ArticlePLoS computational biology2015
Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 2 of them syntheses that pooled it.
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Who cites it
64 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses.Journal of biological rhythms · 2023Pooled it
- Guidelines for Genome-Scale Analysis of Biological Rhythms.Journal of biological rhythms · 2017Guideline
- Short-term sleep restriction in humans alters diurnal circulating metabolite profiles, including those of microbial origin.The Journal of clinical investigation · 2026Trial
- Time-Series RNA Sequencing Reveals Temperature-Specific and Temperature-Compensated Circadian Genes inbioRxiv : the preprint server for biology · 2025Article
- Optimization of experimental designs for biological rhythm discovery.PLoS computational biology · 2025Article
- Maternal food-derived signals oscillate in the fetal suprachiasmatic nucleus before its circadian clock develops.PLoS biology · 2025Article
- PKA-mediated BMAL1 phosphorylation promotes βiScience · 2025Article
- Identification and correction of time-series transcriptomic anomalies.Nucleic acids research · 2025Article
- Pharmacological targeting of BMAL1 modulates circadian and immune pathways.Nature chemical biology · 2025Article
- Circatidal control of gene expression in the deep-sea hot vent shrimpProceedings. Biological sciences · 2025Article
- Chronodisruption that dampens output of the central clock abolishes rhythms in metabolome profiles and elevates acylcarnitine levels in the liver of female rats.Acta physiologica (Oxford, England) · 2025Article
- Latitudinal diversity in circadian and light-sensing genes in an ecologically vital group of marine picoeukaryote algae.The ISME journal · 2025Article
- Bacterial guilds, not genus-level taxa, mediate the protective effects of time-restricted feeding against high-fat diet-induced obesity in mice.ISME communications · 2025Article
- Synergy between time-restricted feeding and time-restricted running is necessary to shift the muscle clock in male wistar rats.Neurobiology of sleep and circadian rhythms · 2024Article
- An Arabidopsis Cell Culture With Weak Circadian Rhythms Under Constant Light Compared With Constant Dark Can Be Rescued by ELF3.Plant direct · 2024Article
- Diurnal expression of Dgat2 induced by time-restricted feeding maintains cardiac health in the Drosophila model of circadian disruption.Aging cell · 2024Article
- A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components.Plants (Basel, Switzerland) · 2024Article
- Autonomous circadian rhythms in the human hepatocyte regulate hepatic drug metabolism and inflammatory responses.Science advances · 2024Article
- Repression of latent NF-κB enhancers by PDX1 regulates β cell functional heterogeneity.Cell metabolism · 2024Article
- Crosstalk between salicylic acid signalling and the circadian clock promotes an effective immune response in plants.Npj biological timing and sleep · 2024Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Robust methods for identifying patterns of expression in genome-wide data are important for generating hypotheses regarding gene function. To this end, several analytic methods have been developed for detecting periodic patterns. We improve one such method, JTK_CYCLE, by explicitly calculating the null distribution such that it accounts for multiple hypothesis testing and by including non-sinusoidal reference waveforms. We term this method empirical JTK_CYCLE with asymmetry search, and we compare its performance to JTK_CYCLE with Bonferroni and Benjamini-Hochberg multiple hypothesis testing correction, as well as to five other methods: cyclohedron test, address reduction, stable persistence, ANOVA, and F24. We find that ANOVA, F24, and JTK_CYCLE consistently outperform the other three methods when data are limited and noisy; empirical JTK_CYCLE with asymmetry search gives the greatest sensitivity while controlling for the false discovery rate. Our analysis also provides insight into experimental design and we find that, for a fixed number of samples, better sensitivity and specificity are achieved with higher numbers of replicates than with higher sampling density. Application of the methods to detecting circadian rhythms in a metadataset of microarrays that quantify time-dependent gene expression in whole heads of Drosophila melanogaster reveals annotations that are enriched among genes with highly asymmetric waveforms. These include a wide range of oxidation reduction and metabolic genes, as well as genes with transcripts that have multiple splice forms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.