Literature DB >> 20934868

Multiscale complexity in the mammalian circadian clock.

Yr Yamada1, Db Forger.   

Abstract

The field of systems biology studies how the interactions among individual components (e.g. genes and proteins) yield interesting and complex behavior. The circadian (daily) timekeeping system in mammals is an ideal system to study complexity because of its many biological scales (from genes to animal behavior). A wealth of data at each of these scales has recently been discovered. Within each scale, modeling can advance our understanding of challenging problems that arise in studying mammalian timekeeping. However, future work must focus on bridging the multiple spatial and temporal scales in the modeling of SCN network. Here we review recent advances, and then delve into a few areas that are promising research directions. We also discuss the flavor of modeling needed (simple or detailed) as well as new techniques that are needed to meet the challenges in modeling data across scales.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID: 20934868      PMCID: PMC3042735          DOI: 10.1016/j.gde.2010.09.006

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  75 in total

1.  Multiple oscillators provide metastability in rhythm generation.

Authors:  H S Chang; K Staras; M P Gilbey
Journal:  J Neurosci       Date:  2000-07-01       Impact factor: 6.167

Review 2.  Modelling biological rhythms.

Authors:  Till Roenneberg; Elaine Jane Chua; Ric Bernardo; Eduardo Mendoza
Journal:  Curr Biol       Date:  2008-09-09       Impact factor: 10.834

Review 3.  Role of phosphorylation in the mammalian circadian clock.

Authors:  K Vanselow; A Kramer
Journal:  Cold Spring Harb Symp Quant Biol       Date:  2007

4.  Model aggregation: a building-block approach to creating large macromolecular regulatory networks.

Authors:  Ranjit Randhawa; Clifford A Shaffer; John J Tyson
Journal:  Bioinformatics       Date:  2009-10-29       Impact factor: 6.937

5.  An opposite role for tau in circadian rhythms revealed by mathematical modeling.

Authors:  Monica Gallego; Erik J Eide; Margaret F Woolf; David M Virshup; Daniel B Forger
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-03       Impact factor: 11.205

6.  A genome-wide RNAi screen for modifiers of the circadian clock in human cells.

Authors:  Eric E Zhang; Andrew C Liu; Tsuyoshi Hirota; Loren J Miraglia; Genevieve Welch; Pagkapol Y Pongsawakul; Xianzhong Liu; Ann Atwood; Jon W Huss; Jeff Janes; Andrew I Su; John B Hogenesch; Steve A Kay
Journal:  Cell       Date:  2009-09-17       Impact factor: 41.582

7.  A molecular model for intercellular synchronization in the mammalian circadian clock.

Authors:  Tsz-Leung To; Michael A Henson; Erik D Herzog; Francis J Doyle
Journal:  Biophys J       Date:  2007-03-16       Impact factor: 4.033

8.  Intrinsic, nondeterministic circadian rhythm generation in identified mammalian neurons.

Authors:  Alexis B Webb; Nikhil Angelo; James E Huettner; Erik D Herzog
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-09       Impact factor: 11.205

9.  Minimum criteria for DNA damage-induced phase advances in circadian rhythms.

Authors:  Christian I Hong; Judit Zámborszky; Attila Csikász-Nagy
Journal:  PLoS Comput Biol       Date:  2009-05-08       Impact factor: 4.475

10.  Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis.

Authors:  Kathryn Moynihan Ramsey; Jun Yoshino; Cynthia S Brace; Dana Abrassart; Yumiko Kobayashi; Biliana Marcheva; Hee-Kyung Hong; Jason L Chong; Ethan D Buhr; Choogon Lee; Joseph S Takahashi; Shin-Ichiro Imai; Joseph Bass
Journal:  Science       Date:  2009-03-19       Impact factor: 47.728

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  11 in total

Review 1.  Genetics of circadian rhythms in Mammalian model organisms.

Authors:  Phillip L Lowrey; Joseph S Takahashi
Journal:  Adv Genet       Date:  2011       Impact factor: 1.944

Review 2.  Systems Level Understanding of Circadian Integration with Cell Physiology.

Authors:  Andrew R Morris; Daniel L Stanton; Destino Roman; Andrew C Liu
Journal:  J Mol Biol       Date:  2020-02-13       Impact factor: 5.469

Review 3.  Cell autonomy and synchrony of suprachiasmatic nucleus circadian oscillators.

Authors:  Jennifer A Mohawk; Joseph S Takahashi
Journal:  Trends Neurosci       Date:  2011-06-12       Impact factor: 13.837

Review 4.  Protein sequestration versus Hill-type repression in circadian clock models.

Authors:  Jae Kyoung Kim
Journal:  IET Syst Biol       Date:  2016-08       Impact factor: 1.615

5.  Chronobiology of Melatonin beyond the Feedback to the Suprachiasmatic Nucleus-Consequences to Melatonin Dysfunction.

Authors:  Rüdiger Hardeland
Journal:  Int J Mol Sci       Date:  2013-03-12       Impact factor: 5.923

Review 6.  Melatonin signaling and its modulation of PfNF-YB transcription factor expression in Plasmodium falciparum.

Authors:  Wânia Rezende Lima; Anthony A Holder; Célia R S Garcia
Journal:  Int J Mol Sci       Date:  2013-07-01       Impact factor: 5.923

7.  Interventions to Minimize Jet Lag After Westward and Eastward Flight.

Authors:  Gregory D Roach; Charli Sargent
Journal:  Front Physiol       Date:  2019-07-31       Impact factor: 4.566

8.  Weakly circadian cells improve resynchrony.

Authors:  Alexis B Webb; Stephanie R Taylor; Kurt A Thoroughman; Francis J Doyle; Erik D Herzog
Journal:  PLoS Comput Biol       Date:  2012-11-29       Impact factor: 4.475

9.  Suppressed cellular oscillations in after-hours mutant mice are associated with enhanced circadian phase-resetting.

Authors:  Clare Guilding; Fiona Scott; David A Bechtold; Timothy M Brown; Sven Wegner; Hugh D Piggins
Journal:  J Physiol       Date:  2012-12-03       Impact factor: 5.182

10.  A mechanism for robust circadian timekeeping via stoichiometric balance.

Authors:  Jae Kyoung Kim; Daniel B Forger
Journal:  Mol Syst Biol       Date:  2012       Impact factor: 11.429

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