{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T12:18:30Z","timestamp":1789042710549,"version":"build-2803163510"},"reference-count":26,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"name":"2024 High-quality Development Research Project of Shenzhen Bao\u2019an Public Hospital","award":["BAGZL2024197"],"award-info":[{"award-number":["BAGZL2024197"]}]}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["J Biol Rhythms"],"abstract":"\n A 12-h (12-h) periodicity in a transcriptomic series is routinely reported as a \u201c12-h rhythm,\u201d yet a single 12-h spectral peak can arise from 3 mechanistically distinct processes: the second harmonic of a non-sinusoidal 24-h waveform (a harmonic), an autonomous 12-h oscillator with its own phase (such as the IRE1\n \n \n \n \u03b1<\/mml:mi>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:inline-formula>\n \u2013XBP1s ER-stress cycle), or the apparent 12-h when 2 anti-phase 24-h processes combine as synthesis minus degradation (an intersection). These origins carry opposite biological meanings but are indistinguishable to standard detectors such as JTK_CYCLE, RAIN, and Cosinor. To resolve the origin of 12-h rhythms, Circadian Harmonic Oscillation Resolution and Disentanglement (CHORD) detects 12-h periodicity and resolves it into this ternary taxonomy. Detection fuses 4 tests through the Cauchy Combination Test; disentanglement rests on 4 complementary statistics, each tied to one identifiable model feature and combined by a calibrated multinomial classifier. On a held-out benchmark, CHORD separates autonomous from driven 12\u2009h at area under the curve (AUC) 0.83 and a genuine oscillator from an intersection at 0.93. An interventional test anchors the classifier to biology: in a liver-specific XBP1 knockout, the hepatic 12-h program collapses when the IRE1\u2013XBP1 clock is ablated (knockout\/wild-type ratio 0.27) while the 24-h circadian clock is preserved (0.91). The canonical autonomous genes are 12-h dominant with little 24\u2009h, which a single series cannot resolve, so CHORD abstains and the intervention resolves them; the confidently classified autonomous set also collapses more than the driven set (0.47 vs. 0.62). Because the program is strongly coregulated, a correlation-adjusted test keeps the program-versus-driven collapse significant (\n \n \n \n p<\/mml:mi>\n =<\/mml:mo>\n 00<\/mml:mn>\n .<\/mml:mo>\n 045<\/mml:mn>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:inline-formula>\n ); this validation covers the autonomous arm in liver only. An identifiability budget shows that 12-h signal-to-noise, not sampling density, bounds classification. CHORD reframes ultradian transcriptomics from whether a 12-h rhythm exists to what kind it is.\n <\/jats:p>","DOI":"10.1177\/07487304261480190","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T10:43:19Z","timestamp":1788777799000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["CHORD: Resolving 12-h Transcriptomic Rhythms Into Harmonic, Autonomous, and Intersection Origins"],"prefix":"10.1177","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0843-7739","authenticated-orcid":false,"given":"Peigen","family":"Chen","sequence":"first","affiliation":[{"name":"Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China"},{"name":"Guangdong Engineering Technology Research Center of Fertility Preservation, Guangzhou, China"},{"name":"Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynaecology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoting","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shenzhen Bao\u2019an District Songgang People\u2019s Hospital, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"e_1_3_2_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1515308112"},{"key":"e_1_3_2_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-020-03730-5"},{"key":"e_1_3_2_4_1","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2018.01178"},{"key":"e_1_3_2_5_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10815-024-03339-8"},{"key":"e_1_3_2_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4682-11-16"},{"key":"e_1_3_2_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2009.11.002"},{"key":"e_1_3_2_8_1","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2024.1497836"},{"key":"e_1_3_2_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000442"},{"key":"e_1_3_2_10_1","doi-asserted-by":"publisher","DOI":"10.1177\/0748730410379711"},{"key":"e_1_3_2_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2023.03.015"},{"key":"e_1_3_2_12_1","doi-asserted-by":"publisher","DOI":"10.1080\/01621459.2018.1554485"},{"key":"e_1_3_2_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00648343"},{"key":"e_1_3_2_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20028-z"},{"key":"e_1_3_2_15_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aao0318"},{"key":"e_1_3_2_16_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000580"},{"key":"e_1_3_2_17_1","doi-asserted-by":"publisher","DOI":"10.1086\/160554"},{"key":"e_1_3_2_18_1","doi-asserted-by":"publisher","DOI":"10.1177\/0748730414553029"},{"key":"e_1_3_2_19_1","doi-asserted-by":"publisher","DOI":"10.1109\/PROC.1982.12433"},{"key":"e_1_3_2_20_1","doi-asserted-by":"publisher","DOI":"10.1096\/fj.201600872R"},{"key":"e_1_3_2_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2013.03.013"},{"key":"e_1_3_2_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks461"},{"key":"e_1_3_2_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw405"},{"key":"e_1_3_2_24_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1011047"},{"key":"e_1_3_2_25_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1408886111"},{"key":"e_1_3_2_26_1","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2023.1195001"},{"key":"e_1_3_2_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2017.05.004"}],"container-title":["Journal 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