{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T14:31:40Z","timestamp":1759588300117},"reference-count":23,"publisher":"World Scientific Pub Co Pte Lt","issue":"05","funder":[{"name":"PhD research startup foundation of Zaozhuang University","award":["2014BS13"],"award-info":[{"award-number":["2014BS13"]}]},{"name":"National Natural Science Foundation of Shandong Province of China","award":["ZR2015PF007"],"award-info":[{"award-number":["ZR2015PF007"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2016,10]]},"abstract":"<jats:p> Inference of gene regulatory networks has been becoming a major area of interest in the field of systems biology over the past decade. In this paper, we present a novel representation of S-system model, named restricted gene expression programming (RGEP), to infer gene regulatory network. A new hybrid evolutionary algorithm based on structure-based evolutionary algorithm and cuckoo search (CS) is proposed to optimize the architecture and corresponding parameters of model, respectively. Two synthetic benchmark datasets and one real biological dataset from SOS DNA repair network in E. coli are used to test the validity of our method. Experimental results demonstrate that our proposed method performs better than previously proposed popular methods. <\/jats:p>","DOI":"10.1142\/s0219720016500219","type":"journal-article","created":{"date-parts":[[2016,5,27]],"date-time":"2016-05-27T06:18:20Z","timestamp":1464329900000},"page":"1650021","source":"Crossref","is-referenced-by-count":6,"title":["Reverse engineering of gene regulatory network using restricted gene expression programming"],"prefix":"10.1142","volume":"14","author":[{"given":"Bin","family":"Yang","sequence":"first","affiliation":[{"name":"School of Information Science and Engineering, Zaozhuang University, Zaozhuang 277160, China"}]},{"given":"Sanrong","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Zaozhuang University, Zaozhuang 277160, China"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Zaozhuang University, Zaozhuang 277160, China"}]}],"member":"219","published-online":{"date-parts":[[2016,11,3]]},"reference":[{"key":"S0219720016500219BIB002","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr628"},{"key":"S0219720016500219BIB003","first-page":"1046","author":"Zavolan M","year":"2015","journal-title":"Methods"},{"key":"S0219720016500219BIB004","doi-asserted-by":"publisher","DOI":"10.1186\/s13637-014-0010-5"},{"key":"S0219720016500219BIB005","volume-title":"Modeling Gene Expression Data using Dynamic Bayesian Network","author":"Murphy K","year":"1999"},{"key":"S0219720016500219BIB006","doi-asserted-by":"publisher","DOI":"10.1016\/j.neucom.2012.07.015"},{"key":"S0219720016500219BIB007","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl1001"},{"issue":"2","key":"S0219720016500219BIB008","first-page":"210","volume":"6","author":"Chaouiyaa C","year":"2008","journal-title":"Brief Bioinform"},{"key":"S0219720016500219BIB009","doi-asserted-by":"publisher","DOI":"10.1088\/1478-3975\/11\/4\/046004"},{"key":"S0219720016500219BIB010","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl522"},{"key":"S0219720016500219BIB011","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg027"},{"key":"S0219720016500219BIB012","doi-asserted-by":"publisher","DOI":"10.1007\/s00521-010-0435-z"},{"key":"S0219720016500219BIB014","doi-asserted-by":"publisher","DOI":"10.1109\/TEVC.2012.2218610"},{"key":"S0219720016500219BIB015","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl122"},{"issue":"2","key":"S0219720016500219BIB017","first-page":"87","volume":"13","author":"Ferreira C","year":"2001","journal-title":"Complex Syst"},{"key":"S0219720016500219BIB018","doi-asserted-by":"publisher","DOI":"10.1049\/iet-syb.2008.0175"},{"issue":"4","key":"S0219720016500219BIB019","first-page":"285","volume":"14","author":"Mihai O","year":"2003","journal-title":"Complex Syst"},{"key":"S0219720016500219BIB020","doi-asserted-by":"publisher","DOI":"10.1007\/s00521-013-1367-1"},{"key":"S0219720016500219BIB021","doi-asserted-by":"publisher","DOI":"10.1007\/s10462-011-9276-0"},{"key":"S0219720016500219BIB023","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti071"},{"key":"S0219720016500219BIB024","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.152046799"},{"key":"S0219720016500219BIB025","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg1071"},{"key":"S0219720016500219BIB026","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-S1-S56"},{"issue":"2","key":"S0219720016500219BIB027","first-page":"205","volume":"16","author":"Noman N","year":"2005","journal-title":"Genome Inform"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720016500219","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T16:14:28Z","timestamp":1565194468000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720016500219"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10]]},"references-count":23,"journal-issue":{"issue":"05","published-online":{"date-parts":[[2016,11,3]]},"published-print":{"date-parts":[[2016,10]]}},"alternative-id":["10.1142\/S0219720016500219"],"URL":"https:\/\/doi.org\/10.1142\/s0219720016500219","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,10]]}}}