{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T10:47:52Z","timestamp":1759402072295},"reference-count":36,"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":480,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Detecting modules of co-ordinated activity is fundamental in the analysis of large biological studies. For two-dimensional data (e.g. genes \u00d7 patients), this is often done via clustering or biclustering. More recently, studies monitoring patients over time have added another dimension. Analysis is much more challenging in this case, especially when time measurements are not synchronized. New methods that can analyze three-way data are thus needed.<\/jats:p>\n               <jats:p>Results: We present a new algorithm for finding coherent and flexible modules in three-way data. Our method can identify both core modules that appear in multiple patients and patient-specific augmentations of these core modules that contain additional genes. Our algorithm is based on a hierarchical Bayesian data model and Gibbs sampling. The algorithm outperforms extant methods on simulated and on real data. The method successfully dissected key components of septic shock response from time series measurements of gene expression. Detected patient-specific module augmentations were informative for disease outcome. In analyzing brain functional magnetic resonance imaging time series of subjects at rest, it detected the pertinent brain regions involved.<\/jats:p>\n               <jats:p>Availability and implementation: R code and data are available at http:\/\/acgt.cs.tau.ac.il\/twigs\/.<\/jats:p>\n               <jats:p>Contact: \u00a0rshamir@tau.ac.il<\/jats:p>\n               <jats:p>Supplementary information \u00a0: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv228","type":"journal-article","created":{"date-parts":[[2015,6,13]],"date-time":"2015-06-13T17:12:36Z","timestamp":1434215556000},"page":"i17-i26","source":"Crossref","is-referenced-by-count":21,"title":["A hierarchical Bayesian model for flexible module discovery in three-way time-series data"],"prefix":"10.1093","volume":"31","author":[{"given":"David","family":"Amar","sequence":"first","affiliation":[{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"}]},{"given":"Daniel","family":"Yekutieli","sequence":"additional","affiliation":[{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"}]},{"given":"Adi","family":"Maron-Katz","sequence":"additional","affiliation":[{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"},{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"},{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"}]},{"given":"Talma","family":"Hendler","sequence":"additional","affiliation":[{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"},{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"}]},{"given":"Ron","family":"Shamir","sequence":"additional","affiliation":[{"name":"1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Statistics and OR, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 3Functional Brain Center, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel and 4Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"}]}],"member":"286","published-online":{"date-parts":[[2015,6,10]]},"reference":[{"key":"2023020115421140200_btv228-B1","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1093\/cercor\/bhs352","article-title":"Tracking whole-brain connectivity dynamics in the resting state","volume":"24","author":"Allen","year":"2014","journal-title":"Cereb. 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