Publications

(2024). Time series-free rhythm profiling using COFE reveals multi-omic circadian rhythms in in-vivo human cancers. Preprint.

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(2024). Quantification of circadian rhythms in mammalian lung tissue snapshot data. Scientific Reports.

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(2023). Are We Finding Functional or Merely Statistically Significant Rhythms?. JBR.

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(2023). Data Integration and Analysis for Circadian Medicine. Acta Physiologica.

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(2022). Inter-layer and inter-subject variability of diurnal gene expression in human skin. NAR Genomics and Bioinformatics.

PDF Code Dataset Project Project DOI

(2022). Ventilator-induced Lung Injury Is Modulated by the Circadian Clock. American Journal of Respiratory and Critical Care Medicine.

PDF Project DOI

(2022). Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. FEBS Journal.

Code Project Project DOI

(2021). Susceptibility rhythm to bacterial endotoxin in myeloid clock-knockout mice. eLife.

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(2021). Circadian rhythms in septic shock patients. Annals of Intensive Care.

PDF DOI

(2020). Regulation of Rest, Rather Than Activity, Underlies Day-Night Activity Differences in Mice. Front. Physiol..

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(2020). Amplitude effects allow short jetlags and large seasonal phase shifts in minimal clock models. Journal of Molecular Biology.

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(2019). Beyond spikes: multiscale computational analysis of in vivo long-term recordings in the cockroach circadian clock. Network Neuroscience.

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(2018). Ultradian Rhythms in the Transcriptome of Neurospora crassa. iScience.

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(2018). High-accuracy determination of internal circadian time from a single blood sample. The Journal of Clinical Investigation.

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(2017). Morning and evening peaking rhythmic genes are regulated by distinct transcription factors in Neurospora crassa. Information and Communication Theory in Molecular Biology.

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(2015). Coupling Controls the Synchrony of Clock Cells in Development and Knockouts. Biophys. J..

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(2015). Mining for novel candidate clock genes in the circadian regulatory network. BMC Systems Biology.

PDF Project Project DOI

(2015). Relating suborganismal processes to ecotoxicological and population level endpoints using a bioenergetic model. Ecological Applications.

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(2014). Positive Feedback Promotes Oscillations in Negative Feedback Loops. PLoS One.

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(2014). Timing of Neuropeptide Coupling Determines Synchrony and Entrainment in the Mammalian Circadian Clock. PLoS Computational Biology.

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(2011). Effects of light dynamics on coral spawning synchrony. Biological Bulletin.

Project DOI

(2011). Entrainment of cell division in phytoplankton with dynamic energy budgets. Journal of Sea Research.

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(2011). Integrate-and-fire models of insolation-driven entrainment of broadcast spawning in corals. Theoretical Ecology.

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(2011). Stochastic growth reduces population fluctuations in Daphnia–algal systems. Ecology.

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