ArticleNucleic acids research2016
ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system.
Article in Nucleic acids research, 2016. 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.
- Guidelines for Genome-Scale Analysis of Biological Rhythms.Journal of biological rhythms · 2017Guideline
- Machine learning identifies a compact gene set for monitoring the circadian clock in human blood.Genome medicine · 2017Pooled it
- BMAL1 in cardiovascular diseases: Molecular mechanisms, circadian regulation and translational perspectives (Review).Molecular medicine reports · 2026Review
- SPIRAL: A versatile online single time-point circadian analysis platform for rice.Science advances · 2026Article
- Transcriptional noise sets fundamental limits to decoding circadian clock phase from single-cell RNA snapshots.iScience · 2026Article
- HairTime: A noninvasive assay for estimating circadian phase from a single hair sample.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- BAYESIAN RHYTHMIC MODEL FOR JOINTLY DETECTING CIRCADIAN BIOMARKERS AND PREDICTING MOLECULAR CIRCADIAN TIME IN HUMAN POST-MORTEM BRAIN TRANSCRIPTOME.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
- Performance of Blood-Based Biomarkers for Human Circadian Pacemaker Phase: Training Sets Matter As Much As Feature-Selection Methods.Journal of biological rhythms · 2025Article
- Chronotherapy as a novel strategy to limit anthracycline-induced cardiotoxicity.Cardiovascular research · 2025Review
- Article
- Blood Clock Correlation Distance (BloodCCD) as a novel marker to detect circadian rhythm disruption in cancer survivors with insomnia.BJC reports · 2025Article
- Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock.Nature communications · 2025Article
- Social jetlag elicits fatty liver via perturbed circulating prolactin rhythm-mediated circadian remodeling of hepatic lipid metabolism.Military Medical Research · 2025Article
- Role of the tendon circadian clock in tendinopathy and implications for therapeutics.International journal of experimental pathology · 2025Review
- Designing and Evaluating Circadian Experiments on Mouse Skin.The Journal of investigative dermatology · 2025Review
- Disruption of day-to-night changes in circadian gene expression with chronic tendinopathy.The Journal of physiology · 2024Article
- AutoXAI4Omics: an automated explainable AI tool for omics and tabular data.Briefings in bioinformatics · 2024Article
- Gene expression clock: an unsupervised deep learning approach for predicting circadian rhythmicity from whole genome expression.Neural computing & applications · 2024Article
- Why does circadian timing of administration matter for immune checkpoint inhibitors' efficacy?British journal of cancer · 2024Review
4 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Numerous biological systems oscillate over time or space. Despite these oscillators' importance, data from an oscillatory system is problematic for existing methods of regularized supervised learning. We present ZeitZeiger, a method to predict a periodic variable (e.g. time of day) from a high-dimensional observation. ZeitZeiger learns a sparse representation of the variation associated with the periodic variable in the training observations, then uses maximum-likelihood to make a prediction for a test observation. We applied ZeitZeiger to a comprehensive dataset of genome-wide gene expression from the mammalian circadian oscillator. Using the expression of 13 genes, ZeitZeiger predicted circadian time (internal time of day) in each of 12 mouse organs to within ∼1 h, resulting in a multi-organ predictor of circadian time. Compared to the state-of-the-art approach, ZeitZeiger was faster, more accurate and used fewer genes. We then validated the multi-organ predictor on 20 additional datasets comprising nearly 800 samples. Our results suggest that ZeitZeiger not only makes accurate predictions, but also gives insight into the behavior and structure of the oscillator from which the data originated. As our ability to collect high-dimensional data from various biological oscillators increases, ZeitZeiger should enhance efforts to convert these data to knowledge.
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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.