{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T00:49:30Z","timestamp":1773103770522,"version":"3.50.1"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T00:00:00Z","timestamp":1630368000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institutes of Health Training Grant","award":["T32 HL007622"],"award-info":[{"award-number":["T32 HL007622"]}]},{"DOI":"10.13039\/501100010446","name":"Institute for Basic Science","doi-asserted-by":"publisher","award":["IBS-R029-C3"],"award-info":[{"award-number":["IBS-R029-C3"]}],"id":[{"id":"10.13039\/501100010446","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014364","name":"Samsung Science and Technology Foundation","doi-asserted-by":"publisher","award":["SSTF-BA1902-01"],"award-info":[{"award-number":["SSTF-BA1902-01"]}],"id":[{"id":"10.13039\/501100014364","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Fundamental to biological study is identifying regulatory interactions. The recent surge in time-series data collection in biology provides a unique opportunity to infer regulations computationally. However, when components oscillate, model-free inference methods, while easily implemented, struggle to distinguish periodic synchrony and causality. Alternatively, model-based methods test the reproducibility of time series given a specific model but require inefficient simulations and have limited applicability.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We develop an inference method based on a general model of molecular, neuronal and ecological oscillatory systems that merges the advantages of both model-based and model-free methods, namely accuracy, broad applicability and usability. Our method successfully infers the positive and negative regulations within various oscillatory networks, e.g. the repressilator and a network of cofactors at the pS2 promoter, outperforming popular inference methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>We provide a computational package, ION (Inferring Oscillatory Networks), that users can easily apply to noisy, oscillatory time series to uncover the mechanisms by which diverse systems generate oscillations. Accompanying MATLAB code under a BSD-style license and examples are available at https:\/\/github.com\/Mathbiomed\/ION. Additionally, the code is available under a CC-BY 4.0 License at https:\/\/doi.org\/10.6084\/m9.figshare.16431408.v1.<\/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\/btab623","type":"journal-article","created":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T11:21:35Z","timestamp":1630408895000},"page":"196-203","source":"Crossref","is-referenced-by-count":6,"title":["Inferring causality in biological oscillators"],"prefix":"10.1093","volume":"38","author":[{"given":"Jonathan","family":"Tyler","sequence":"first","affiliation":[{"name":"Department of Mathematics, University of Michigan , Ann Arbor, MI 48109, USA"},{"name":"Department of Pediatrics, University of Michigan , Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Forger","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Michigan , Ann Arbor, MI 48109, USA"},{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7842-2172","authenticated-orcid":false,"given":"Jae Kyoung","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology , Daejeon 34141, Republic of Kore a"},{"name":"Biomedical Mathematics Group, Institute for Basic Science , Daejeon 34126, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,8,31]]},"reference":[{"key":"2023020108400804300_btab623-B1","doi-asserted-by":"crossref","first-page":"4512","DOI":"10.1073\/pnas.1521178113","article-title":"Functional network inference of the suprachiasmatic nucleus","volume":"113","author":"Abel","year":"2016","journal-title":"Proc. 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