{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T16:50:01Z","timestamp":1776012601754,"version":"3.50.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T00:00:00Z","timestamp":1626048000000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"JSPS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"MEXT","doi-asserted-by":"publisher","award":["JP19J20117"],"award-info":[{"award-number":["JP19J20117"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"MEXT","doi-asserted-by":"publisher","award":["JP20H05582"],"award-info":[{"award-number":["JP20H05582"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"MEXT","doi-asserted-by":"publisher","award":["JP20H00624"],"award-info":[{"award-number":["JP20H00624"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"MEXT","doi-asserted-by":"publisher","award":["JP19H01152"],"award-info":[{"award-number":["JP19H01152"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"MEXT","doi-asserted-by":"publisher","award":["JP18KT0016"],"award-info":[{"award-number":["JP18KT0016"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Accumulating evidence has highlighted the importance of microbial interaction networks. Methods have been developed for estimating microbial interaction networks, of which the generalized Lotka\u2013Volterra equation (gLVE)-based method can estimate a directed interaction network. The previous gLVE-based method for estimating microbial interaction networks did not consider time-varying interactions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, we developed unsupervised learning-based microbial interaction inference method using Bayesian estimation (Umibato), a method for estimating time-varying microbial interactions. The Umibato algorithm comprises Gaussian process regression (GPR) and a new Bayesian probabilistic model, the continuous-time regression hidden Markov model (CTRHMM). Growth rates are estimated by GPR, and interaction networks are estimated by CTRHMM. CTRHMM can estimate time-varying interaction networks using interaction states, which are defined as hidden variables. Umibato outperformed the existing methods on synthetic datasets. In addition, it yielded reasonable estimations in experiments on a mouse gut microbiota dataset, thus providing novel insights into the relationship between consumed diets and the gut microbiota.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The C++ and python source codes of the Umibato software are available at https:\/\/github.com\/shion-h\/Umibato.<\/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\/btab287","type":"journal-article","created":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T16:46:37Z","timestamp":1619455597000},"page":"i16-i24","source":"Crossref","is-referenced-by-count":5,"title":["Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model"],"prefix":"10.1093","volume":"37","author":[{"given":"Shion","family":"Hosoda","sequence":"first","affiliation":[{"name":"Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan"},{"name":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , Tokyo 169-8555, Japan"}]},{"given":"Tsukasa","family":"Fukunaga","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan"},{"name":"Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo , Tokyo 113-8656, Japan"}]},{"given":"Michiaki","family":"Hamada","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan"},{"name":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , Tokyo 169-8555, Japan"},{"name":"Graduate School of Medicine, Nippon Medical School , Tokyo 113-8602, Japan"}]}],"member":"286","published-online":{"date-parts":[[2021,7,12]]},"reference":[{"key":"2023062410173515700_btab287-B1","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature12331","article-title":"T reg induction by a rationally selected mixture of Clostridia strains from the human microbiota","volume":"500","author":"Atarashi","year":"2013","journal-title":"Nature"},{"key":"2023062410173515700_btab287-B2","first-page":"546","article-title":"Strain competition keeps a lid on gut pathogens","volume":"14","author":"Attar","year":"2016","journal-title":"Nat. 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