ArticleBriefings in bioinformatics2021
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Remodeling of the hepatic circadian transcriptome across the estrous cycle.bioRxiv : the preprint server for biology · 2026Article
- CCorGsDB: a database for clock correlated genes in the mouse and human central nervous systems.Npj biological timing and sleep · 2026Article
- Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus.Communications biology · 2025Article
- Composition and rhythmic variations in the microbiome of Southwestern Atlantic corals.Environmental microbiome · 2025Article
- Single-Cell Multiomic Analysis of Circadian Rhythmicity in Mouse Liver.bioRxiv : the preprint server for biology · 2025Article
- Aggregating dependent signals with heavy-tailed combination tests.Biometrika · 2025Article
- Spontaneous oxycodone withdrawal disrupts sleep, diurnal, and electrophysiological dynamics in rats.PloS one · 2025Article
- Detecting Rhythmic Gene Expression in Single-cell Transcriptomics.Journal of biological rhythms · 2024Article
- Circadian regulation of endoplasmic reticulum calcium response in cultured mouse astrocytes.eLife · 2024Article
- Fibroblasts as an in vitro model of circadian genetic and genomic studies.Mammalian genome : official journal of the International Mammalian Genome Society · 2024Article
- Detecting Rhythmic Gene Expression in Single Cell Transcriptomics.bioRxiv : the preprint server for biology · 2024Article
- Circadian regulation of macromolecular complex turnover and proteome renewal.The EMBO journal · 2024Article
- Environmental circadian disruption re-writes liver circadian proteomes.Nature communications · 2024Article
- Fibroblasts as an in vitro model of circadian genetic and genomic studies: A temporal analysis.bioRxiv : the preprint server for biology · 2024Article
- Circadian organization of lipid landscape is perturbed in type 2 diabetic patients.Cell reports. Medicine · 2023Article
- Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations.iScience · 2023Article
- An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells.Bioinformatics (Oxford, England) · 2023Article
- Review
- Keep It Simple: Using README Files to Advance Standardization in Chronobiology.Clocks & sleep · 2023Article
- Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model.Statistics in medicine · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Circadian rhythms are oscillations of behavior, physiology and metabolism in many organisms. Recent advancements in omics technology make it possible for genome-wide profiling of circadian rhythms. Here, we conducted a comprehensive analysis of seven existing algorithms commonly used for circadian rhythm detection. Using gold-standard circadian and non-circadian genes, we systematically evaluated the accuracy and reproducibility of the algorithms on empirical datasets generated from various omics platforms under different experimental designs. We also carried out extensive simulation studies to test each algorithm's robustness to key variables, including sampling patterns, replicates, waveforms, signal-to-noise ratios, uneven samplings and missing values. Furthermore, we examined the distributions of the nominal $P$-values under the null and raised issues with multiple testing corrections using traditional approaches. With our assessment, we provide method selection guidelines for circadian rhythm detection, which are applicable to different types of high-throughput omics data.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.