{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T09:47:40Z","timestamp":1781948860144,"version":"3.54.5"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,12,15]],"date-time":"2016-12-15T00:00:00Z","timestamp":1481760000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Council of Scientific and Industrial Research (CSIR) Network Project","award":["BSC0121"],"award-info":[{"award-number":["BSC0121"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that \u2013 is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Implemented on the Agent Modelling Framework developed in-house. C\u2009++ code templates available in Supplementary material.<\/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\/btw709","type":"journal-article","created":{"date-parts":[[2016,11,8]],"date-time":"2016-11-08T12:05:48Z","timestamp":1478606748000},"page":"726-732","source":"Crossref","is-referenced-by-count":7,"title":["Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems\u00a0biology"],"prefix":"10.1093","volume":"33","author":[{"given":"Arya A","family":"Das","sequence":"first","affiliation":[{"name":"Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T","family":"Ajayakumar Darsana","sequence":"additional","affiliation":[{"name":"Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Jacob","sequence":"additional","affiliation":[{"name":"Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,12,15]]},"reference":[{"key":"2023020204501971300_btw709-B1","doi-asserted-by":"crossref","first-page":"16392","DOI":"10.1073\/pnas.1101263108","article-title":"HER2 overcomes PTEN (loss)-induced senescence to cause aggressive prostate cancer","volume":"108","author":"Ahmad","year":"2011","journal-title":"Proc. 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