{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T15:52:58Z","timestamp":1718121178887},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2019,8,16]],"date-time":"2019-08-16T00:00:00Z","timestamp":1565913600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007678","name":"Center for Modelling and Simulation in the Biosciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007678","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Deutsche Forschungs Gemeinschaft (DFG)","award":["SFB1129 (project 8)"]},{"name":"Chica and Heinz Schaller Foundation"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007230","type":"journal-article","created":{"date-parts":[[2019,8,16]],"date-time":"2019-08-16T17:23:40Z","timestamp":1565976220000},"page":"e1007230","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics"],"prefix":"10.1371","volume":"15","author":[{"given":"Michael","family":"Gabel","sequence":"first","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-2229-4391","authenticated-orcid":true,"given":"Tobias","family":"Hohl","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-8740-1477","authenticated-orcid":true,"given":"Andrea","family":"Imle","sequence":"additional","affiliation":[]},{"given":"Oliver T.","family":"Fackler","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-1198-6632","authenticated-orcid":true,"given":"Frederik","family":"Graw","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,8,16]]},"reference":[{"issue":"9","key":"pcbi.1007230.ref001","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/nbt1330","article-title":"Ensemble modeling for analysis of cell signaling dynamics","volume":"25","author":"L Kuepfer","year":"2007","journal-title":"Nat Biotechnol"},{"key":"pcbi.1007230.ref002","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/978-1-60761-842-3_18","article-title":"Parameter inference and model selection in signaling pathway models","volume":"673","author":"T Toni","year":"2010","journal-title":"Methods Mol Biol"},{"issue":"8","key":"pcbi.1007230.ref003","doi-asserted-by":"crossref","first-page":"e1003561","DOI":"10.1371\/journal.ppat.1003561","article-title":"Replication vesicles are load- and choke-points in the hepatitis C virus lifecycle","volume":"9","author":"M Binder","year":"2013","journal-title":"PLoS Pathog"},{"issue":"2","key":"pcbi.1007230.ref004","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1128\/JVI.01304-06","article-title":"Mathematical modeling of subgenomic hepatitis C virus replication in Huh-7 cells","volume":"81","author":"H Dahari","year":"2007","journal-title":"J Virol"},{"issue":"13","key":"pcbi.1007230.ref005","doi-asserted-by":"crossref","first-page":"6383","DOI":"10.1128\/JVI.02612-08","article-title":"Modeling subgenomic hepatitis C virus RNA kinetics during treatment with alpha interferon","volume":"83","author":"H Dahari","year":"2009","journal-title":"J Virol"},{"key":"pcbi.1007230.ref006","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2018.01137","article-title":"Varying Immunizations With Plasmodium Radiation-Attenuated Sporozoites Alter Tissue-Specific CD8+ T Cell Dynamics","volume":"9","author":"R Frank","year":"2018","journal-title":"Front. Immunol"},{"issue":"3","key":"pcbi.1007230.ref007","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/j.cels.2017.01.014","article-title":"Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny","volume":"4","author":"F Crauste","year":"2017","journal-title":"Cell Syst"},{"issue":"6132","key":"pcbi.1007230.ref008","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1126\/science.1235454","article-title":"Disparate individual fates compose robust CD8+ T cell immunity","volume":"340","author":"VR Buchholz","year":"2013","journal-title":"Science"},{"key":"pcbi.1007230.ref009","volume-title":"Model selection and multimodel inference","author":"KP Burnham","year":"2003","edition":"2nd ed"},{"issue":"12","key":"pcbi.1007230.ref010","first-page":"1","article-title":"glmulti: An R Package for Easy Automated Model Selection with (Generalized) Linear Models","volume":"34","author":"V Calcagno","year":"2010","journal-title":"J Statistic Software"},{"key":"pcbi.1007230.ref011","unstructured":"Lumley T, Miller A. leaps: Regression Subset Selection.; 2009."},{"key":"pcbi.1007230.ref012","unstructured":"Barton K. MuMIn: Multi-Model Inference; 2009."},{"key":"pcbi.1007230.ref013","unstructured":"Sestelo M, Villanueva NM, Roca-Pardinas J. FWDselect: Selecting Variables in Regression Models; 2015."},{"issue":"1","key":"pcbi.1007230.ref014","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1093\/bioinformatics\/btp619","article-title":"Simulation-based model selection for dynamical systems in systems and population biology","volume":"26","author":"T Toni","year":"2010","journal-title":"Bioinformatics"},{"issue":"15","key":"pcbi.1007230.ref015","doi-asserted-by":"crossref","first-page":"3932","DOI":"10.1073\/pnas.1517384113","article-title":"Discovering governing equations from data by sparse identification of nonlinear dynamical systems","volume":"113","author":"SL Brunton","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2204","key":"pcbi.1007230.ref016","doi-asserted-by":"crossref","first-page":"20170009","DOI":"10.1098\/rspa.2017.0009","article-title":"Model selection for dynamical systems via sparse regression and information criteria","volume":"473","author":"NM Mangan","year":"2017","journal-title":"Proc Math Phys Eng Sci"},{"issue":"18","key":"pcbi.1007230.ref017","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1093\/bioinformatics\/btv314","article-title":"Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach","volume":"31","author":"D Henriques","year":"2015","journal-title":"Bioinformatics"},{"issue":"2","key":"pcbi.1007230.ref018","doi-asserted-by":"crossref","first-page":"e1005379","DOI":"10.1371\/journal.pcbi.1005379","article-title":"Data-driven reverse engineering of signaling pathways using ensembles of dynamic models","volume":"13","author":"D Henriques","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1007230.ref019","doi-asserted-by":"crossref","first-page":"391","DOI":"10.3934\/ipi.2011.5.391","article-title":"A refinement and coarsening indicator algorithm for finding sparse solutions of inverse problems","volume":"5","author":"B Kaltenbacher","year":"2011","journal-title":"Inv Problems & Imaging"},{"key":"pcbi.1007230.ref020","unstructured":"Akaike H. Information theory and an extension of the maximum likelihood principle. 2nd Int Symp on information theory (BN Petrov, F Casaki), Budapest, Hungary. 1973; p. 267\u2013281."},{"key":"pcbi.1007230.ref021","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification","volume":"19","author":"H Akaike","year":"1974","journal-title":"IEEE Trans Automat Control"},{"key":"pcbi.1007230.ref022","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1214\/aos\/1176344136","article-title":"Estimating the dimension of a model","volume":"6","author":"G Schwarz","year":"1978","journal-title":"Ann Stat"},{"key":"pcbi.1007230.ref023","doi-asserted-by":"crossref","DOI":"10.1201\/9781420035933","volume-title":"Subset selection in regression","author":"AJ Miller","year":"2002","edition":"2nd ed"},{"key":"pcbi.1007230.ref024","unstructured":"R Development Core Team. R: A Language and Environment for Statistical Computing, http:\/\/www.R-project.org."},{"key":"pcbi.1007230.ref025","unstructured":"Bengtsson H. future: Unified Parallel and Distributed Processing in R for Everyone; 2017."},{"key":"pcbi.1007230.ref026","unstructured":"Johnson P. adaptivetau: Tau-Leaping Stochastic Simulation; 2016."},{"issue":"1","key":"pcbi.1007230.ref027","doi-asserted-by":"crossref","first-page":"2144","DOI":"10.1038\/s41467-019-09879-3","article-title":"Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures","volume":"10","author":"A Imle","year":"2019","journal-title":"Nat Commun"},{"issue":"45","key":"pcbi.1007230.ref028","doi-asserted-by":"crossref","first-page":"18541","DOI":"10.1073\/pnas.1204322109","article-title":"HIV-1 Nef interferes with T-lymphocyte circulation through confined environments in vivo","volume":"109","author":"B Stolp","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"issue":"15","key":"pcbi.1007230.ref029","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1093\/bioinformatics\/btp358","article-title":"Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood","volume":"25","author":"A Raue","year":"2009","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1007230.ref030","doi-asserted-by":"crossref","first-page":"192","DOI":"10.3758\/BF03206482","article-title":"AIC model selection using Akaike weights","volume":"11","author":"EJ Wagenmakers","year":"2004","journal-title":"Psychon Bull Rev"},{"key":"pcbi.1007230.ref031","first-page":"1","article-title":"Dynamic Modeling, Parameter Estimation, and Uncertainty Analysis in R","volume":"88","author":"D Kaschek","year":"2019","journal-title":"J Statistic Software"},{"key":"pcbi.1007230.ref032","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-2719-7","volume-title":"Modern Applied Statistics with S-PLUS","author":"WN Venables","year":"1997","edition":"3rd ed"},{"key":"pcbi.1007230.ref033","first-page":"77","article-title":"Reconstructing leukocyte migration in 3D extracellular matrix by time-lapse videomicroscopy and computer-assisted tracking","volume":"239","author":"P Friedl","year":"2004","journal-title":"Methods Mol Biol"},{"key":"pcbi.1007230.ref034","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.jtbi.2012.12.025","article-title":"Quantifying T lymphocyte turnover","volume":"327","author":"RJ De Boer","year":"2013","journal-title":"J Theor Biol"},{"key":"pcbi.1007230.ref035","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1186\/1471-2105-8-196","article-title":"Reconstruction of cell population dynamics using CFSE","volume":"8","author":"A Yates","year":"2007","journal-title":"BMC Bioinformatics"},{"issue":"26","key":"pcbi.1007230.ref036","doi-asserted-by":"crossref","first-page":"6772","DOI":"10.1182\/blood-2010-12-319780","article-title":"Preculture of PBMCs at high cell density increases sensitivity of T-cell responses, revealing cytokine release by CD28 superagonist TGN1412","volume":"118","author":"PS R\u00f6mer","year":"2011","journal-title":"Blood"},{"issue":"6132","key":"pcbi.1007230.ref037","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1126\/science.1235487","article-title":"Heterogeneous differentiation patterns of individual CD8+ T cells","volume":"340","author":"C Gerlach","year":"2013","journal-title":"Science"},{"issue":"12","key":"pcbi.1007230.ref038","doi-asserted-by":"crossref","first-page":"5032","DOI":"10.1073\/pnas.0700026104","article-title":"A model of immune regulation as a consequence of randomized lymphocyte division and death times","volume":"104","author":"ED Hawkins","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"issue":"48","key":"pcbi.1007230.ref039","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1098\/rsif.2009.0488","article-title":"A minimum of two distinct heritable factors are required to explain correlation structures in proliferating lymphocytes","volume":"7","author":"JF Markham","year":"2010","journal-title":"J R Soc Interface"},{"issue":"6066","key":"pcbi.1007230.ref040","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1126\/science.1213230","article-title":"Activation-induced B cell fates are selected by intracellular stochastic competition","volume":"335","author":"KR Duffy","year":"2012","journal-title":"Science"},{"issue":"9","key":"pcbi.1007230.ref041","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0012775","article-title":"Stochastic models of lymphocyte proliferation and death","volume":"5","author":"A Zilman","year":"2010","journal-title":"PLoS ONE"},{"issue":"1-2","key":"pcbi.1007230.ref042","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.jim.2005.01.011","article-title":"Quantifying cell turnover using CFSE data","volume":"298","author":"VV Ganusov","year":"2005","journal-title":"J Immunol Methods"},{"issue":"6","key":"pcbi.1007230.ref043","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1007\/s00285-007-0142-2","article-title":"Determining the expected variability of immune responses using the cyton model","volume":"56","author":"VG Subramanian","year":"2008","journal-title":"J Math Biol"},{"issue":"430","key":"pcbi.1007230.ref044","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1080\/01621459.1995.10476572","article-title":"Bayes factor","volume":"90","author":"RE Kass","year":"1995","journal-title":"J Am Stat Assoc"},{"key":"pcbi.1007230.ref045","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1007\/s11222-013-9416-2","article-title":"Understanding predictive information criteria for Bayesian models","volume":"24","author":"A Gelman","year":"2014","journal-title":"Stat Comput"},{"key":"pcbi.1007230.ref046","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/msb.2009.87","article-title":"Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction","volume":"5","author":"J Saez-Rodriguez","year":"2009","journal-title":"Mol Syst Biol"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007230","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T23:53:51Z","timestamp":1588982031000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007230"}},"subtitle":[],"editor":[{"given":"Becca","family":"Asquith","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,8,16]]},"references-count":46,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2019,8,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007230","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,16]]}}}