{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T15:58:52Z","timestamp":1791215932291,"version":"4.1.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM123558"],"award-info":[{"award-number":["R01GM123558"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Circadian rhythms are fundamental to biology: they occur at the molecular level across all species and are critical to homeostasis and biological functions. They are also essential for health and medicine, as disruption of circadian regulation has been linked to numerous health problems, and many drug targets exhibit circadian oscillations, highlighting the importance of molecular-level circadian insight for precision medicine. Despite the rapid growth of circadian omic time series datasets, informatics tools for processing and analyzing this growing wealth of data remain limited.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>CircadiOmics provides, to the best of our knowledge, the largest repository and analytical platform for circadian omic data, consisting primarily of transcriptomic data, along with metabolomic, proteomic, and acetylomic datasets. CircadiOmics contains 704 omic datasets across 18 species, 30 tissue\/organ categories, and 21 experiment types, including genetic manipulations, dietary interventions, and disease-associated conditions. By leveraging this repository, users can access an environment for comparing and visualizing molecular-level circadian oscillations. Periodicity statistics computed using BIO_CYCLE, including period, amplitude, phase, p-values, and q-values, are available as interactive plots and downloadable tables. This updated version of CircadiOmics introduces new features and substantially expanded data coverage, establishing it as a comprehensive resource for the exploration and analysis of circadian omic data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CircadiOmics is freely accessible at: https:\/\/circadiomics.igb.uci.edu. The source code for BIO_CYCLE is available on GitHub: https:\/\/github.com\/BaldiLab\/BIO_CYCLE and archived on Zenodo: https:\/\/doi.org\/10.5281\/zenodo.22108329.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag716","type":"journal-article","created":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T11:32:59Z","timestamp":1790508779000},"source":"Crossref","is-referenced-by-count":0,"title":["CircadiOmics: bioinformatics platform for circadian rhythms"],"prefix":"10.1093","volume":"42","author":[{"given":"Kousha","family":"Changizi Ashtiani","sequence":"first","affiliation":[{"name":"Artificial Intelligence in Science Institute, University of California , Irvine, CA 92697,","place":["United States"]},{"name":"Department of Computer Science, University of California , Irvine, CA 92697,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8752-4664","authenticated-orcid":false,"given":"Pierre","family":"Baldi","sequence":"additional","affiliation":[{"name":"Artificial Intelligence in Science Institute, University of California , Irvine, CA 92697,","place":["United States"]},{"name":"Department of Computer Science, University of California , Irvine, CA 92697,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"key":"2026100511420937200_btag716-B1","doi-asserted-by":"publisher","first-page":"3051","DOI":"10.1093\/bioinformatics\/btw504","article-title":"What time is it? Deep learning approaches for circadian rhythms","volume":"32","author":"Agostinelli","year":"2016","journal-title":"Bioinformatics"},{"key":"2026100511420937200_btag716-B2","doi-asserted-by":"publisher","first-page":"9897","DOI":"10.1073\/pnas.1120636110","article-title":"Circadian clock regulates the host response to Salmonella","volume":"110","author":"Bellet","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026100511420937200_btag716-B3","doi-asserted-by":"publisher","first-page":"882044","DOI":"10.3389\/fgene.2022.882044","article-title":"RhythmicDB: a database of predicted multi-frequency rhythmic transcripts","volume":"13","author":"Castellana","year":"2022","journal-title":"Front Genet"},{"key":"2026100511420937200_btag716-B4","doi-asserted-by":"publisher","first-page":"W157","DOI":"10.1093\/nar\/gky441","article-title":"CircadiOmics: circadian omic web portal","volume":"46","author":"Ceglia","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026100511420937200_btag716-B5","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/s13041-024-01143-0","article-title":"Circadian cilia transcriptome in mouse brain across physiological and pathological states","volume":"17","author":"Chen","year":"2024","journal-title":"Mol Brain"},{"key":"2026100511420937200_btag716-B6","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1016\/j.cell.2018.08.042","article-title":"Atlas of circadian metabolism reveals system-wide coordination and communication between clocks","volume":"174","author":"Dyar","year":"2018","journal-title":"Cell"},{"key":"2026100511420937200_btag716-B7","doi-asserted-by":"publisher","first-page":"5541","DOI":"10.1073\/pnas.1118726109","article-title":"Coordination of the transcriptome and metabolome by the circadian clock","volume":"109","author":"Eckel-Mahan","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026100511420937200_btag716-B8","doi-asserted-by":"publisher","first-page":"1464","DOI":"10.1016\/j.cell.2013.11.034","article-title":"Reprogramming of the circadian clock by nutritional challenge","volume":"155","author":"Eckel-Mahan","year":"2013","journal-title":"Cell"},{"key":"2026100511420937200_btag716-B9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1210\/er.2009-0014","article-title":"Metabolism and circadian rhythms\u2013implications for obesity","volume":"31","author":"Froy","year":"2010","journal-title":"Endocr Rev"},{"key":"2026100511420937200_btag716-B10","doi-asserted-by":"publisher","first-page":"12824","DOI":"10.1523\/JNEUROSCI.3353-09.2009","article-title":"Cycling behavior and memory formation","volume":"29","author":"Gerstner","year":"2009","journal-title":"J Neurosci"},{"key":"2026100511420937200_btag716-B11","doi-asserted-by":"publisher","first-page":"8175","DOI":"10.1038\/s41467-023-44039-8","article-title":"Astrocytic insulin receptor controls circadian behavior via dopamine signaling in a sexually dimorphic manner","volume":"14","author":"Gonz\u00e1lez-Vila","year":"2023","journal-title":"Nat Commun"},{"key":"2026100511420937200_btag716-B12","doi-asserted-by":"publisher","first-page":"4753","DOI":"10.1038\/ncomms5753","article-title":"Circadian rhythm reprogramming during lung inflammation","volume":"5","author":"Haspel","year":"2014","journal-title":"Nat Commun"},{"key":"2026100511420937200_btag716-B13","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkh453","article-title":"PubCrawler: keeping up comfortably with PubMed and GenBank","volume":"32","author":"Hokamp","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2026100511420937200_btag716-B14","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1177\/0748730410379711","article-title":"JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets","volume":"25","author":"Hughes","year":"2010","journal-title":"J Biol Rhythms"},{"key":"2026100511420937200_btag716-B15","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2026100511420937200_btag716-B16","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1093\/occmed\/kqg048","article-title":"Health disorders of shift workers","volume":"53","author":"Knutsson","year":"2003","journal-title":"Occup Med (Lond)"},{"key":"2026100511420937200_btag716-B17","doi-asserted-by":"publisher","first-page":"R271","DOI":"10.1093\/hmg\/ddl207","article-title":"Molecular components of the mammalian circadian clock","volume":"15 Spec No 2","author":"Ko","year":"2006","journal-title":"Human Molecular Genetics"},{"key":"2026100511420937200_btag716-B18","doi-asserted-by":"publisher","first-page":"1868","DOI":"10.1101\/gad.1432206","article-title":"Early aging and age-related pathologies in mice deficient in BMAL1, the core component of the circadian clock","volume":"20","author":"Kondratov","year":"2006","journal-title":"Genes Dev"},{"key":"2026100511420937200_btag716-B19","doi-asserted-by":"publisher","first-page":"107810","DOI":"10.1016\/j.isci.2023.107810","article-title":"Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations","volume":"26","author":"Lee","year":"2023","journal-title":"iScience"},{"key":"2026100511420937200_btag716-B20","doi-asserted-by":"publisher","first-page":"D64","DOI":"10.1093\/nar\/gkx944","article-title":"CirGRDB: a database for the genome-wide deciphering circadian genes and regulators","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026100511420937200_btag716-B21","doi-asserted-by":"publisher","first-page":"3339","DOI":"10.1073\/pnas.1217632110","article-title":"Circadian acetylome reveals regulation of mitochondrial metabolic pathways","volume":"110","author":"Masri","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100511420937200_btag716-B22","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/j.cell.2014.06.050","article-title":"Partitioning circadian transcription by SIRT6 leads to segregated control of cellular metabolism","volume":"158","author":"Masri","year":"2014","journal-title":"Cell"},{"key":"2026100511420937200_btag716-B23","doi-asserted-by":"publisher","first-page":"eaeb3756","DOI":"10.1126\/sciadv.aeb3756","article-title":"Chronic intermittent hypoxia reshapes circadian metabolic architecture in a model of sleep apnea","volume":"12","author":"Montellier","year":"2026","journal-title":"Sci Adv"},{"key":"2026100511420937200_btag716-B24","doi-asserted-by":"publisher","first-page":"1292","DOI":"10.15252\/embr.201642463","article-title":"Gut microbiota directs PPAR\u03b3-driven reprogramming of the liver circadian clock by nutritional challenge","volume":"17","author":"Murakami","year":"2016","journal-title":"EMBO Rep"},{"key":"2026100511420937200_btag716-B25","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/s0092-8674(02)00722-5","article-title":"Coordinated transcription of key pathways in the mouse by the circadian clock","volume":"109","author":"Panda","year":"2002","journal-title":"Cell"},{"key":"2026100511420937200_btag716-B26","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/417329a","article-title":"Circadian rhythms from flies to human","volume":"417","author":"Panda","year":"2002","journal-title":"Nature"},{"key":"2026100511420937200_btag716-B27","doi-asserted-by":"publisher","first-page":"3181","DOI":"10.1093\/bioinformatics\/btv353","article-title":"The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework","volume":"31","author":"Patel","year":"2015","journal-title":"Bioinformatics"},{"key":"2026100511420937200_btag716-B28","doi-asserted-by":"publisher","first-page":"D1009","DOI":"10.1093\/nar\/gks1161","article-title":"CircaDB: a database of mammalian circadian gene expression profiles","volume":"41","author":"Pizarro","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026100511420937200_btag716-B29","doi-asserted-by":"publisher","first-page":"W183","DOI":"10.1093\/nar\/gkac419","article-title":"CircadiOmics: circadian omic web portal","volume":"50","author":"Samad","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026100511420937200_btag716-B30","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1177\/07487304251386926","article-title":"The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function","volume":"41","author":"Sica","year":"2026","journal-title":"J Biol Rhythms"},{"key":"2026100511420937200_btag716-B31","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1038\/nature744","article-title":"Extensive and divergent circadian gene expression in liver and heart","volume":"417","author":"Storch","year":"2002","journal-title":"Nature"},{"key":"2026100511420937200_btag716-B32","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1038\/nrg2430","article-title":"The genetics of mammalian circadian order and disorder: implications for physiology and disease","volume":"9","author":"Takahashi","year":"2008","journal-title":"Nat Rev Genet"},{"key":"2026100511420937200_btag716-B33","doi-asserted-by":"publisher","first-page":"eady9244","DOI":"10.1126\/sciadv.ady9244","article-title":"Circadian reprogramming by timed sodium intake reveals transcriptional pathways of daily salt handling in the colon","volume":"12","author":"Torimitsu","year":"2026","journal-title":"Sci Adv"},{"key":"2026100511420937200_btag716-B34","doi-asserted-by":"publisher","first-page":"22564","DOI":"10.1073\/pnas.0912673106","article-title":"Oscillations in supercoiling drive circadian gene expression in cyanobacteria","volume":"106","author":"Vijayan","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100511420937200_btag716-B35","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1016\/j.cmet.2023.03.004","article-title":"SUCNR1 signaling in adipocytes controls energy metabolism by modulating circadian clock and leptin expression","volume":"35","author":"Villanueva-Carmona","year":"2023","journal-title":"Cell Metab"},{"key":"2026100511420937200_btag716-B36","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2026100511420937200_btag716-B37","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1016\/j.cmet.2024.12.002","article-title":"Maternal circadian rhythms during pregnancy dictate metabolic plasticity in offspring","volume":"37","author":"Yao","year":"2025","journal-title":"Cell Metab"},{"key":"2026100511420937200_btag716-B38","doi-asserted-by":"publisher","first-page":"16219","DOI":"10.1073\/pnas.1408886111","article-title":"A circadian gene expression atlas in mammals: implications for biology and medicine","volume":"111","author":"Zhang","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026100511420937200_btag716-B39","doi-asserted-by":"publisher","first-page":"D67","DOI":"10.1093\/nar\/gkae817","article-title":"CircaKB: a comprehensive knowledgebase of circadian genes across multiple species","volume":"53","author":"Zhu","year":"2025","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag716\/71438295\/btag716.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/10\/btag716\/71438295\/btag716.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/10\/btag716\/71438295\/btag716.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T15:42:13Z","timestamp":1791214933000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag716\/8841215"}},"subtitle":[],"editor":[{"given":"Macha","family":"Nikolski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,28]]},"references-count":39,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag716","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,9,28]]},"article-number":"btag716"}}