{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T01:34:44Z","timestamp":1755221684458,"version":"3.43.0"},"reference-count":51,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"4","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"}],"funder":[{"name":"Brazilian National Council for Scientific and Technological Development","award":["301061\/2025-4"],"award-info":[{"award-number":["301061\/2025-4"]}]},{"name":"NCI","award":["U01-CA232137","1720625","1818187"],"award-info":[{"award-number":["U01-CA232137","1720625","1818187"]}]},{"DOI":"10.13039\/100001006","name":"Breast Cancer Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001006","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Giovanis Foundation for Health and Policy"},{"name":"Carlos Chagas Filho Foundation for Supporting Research","award":["E-26\/210.430\/2024"],"award-info":[{"award-number":["E-26\/210.430\/2024"]}]},{"name":"Brazilian National Council for Scientific and Technological Development","award":["306588\/2022-6"],"award-info":[{"award-number":["306588\/2022-6"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE Trans. Comput. Biol. Bioinform."],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1109\/tcbbio.2025.3565543","type":"journal-article","created":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T13:30:58Z","timestamp":1745933458000},"page":"1690-1702","source":"Crossref","is-referenced-by-count":0,"title":["Connecting Different Approaches for Cell Cycle Modeling: Learning Ordinary Differential Equations from Individual-Based Models"],"prefix":"10.1109","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7331-9763","authenticated-orcid":false,"given":"Gustavo T.","family":"Naozuka","sequence":"first","affiliation":[{"name":"Coordenação de Modelagem Computacional, Laboratório Nacional de Computação Científica, Petrópolis, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5876-2644","authenticated-orcid":false,"given":"Heber L.","family":"Rocha","sequence":"additional","affiliation":[{"name":"Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7934-028X","authenticated-orcid":false,"given":"Thiago J.","family":"Pereira","sequence":"additional","affiliation":[{"name":"Departamento de Ciências Exatas, Biológicas e da Terra, Universidade Federal Fluminense, Santo Antônio de Pádua, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4583-6026","authenticated-orcid":false,"given":"Gustavo B.","family":"Libotte","sequence":"additional","affiliation":[{"name":"Departamento de Modelagem Computacional, Universidade do Estado do Rio de Janeiro, Nova Friburgo, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9756-8131","authenticated-orcid":false,"given":"Regina C.","family":"Almeida","sequence":"additional","affiliation":[{"name":"Coordenação de Modelagem Computacional, Laboratório Nacional de Computação Científica, Petrópolis, Brazil"}]}],"member":"263","reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1200\/cci.18.00069"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1002\/wsbm.1461"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1186\/s12982-021-00102-7"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcaa043"},{"issue":"2022-10","key":"ref5","first-page":"1","article-title":"Agent-based modeling in economics and finance: Past, present, and future","author":"Axtell","year":"2022","journal-title":"Inst. New Econ. Thinking Oxford Martin Sch."},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1177\/0049124113506405"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.3389\/fbioe.2020.00249"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa969"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1007\/s00366-022-01625-6"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1177\/1176935118790262"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-17-2649"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1016\/j.tcb.2022.10.006"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005991"},{"key":"ref14","article-title":"Digitize your biology! modeling multicellular systems through interpretable cell behavior","author":"Johnson","year":"2023","journal-title":"bioRxiv"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv730"},{"key":"ref16","article-title":"Iterative community-driven development of a SARS-CoV-2 tissue simulator","author":"Getz","year":"2021","journal-title":"bioRxiv"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1039\/C9ME00036D"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1038\/s41540-024-00472-z"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-78780-7"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.102935"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.0c00356"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cma.2022.115412"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-540-78841-6_5"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1016\/j.cma.2016.03.025"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1016\/j.eswa.2023.123070"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2006.10.010"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1017\/S0962492921000064"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1007\/s00500-022-07362-8"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1517384113"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1098\/rspa.2021.0904"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1098\/rsos.211823"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1098\/rspa.2020.0279"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1098\/rspa.2018.0335"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2021.110525"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2022.111203"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-1418-1"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1007\/s11071-022-07755-2"},{"key":"ref38","article-title":"Estimating cell cycle model parameters using systems identification","author":"Juarez","year":"2015","journal-title":"bioRxiv"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2020.0987"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0095150"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.46471\/gigabyte.128"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.jtbi.2012.02.002","article-title":"Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): From microscopic measurements to macroscopic predictions of clinical progression","volume":"301","author":"Macklin","year":"2012","journal-title":"J. Theor. Biol."},{"volume-title":"PhysiCell User Guide","year":"2020","author":"Macklin","key":"ref43"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2018.08.004"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1023\/A:1008202821328"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1049\/iet-syb:20060067"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/S0076-6879(85)17018-7","article-title":"Nonlinear least-squares analysis","volume-title":"Enzyme Structure Part J","volume":"117","author":"Johnson","year":"1985"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-34931-0"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1109\/TMBMC.2016.2633265"},{"key":"ref50","doi-asserted-by":"publisher","DOI":"10.1021\/ac60214a047"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.103.042310"}],"container-title":["IEEE Transactions on Computational Biology and Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx8\/10723156\/11121392\/10979884.pdf?arnumber=10979884","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,9]],"date-time":"2025-08-09T04:43:10Z","timestamp":1754714590000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/10979884\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":51,"journal-issue":{"issue":"4"},"URL":"https:\/\/doi.org\/10.1109\/tcbbio.2025.3565543","relation":{},"ISSN":["2998-4165"],"issn-type":[{"type":"electronic","value":"2998-4165"}],"subject":[],"published":{"date-parts":[[2025,7]]}}}