Literature DB >> 18931366

WAVECLOCK: wavelet analysis of circadian oscillation.

Tom S Price1, Julie E Baggs, Anne M Curtis, Garret A Fitzgerald, John B Hogenesch.   

Abstract

UNLABELLED: Oscillations in mRNA and protein of circadian clock components can be continuously monitored in vitro using synchronized cell lines. These rhythms can be highly variable due to culture conditions and are non-stationary due to baseline trends, damping and drift in period length. We present a technique for characterizing the modal frequencies of oscillation using continuous wavelet decomposition to non-parametrically model changes in amplitude and period while removing baseline effects and noise. AVAILABILITY: The method has been implemented as the package waveclock for the free statistical software program R and is available for download from http://cran.r-project.org/

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Year:  2008        PMID： 18931366      PMCID： PMC2639275          DOI： 10.1093/bioinformatics/btn521

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

1.  Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells.

Authors:  Emi Nagoshi; Camille Saini; Christoph Bauer; Thierry Laroche; Felix Naef; Ueli Schibler
Journal:  Cell       Date:  2004-11-24       Impact factor: 41.582

Review 2.  Circadian biology: fibroblast clocks keep ticking.

Authors:  Michael H Hastings
Journal:  Curr Biol       Date:  2005-01-11       Impact factor: 10.834

Review 3.  Properties, entrainment, and physiological functions of mammalian peripheral oscillators.

Authors:  Markus Stratmann; Ueli Schibler
Journal:  J Biol Rhythms       Date:  2006-12       Impact factor: 3.182

4.  Circadian variation of blood pressure and the vascular response to asynchronous stress.

Authors:  Anne M Curtis; Yan Cheng; Shiv Kapoor; Dermot Reilly; Tom S Price; Garret A Fitzgerald
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-20       Impact factor: 11.205

5.  Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks.

Authors:  Jacques Rougemont; Felix Naef
Journal:  Mol Syst Biol       Date:  2007-03-13       Impact factor: 11.429

6.  Quantitative analyses of circadian gene expression in mammalian cell cultures.

Authors:  Mariko Izumo; Takashi R Sato; Martin Straume; Carl Hirschie Johnson
Journal:  PLoS Comput Biol       Date:  2006-10       Impact factor: 4.475

7.  PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues.

Authors:  Seung-Hee Yoo; Shin Yamazaki; Phillip L Lowrey; Kazuhiro Shimomura; Caroline H Ko; Ethan D Buhr; Sandra M Siepka; Hee-Kyung Hong; Won Jun Oh; Ook Joon Yoo; Michael Menaker; Joseph S Takahashi
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-12       Impact factor: 11.205
  7 in total
  26 in total

1.  Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock.

Authors:  Jason P DeBruyne; Julie E Baggs; Trey K Sato; John B Hogenesch
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-21       Impact factor: 11.205

2.  High-throughput and quantitative approaches for measuring circadian rhythms in cyanobacteria using bioluminescence.

Authors:  Ryan K Shultzaberger; Mark L Paddock; Takeo Katsuki; Ralph J Greenspan; Susan S Golden
Journal:  Methods Enzymol       Date:  2014-12-26       Impact factor: 1.600

3.  Ultradian rhythm unmasked in the Pdf clock mutant of Drosophila.

Authors:  Yuuichi Seki; Teiichi Tanimura
Journal:  J Biosci       Date:  2014-09       Impact factor: 1.826

Review 4.  Measuring synchrony in the mammalian central circadian circuit.

Authors:  Erik D Herzog; István Z Kiss; Cristina Mazuski
Journal:  Methods Enzymol       Date:  2014-12-26       Impact factor: 1.600

5.  Wavelet measurement suggests cause of period instability in mammalian circadian neurons.

Authors:  Kirsten Meeker; Richard Harang; Alexis B Webb; David K Welsh; Francis J Doyle; Guillaume Bonnet; Erik D Herzog; Linda R Petzold
Journal:  J Biol Rhythms       Date:  2011-08       Impact factor: 3.182

6.  Wavelet meets actogram.

Authors:  Tanya L Leise; Premananda Indic; Matthew J Paul; William J Schwartz
Journal:  J Biol Rhythms       Date:  2013-02       Impact factor: 3.182

7.  Casein kinase 1 delta (CK1delta) regulates period length of the mouse suprachiasmatic circadian clock in vitro.

Authors:  Jean-Pierre Etchegaray; Elizabeth A Yu; Premananda Indic; Robert Dallmann; David R Weaver
Journal:  PLoS One       Date:  2010-04-22       Impact factor: 3.240

8.  Bayesian statistical analysis of circadian oscillations in fibroblasts.

Authors:  Andrew L Cohen; Tanya L Leise; David K Welsh
Journal:  J Theor Biol       Date:  2012-09-08       Impact factor: 2.691

9.  Role for LSM genes in the regulation of circadian rhythms.

Authors:  Soledad Perez-Santángelo; Estefanía Mancini; Lauren J Francey; Ruben Gustavo Schlaen; Ariel Chernomoretz; John B Hogenesch; Marcelo J Yanovsky
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-06       Impact factor: 11.205

10.  Network features of the mammalian circadian clock.

Authors:  Julie E Baggs; Tom S Price; Luciano DiTacchio; Satchidananda Panda; Garret A Fitzgerald; John B Hogenesch
Journal:  PLoS Biol       Date:  2009-03-10       Impact factor: 8.029
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