{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:17Z","timestamp":1772138057290,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,2,24]],"date-time":"2023-02-24T00:00:00Z","timestamp":1677196800000},"content-version":"vor","delay-in-days":23,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004759","name":"Isfahan University of Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004759","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003970","name":"Isfahan University of Medical Sciences","doi-asserted-by":"publisher","award":["199503"],"award-info":[{"award-number":["199503"]}],"id":[{"id":"10.13039\/501100003970","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The recent availability of omics data allows the construction of holistic maps of interactions between numerous role-playing biomolecules. However, these networks are often static, ignoring the dynamic behavior of biological processes. On the other hand, dynamic models are commonly constructed on small scales. Hence, the construction of large-scale dynamic models that can quantitatively predict the time-course cellular behaviors remains a big challenge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, a pipeline is proposed for the automatic construction of large-scale dynamic models. The pipeline uses a list of biomolecules and their time-course trajectories in a given phenomenon as input. First, the interaction network of the biomolecules is constructed. To state the underlying molecular events of each interaction, it is translated into a map of biochemical reactions. Next, to define the kinetics of the reactions, an ordinary differential equation (ODE) is generated for each involved biomolecule. Finally, the parameters of the ODE system are estimated by a novel large-scale parameter approximation method. The high performance of the pipeline is demonstrated by modeling the response of a colorectal cancer cell line to different chemotherapy regimens. In conclusion, Systematic Protein Association Dynamic ANalyzer constructs genome-scale dynamic models, filling the gap between large-scale static and small-scale dynamic modeling strategies. This simulation approach allows for holistic quantitative predictions which are critical for the simulation of therapeutic interventions in precision medicine.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Detailed information about the constructed large-scale model of colorectal cancer is available in supplementary data. The SPADAN toolbox source code is also available on GitHub (https:\/\/github.com\/PooyaBorzou\/SPADAN).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad079","type":"journal-article","created":{"date-parts":[[2023,2,24]],"date-time":"2023-02-24T08:34:53Z","timestamp":1677227693000},"source":"Crossref","is-referenced-by-count":9,"title":["A novel strategy for dynamic modeling of genome-scale interaction networks"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0249-959X","authenticated-orcid":false,"given":"Pooya","family":"Borzou","sequence":"first","affiliation":[{"name":"Department of Electrical and Computer Engineering, Isfahan University of Technology , Isfahan 84156-83111, Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jafar","family":"Ghaisari","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Isfahan University of Technology , Isfahan 84156-83111, Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iman","family":"Izadi","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Isfahan University of Technology , Isfahan 84156-83111, Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasin","family":"Eshraghi","sequence":"additional","affiliation":[{"name":"Regenerative Medicine Research Center, Isfahan University of Medical Sciences , Isfahan 81746-73476, Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yousof","family":"Gheisari","sequence":"additional","affiliation":[{"name":"Regenerative Medicine Research Center, Isfahan University of Medical Sciences , Isfahan 81746-73476, Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,2,24]]},"reference":[{"key":"2023022713393496000_","first-page":"111","author":"Agrawal","year":"2018"},{"key":"2023022713393496000_","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1752-0509-4-11","article-title":"An iterative identification procedure for dynamic modeling of biochemical networks","volume":"4","author":"Balsa-Canto","year":"2010","journal-title":"BMC Syst. 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