{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:31:39Z","timestamp":1740137499017,"version":"3.37.3"},"reference-count":24,"publisher":"World Scientific Pub Co Pte Ltd","issue":"04","funder":[{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"crossref","award":["61070130"],"award-info":[{"award-number":["61070130"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"the Key Project of Natural Science Foundation of Shandong Province","award":["ZR2011FZ001"],"award-info":[{"award-number":["ZR2011FZ001"]}]},{"name":"National Natural Science Foundation of Shandong Province of China","award":["ZR2010FM040"],"award-info":[{"award-number":["ZR2010FM040"]}]},{"name":"Special Funding Project for Independent Innovation Achievements transform of Shandong Province","award":["2012CX30202"],"award-info":[{"award-number":["2012CX30202"]}]},{"name":"Foundation of Shandong University for Independent Innovation","award":["2012DZ038"],"award-info":[{"award-number":["2012DZ038"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2016,8]]},"abstract":"<jats:p> This paper demonstrates a new time-delayed mass action model which applies a set of delay differential equations (DDEs) to represent the dynamics of gene regulatory networks (GRNs). The mass action model is a classical model which is often used to describe the kinetics of biochemical processes, so it is fit for GRN modeling. The ability to incorporate time-delayed parameters in this model enables different time delays of interaction between genes. Moreover, an efficient learning method which employs population-based incremental learning (PBIL) algorithm and trigonometric differential evolution (TDE) algorithm TDE is proposed to automatically evolve the structure of the network and infer the optimal parameters from observed time-series gene expression data. Experiments on three well-known motifs of GRN and a real budding yeast cell cycle network show that the proposal can not only successfully infer the network structure and parameters but also has a strong anti-noise ability. Compared with other works, this method also has a great improvement in performances. <\/jats:p>","DOI":"10.1142\/s0219720016500128","type":"journal-article","created":{"date-parts":[[2016,2,18]],"date-time":"2016-02-18T02:26:27Z","timestamp":1455762387000},"page":"1650012","source":"Crossref","is-referenced-by-count":1,"title":["Inferring gene regulatory networks using a time-delayed mass action model"],"prefix":"10.1142","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4134-2352","authenticated-orcid":false,"given":"Yaou","family":"Zhao","sequence":"first","affiliation":[{"name":"School of Information Science and Engineering, University of Jinan, Jinan, Shandong Province 250100, P. R. China"},{"name":"Shandong Provincial Key Laboratory of Network Based, Intelligent Computing, University of Jinan, Jinan, Shandong Province 250022, P. R. China"}]},{"given":"Mingyan","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, University of Jinan, Jinan, Shandong Province 250100, P. R. China"}]},{"given":"Yuehui","family":"Chen","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Network Based, Intelligent Computing, University of Jinan, Jinan, Shandong Province 250022, P. R. China"}]}],"member":"219","published-online":{"date-parts":[[2016,8,25]]},"reference":[{"key":"S0219720016500128BIB001","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2013.09.004"},{"key":"S0219720016500128BIB002","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2014.02.011"},{"key":"S0219720016500128BIB003","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2008.0132.focus"},{"key":"S0219720016500128BIB004","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030129"},{"key":"S0219720016500128BIB005","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.12.1183"},{"key":"S0219720016500128BIB006","doi-asserted-by":"publisher","DOI":"10.1126\/science.1081900"},{"key":"S0219720016500128BIB007","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0933416100"},{"key":"S0219720016500128BIB008","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl003"},{"key":"S0219720016500128BIB009","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-93107-9"},{"key":"S0219720016500128BIB010","doi-asserted-by":"publisher","DOI":"10.1016\/j.na.2010.01.016"},{"key":"S0219720016500128BIB011","doi-asserted-by":"publisher","DOI":"10.1126\/science.1074560"},{"key":"S0219720016500128BIB012","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.01.055"},{"key":"S0219720016500128BIB013","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2007.03.013"},{"key":"S0219720016500128BIB014","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.152046799"},{"key":"S0219720016500128BIB015","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.106.101717"},{"key":"S0219720016500128BIB016","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/msb.2008.74","volume":"5","author":"Chen WW","year":"2009","journal-title":"Mol Sys Biol"},{"key":"S0219720016500128BIB017","doi-asserted-by":"publisher","DOI":"10.1016\/S0014-5793(03)00279-5"},{"key":"S0219720016500128BIB018","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(03)00494-9"},{"key":"S0219720016500128BIB021","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth140"},{"key":"S0219720016500128BIB022","doi-asserted-by":"publisher","DOI":"10.1023\/A:1024653025686"},{"key":"S0219720016500128BIB023","doi-asserted-by":"publisher","DOI":"10.1016\/j.compchemeng.2006.09.015"},{"key":"S0219720016500128BIB024","doi-asserted-by":"publisher","DOI":"10.1080\/10635150490522304"},{"key":"S0219720016500128BIB026","doi-asserted-by":"publisher","DOI":"10.1038\/ng881"},{"key":"S0219720016500128BIB027","doi-asserted-by":"publisher","DOI":"10.1126\/science.1075090"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720016500128","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T14:09:19Z","timestamp":1565186959000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720016500128"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8]]},"references-count":24,"journal-issue":{"issue":"04","published-online":{"date-parts":[[2016,8,25]]},"published-print":{"date-parts":[[2016,8]]}},"alternative-id":["10.1142\/S0219720016500128"],"URL":"https:\/\/doi.org\/10.1142\/s0219720016500128","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"type":"print","value":"0219-7200"},{"type":"electronic","value":"1757-6334"}],"subject":[],"published":{"date-parts":[[2016,8]]}}}