{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T06:33:47Z","timestamp":1774074827368,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Circadian oscillations of gene expression regulate daily physiological processes, and their disruption is linked to many diseases. Circadian rhythms can be disrupted in a variety of ways, including differential phase, amplitude and rhythm fitness. Although many differential circadian biomarker detection methods have been proposed, a workflow for systematic detection of multifaceted differential circadian characteristics with accurate false positive control is not currently available. We propose a comprehensive and interactive pipeline to capture the multifaceted characteristics of differentially rhythmic biomarkers. Analysis outputs are accompanied by informative visualization and interactive exploration. The workflow is demonstrated in multiple case studies and is extensible to general omics applications.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>R package, Shiny app and source code are available in GitHub (https:\/\/github.com\/DiffCircaPipeline) and Zenodo (https:\/\/doi.org\/10.5281\/zenodo.7507989)<\/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\/btad039","type":"journal-article","created":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T12:01:17Z","timestamp":1674129677000},"source":"Crossref","is-referenced-by-count":9,"title":["DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity"],"prefix":"10.1093","volume":"39","author":[{"given":"Xiangning","family":"Xue","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh , Pittsburgh, PA 15213, USA"}]},{"given":"Wei","family":"Zong","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh , Pittsburgh, PA 15213, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8032-4392","authenticated-orcid":false,"given":"Zhiguang","family":"Huo","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Florida , Gainesville, FL 32603, USA"}]},{"given":"Kyle D","family":"Ketchesin","sequence":"additional","affiliation":[{"name":"Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine , Pittsburgh, PA 15219, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2059-2256","authenticated-orcid":false,"given":"Madeline R","family":"Scott","sequence":"additional","affiliation":[{"name":"Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine , Pittsburgh, PA 15219, USA"}]},{"given":"Kaitlyn A","family":"Petersen","sequence":"additional","affiliation":[{"name":"Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine , Pittsburgh, PA 15219, USA"}]},{"given":"Ryan W","family":"Logan","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine , Boston, MA 02118, USA"}]},{"given":"Marianne L","family":"Seney","sequence":"additional","affiliation":[{"name":"Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine , Pittsburgh, PA 15219, USA"}]},{"given":"Colleen","family":"McClung","sequence":"additional","affiliation":[{"name":"Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine , Pittsburgh, PA 15219, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5447-1014","authenticated-orcid":false,"given":"George","family":"Tseng","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh , Pittsburgh, PA 15213, USA"}]}],"member":"286","published-online":{"date-parts":[[2023,1,19]]},"reference":[{"key":"2023020105451690800_btad039-B1","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1073\/pnas.1508249112","article-title":"Effects of aging on circadian patterns of gene expression in the human prefrontal cortex","volume":"113","author":"Chen","year":"2016","journal-title":"Proc. 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