{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:11:11Z","timestamp":1772165471331,"version":"3.50.1"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,11,8]],"date-time":"2024-11-08T00:00:00Z","timestamp":1731024000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,11,8]],"date-time":"2024-11-08T00:00:00Z","timestamp":1731024000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["378803395"],"award-info":[{"award-number":["378803395"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["378803395"],"award-info":[{"award-number":["378803395"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERC Advanced Grant","award":["787367"],"award-info":[{"award-number":["787367"]}]},{"DOI":"10.13039\/501100001824","name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["GJ20-02328Y"],"award-info":[{"award-number":["GJ20-02328Y"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001824","name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["GJ20-02328Y"],"award-info":[{"award-number":["GJ20-02328Y"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001824","name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["GJ20-02328Y"],"award-info":[{"award-number":["GJ20-02328Y"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017520","name":"Fakulta Informa\u010dn\u00edch Technologi\u00ed, Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Brn\u011b","doi-asserted-by":"publisher","award":["internal project FIT-S-23-8151,"],"award-info":[{"award-number":["internal project FIT-S-23-8151,"]}],"id":[{"id":"10.13039\/501100017520","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Grant Agency of Masaryk University","award":["MUNI\/I\/1757\/2021"],"award-info":[{"award-number":["MUNI\/I\/1757\/2021"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/s12859-024-05966-5","type":"journal-article","created":{"date-parts":[[2024,11,8]],"date-time":"2024-11-08T07:24:47Z","timestamp":1731050687000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Abstraction-based segmental simulation of reaction networks using adaptive memoization"],"prefix":"10.1186","volume":"25","author":[{"given":"Martin","family":"Helfrich","sequence":"first","affiliation":[]},{"given":"Roman","family":"Andriushchenko","sequence":"additional","affiliation":[]},{"given":"Milan","family":"\u010ce\u0161ka","sequence":"additional","affiliation":[]},{"given":"Jan","family":"K\u0159et\u00ednsk\u00fd","sequence":"additional","affiliation":[]},{"given":"\u0160tefan","family":"Marti\u010dek","sequence":"additional","affiliation":[]},{"given":"David","family":"\u0160afr\u00e1nek","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,11,8]]},"reference":[{"issue":"5584","key":"5966_CR1","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1126\/science.1070919","volume":"297","author":"MB Elowitz","year":"2002","unstructured":"Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002;297(5584):1183\u20136.","journal-title":"Science"},{"issue":"25","key":"5966_CR2","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"DT Gillespie","year":"1977","unstructured":"Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem. 1977;81(25):2340\u201381.","journal-title":"J Phys Chem"},{"issue":"4","key":"5966_CR3","doi-asserted-by":"publisher","first-page":"044109","DOI":"10.1063\/1.2159468","volume":"124","author":"Y Cao","year":"2006","unstructured":"Cao Y, Gillespie DT, Petzold LR. Efficient step size selection for the tau-leaping simulation method. J Chem Phys. 2006;124(4):044109.","journal-title":"J Chem Phys"},{"issue":"2","key":"5966_CR4","doi-asserted-by":"publisher","first-page":"024113","DOI":"10.1063\/1.4904980","volume":"142","author":"C Lester","year":"2015","unstructured":"Lester C, Yates CA, Giles MB, Baker RE. An adaptive multi-level simulation algorithm for stochastic biological systems. J Chem Phys. 2015;142(2):024113.","journal-title":"J Chem Phys"},{"issue":"18","key":"5966_CR5","doi-asserted-by":"publisher","first-page":"184102","DOI":"10.1063\/1.1889434","volume":"122","author":"J Goutsias","year":"2005","unstructured":"Goutsias J. Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems. J Chem Phys. 2005;122(18):184102.","journal-title":"J Chem Phys"},{"issue":"4","key":"5966_CR6","doi-asserted-by":"publisher","first-page":"1390","DOI":"10.1137\/140983471","volume":"13","author":"A Ganguly","year":"2015","unstructured":"Ganguly A, Altintan D, Koeppl H. Jump-diffusion approximation of stochastic reaction dynamics: error bounds and algorithms. Multiscale Model Simul. 2015;13(4):1390\u2013419.","journal-title":"Multiscale Model Simul"},{"issue":"3","key":"5966_CR7","doi-asserted-by":"publisher","first-page":"034118","DOI":"10.1063\/1.4905196","volume":"142","author":"B Hepp","year":"2015","unstructured":"Hepp B, Gupta A, Khammash M. Adaptive hybrid simulations for multiscale stochastic reaction networks. J Chem Phys. 2015;142(3):034118.","journal-title":"J Chem Phys"},{"key":"5966_CR8","doi-asserted-by":"crossref","unstructured":"Cairoli F, Carbone G, Bortolussi L. Abstraction of markov population dynamics via generative adversarial nets. In: Computational Methods in Systems Biology (CMSB), 2021;19\u201335. Springer","DOI":"10.1007\/978-3-030-85633-5_2"},{"issue":"12","key":"5966_CR9","doi-asserted-by":"publisher","first-page":"1009623","DOI":"10.1371\/journal.pcbi.1009623","volume":"17","author":"A Gupta","year":"2021","unstructured":"Gupta A, Schwab C, Khammash M. DeepCME: a deep learning framework for computing solution statistics of the chemical master equation. PLoS Comput Biol. 2021;17(12):1009623.","journal-title":"PLoS Comput Biol"},{"issue":"17","key":"5966_CR10","doi-asserted-by":"publisher","first-page":"2457","DOI":"10.1093\/bioinformatics\/btr401","volume":"27","author":"KR Sanft","year":"2011","unstructured":"Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR. StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics. 2011;27(17):2457\u20138.","journal-title":"Bioinformatics"},{"issue":"24","key":"5966_CR11","doi-asserted-by":"publisher","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","volume":"22","author":"S Hoops","year":"2006","unstructured":"Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. COPASI - a COmplex PAthway SImulator. Bioinformatics. 2006;22(24):3067\u201374.","journal-title":"Bioinformatics"},{"issue":"11","key":"5966_CR12","doi-asserted-by":"publisher","first-page":"79345","DOI":"10.1371\/journal.pone.0079345","volume":"8","author":"TR Maarleveld","year":"2013","unstructured":"Maarleveld TR, Olivier BG, Bruggeman FJ. Stochpy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PLoS ONE. 2013;8(11):79345.","journal-title":"PLoS ONE"},{"issue":"21","key":"5966_CR13","doi-asserted-by":"publisher","first-page":"2848","DOI":"10.1093\/bioinformatics\/btp457","volume":"25","author":"CJ Myers","year":"2009","unstructured":"Myers CJ, Barker N, Jones K, Kuwahara H, Madsen C, Nguyen N-PD. ibiosim: a tool for the analysis and design of genetic circuits. Bioinformatics. 2009;25(21):2848\u20139.","journal-title":"Bioinformatics"},{"issue":"1","key":"5966_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0146732","volume":"11","author":"A Kazeroonian","year":"2016","unstructured":"Kazeroonian A, Frohlich F, Raue A, Theis FJ, Hasenauer J. Cerena: Chemical reaction network analyzer: a toolbox for the simulation and analysis of stochastic chemical kinetics. PLoS ONE. 2016;11(1):1\u201315.","journal-title":"PLoS ONE"},{"issue":"1","key":"5966_CR15","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1109\/TCBB.2009.47","volume":"8","author":"S Mauch","year":"2009","unstructured":"Mauch S, Stalzer M. Efficient formulations for exact stochastic simulation of chemical systems. IEEE\/ACM Trans Comput Biol Bioinf. 2009;8(1):27\u201335.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"issue":"8","key":"5966_CR16","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1093\/bioinformatics\/btr068","volume":"27","author":"G Klingbeil","year":"2011","unstructured":"Klingbeil G, Erban R, Giles M, Maini PK. Stochsimgpu: parallel stochastic simulation for the systems biology toolbox 2 for matlab. Bioinformatics. 2011;27(8):1170\u20131.","journal-title":"Bioinformatics"},{"issue":"3","key":"5966_CR17","doi-asserted-by":"publisher","first-page":"91963","DOI":"10.1371\/journal.pone.0091963","volume":"9","author":"MS Nobile","year":"2014","unstructured":"Nobile MS, Cazzaniga P, Besozzi D, Pescini D, Mauri G. cutauleaping: a gpu-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems. PLoS ONE. 2014;9(3):91963.","journal-title":"PLoS ONE"},{"key":"5966_CR18","doi-asserted-by":"publisher","first-page":"044104","DOI":"10.1063\/1.2145882","volume":"124","author":"B Munsky","year":"2006","unstructured":"Munsky B, Khammash M. The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys. 2006;124:044104.","journal-title":"J Chem Phys"},{"issue":"2","key":"5966_CR19","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1504\/IJCBDD.2009.028825","volume":"2","author":"J Zhang","year":"2009","unstructured":"Zhang J, Watson LT, Cao Y. Adaptive aggregation method for the chemical master equation. Int J Comput Biol Drug Des. 2009;2(2):134\u201348.","journal-title":"Int J Comput Biol Drug Des"},{"key":"5966_CR20","doi-asserted-by":"crossref","unstructured":"Hasenauer J, Wolf V, Kazeroonian A, Theis FJ. Method of conditional moments (MCM) for the chemical master equation. J Math Biol. 2013;1\u201349.","DOI":"10.1007\/s00285-013-0711-5"},{"key":"5966_CR21","doi-asserted-by":"publisher","first-page":"102207","DOI":"10.1016\/j.peva.2021.102207","volume":"148","author":"A Abate","year":"2021","unstructured":"Abate A, Andriushchenko R, \u010ce\u0161ka M, Kwiatkowska M. Adaptive formal approximations of markov chains. Perform Eval. 2021;148:102207.","journal-title":"Perform Eval"},{"issue":"8","key":"5966_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0255880","volume":"16","author":"A Singh","year":"2021","unstructured":"Singh A. Stochastic dynamics of predator-prey interactions. PLoS ONE. 2021;16(8):1\u201314. https:\/\/doi.org\/10.1371\/journal.pone.0255880.","journal-title":"PLoS ONE"},{"key":"5966_CR23","doi-asserted-by":"crossref","unstructured":"Helfrich M, \u010ce\u0161ka M, K\u0159et\u00ednsk\u00fd J, Marti\u010dek \u0160. Abstraction-based segmental simulation of chemical reaction networks. In: Computational Methods in Systems Biology (CMSB), 2022;41\u201360. Springer.","DOI":"10.1007\/978-3-031-15034-0_3"},{"key":"5966_CR24","doi-asserted-by":"crossref","unstructured":"Sukys A, \u00d6cal K, Grima R. Approximating solutions of the chemical master equation using neural networks. Iscience 2022;25(9)","DOI":"10.1016\/j.isci.2022.105010"},{"issue":"1","key":"5966_CR25","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.jtbi.2008.04.011","volume":"254","author":"S Marino","year":"2008","unstructured":"Marino S, Hogue IB, Ray CJ, Kirschner DE. A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol. 2008;254(1):178\u201396.","journal-title":"J Theor Biol"},{"issue":"4","key":"5966_CR26","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1109\/MCS.2009.932926","volume":"29","author":"V Chellaboina","year":"2009","unstructured":"Chellaboina V, Bhat SP, Haddad WM, Bernstein DS. Modeling and analysis of mass-action kinetics. IEEE Control Syst Mag. 2009;29(4):60\u201378.","journal-title":"IEEE Control Syst Mag"},{"issue":"12","key":"5966_CR27","doi-asserted-by":"publisher","first-page":"5393","DOI":"10.1073\/pnas.0909380107","volume":"107","author":"D Soloveichik","year":"2010","unstructured":"Soloveichik D, Seelig G, Winfree E. DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci USA. 2010;107(12):5393\u20138.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1\u20133","key":"5966_CR28","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/0378-4371(92)90283-V","volume":"188","author":"DT Gillespie","year":"1992","unstructured":"Gillespie DT. A rigorous derivation of the chemical master equation. Physica A. 1992;188(1\u20133):404\u201325.","journal-title":"Physica A"},{"issue":"2","key":"5966_CR29","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/0022-5193(71)90054-3","volume":"30","author":"R Lefever","year":"1971","unstructured":"Lefever R, Nicolis G. Chemical instabilities and sustained oscillations. J Theor Biol. 1971;30(2):267\u201384.","journal-title":"J Theor Biol"},{"key":"5966_CR30","doi-asserted-by":"crossref","unstructured":"Madsen C, Myers CJ, Roehner N, Winstead C, Zhang Z. Utilizing stochastic model checking to analyze genetic circuits. In: Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2012;379\u2013386. IEEE.","DOI":"10.1109\/CIBCB.2012.6217255"},{"issue":"25","key":"5966_CR31","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"DT Gillespie","year":"1977","unstructured":"Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem. 1977;81(25):2340\u201361.","journal-title":"J Phys Chem"},{"key":"5966_CR32","doi-asserted-by":"crossref","unstructured":"Robinson JT, Devarakonda MV. Data cache management using frequency-based replacement. In: Conference on Measurement and Modeling of Computer Systems, 1990;134\u2013142. Association for Computing Machinery.","DOI":"10.1145\/98457.98523"},{"issue":"3","key":"5966_CR33","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1006\/jtbi.2002.3078","volume":"218","author":"R Srivastava","year":"2002","unstructured":"Srivastava R, You L, Summers J, Yin J. Stochastic vs. deterministic modeling of intracellular viral kinetics. J Theor Biol. 2002;218(3):309\u201321.","journal-title":"J Theor Biol"},{"issue":"2\u20133","key":"5966_CR34","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.pbiomolbio.2004.01.014","volume":"85","author":"K Burrage","year":"2004","unstructured":"Burrage K, Tian T, Burrage P. A multi-scaled approach for simulating chemical reaction systems. Prog Biophys Mol Biol. 2004;85(2\u20133):217\u201334.","journal-title":"Prog Biophys Mol Biol"},{"key":"5966_CR35","doi-asserted-by":"crossref","unstructured":"\u010ce\u0161ka M, Chau C, K\u0159et\u00ednsk\u00fd J. SeQuaiA: A scalable tool for semi-quantitative analysis of chemical reaction networks. In: Computer Aided Verification (CAV), 2020;653\u2013666. Springer.","DOI":"10.1007\/978-3-030-53288-8_32"},{"issue":"9","key":"5966_CR36","doi-asserted-by":"publisher","first-page":"4059","DOI":"10.1063\/1.1778376","volume":"121","author":"Y Cao","year":"2004","unstructured":"Cao Y, Li H, Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J Chem Phys. 2004;121(9):4059\u201367.","journal-title":"J Chem Phys"},{"issue":"1","key":"5966_CR37","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.compbiolchem.2005.10.007","volume":"30","author":"JM McCollum","year":"2006","unstructured":"McCollum JM, Peterson GD, Cox CD, Simpson ML, Samatova NF. The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Comput Biol Chem. 2006;30(1):39\u201349.","journal-title":"Comput Biol Chem"},{"issue":"11","key":"5966_CR38","doi-asserted-by":"publisher","first-page":"4999","DOI":"10.1063\/1.1545446","volume":"118","author":"CV Rao","year":"2003","unstructured":"Rao CV, Arkin AP. Stochastic chemical kinetics and the quasi-steady-state assumption: application to the gillespie algorithm. J Chem Phys. 2003;118(11):4999\u20135010.","journal-title":"J Chem Phys"},{"issue":"1","key":"5966_CR39","doi-asserted-by":"publisher","first-page":"014116","DOI":"10.1063\/1.1824902","volume":"122","author":"Y Cao","year":"2005","unstructured":"Cao Y, Gillespie DT, Petzold LR. The slow-scale stochastic simulation algorithm. J Chem Phys. 2005;122(1):014116.","journal-title":"J Chem Phys"},{"issue":"2","key":"5966_CR40","first-page":"498","volume":"180","author":"S Engblom","year":"2006","unstructured":"Engblom S. Computing the moments of high dimensional solutions of the master equation. Appl Math Comput. 2006;180(2):498\u2013515.","journal-title":"Appl Math Comput"},{"key":"5966_CR41","unstructured":"Van\u00a0Kampen NG. Stochastic Processes in Physics and Chemistry vol. 1, Elsevier 1992."},{"key":"5966_CR42","unstructured":"Ethier SN, Kurtz TG. Markov Processes - Characterization and Convergence, vol. 282. Wiley; 2009."},{"issue":"1","key":"5966_CR43","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1063\/1.481811","volume":"113","author":"DT Gillespie","year":"2000","unstructured":"Gillespie DT. The chemical Langevin equation. J Chem Phys. 2000;113(1):297\u2013306.","journal-title":"J Chem Phys"},{"key":"5966_CR44","doi-asserted-by":"crossref","unstructured":"Feret J, Salazar A. A generic framework to coarse-grain stochastic reaction networks by abstract interpretation. In: Verification, Model Checking, and Abstract Interpretation (VMCAI), 2023;228\u2013251. Springer","DOI":"10.1007\/978-3-031-24950-1_11"},{"key":"5966_CR45","doi-asserted-by":"publisher","first-page":"114169","DOI":"10.1016\/j.tcs.2023.114169","volume":"977","author":"F Cairoli","year":"2023","unstructured":"Cairoli F, Anselmi F, d\u2019Onofrio A, Bortolussi L. Generative abstraction of markov population processes. Theoret Comput Sci. 2023;977:114169.","journal-title":"Theoret Comput Sci"},{"key":"5966_CR46","doi-asserted-by":"publisher","first-page":"104788","DOI":"10.1016\/j.ic.2021.104788","volume":"281","author":"D Repin","year":"2021","unstructured":"Repin D, Petrov T. Automated deep abstractions for stochastic chemical reaction networks. Inf Comput. 2021;281:104788.","journal-title":"Inf Comput"},{"key":"5966_CR47","doi-asserted-by":"crossref","unstructured":"Cardelli L, Csik\u00e1sz-Nagy A. The cell cycle switch computes approximate majority. Scientific reports 2012;2.","DOI":"10.1038\/srep00656"},{"issue":"22","key":"5966_CR48","doi-asserted-by":"publisher","first-page":"3211","DOI":"10.1093\/bioinformatics\/btr543","volume":"27","author":"MR Lakin","year":"2011","unstructured":"Lakin MR, Youssef S, Polo F, Emmott S, Phillips A. Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics. 2011;27(22):3211\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/btr543.","journal-title":"Bioinformatics"},{"issue":"52","key":"5966_CR49","doi-asserted-by":"publisher","first-page":"12182","DOI":"10.1073\/pnas.1806859115","volume":"115","author":"B Wang","year":"2018","unstructured":"Wang B, Thachuk C, Ellington AD, Winfree E, Soloveichik D. Effective design principles for leakless strand displacement systems. Proc Natl Acad Sci. 2018;115(52):12182\u201391.","journal-title":"Proc Natl Acad Sci"},{"issue":"23","key":"5966_CR50","doi-asserted-by":"publisher","first-page":"5231","DOI":"10.1016\/j.bpj.2021.10.038","volume":"120","author":"DS Tourigny","year":"2021","unstructured":"Tourigny DS, Goldberg AP, Karr JR. Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm. Biophys J. 2021;120(23):5231\u201342.","journal-title":"Biophys J"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05966-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-024-05966-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05966-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,8]],"date-time":"2024-11-08T08:03:29Z","timestamp":1731053009000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-024-05966-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,8]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["5966"],"URL":"https:\/\/doi.org\/10.1186\/s12859-024-05966-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-4905477\/v1","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,8]]},"assertion":[{"value":"13 August 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 October 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"350"}}