Kim JK, Forger DB. (2012). A mechanism for robust circadian timekeeping via stoichiometric balance. Molecular systems biology. 8 [PubMed]

See more from authors: Kim JK · Forger DB

References and models cited by this paper

Baggs JE et al. (2009). Network features of the mammalian circadian clock. PLoS biology. 7 [PubMed]

Baker CL, Loros JJ, Dunlap JC. (2012). The circadian clock of Neurospora crassa. FEMS microbiology reviews. 36 [PubMed]

Barkai N, Leibler S. (2000). Circadian clocks limited by noise. Nature. 403 [PubMed]

Becker-Weimann S, Wolf J, Herzel H, Kramer A. (2004). Modeling feedback loops of the Mammalian circadian oscillator. Biophysical journal. 87 [PubMed]

Benito J, Zheng H, Hardin PE. (2007). PDP1epsilon functions downstream of the circadian oscillator to mediate behavioral rhythms. The Journal of neuroscience : the official journal of the Society for Neuroscience. 27 [PubMed]

Blau J, Young MW. (1999). Cycling vrille expression is required for a functional Drosophila clock. Cell. 99 [PubMed]

Buchler NE, Cross FR. (2009). Protein sequestration generates a flexible ultrasensitive response in a genetic network. Molecular systems biology. 5 [PubMed]

Buchler NE, Louis M. (2008). Molecular titration and ultrasensitivity in regulatory networks. Journal of molecular biology. 384 [PubMed]

Bugge A et al. (2012). Rev-erba and Rev-erbß coordinately protect the circadian clock and normal metabolic function. Genes & development. 26 [PubMed]

Busino L et al. (2007). SCFFbxl3 controls the oscillation of the circadian clock by directing the degradation of cryptochrome proteins. Science (New York, N.Y.). 316 [PubMed]

Challet E, Poirel VJ, Malan A, Pévet P. (2003). Light exposure during daytime modulates expression of Per1 and Per2 clock genes in the suprachiasmatic nuclei of mice. Journal of neuroscience research. 72 [PubMed]

Chen R et al. (2009). Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism. Molecular cell. 36 [PubMed]

Cho H et al. (2012). Regulation of circadian behaviour and metabolism by REV-ERB-a and REV-ERB-ß. Nature. 485 [PubMed]

Dardente H, Fortier EE, Martineau V, Cermakian N. (2007). Cryptochromes impair phosphorylation of transcriptional activators in the clock: a general mechanism for circadian repression. The Biochemical journal. 402 [PubMed]

Debruyne JP et al. (2006). A clock shock: mouse CLOCK is not required for circadian oscillator function. Neuron. 50 [PubMed]

Dibner C et al. (2009). Circadian gene expression is resilient to large fluctuations in overall transcription rates. The EMBO journal. 28 [PubMed]

Etchegaray JP et al. (2009). Casein kinase 1 delta regulates the pace of the mammalian circadian clock. Molecular and cellular biology. 29 [PubMed]

Fan Y, Hida A, Anderson DA, Izumo M, Johnson CH. (2007). Cycling of CRYPTOCHROME proteins is not necessary for circadian-clock function in mammalian fibroblasts. Current biology : CB. 17 [PubMed]

Forger DB. (2011). Signal processing in cellular clocks. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]

Forger DB, Peskin CS. (2003). A detailed predictive model of the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 100 [PubMed]

Forger DB, Peskin CS. (2005). Stochastic simulation of the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 102 [PubMed]

François P, Hakim V. (2005). Core genetic module: the mixed feedback loop. Physical review. E, Statistical, nonlinear, and soft matter physics. 72 [PubMed]

Froy O, Chang DC, Reppert SM. (2002). Redox potential: differential roles in dCRY and mCRY1 functions. Current biology : CB. 12 [PubMed]

Gallego M, Eide EJ, Woolf MF, Virshup DM, Forger DB. (2006). An opposite role for tau in circadian rhythms revealed by mathematical modeling. Proceedings of the National Academy of Sciences of the United States of America. 103 [PubMed]

Glossop NR, Lyons LC, Hardin PE. (1999). Interlocked feedback loops within the Drosophila circadian oscillator. Science (New York, N.Y.). 286 [PubMed]

Gonzalez OR, Küper C, Jung K, Naval PC, Mendoza E. (2007). Parameter estimation using Simulated Annealing for S-system models of biochemical networks. Bioinformatics (Oxford, England). 23 [PubMed]

Goodwin BC. (1965). Oscillatory behavior in enzymatic control processes. Advances in enzyme regulation. 3 [PubMed]

Griffith JS. (1968). Mathematics of cellular control processes. I. Negative feedback to one gene. Journal of theoretical biology. 20 [PubMed]

He Q et al. (2005). Light-independent phosphorylation of WHITE COLLAR-1 regulates its function in the Neurospora circadian negative feedback loop. The Journal of biological chemistry. 280 [PubMed]

Herzog ED, Takahashi JS, Block GD. (1998). Clock controls circadian period in isolated suprachiasmatic nucleus neurons. Nature neuroscience. 1 [PubMed]

Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM. (2004). ModelDB: A Database to Support Computational Neuroscience. Journal of computational neuroscience. 17 [PubMed]

Huang G et al. (2007). Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop. Genes & development. 21 [PubMed]

Iitaka C, Miyazaki K, Akaike T, Ishida N. (2005). A role for glycogen synthase kinase-3beta in the mammalian circadian clock. The Journal of biological chemistry. 280 [PubMed]

Khan SK et al. (2012). Identification of a novel cryptochrome differentiating domain required for feedback repression in circadian clock function. The Journal of biological chemistry. 287 [PubMed]

Kim SY, Ferrell JE. (2007). Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell. 128 [PubMed]

Ko CH, Takahashi JS. (2006). Molecular components of the mammalian circadian clock. Human molecular genetics. 15 Spec No 2 [PubMed]

Ko CH et al. (2010). Emergence of noise-induced oscillations in the central circadian pacemaker. PLoS biology. 8 [PubMed]

Kondratov RV et al. (2006). Post-translational regulation of circadian transcriptional CLOCK(NPAS2)/BMAL1 complex by CRYPTOCHROMES. Cell cycle (Georgetown, Tex.). 5 [PubMed]

Kronauer RE, Forger DB, Jewett ME. (1999). Quantifying human circadian pacemaker response to brief, extended, and repeated light stimuli over the phototopic range. Journal of biological rhythms. 14 [PubMed]

Kwon I et al. (2006). BMAL1 shuttling controls transactivation and degradation of the CLOCK/BMAL1 heterodimer. Molecular and cellular biology. 26 [PubMed]

Langmesser S, Tallone T, Bordon A, Rusconi S, Albrecht U. (2008). Interaction of circadian clock proteins PER2 and CRY with BMAL1 and CLOCK. BMC molecular biology. 9 [PubMed]

Lee C, Etchegaray JP, Cagampang FR, Loudon AS, Reppert SM. (2001). Posttranslational mechanisms regulate the mammalian circadian clock. Cell. 107 [PubMed]

Lee H, Chen R, Lee Y, Yoo S, Lee C. (2009). Essential roles of CKIdelta and CKIepsilon in the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]

Lee Y, Chen R, Lee HM, Lee C. (2011). Stoichiometric relationship among clock proteins determines robustness of circadian rhythms. The Journal of biological chemistry. 286 [PubMed]

Leise TL, Wang CW, Gitis PJ, Welsh DK. (2012). Persistent cell-autonomous circadian oscillations in fibroblasts revealed by six-week single-cell imaging of PER2::LUC bioluminescence. PloS one. 7 [PubMed]

Leloup JC, Goldbeter A. (2003). Toward a detailed computational model for the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 100 [PubMed]

Leloup JC, Goldbeter A. (2004). Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms. Journal of theoretical biology. 230 [PubMed]

Li D, Li C. (2008). Noise-induced dynamics in the mixed-feedback-loop network motif. Physical review. E, Statistical, nonlinear, and soft matter physics. 77 [PubMed]

Liu AC et al. (2008). Redundant function of REV-ERBalpha and beta and non-essential role for Bmal1 cycling in transcriptional regulation of intracellular circadian rhythms. PLoS genetics. 4 [PubMed]

Liu AC et al. (2007). Intercellular coupling confers robustness against mutations in the SCN circadian clock network. Cell. 129 [PubMed]

Loros JJ, Dunlap JC, Decoursey PJ. (2004). Chronobiology: Biological Timekeeping.

Mendes P et al. (2009). Computational modeling of biochemical networks using COPASI. Methods in molecular biology (Clifton, N.J.). 500 [PubMed]

Menet JS, Abruzzi KC, Desrochers J, Rodriguez J, Rosbash M. (2010). Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA. Genes & development. 24 [PubMed]

Miller MM, Gould BE, Nelson JF. (1989). Aging and long-term ovariectomy alter the cytoarchitecture of the hypothalamic-preoptic area of the C57BL/6J mouse. Neurobiology of aging. 10 [PubMed]

Mirsky HP, Liu AC, Welsh DK, Kay SA, Doyle FJ. (2009). A model of the cell-autonomous mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]

Novák B, Tyson JJ. (2008). Design principles of biochemical oscillators. Nature reviews. Molecular cell biology. 9 [PubMed]

Pokhilko A et al. (2012). The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Molecular systems biology. 8 [PubMed]

Preitner N et al. (2002). The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell. 110 [PubMed]

Relógio A et al. (2011). Tuning the mammalian circadian clock: robust synergy of two loops. PLoS computational biology. 7 [PubMed]

Reppert SM, Weaver DR. (2001). Molecular analysis of mammalian circadian rhythms. Annual review of physiology. 63 [PubMed]

Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK. (2007). Ordered phosphorylation governs oscillation of a three-protein circadian clock. Science (New York, N.Y.). 318 [PubMed]

Sahar S, Zocchi L, Kinoshita C, Borrelli E, Sassone-Corsi P. (2010). Regulation of BMAL1 protein stability and circadian function by GSK3beta-mediated phosphorylation. PloS one. 5 [PubMed]

Sato TK et al. (2006). Feedback repression is required for mammalian circadian clock function. Nature genetics. 38 [PubMed]

Schmidt H, Jirstrand M. (2006). Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics (Oxford, England). 22 [PubMed]

Shearman LP et al. (2000). Interacting molecular loops in the mammalian circadian clock. Science (New York, N.Y.). 288 [PubMed]

Siepka SM et al. (2007). Circadian mutant Overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression. Cell. 129 [PubMed]

Smolen P, Baxter DA, Byrne JH. (2002). A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator. Biophysical journal. 83 [PubMed]

Stricker J et al. (2008). A fast, robust and tunable synthetic gene oscillator. Nature. 456 [PubMed]

Suter DM et al. (2011). Mammalian genes are transcribed with widely different bursting kinetics. Science (New York, N.Y.). 332 [PubMed]

Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M. (2009). A tunable synthetic mammalian oscillator. Nature. 457 [PubMed]

Tsai TY et al. (2008). Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science (New York, N.Y.). 321 [PubMed]

Ueda HR et al. (2005). System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nature genetics. 37 [PubMed]

Ukai-Tadenuma M et al. (2011). Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell. 144 [PubMed]

Vitaterna MH et al. (1994). Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science (New York, N.Y.). 264 [PubMed]

Welsh DK, Yoo SH, Liu AC, Takahashi JS, Kay SA. (2004). Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Current biology : CB. 14 [PubMed]

Wilkins AK, Barton PI, Tidor B. (2007). The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS computational biology. 3 [PubMed]

Yamada Y, Forger D. (2010). Multiscale complexity in the mammalian circadian clock. Current opinion in genetics & development. 20 [PubMed]

Yamaguchi S et al. (2003). Synchronization of cellular clocks in the suprachiasmatic nucleus. Science (New York, N.Y.). 302 [PubMed]

Ye R, Selby CP, Ozturk N, Annayev Y, Sancar A. (2011). Biochemical analysis of the canonical model for the mammalian circadian clock. The Journal of biological chemistry. 286 [PubMed]

Yin L, Wang J, Klein PS, Lazar MA. (2006). Nuclear receptor Rev-erbalpha is a critical lithium-sensitive component of the circadian clock. Science (New York, N.Y.). 311 [PubMed]

Yoo SH et al. (2005). A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo. Proceedings of the National Academy of Sciences of the United States of America. 102 [PubMed]

References and models that cite this paper

Cao F, Ralph MR, Stinchcombe AR. (2022). A Phenomenological Mouse Circadian Pacemaker Model Journal of biological rhythms. 37 [PubMed]

DeWoskin D et al. (2015). Distinct roles for GABA across multiple timescales in mammalian circadian timekeeping. Proceedings of the National Academy of Sciences of the United States of America. 112 [PubMed]

Gleit RD, Diniz Behn CG, Booth V. (2013). Modeling interindividual differences in spontaneous internal desynchrony patterns. Journal of biological rhythms. 28 [PubMed]

Paul JR et al. (2016). Regulation of persistent sodium currents by glycogen synthase kinase 3 encodes daily rhythms of neuronal excitability. Nature communications. 7 [PubMed]

Podkolodnyy NL, Tverdokhleb NN, Podkolodnaya OA. (2017). Computational model of circadian oscillator in mammals: Interaction with NAD+/SIRT1 system and age-related changes in the expression of circadian oscillator genes Russian Journal of Genetics: Applied Research. 7

Wood D et al. (2013). Modeling and validating chronic pharmacological manipulation of circadian rhythms CPT: Pharmacometrics & Systems Pharmacology. 2(7)

This website requires cookies and limited processing of your personal data in order to function. By continuing to browse or otherwise use this site, you are agreeing to this use. See our Privacy policy and how to cite and terms of use.