{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T20:52:08Z","timestamp":1769719928504,"version":"3.49.0"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Periodic patterns in time series resulting from biological experiments are of great interest. The commonly used Fast Fourier Transform (FFT) algorithm is applicable only when data are evenly spaced and when no values are missing, which is not always the case in high-throughput measurements. The choice of statistic to evaluate the significance of the periodic patterns for unevenly spaced gene expression time series has not been well substantiated.<\/jats:p><jats:p>Methods: The Lomb\u2013Scargle periodogram approach is used to search time series of gene expression to quantify the periodic behavior of every gene represented on the DNA array. The Lomb\u2013Scargle periodogram analysis provides a direct method to treat missing values and unevenly spaced time points. We propose the combination of a Lomb\u2013Scargle test statistic for periodicity and a multiple hypothesis testing procedure with controlled false discovery rate to detect significant periodic gene expression patterns.<\/jats:p><jats:p>Results: We analyzed the Plasmodium falciparum gene expression dataset. In the Quality Control Dataset of 5080 expression patterns, we found 4112 periodic probes. In addition, we identified 243 probes with periodic expression in the Complete Dataset, which could not be examined in the original study by the FFT analysis due to an excessive number of missing values. While most periodic genes had a period of 48 h, some had a period close to 24 h. Our approach should be applicable for detection and quantification of periodic patterns in any unevenly spaced gene expression time-series data.<\/jats:p><jats:p>Availability: The computations were performed in R. The R code is available from<\/jats:p><jats:p>Contact: \u00a0chenj@umkc.edu<\/jats:p><jats:p>Supplementary information: The online supplement is available at<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti789","type":"journal-article","created":{"date-parts":[[2005,11,23]],"date-time":"2005-11-23T01:24:56Z","timestamp":1132709096000},"page":"310-316","source":"Crossref","is-referenced-by-count":223,"title":["Detecting periodic patterns in unevenly spaced gene expression time series using Lomb\u2013Scargle periodograms"],"prefix":"10.1093","volume":"22","author":[{"given":"Earl F.","family":"Glynn","sequence":"first","affiliation":[{"name":"Stowers Institute for Medical Research 1 \u00a0 1 \u00a0 \u00a0 1000 East 50th Street, Kansas City, MO 64110, USA"}]},{"given":"Jie","family":"Chen","sequence":"additional","affiliation":[{"name":"Stowers Institute for Medical Research 1 \u00a0 1 \u00a0 \u00a0 1000 East 50th Street, Kansas City, MO 64110, USA"},{"name":"Department of Mathematics and Statistics, University of Missouri-Kansas City 2 \u00a0 2 \u00a0 \u00a0 5100 Rockhill Road, Kansas City, MO 64110, USA"}]},{"given":"Arcady R.","family":"Mushegian","sequence":"additional","affiliation":[{"name":"Stowers Institute for Medical Research 1 \u00a0 1 \u00a0 \u00a0 1000 East 50th Street, Kansas City, MO 64110, USA"},{"name":"Department of Microbiology, Immunology and Molecular Genetics, University of Kansas Medical Center 3 \u00a0 3 \u00a0 \u00a0 Kansas City, KS 66160, USA"}]}],"member":"286","published-online":{"date-parts":[[2005,11,22]]},"reference":[{"key":"2023012408340270900_b1","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/S0092-8674(03)01023-7","article-title":"Plasmodium biology: genomic gleanings","volume":"115","author":"Aravind","year":"2003","journal-title":"Cell"},{"key":"2023012408340270900_b2","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1089\/10665270360688057","article-title":"Continuous representations of time series gene expression data","volume":"10","author":"Bar-Joseph","year":"2003","journal-title":"J. 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