{"key":"5_CR4","series-title":"LNCS","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1007\/978-3-031-68150-9_2","volume-title":"FMICS 2024","author":"V Castiglioni","year":"2024","unstructured":"Castiglioni, V., Lanotte, R., Loreti, M., Tini, S.: Evaluating the effectiveness of digital twins through statistical model checking with feedback and perturbations. In: Haxthausen, A.E., Serwe, W. (eds.) FMICS 2024. LNCS, vol. 14952, pp. 21\u201339. Springer, Cham (2024). https:\/\/doi.org\/10.1007\/978-3-031-68150-9_2"},{"key":"5_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1007\/978-3-030-61470-6_23","volume-title":"Leveraging Applications of Formal Methods, Verification and Validation: Engineering Principles","author":"V Castiglioni","year":"2020","unstructured":"Castiglioni, V., Loreti, M., Tini, S.: Measuring adaptability and reliability of large scale systems. In: Margaria, T., Steffen, B. (eds.) ISoLA 2020, Part II. LNCS, vol. 12477, pp. 380\u2013396. Springer, Cham (2020). https:\/\/doi.org\/10.1007\/978-3-030-61470-6_23"},{"key":"5_CR6","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1007\/978-3-030-78089-0_4","volume-title":"Formal Techniques for Distributed Objects, Components, and Systems","author":"V Castiglioni","year":"2021","unstructured":"Castiglioni, V., Loreti, M., Tini, S.: How adaptive and reliable is your program? In: Peters, K., Willemse, T.A.C. (eds.) FORTE 2021. LNCS, vol. 12719, pp. 60\u201379. Springer, Cham (2021). https:\/\/doi.org\/10.1007\/978-3-030-78089-0_4"},{"doi-asserted-by":"publisher","unstructured":"Castiglioni, V., Loreti, M., Tini, S.: RobTL: a temporal logic for the robustness of cyber-physical systems. CoRR abs\/2212.11158 (2022). https:\/\/doi.org\/10.48550\/arXiv.2212.11158","key":"5_CR7","DOI":"10.48550\/arXiv.2212.11158"},{"doi-asserted-by":"publisher","unstructured":"Castiglioni, V., Loreti, M., Tini, S.: A framework to measure the robustness of programs in the unpredictable environment. Log. Methods Comput. Sci. 19(3) (2023). https:\/\/doi.org\/10.46298\/LMCS-19(3:2)2023","key":"5_CR8","DOI":"10.46298\/LMCS-19(3:2)2023"},{"key":"5_CR9","series-title":"LNCS","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1007\/978-3-031-35361-1_6","volume-title":"COORDINATION 2023","author":"V Castiglioni","year":"2023","unstructured":"Castiglioni, V., Loreti, M., Tini, S.: STARK: a software tool for the analysis of robustness in the unknown environment. In: Jongmans, S.S., Lopes, A. (eds.) COORDINATION 2023. LNCS, vol. 13908, pp. 115\u2013132. Springer, Cham (2023). https:\/\/doi.org\/10.1007\/978-3-031-35361-1_6"},{"unstructured":"Castiglioni, V., Loreti, M., Tini, S.: RobTL: robustness temporal logic for CPS. In: Proceedings of CONCUR 2024. LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum f\u00fcr Informatik (2024, to appear)","key":"5_CR10"},{"key":"5_CR11","doi-asserted-by":"publisher","DOI":"10.1016\/j.scico.2024.103134","volume":"236","author":"V Castiglioni","year":"2024","unstructured":"Castiglioni, V., Loreti, M., Tini, S.: STARK: a tool for the analysis of CPSs robustness. Sci. Comput. Program. 236, 103134 (2024). https:\/\/doi.org\/10.1016\/j.scico.2024.103134","journal-title":"Sci. Comput. Program."},{"issue":"8","key":"5_CR12","doi-asserted-by":"publisher","first-page":"5770","DOI":"10.1074\/jbc.M112.339226","volume":"288","author":"JP Dexter","year":"2013","unstructured":"Dexter, J.P., Gunawardena, J.: Dimerization and bifunctionality confer robustness to the Isocitrate Dehydrogenase regulatory system in Escherichia coli. J. Biol. Chem. 288(8), 5770\u20135778 (2013). https:\/\/doi.org\/10.1074\/jbc.M112.339226","journal-title":"J. Biol. Chem."},{"key":"5_CR13","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/35002125","volume":"403","author":"MB Elowitz","year":"2000","unstructured":"Elowitz, M.B., Leibler, S.: A synthetic oscillatory network of transcriptional regulators. Nature 403, 335\u2013338 (2000). https:\/\/doi.org\/10.1038\/35002125","journal-title":"Nature"},{"issue":"25","key":"5_CR14","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"DT Gillespie","year":"1977","unstructured":"Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340\u20132361 (1977)","journal-title":"J. Phys. Chem."},{"key":"5_CR15","series-title":"LNCS","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1007\/978-3-031-42697-1_7","volume-title":"CMSB 2023","author":"U Herbach","year":"2023","unstructured":"Herbach, U.: Harissa: stochastic simulation and inference of gene regulatory networks based on transcriptional bursting. In: Pang, J., Niehren, J. (eds.) CMSB 2023. LNCS, vol. 14137, pp. 97\u2013105. Springer, Cham (2023). https:\/\/doi.org\/10.1007\/978-3-031-42697-1_7"},{"key":"5_CR16","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1186\/s12918-017-0487-0","volume":"11","author":"U Herbach","year":"2017","unstructured":"Herbach, U., Bonnaffoux, A., Espinasse, T., Gandrillon, O.: Inferring gene regulatory networks from single-cell data: a mechanistic approach. BMC Syst. Biol. 11, 335\u2013338 (2017). https:\/\/doi.org\/10.1186\/s12918-017-0487-0","journal-title":"BMC Syst. Biol."},{"issue":"44","key":"5_CR17","doi-asserted-by":"publisher","first-page":"2786","DOI":"10.1038\/s41392-024-01749-9","volume":"9","author":"X Jia","year":"2024","unstructured":"Jia, X., He, X., Huang, C., Li, J., Dong, Z., Liu, K.: Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct. Target. Ther. 9(44), 2786\u20132791 (2024). https:\/\/doi.org\/10.1038\/s41392-024-01749-9","journal-title":"Signal Transduct. Target. Ther."},{"key":"5_CR18","doi-asserted-by":"publisher","first-page":"20200031","DOI":"10.1098\/rsif.2020.0031","volume":"17","author":"J Kim","year":"2020","unstructured":"Kim, J., Enciso, G.: Absolutely robust controllers for chemical reaction networks. J. R. Soc. Interface 17, 20200031 (2020). https:\/\/doi.org\/10.1098\/rsif.2020.0031","journal-title":"J. R. Soc. Interface"},{"issue":"1","key":"5_CR19","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/msb4100179","volume":"3","author":"H Kitano","year":"2007","unstructured":"Kitano, H.: Towards a theory of biological robustness. Mol. Syst. Biol. 3(1), 137 (2007). https:\/\/doi.org\/10.1038\/msb4100179","journal-title":"Mol. Syst. Biol."},{"unstructured":"Lanotte, R., Manicardi, D., Tini, S.: Step-by-step robustness for biochemical networks. In: Proceedings of ICTCS 2023. CEUR Workshop Proceedings, vol.\u00a03587, pp. 299\u2013313. CEUR-WS.org (2023). https:\/\/ceur-ws.org\/Vol-3587\/2906.pdf","key":"5_CR20"},{"unstructured":"Nasti, L.: Verification of robustness property in chemical reaction networks. Ph.D. thesis, University of Pisa, Italy (2020). https:\/\/etd.adm.unipi.it\/theses\/available\/etd-02172020-165444\/","key":"5_CR21"},{"key":"5_CR22","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1007\/978-3-030-04771-9_8","volume-title":"Software Technologies: Applications and Foundations","author":"L Nasti","year":"2018","unstructured":"Nasti, L., Gori, R., Milazzo, P.: Formalizing a notion of concentration robustness for biochemical networks. In: Mazzara, M., Ober, I., Sala\u00fcn, G. (eds.) STAF 2018. LNCS, vol. 11176, pp. 81\u201397. Springer, Cham (2018). https:\/\/doi.org\/10.1007\/978-3-030-04771-9_8"},{"doi-asserted-by":"publisher","unstructured":"Pernice, S., et al.: Computational modeling of the immune response in multiple sclerosis using epimod framework. BMC Bioinform. 21-S(17), 550 (2020). https:\/\/doi.org\/10.1186\/S12859-020-03823-9","key":"5_CR23","DOI":"10.1186\/S12859-020-03823-9"},{"issue":"10","key":"5_CR24","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.4161\/15476286.2014.972852","volume":"11","author":"E Petrillo","year":"2014","unstructured":"Petrillo, E., Herz, M., Barta, A., Kalyna, M., Kornblihtt, A.: Let there be light: regulation of gene expression in plants. RNA Biol. 11(10), 1215\u20131220 (2014). https:\/\/doi.org\/10.4161\/15476286.2014.972852","journal-title":"RNA Biol."},{"issue":"6","key":"5_CR25","doi-asserted-by":"publisher","first-page":"2786","DOI":"10.2134\/agronj2019.04.0291","volume":"111","author":"WR Raun","year":"2019","unstructured":"Raun, W.R., et al.: Unpredictable nature of environment on nitrogen supply and demand. Agron. J. 111(6), 2786\u20132791 (2019). https:\/\/doi.org\/10.2134\/agronj2019.04.0291","journal-title":"Agron. J."},{"doi-asserted-by":"publisher","unstructured":"Rizk, A., Batt, G., Fages, F., Soliman, S.: A general computational method for robustness analysis with applications to synthetic gene networks. Bioinform. 25(12) (2009). https:\/\/doi.org\/10.1093\/bioinformatics\/btp200","key":"5_CR26","DOI":"10.1093\/bioinformatics\/btp200"},{"issue":"26","key":"5_CR27","doi-asserted-by":"publisher","first-page":"2827","DOI":"10.1016\/j.tcs.2010.05.008","volume":"412","author":"A Rizk","year":"2011","unstructured":"Rizk, A., Batt, G., Fages, F., Soliman, S.: Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures. Theor. Comput. Sci. 412(26), 2827\u20132839 (2011). https:\/\/doi.org\/10.1016\/j.tcs.2010.05.008","journal-title":"Theor. Comput. Sci."},{"issue":"5971","key":"5_CR28","doi-asserted-by":"publisher","first-page":"1389","DOI":"10.1126\/science.1183372","volume":"327","author":"G Shinar","year":"2010","unstructured":"Shinar, G., Feinberg, M.: Structural sources of robustness in biochemical reaction networks. Science 327(5971), 1389\u20131391 (2010). https:\/\/doi.org\/10.1126\/science.1183372","journal-title":"Science"},{"issue":"1","key":"5_CR29","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.mbs","volume":"231","author":"G Shinar","year":"2011","unstructured":"Shinar, G., Feinberg, M.: Design principles for robust biochemical reaction networks: what works, what cannot work, and what might almost work. Mathe. Biosci. 231(1), 39\u201348 (2011). https:\/\/doi.org\/10.1016\/j.mbs","journal-title":"Mathe. Biosci."},{"issue":"4","key":"5_CR30","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1016\/j.tig.2020.01.003","volume":"36","author":"E Tunnacliffe","year":"2020","unstructured":"Tunnacliffe, E., Chubb, J.R.: What is a transcriptional burst? Trends Genet. 36(4), 288\u2013297 (2020). https:\/\/doi.org\/10.1016\/j.tig.2020.01.003","journal-title":"Trends Genet."},{"unstructured":"Uri, A.: An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall\/CRC (2006)","key":"5_CR31"},{"issue":"3","key":"5_CR32","first-page":"64","volume":"5","author":"LN Vaserstein","year":"1969","unstructured":"Vaserstein, L.N.: Markovian processes on countable space product describing large systems of automata. Probl. Peredachi Inf. 5(3), 64\u201372 (1969)","journal-title":"Probl. Peredachi Inf."}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-71671-3_5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,19]],"date-time":"2024-09-19T22:46:14Z","timestamp":1726785974000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-71671-3_5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"ISBN":["9783031716706","9783031716713"],"references-count":32,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-71671-3_5","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2024]]},"assertion":[{"value":"19 September 2024","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"CMSB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Computational Methods in Systems Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Pisa","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Italy","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2024","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"17 September 2024","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"19 September 2024","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"22","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"cmsb2024","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/cmsb.sciencesconf.org\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}