{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T08:46:40Z","timestamp":1759826800564},"publisher-location":"Cham","reference-count":24,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030313036"},{"type":"electronic","value":"9783030313043"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1007\/978-3-030-31304-3_1","type":"book-chapter","created":{"date-parts":[[2019,9,16]],"date-time":"2019-09-16T16:02:46Z","timestamp":1568649766000},"page":"3-19","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Sequential Reprogramming of Boolean Networks Made Practical"],"prefix":"10.1007","author":[{"given":"Hugues","family":"Mandon","sequence":"first","affiliation":[]},{"given":"Cui","family":"Su","sequence":"additional","affiliation":[]},{"given":"Stefan","family":"Haar","sequence":"additional","affiliation":[]},{"given":"Jun","family":"Pang","sequence":"additional","affiliation":[]},{"given":"Lo\u00efc","family":"Paulev\u00e9","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,9,17]]},"reference":[{"key":"1_CR1","first-page":"86","volume":"2","author":"W Abou-Jaoud\u00e9","year":"2015","unstructured":"Abou-Jaoud\u00e9, W., et al.: Model checking to assess T-helper cell plasticity. Front. Bioeng. Biotechnol. 2, 86 (2015)","journal-title":"Front. Bioeng. Biotechnol."},{"key":"1_CR2","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1007\/978-3-319-67471-1_4","volume-title":"Computational Methods in Systems Biology","author":"C Biane","year":"2017","unstructured":"Biane, C., Delaplace, F.: Abduction based drug target discovery using Boolean control network. In: Feret, J., Koeppl, H. (eds.) CMSB 2017. LNCS, vol. 10545, pp. 57\u201373. Springer, Cham (2017). \n                      https:\/\/doi.org\/10.1007\/978-3-319-67471-1_4"},{"issue":"12","key":"1_CR3","doi-asserted-by":"publisher","first-page":"e1002300","DOI":"10.1371\/journal.pcbi.1002300","volume":"7","author":"R Chang","year":"2011","unstructured":"Chang, R., Shoemaker, R., Wang, W.: Systematic search for recipes to generate induced pluripotent stem cells. PLoS Comput. Biol. 7(12), e1002300 (2011)","journal-title":"PLoS Comput. Biol."},{"issue":"3","key":"1_CR4","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1124\/jpet.115.224766","volume":"354","author":"V Chudasama","year":"2015","unstructured":"Chudasama, V., Ovacik, M., Abernethy, D., Mager, D.: Logic-based and cellular pharmacodynamic modeling of Bortezomib responses in U266 human myeloma cells. J. Pharmacol. Exp. Ther. 354(3), 448\u2013458 (2015)","journal-title":"J. Pharmacol. Exp. Ther."},{"issue":"11","key":"1_CR5","doi-asserted-by":"publisher","first-page":"e1004571","DOI":"10.1371\/journal.pcbi.1004571","volume":"11","author":"DPA Cohen","year":"2015","unstructured":"Cohen, D.P.A., Martignetti, L., Robine, S., Barillot, E., Zinovyev, A., Calzone, L.: Mathematical modelling of molecular pathways enabling tumour cell invasion and migration. PLoS Comput. Biol. 11(11), e1004571 (2015)","journal-title":"PLoS Comput. Biol."},{"issue":"23","key":"1_CR6","doi-asserted-by":"publisher","first-page":"5792","DOI":"10.1073\/pnas.1610622114","volume":"114","author":"S Collombet","year":"2017","unstructured":"Collombet, S., et al.: Logical modeling of lymphoid and myeloid cell specification and transdifferentiation. Proc. Nat. Acad. Sci. 114(23), 5792\u20135799 (2017)","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"1","key":"1_CR7","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/1752-0509-7-140","volume":"7","author":"I Crespo","year":"2013","unstructured":"Crespo, I., Perumal, T.M., Jurkowski, W., del Sol, A.: Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks. BMC Syst. Biol. 7(1), 140 (2013)","journal-title":"BMC Syst. Biol."},{"issue":"7273","key":"1_CR8","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nature08533","volume":"462","author":"T Graf","year":"2009","unstructured":"Graf, T., Enver, T.: Forcing cells to change lineages. Nature 462(7273), 587\u2013594 (2009)","journal-title":"Nature"},{"key":"1_CR9","first-page":"1","volume":"7","author":"F Herrmann","year":"2012","unstructured":"Herrmann, F., Gro\u00df, A., Zhou, D., Kestler, H.A., K\u00fchl, M.: A Boolean model of the cardiac gene regulatory network determining first and second heart field identity. PLoS ONE 7, 1\u201310 (2012)","journal-title":"PLoS ONE"},{"issue":"3","key":"1_CR10","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1093\/nar\/gkv1468","volume":"44","author":"J Jo","year":"2016","unstructured":"Jo, J., et al.: An integrated systems biology approach identifies positive cofactor 4 as a factor that increases reprogramming efficiency. Nucleic Acids Res. 44(3), 1203\u20131215 (2016)","journal-title":"Nucleic Acids Res."},{"issue":"8","key":"1_CR11","doi-asserted-by":"publisher","first-page":"e22649","DOI":"10.1371\/journal.pone.0022649","volume":"6","author":"J Krumsiek","year":"2011","unstructured":"Krumsiek, J., Marr, C., Schroeder, T., Theis, F.J.: Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network. PLoS ONE 6(8), e22649 (2011)","journal-title":"PLoS ONE"},{"key":"1_CR12","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1007\/978-3-319-67471-1_11","volume-title":"Computational Methods in Systems Biology","author":"H Mandon","year":"2017","unstructured":"Mandon, H., Haar, S., Paulev\u00e9, L.: Temporal reprogramming of Boolean networks. In: Feret, J., Koeppl, H. (eds.) CMSB 2017. LNCS, vol. 10545, pp. 179\u2013195. Springer, Cham (2017). \n                      https:\/\/doi.org\/10.1007\/978-3-319-67471-1_11"},{"issue":"1","key":"1_CR13","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1109\/TCBB.2018.2850901","volume":"16","author":"A Mizera","year":"2018","unstructured":"Mizera, A., Pang, J., Qu, H., Yuan, Q.: Taming asynchrony for attractor detection in large Boolean networks. IEEE\/ACM Trans. Comput. Biol. Bioinf. 16(1), 31\u201342 (2018)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf."},{"issue":"4","key":"1_CR14","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1109\/TCBB.2017.2773477","volume":"15","author":"A Mizera","year":"2018","unstructured":"Mizera, A., Pang, J., Su, C., Yuan, Q.: ASSA-PBN: a toolbox for probabilistic Boolean networks. IEEE\/ACM Trans. Comput. Biol. Bioinf. 15(4), 1203\u20131216 (2018)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf."},{"key":"1_CR15","doi-asserted-by":"publisher","first-page":"44","DOI":"10.3389\/fgene.2016.00044","volume":"7","author":"B Offermann","year":"2016","unstructured":"Offermann, B., et al.: Boolean modeling reveals the necessity of transcriptional regulation for bistability in PC12 cell differentiation. Front. Genet. 7, 44 (2016)","journal-title":"Front. Genet."},{"doi-asserted-by":"crossref","unstructured":"Paul, S., Su, C., Pang, J., Mizera, A.: A decomposition-based approach towards the control of Boolean networks. In: Proceedings 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 11\u201320. ACM Press (2018)","key":"1_CR16","DOI":"10.1145\/3233547.3233550"},{"doi-asserted-by":"crossref","unstructured":"Paul, S., Su, C., Pang, J., Mizera, A.: An efficient approach towards the source-target control of Boolean networks. IEEE\/ACM Trans. Comput. Biol. Bioinf. (2019, accepted)","key":"1_CR17","DOI":"10.1109\/TCBB.2019.2915081"},{"key":"1_CR18","doi-asserted-by":"publisher","first-page":"4042","DOI":"10.1158\/0008-5472.CAN-15-0602","volume":"75","author":"E Remy","year":"2015","unstructured":"Remy, E., Rebouissou, S., Chaouiya, C., Zinovyev, A., Radvanyi, F., Calzone, L.: A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis. Cancer Res. 75, 4042\u20134052 (2015). \n                      https:\/\/doi.org\/10.1158\/0008-5472.CAN-15-0602","journal-title":"Cancer Res."},{"issue":"45","key":"1_CR19","doi-asserted-by":"publisher","first-page":"11832","DOI":"10.1073\/pnas.1712350114","volume":"114","author":"S Ronquist","year":"2017","unstructured":"Ronquist, S., et al.: Algorithm for cellular reprogramming. Proc. Nat. Acad. Sci. 114(45), 11832\u201311837 (2017)","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"1","key":"1_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1752-0509-3-1","volume":"3","author":"\u00d6 Sahin","year":"2009","unstructured":"Sahin, \u00d6., et al.: Modeling ERBB receptor-regulated G1\/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 3(1), 1 (2009)","journal-title":"BMC Syst. Biol."},{"issue":"1","key":"1_CR21","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1089\/cmb.2009.0121","volume":"17","author":"R Samaga","year":"2010","unstructured":"Samaga, R., Von Kamp, A., Klamt, S.: Computing combinatorial intervention strategies and failure modes in signaling networks. J. Comput. Biol. 17(1), 39\u201353 (2010)","journal-title":"J. Comput. Biol."},{"issue":"6","key":"1_CR22","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1002\/stem.1627","volume":"32","author":"A Sol del","year":"2014","unstructured":"del Sol, A., Buckley, N.J.: Concise review: a population shift view of cellular reprogramming. Stem Cells 32(6), 1367\u20131372 (2014)","journal-title":"Stem Cells"},{"issue":"3","key":"1_CR23","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1038\/nrm.2016.8","volume":"17","author":"K Takahashi","year":"2016","unstructured":"Takahashi, K., Yamanaka, S.: A decade of transcription factor-mediated reprogramming to pluripotency. Nat. Rev. Mol. Cell Biol. 17(3), 183\u2013193 (2016)","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"1_CR24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1004193","volume":"11","author":"JGT Za\u00f1udo","year":"2015","unstructured":"Za\u00f1udo, J.G.T., Albert, R.: Cell fate reprogramming by control of intracellular network dynamics. PLoS Comput. Biol. 11, 1\u201324 (2015)","journal-title":"PLoS Comput. Biol."}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-31304-3_1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,16]],"date-time":"2019-09-16T16:02:55Z","timestamp":1568649775000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-31304-3_1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030313036","9783030313043"],"references-count":24,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-31304-3_1","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"17 September 2019","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":"Trieste","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":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"18 September 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"20 September 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"17","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"cmsb2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/cmsb2019.units.it\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"53","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"14","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"11","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"26% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"2.5","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"No","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"7 tool papers were accepted; average number of reviewers\/paper for the short papers: 1.5","order":10,"name":"additional_info_on_review_process","label":"Additional Info on Review Process","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}