ArticleBioinformatics (Oxford, England)2020
ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- The circadian gene Dec2 promotes pancreatic cancer progression and dormancy through immune evasion.Developmental cell · 2026Article
- Core clock protein subcellular dynamics coordinate local and global circadian control in syncytia.The Journal of cell biology · 2026Article
- Alzheimer's Disease and circadian disruption sex-specifically contribute to a loss of bone maintenance in APP/PS1 model mice.bioRxiv : the preprint server for biology · 2026Article
- Article
- Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.Cell reports · 2025Article
- Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data.BMC bioinformatics · 2025Article
- Circatidal control of gene expression in the deep-sea hot vent shrimpProceedings. Biological sciences · 2025Article
- Challenges and opportunities for statistical power and biomarker identification arising from rhythmic variation in proteomics.Npj biological timing and sleep · 2025Article
- Dual-Approach Co-expression Analysis Framework (D-CAF) Enables Identification of Novel Circadian Regulation From Multi-Omic Timeseries Data.bioRxiv : the preprint server for biology · 2024Article
- Nighttime-specific differential gene expression in suprachiasmatic nucleus and habenula is associated with resilience to chronic social stress.Translational psychiatry · 2024Article
- Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator.Nature communications · 2024Article
- MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis.bioRxiv : the preprint server for biology · 2023Article
- MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis.PLoS genetics · 2023Article
- Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock.Genome research · 2023Article
- Conformational changes in the negative arm of the circadian clock correlate with dynamic interactomes involved in post-transcriptional regulation.Cell reports · 2023Article
- Article
- NOX2 inhibition enables retention of the circadian clock in BV2 microglia and primary macrophages.Frontiers in immunology · 2023Article
- Regulation of feeding dynamics by the circadian clock, light and sex in an adult nocturnal insect.Frontiers in physiology · 2023Article
- Integrative Analysis of Rhythmicity: From Biology to Urban Environments and Sustainability.International journal of environmental research and public health · 2022Review
- A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules.Cell reports · 2022Article
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Authors and funding
7 authors.
Funding
Abstract
motivationTime courses utilizing genome scale data are a common approach to identifying the biological pathways that are controlled by the circadian clock, an important regulator of organismal fitness. However, the methods used to detect circadian oscillations in these datasets are not able to accommodate changes in the amplitude of the oscillations over time, leading to an underestimation of the impact of the clock on biological systems.
resultsWe have created a program to efficaciously identify oscillations in large-scale datasets, called the Extended Circadian Harmonic Oscillator application, or ECHO. ECHO utilizes an extended solution of the fixed amplitude oscillator that incorporates the amplitude change coefficient. Employing synthetic datasets, we determined that ECHO outperforms existing methods in detecting rhythms with decreasing oscillation amplitudes and in recovering phase shift. Rhythms with changing amplitudes identified from published biological datasets revealed distinct functions from those oscillations that were harmonic, suggesting purposeful biologic regulation to create this subtype of circadian rhythms. AVAILABILITY AND IMPLEMENTATION: ECHO's full interface is available at https://github.com/delosh653/ECHO. An R package for this functionality, echo.find, can be downloaded at https://CRAN.R-project.org/package=echo.find. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.