Analysis of Nonstationary Time Series for Biological Rhythms Research

This article is part of a Journal of Biological Rhythms series exploring analysis and statistics topics relevant to researchers in biological rhythms and sleep research. The goal is to provide an overview of the most common issues that arise in the analysis and interpretation of data in these fields. In this article on time series analysis for biological rhythms, we describe some methods for assessing the rhythmic properties of time series, including tests of whether a time series is indeed rhythmic. Because biological rhythms can exhibit significant fluctuations in their period, phase, and amplitude, their analysis may require methods appropriate for nonstationary time series, such as wavelet transforms, which can measure how these rhythmic parameters change over time. We illustrate these methods using simulated and real time series.

[1]  G. Cornelissen,et al.  Procedures for numerical analysis of circadian rhythms , 2007, Biological rhythm research.

[2]  Boualem Boashash,et al.  Estimating and interpreting the instantaneous frequency of a signal. I. Fundamentals , 1992, Proc. IEEE.

[3]  Joel D Levine,et al.  Signal analysis of behavioral and molecular cycles , 2002, BMC Neuroscience.

[4]  Aslak Grinsted,et al.  Nonlinear Processes in Geophysics Application of the Cross Wavelet Transform and Wavelet Coherence to Geophysical Time Series , 2022 .

[5]  Jie Chen,et al.  Bioinformatics Original Paper Detecting Periodic Patterns in Unevenly Spaced Gene Expression Time Series Using Lomb–scargle Periodograms , 2022 .

[6]  Todd R. Ogden,et al.  Wavelet Methods for Time Series Analysis , 2002 .

[7]  Steve A. Kay,et al.  Bioluminescence Imaging of Individual Fibroblasts Reveals Persistent, Independently Phased Circadian Rhythms of Clock Gene Expression , 2004, Current Biology.

[8]  Tanya L Leise,et al.  Wavelet-based analysis of circadian behavioral rhythms. , 2015, Methods in enzymology.

[9]  R. Refinetti Non-stationary time series and the robustness of circadian rhythms. , 2004, Journal of theoretical biology.

[10]  Yannick Bornat,et al.  Wavelet Transform for Real-Time Detection of Action Potentials in Neural Signals , 2011, Front. Neuroeng..

[11]  Francis J. Doyle,et al.  Intercellular Coupling Confers Robustness against Mutations in the SCN Circadian Clock Network , 2007, Cell.

[12]  Stéphane Mallat,et al.  A Wavelet Tour of Signal Processing - The Sparse Way, 3rd Edition , 2008 .

[13]  P. Welch The use of fast Fourier transform for the estimation of power spectra: A method based on time averaging over short, modified periodograms , 1967 .

[14]  Craig K. Enders,et al.  Applied Missing Data Analysis , 2010 .

[15]  Guy P. Nason,et al.  Spectral estimation for locally stationary time series with missing observations , 2012, Stat. Comput..

[16]  A. Phillips,et al.  Statistics for Sleep and Biological Rhythms Research: Longitudinal Analysis of Biological Rhythms Data , 2019 .

[17]  Piotr Fryzlewicz,et al.  Complex-Valued Wavelet Lifting and Applications , 2018, Technometrics.

[18]  Richard Baraniuk,et al.  The Dual-tree Complex Wavelet Transform , 2007 .

[19]  Aneta Stefanovska,et al.  Nonlinear mode decomposition: a noise-robust, adaptive decomposition method. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[20]  Harold B Dowse,et al.  Analyses for physiological and behavioral rhythmicity. , 2009, Methods in enzymology.

[21]  Sofia C. Olhede,et al.  On the Analytic Wavelet Transform , 2007, IEEE Transactions on Information Theory.

[22]  Germaine Cornelissen,et al.  Cosinor-based rhythmometry , 2014, Theoretical Biology and Medical Modelling.

[23]  David K. Welsh,et al.  Persistent Cell-Autonomous Circadian Oscillations in Fibroblasts Revealed by Six-Week Single-Cell Imaging of PER2::LUC Bioluminescence , 2012, PloS one.

[24]  Gang Wu,et al.  MetaCycle: an integrated R package to evaluate periodicity in large scale data , 2016, bioRxiv.

[25]  D. Pfaff,et al.  Phase-Amplitude Coupling in Spontaneous Mouse Behavior , 2016, PloS one.

[26]  Korbinian Strimmer,et al.  Identifying periodically expressed transcripts in microarray time series data , 2008, Bioinform..

[27]  Andrew J. Millar,et al.  Strengths and Limitations of Period Estimation Methods for Circadian Data , 2014, PloS one.

[28]  Andrew L Cohen,et al.  Bayesian statistical analysis of circadian oscillations in fibroblasts. , 2012, Journal of theoretical biology.

[29]  C. Torrence,et al.  A Practical Guide to Wavelet Analysis. , 1998 .

[30]  Mary E Harrington,et al.  Wavelet-Based Time Series Analysis of Circadian Rhythms , 2011, Journal of biological rhythms.

[31]  A. Phillips,et al.  Statistics for Sleep and Biological Rhythms Research , 2017, Journal of biological rhythms.