ArticleProceedings of the National Academy of Sciences of the United States of America2017
CYCLOPS reveals human transcriptional rhythms in health and disease.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers, 1 of them a synthesis that pooled it.
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Who cites it
155 citing papers in PubMed, 1 synthesis or guideline pooled it, 258 citations in OpenAlex.
- Chronotype in Patients With Immune-Mediated Inflammatory Disease: A Systematic Review.Journal of biological rhythms · 2023Pooled it
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- The circadian clock controls hepatic stellate cell activation via a BMAL1/CK1ε/REV-ERBα/transgelin signaling pathway.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Review
- Biology and Time Course of Obstruction-Induced Detrusor Underactivity Causing Postvoid Residual Urine.International neurourology journal · 2026Article
- Intracellular potassium levels orchestrate circadian rhythmicity and cell division.Nature communications · 2026Article
- Translational applications of circadian research: connecting chronobiology to medicine.Npj biological timing and sleep · 2026Review
- Transcriptional noise sets fundamental limits to decoding circadian clock phase from single-cell RNA snapshots.iScience · 2026Article
- Deciphering Cell Cycle Dynamics and Cell States in Single-cell RNA-seq data with SPAE.bioRxiv : the preprint server for biology · 2026Article
- Diurnal Regulation and Gene-Specific Vulnerability of Oxidative Alcohol-Metabolizing Enzymes to Circadian Disruption.International journal of molecular sciences · 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
- VIST: variational inference for single cell time series.Genome biology · 2026Article
- Hepatocellular Carcinoma Around the Clock.Current oncology (Toronto, Ont.) · 2026Review
- DCPR: a deep learning framework for circadian phase reconstruction.BMC bioinformatics · 2025Article
- Tuned by time: the role of circadian rhythms in metabolic energy sensing and chronotherapy.Annals of medicine · 2025Review
- Chronotherapy as a novel strategy to limit anthracycline-induced cardiotoxicity.Cardiovascular research · 2025Review
- Circadian regulation of extracellular vesicle biogenesis, composition, and release.Npj biological timing and sleep · 2025Review
- A glial circadian gene expression atlas reveals cell-type and disease-specific reprogramming in response to amyloid pathology or aging.Nature neuroscience · 2025Article
- Article
95 more citing papers are in PubMed but not listed here.
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4 authors at 2 institutions in 1 country.
Funding
Abstract
Circadian rhythms modulate many aspects of physiology. Knowledge of the molecular basis of these rhythms has exploded in the last 20 years. However, most of these data are from model organisms, and translation to clinical practice has been limited. Here, we present an approach to identify molecular rhythms in humans from thousands of unordered expression measurements. Our algorithm, cyclic ordering by periodic structure (CYCLOPS), uses evolutionary conservation and machine learning to identify elliptical structure in high-dimensional data. From this structure, CYCLOPS estimates the phase of each sample. We validated CYCLOPS using temporally ordered mouse and human data and demonstrated its consistency on human data from two independent research sites. We used this approach to identify rhythmic transcripts in human liver and lung, including hundreds of drug targets and disease genes. Importantly, for many genes, the circadian variation in expression exceeded variation from genetic and other environmental factors. We also analyzed hepatocellular carcinoma samples and show these solid tumors maintain circadian function but with aberrant output. Finally, to show how this method can catalyze medical translation, we show that dosage time can temporally segregate efficacy from dose-limiting toxicity of streptozocin, a chemotherapeutic drug. In sum, these data show the power of CYCLOPS and temporal reconstruction in bridging basic circadian research and clinical medicine.
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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.