AIMC Topic: Circadian Clocks
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System-level time computation and representation in the suprachiasmatic nucleus revealed by large-scale calcium imaging and machine learning.
Cell research
Apr 11, 2024
The suprachiasmatic nucleus (SCN) is the mammalian central circadian pacemaker with heterogeneous neurons acting in concert while each neuron harbors a self-sustained molecular clockwork. Nevertheless, how system-level SCN signals encode time of the ...
Universal method for robust detection of circadian state from gene expression.
Proceedings of the National Academy of Sciences of the United States of America
Sep 10, 2018
Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessment of physiological time using transcriptional biomarkers found in human blood can significantly imp...
Machine learning identifies a compact gene set for monitoring the circadian clock in human blood.
Genome medicine
Feb 28, 2017
BACKGROUND: The circadian clock and the daily rhythms it produces are crucial for human health, but are often disrupted by the modern environment. At the same time, circadian rhythms may influence the efficacy and toxicity of therapeutics and the met...
Modelling with ANIMO: between fuzzy logic and differential equations.
BMC systems biology
Jul 27, 2016
BACKGROUND: Computational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computational support and allow insigh...
ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system.
Nucleic acids research
Jan 26, 2016
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 peri...
Rhythm profiling using COFE reveals multi-omic circadian rhythms in human cancers in vivo.
PLoS biology
May 1, 2025
The study of ubiquitous circadian rhythms in human physiology requires regular measurements across time. Repeated sampling of the different internal tissues that house circadian clocks is both practically and ethically infeasible. Here, we present a ...
Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function.
Proceedings of the National Academy of Sciences of the United States of America
Aug 10, 2021
The circadian clock is an important adaptation to life on Earth. Here, we use machine learning to predict complex, temporal, and circadian gene expression patterns in Most significantly, we classify circadian genes using DNA sequence features genera...
[Effect of Acupuncture at Points in Heel Vessel for Circadian Genes of 1 and 2 mRNAs in the Suprachiasmatic Nucleus in Insomnia Rats].
Zhen ci yan jiu = Acupuncture research
Dec 25, 2017
OBJECTIVE: To investigate the influence and mechanism of acupuncture at the points in Heel Vessel for the circadian clock genes of Period () 1 and 2 mRNAs in the suprachiasmatic nucleus (SCN) in insomnia rats.
What time is it? Deep learning approaches for circadian rhythms.
Bioinformatics (Oxford, England)
Jun 15, 2016
MOTIVATION: Circadian rhythms date back to the origins of life, are found in virtually every species and every cell, and play fundamental roles in functions ranging from metabolism to cognition. Modern high-throughput technologies allow the measureme...
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