{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T21:36:37Z","timestamp":1771018597713,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1576,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The generation of time series transcriptomic datasets collected under multiple experimental conditions has proven to be a powerful approach for disentangling complex biological processes, allowing for the reverse engineering of gene regulatory networks (GRNs). Most methods for reverse engineering GRNs from multiple datasets assume that each of the time series were generated from networks with identical topology. In this study, we outline a hierarchical, non-parametric Bayesian approach for reverse engineering GRNs using multiple time series that can be applied in a number of novel situations including: (i) where different, but overlapping sets of transcription factors are expected to bind in the different experimental conditions; that is, where switching events could potentially arise under the different treatments and (ii) for inference in evolutionary related species in which orthologous GRNs exist. More generally, the method can be used to identify context-specific regulation by leveraging time series gene expression data alongside methods that can identify putative lists of transcription factors or transcription factor targets.<\/jats:p>\n               <jats:p>Results: The hierarchical inference outperforms related (but non-hierarchical) approaches when the networks used to generate the data were identical, and performs comparably even when the networks used to generate data were independent. The method was subsequently used alongside yeast one hybrid and microarray time series data to infer potential transcriptional switches in Arabidopsis thaliana response to stress. The results confirm previous biological studies and allow for additional insights into gene regulation under various abiotic stresses.<\/jats:p>\n               <jats:p>Availability: The methods outlined in this article have been implemented in Matlab and are available on request.<\/jats:p>\n               <jats:p>Contact: \u00a0d.l.wild@warwick.ac.uk<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data is available for this article.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts222","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T14:09:18Z","timestamp":1339423758000},"page":"i233-i241","source":"Crossref","is-referenced-by-count":44,"title":["Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks"],"prefix":"10.1093","volume":"28","author":[{"given":"Christopher A.","family":"Penfold","sequence":"first","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL and 2School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK"}]},{"given":"Vicky","family":"Buchanan-Wollaston","sequence":"additional","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL and 2School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK"},{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL and 2School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK"}]},{"given":"Katherine J.","family":"Denby","sequence":"additional","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL and 2School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK"},{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL and 2School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK"}]},{"given":"David L.","family":"Wild","sequence":"additional","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL and 2School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512345068000_B1","doi-asserted-by":"crossref","first-page":"2937","DOI":"10.1093\/bioinformatics\/btp511","article-title":"Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics","volume":"25","author":"\u00c4ij\u00f6","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512345068000_B2","article-title":"Reliable transfer of transcriptional gene regulatory networks between taxanomically related organisms","volume":"3","author":"Baumbach","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012512345068000_B3","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1105\/tpc.111.083345","article-title":"High resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation","volume":"23","author":"Breeze","year":"2011","journal-title":"Plant Cell"},{"key":"2023012512345068000_B4","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1038\/nbt0805-942","article-title":"Discovering DNA regulatory elements with bacteria","volume":"23","author":"Bulyk","year":"2005","journal-title":"Nat. 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