{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,3]],"date-time":"2023-10-03T12:26:24Z","timestamp":1696335984457},"reference-count":22,"publisher":"Hindawi Limited","license":[{"start":{"date-parts":[[2010,7,20]],"date-time":"2010-07-20T00:00:00Z","timestamp":1279584000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"funder":[{"name":"Rural and Environment Research and Analysis Directorate"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Advances in Bioinformatics"],"published-print":{"date-parts":[[2010,7,20]]},"abstract":"<jats:p>An important objective in systems biology is to infer gene regulatory networks from postgenomic data, and dynamic Bayesian networks have been widely applied as a popular tool to this end. The standard approach for nondiscretised data is restricted to a linear model and a homogeneous Markov chain. Recently, various generalisations based on changepoint processes and free allocation mixture models have been proposed. The former aim to relax the homogeneity assumption, whereas the latter are more flexible and, in principle, more adequate for modelling nonlinear processes. In our paper, we compare both paradigms and discuss theoretical shortcomings of the latter approach. We show that a model based on the changepoint process yields systematically better results than the free allocation model when inferring nonstationary gene regulatory processes from simulated gene expression time series. We further cross-compare the performance of both models on three biological systems: macrophages challenged with viral infection, circadian regulation in <jats:italic>Arabidopsis thaliana<\/jats:italic>, and morphogenesis in <jats:italic>Drosophila melanogaster<\/jats:italic>.<\/jats:p>","DOI":"10.1155\/2010\/749848","type":"journal-article","created":{"date-parts":[[2010,7,21]],"date-time":"2010-07-21T06:18:31Z","timestamp":1279693111000},"page":"1-17","source":"Crossref","is-referenced-by-count":3,"title":["Modelling Nonstationary Gene Regulatory Processes"],"prefix":"10.1155","volume":"2010","author":[{"given":"Marco","family":"Grzegorcyzk","sequence":"first","affiliation":[{"name":"Department of Statistics, TU Dortmund University, 44221 Dortmund, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Husmeier","sequence":"additional","affiliation":[{"name":"Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Edinburgh EH93JZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Rahnenf\u00fchrer","sequence":"additional","affiliation":[{"name":"Department of Statistics, TU Dortmund University, 44221 Dortmund, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"98","reference":[{"key":"21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030129"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1023\/A:1020249912095"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1007\/s10994-008-5057-7"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn367"},{"key":"22","doi-asserted-by":"publisher","DOI":"10.1007\/s11222-006-9014-7"},{"key":"27","doi-asserted-by":"publisher","DOI":"10.1198\/016214503000215"},{"issue":"2","key":"13","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1142\/S0219720003000071","volume":"1","year":"2003","journal-title":"Journal of Bioinformatics and Computational Biology"},{"key":"15","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-3-54"},{"key":"26","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1214\/aos\/1176344136","volume":"6","year":"1978","journal-title":"Annals of Statistics"},{"key":"24","first-page":"1369","volume-title":"Non-stationary dynamic Bayesian networks","year":"2009"},{"key":"2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00994110"},{"key":"6","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1093\/biomet\/82.4.711","volume":"82","year":"1995","journal-title":"Biometrika"},{"key":"18","doi-asserted-by":"crossref","first-page":"215","DOI":"10.2307\/1403615","volume":"63","year":"1995","journal-title":"International Statistical Review"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2006.08.009"},{"key":"25","doi-asserted-by":"publisher","DOI":"10.1177\/0748730404268112"},{"key":"19","doi-asserted-by":"publisher","DOI":"10.1016\/j.tcb.2008.03.005"},{"key":"1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1072152"},{"key":"5","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1214\/ss\/1177011136","volume":"7","year":"1992","journal-title":"Statistical Science"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg313"},{"key":"20","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.106.040980"},{"key":"17","volume":"1, article 13","year":"2005","journal-title":"Molecular Systems Biology"},{"key":"28","doi-asserted-by":"publisher","DOI":"10.1142\/S0219720008003539"}],"container-title":["Advances in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/749848.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/749848.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/749848.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T00:15:28Z","timestamp":1607472928000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.hindawi.com\/journals\/abi\/2010\/749848\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,7,20]]},"references-count":22,"alternative-id":["749848","749848"],"URL":"https:\/\/doi.org\/10.1155\/2010\/749848","relation":{},"ISSN":["1687-8027","1687-8035"],"issn-type":[{"value":"1687-8027","type":"print"},{"value":"1687-8035","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,7,20]]}}}