{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T20:27:54Z","timestamp":1784147274609,"version":"3.55.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,7,17]],"date-time":"2019-07-17T00:00:00Z","timestamp":1563321600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61871272"],"award-info":[{"award-number":["61871272"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Scientific Research and Development Funding Program","award":["JCYJ20170302154328155"],"award-info":[{"award-number":["JCYJ20170302154328155"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Inferring gene regulatory networks from gene expression time series data is important for gaining insights into the complex processes of cell life. A popular approach is to infer Boolean networks. However, it is still a pressing open problem to infer accurate Boolean networks from experimental data that are typically short and noisy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address the problem, we propose a Boolean network inference algorithm which is able to infer accurate Boolean network topology and dynamics from short and noisy time series data. The main idea is that, for each target gene, we use an And\/Or tree ensemble algorithm to select prime implicants of which each is a conjunction of a set of input genes. The selected prime implicants are important features for predicting the states of the target gene. Using these important features we then infer the Boolean function of the target gene. Finally, the Boolean functions of all target genes are combined as a Boolean network. Using the data generated from artificial and real-world gene regulatory networks, we show that our algorithm can infer more accurate Boolean network topology and dynamics from short and noisy time series data than other algorithms. Our algorithm enables us to gain better insights into complex regulatory mechanisms of cell life.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Package ATEN is freely available at https:\/\/github.com\/ningshi\/ATEN.<\/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\/btz563","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T19:17:27Z","timestamp":1563995847000},"page":"578-585","source":"Crossref","is-referenced-by-count":27,"title":["ATEN: And\/Or tree ensemble for inferring accurate Boolean network topology and dynamics"],"prefix":"10.1093","volume":"36","author":[{"given":"Ning","family":"Shi","sequence":"first","affiliation":[{"name":"School of Computer Science , University of Birmingham, Birmingham B15 2TT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zexuan","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Software Engineering , Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering , Southern University of Science and Technology, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Parker","sequence":"additional","affiliation":[{"name":"School of Computer Science , University of Birmingham, Birmingham B15 2TT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan","family":"He","sequence":"additional","affiliation":[{"name":"School of Computer Science , University of Birmingham, Birmingham B15 2TT, UK"},{"name":"Department of Computer Science and Engineering , Southern University of Science and Technology, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,7,17]]},"reference":[{"key":"2023013112062151700_btz563-B1","first-page":"17","article-title":"Identification of genetic networks from a small number of gene expression patterns under the Boolean network model","volume":"5","author":"Akutsu","year":"1999","journal-title":"Pac. Symp. Biocomput"},{"key":"2023013112062151700_btz563-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(03)00035-3","article-title":"The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster","volume":"223","author":"Albert","year":"2003","journal-title":"J. Theor. Biol"},{"key":"2023013112062151700_btz563-B3","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","article-title":"Inference of gene regulatory networks and compound mode of action from time course gene expression profiles","volume":"22","author":"Bansal","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B4","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1093\/bioinformatics\/bth283","article-title":"Analyzing time series gene expression data","volume":"20","author":"Bar-Joseph","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B5","doi-asserted-by":"crossref","first-page":"e0171097.","DOI":"10.1371\/journal.pone.0171097","article-title":"A novel mutual information-based Boolean network inference method from time series gene expression data","volume":"12","author":"Barman","year":"2017","journal-title":"PLoS One"},{"key":"2023013112062151700_btz563-B6","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.compbiomed.2014.02.011","article-title":"A review on the computational approaches for gene regulatory network construction","volume":"48","author":"Chai","year":"2014","journal-title":"Comput. Biol. Med"},{"key":"2023013112062151700_btz563-B7","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1089\/10665270252833208","article-title":"Modeling and simulation of genetic regulatory systems: a literature review","volume":"9","author":"de Jong","year":"2002","journal-title":"J. Comp. Biol"},{"key":"2023013112062151700_btz563-B8","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1089\/106652700750050961","article-title":"Using Bayesian networks to analyze expression data","volume":"7","author":"Friedman","year":"2000","journal-title":"J. Comput. Biol. J. Comput. Mol. Cell Biol"},{"key":"2023013112062151700_btz563-B9","doi-asserted-by":"crossref","first-page":"24456.","DOI":"10.1038\/srep24456","article-title":"Control of complex networks requires both structure and dynamics","volume":"6","author":"Gates","year":"2016","journal-title":"Sci. Rep"},{"key":"2023013112062151700_btz563-B10","doi-asserted-by":"crossref","first-page":"2225","DOI":"10.1016\/j.patrec.2010.03.014","article-title":"Variable selection using random forests","volume":"31","author":"Genuer","year":"2010","journal-title":"Pattern Recognit. Lett"},{"key":"2023013112062151700_btz563-B11","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.biosystems.2008.12.004","article-title":"Gene regulatory network inference: data integration in dynamic models - a review","volume":"96","author":"Hecker","year":"2009","journal-title":"Biosystems"},{"key":"2023013112062151700_btz563-B12","doi-asserted-by":"crossref","first-page":"e12776.","DOI":"10.1371\/journal.pone.0012776","article-title":"Inferring regulatory networks from expression data using tree-based methods","volume":"5","author":"Huynh-Thu","year":"2010","journal-title":"PLoS One"},{"key":"2023013112062151700_btz563-B13","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1038\/nrm2503","article-title":"Modelling and analysis of gene regulatory networks","volume":"9","author":"Karlebach","year":"2008","journal-title":"Nat. Rev. Mol. Cell Biol"},{"key":"2023013112062151700_btz563-B14","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/0022-5193(69)90015-0","article-title":"Metabolic stability and epigensis in randomly constructed genetic nets","volume":"22","author":"Kauffman","year":"1969","journal-title":"J. Theor. Biol"},{"key":"2023013112062151700_btz563-B15","doi-asserted-by":"crossref","first-page":"36812","DOI":"10.1038\/srep36812","article-title":"Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy","volume":"6","author":"Knijnenburg","year":"2016","journal-title":"Sci. Rep"},{"key":"2023013112062151700_btz563-B16","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1023\/A:1023905711304","article-title":"On learning gene regulatory networks under the Boolean network model","volume":"52","author":"L\u00e4hdesm\u00e4ki","year":"2003","journal-title":"Mach. Learn"},{"key":"2023013112062151700_btz563-B17","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.jtbi.2004.04.037","article-title":"A computational algebra approach to the reverse engineering of gene regulatory networks","volume":"229","author":"Laubenbacher","year":"2004","journal-title":"J. Theor. Biol"},{"key":"2023013112062151700_btz563-B18","first-page":"18","article-title":"REVEAL, a general reverse engineering algorithm for inference of genetic network architectures","volume":"3","author":"Liang","year":"1998","journal-title":"Pac. Symp. Biocomp"},{"key":"2023013112062151700_btz563-B19","doi-asserted-by":"crossref","first-page":"355.","DOI":"10.1186\/s12859-016-1235-y","article-title":"BTR: training asynchronous Boolean models using single-cell expression data","volume":"17","author":"Lim","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2023013112062151700_btz563-B20","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1016\/j.artint.2009.07.003","article-title":"AND\/OR Branch-and-Bound search for combinatorial optimization in graphical models","volume":"173","author":"Marinescu","year":"2009","journal-title":"Artif. Intell"},{"key":"2023013112062151700_btz563-B21","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.1093\/bioinformatics\/btr166","article-title":"Inferring Boolean network structure via correlation","volume":"27","author":"Maucher","year":"2011","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B22","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1002\/j.1538-7305.1956.tb03835.x","article-title":"Minimization of Boolean functions","volume":"62","author":"McCluskey","year":"1956","journal-title":"Bell Syst. Tech. J"},{"key":"2023013112062151700_btz563-B23","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","article-title":"Boolnet - an R package for generation, reconstruction, and analysis of Boolean networks","volume":"26","author":"M\u00fcssel","year":"2010","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B24","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1093\/bioinformatics\/btv680","article-title":"Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models","volume":"32","author":"Pirkl","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B25","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1080\/00029890.1955.11988710","article-title":"A way to simplify truth functions","volume":"62","author":"Quine","year":"1955","journal-title":"Am. Math. Mon"},{"key":"2023013112062151700_btz563-B26","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1198\/1061860032238","article-title":"Logic regression","volume":"12","author":"Ruczinski","year":"2003","journal-title":"J. Comput. Graph. Stat"},{"key":"2023013112062151700_btz563-B27","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ymeth.2012.10.012","article-title":"Boolean modeling of biological regulatory networks: a methodology tutorial","volume":"62","author":"Saadatpour","year":"2013","journal-title":"Methods"},{"key":"2023013112062151700_btz563-B28","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/bioinformatics\/btx605","article-title":"A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data","volume":"34","author":"Sanchez-Castillo","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B29","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1093\/biostatistics\/kxm024","article-title":"Identification of SNP interactions using logic regression","volume":"9","author":"Schwender","year":"2008","journal-title":"Biostatistics"},{"key":"2023013112062151700_btz563-B30","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/bioinformatics\/18.2.261","article-title":"Probabilistic Boolean networks: a rule-based uncertainty model for gene-regulatory networks","volume":"18","author":"Shmulevich","year":"2002","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B31","doi-asserted-by":"crossref","first-page":"1778","DOI":"10.1109\/JPROC.2002.804686","article-title":"From Boolean to probabalistic Boolean networks as models of genetic regulatory networks","volume":"90","author":"Shmulevich","year":"2002","journal-title":"Proc. IEEE"},{"key":"2023013112062151700_btz563-B32","doi-asserted-by":"crossref","first-page":"i130","DOI":"10.1093\/bioinformatics\/btu285","article-title":"Functional association networks as priors for gene regulatory network inference","volume":"30","author":"Studham","year":"2014","journal-title":"Bioinformatics"},{"key":"2023013112062151700_btz563-B33","doi-asserted-by":"crossref","DOI":"10.1007\/978-94-015-7744-1","volume-title":"Simulated Annealing: Theory and Applications","author":"van Laarhoven","year":"1987"},{"key":"2023013112062151700_btz563-B34","doi-asserted-by":"crossref","first-page":"37.","DOI":"10.1186\/1752-0509-8-37","article-title":"An algebra-based method for inferring gene regulatory networks","volume":"8","author":"Vera-Licona","year":"2014","journal-title":"BMC Syst. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz563\/29106184\/btz563.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/2\/578\/48990734\/btz563.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/2\/578\/48990734\/btz563.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:22:24Z","timestamp":1675200144000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/2\/578\/5542393"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,7,17]]},"references-count":34,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz563","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1,15]]},"published":{"date-parts":[[2019,7,17]]}}}