Citation Relationships

Legends: Link to a Model Reference cited by multiple papers


Kim JK, Forger DB (2012) A mechanism for robust circadian timekeeping via stoichiometric balance. Mol Syst Biol 8:630 [PubMed]

   Circadian clock model based on protein sequestration (simple version) (Kim & Forger 2012)

   Circadian clock model in mammals (detailed version) (Kim & Forger 2012)

References and models cited by this paper

References and models that cite this paper

Baggs JE, Price TS, DiTacchio L, Panda S, Fitzgerald GA, Hogenesch JB (2009) Network features of the mammalian circadian clock. PLoS Biol 7:e52 [Journal] [PubMed]
Baker CL, Loros JJ, Dunlap JC (2012) The circadian clock of Neurospora crassa. FEMS Microbiol Rev 36:95-110 [Journal] [PubMed]
Barkai N, Leibler S (2000) Circadian clocks limited by noise. Nature 403:267-8 [Journal] [PubMed]
Becker-Weimann S, Wolf J, Herzel H, Kramer A (2004) Modeling feedback loops of the Mammalian circadian oscillator. Biophys J 87:3023-34 [Journal] [PubMed]
Benito J, Zheng H, Hardin PE (2007) PDP1epsilon functions downstream of the circadian oscillator to mediate behavioral rhythms. J Neurosci 27:2539-47 [Journal] [PubMed]
Blau J, Young MW (1999) Cycling vrille expression is required for a functional Drosophila clock. Cell 99:661-71 [PubMed]
Buchler NE, Cross FR (2009) Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol Syst Biol 5:272 [Journal] [PubMed]
Buchler NE, Louis M (2008) Molecular titration and ultrasensitivity in regulatory networks. J Mol Biol 384:1106-19 [Journal] [PubMed]
Bugge A, Feng D, Everett LJ, Briggs ER, Mullican SE, Wang F, Jager J, Lazar MA (2012) Rev-erba and Rev-erbß coordinately protect the circadian clock and normal metabolic function. Genes Dev 26:657-67 [Journal] [PubMed]
Busino L, Bassermann F, Maiolica A, Lee C, Nolan PM, Godinho SI, Draetta GF, Pagano M (2007) SCFFbxl3 controls the oscillation of the circadian clock by directing the degradation of cryptochrome proteins. Science 316:900-4 [Journal] [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. J Neurosci Res 72:629-37 [Journal] [PubMed]
Chen R, Schirmer A, Lee Y, Lee H, Kumar V, Yoo SH, Takahashi JS, Lee C (2009) Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism. Mol Cell 36:417-30 [Journal] [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. Biochem J 402:525-36 [Journal] [PubMed]
Debruyne JP, Noton E, Lambert CM, Maywood ES, Weaver DR, Reppert SM (2006) A clock shock: mouse CLOCK is not required for circadian oscillator function. Neuron 50:465-77 [Journal] [PubMed]
Dibner C, Sage D, Unser M, Bauer C, d'Eysmond T, Naef F, Schibler U (2009) Circadian gene expression is resilient to large fluctuations in overall transcription rates. EMBO J 28:123-34 [Journal] [PubMed]
Dunlap JC, Loros JJ, Decoursey PJ (2004) Chronobiology: Biological Timekeeping
Etchegaray JP, Machida KK, Noton E, Constance CM, Dallmann R, Di Napoli MN, DeBruyne JP, Lambert CM, Yu EA, Reppert SM, Weaver DR (2009) Casein kinase 1 delta regulates the pace of the mammalian circadian clock. Mol Cell Biol 29:3853-66 [Journal] [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. Curr Biol 17:1091-100 [Journal] [PubMed]
Forger DB (2011) Signal processing in cellular clocks. Proc Natl Acad Sci U S A 108:4281-5 [Journal] [PubMed]
Forger DB, Peskin CS (2003) A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci U S A 100:14806-11 [Journal] [PubMed]
Forger DB, Peskin CS (2005) Stochastic simulation of the mammalian circadian clock. Proc Natl Acad Sci U S A 102:321-4 [Journal] [PubMed]
François P, Hakim V (2005) Core genetic module: the mixed feedback loop. Phys Rev E Stat Nonlin Soft Matter Phys 72:031908 [Journal] [PubMed]
Froy O, Chang DC, Reppert SM (2002) Redox potential: differential roles in dCRY and mCRY1 functions. Curr Biol 12:147-52 [PubMed]
Gallego M, Eide EJ, Woolf MF, Virshup DM, Forger DB (2006) An opposite role for tau in circadian rhythms revealed by mathematical modeling. Proc Natl Acad Sci U S A 103:10618-23 [Journal] [PubMed]
Glossop NR, Lyons LC, Hardin PE (1999) Interlocked feedback loops within the Drosophila circadian oscillator. Science 286:766-8 [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 23:480-6 [Journal] [PubMed]
Goodwin BC (1965) Oscillatory behavior in enzymatic control processes. Adv Enzyme Regul 3:425-38 [PubMed]
Griffith JS (1968) Mathematics of cellular control processes. I. Negative feedback to one gene. J Theor Biol 20:202-8 [PubMed]
He Q, Shu H, Cheng P, Chen S, Wang L, Liu Y (2005) Light-independent phosphorylation of WHITE COLLAR-1 regulates its function in the Neurospora circadian negative feedback loop. J Biol Chem 280:17526-32 [Journal] [PubMed]
Herzog ED, Takahashi JS, Block GD (1998) Clock controls circadian period in isolated suprachiasmatic nucleus neurons. Nat Neurosci 1:708-13 [Journal] [PubMed]
Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM (2004) ModelDB: A Database to Support Computational Neuroscience. J Comput Neurosci 17:7-11 [Journal] [PubMed]
Huang G, Chen S, Li S, Cha J, Long C, Li L, He Q, Liu Y (2007) Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop. Genes Dev 21:3283-95 [Journal] [PubMed]
Iitaka C, Miyazaki K, Akaike T, Ishida N (2005) A role for glycogen synthase kinase-3beta in the mammalian circadian clock. J Biol Chem 280:29397-402 [Journal] [PubMed]
Khan SK, Xu H, Ukai-Tadenuma M, Burton B, Wang Y, Ueda HR, Liu AC (2012) Identification of a novel cryptochrome differentiating domain required for feedback repression in circadian clock function. J Biol Chem 287:25917-26 [Journal] [PubMed]
Kim SY, Ferrell JE (2007) Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell 128:1133-45 [Journal] [PubMed]
Ko CH, Takahashi JS (2006) Molecular components of the mammalian circadian clock. Hum Mol Genet 15 Spec No 2:R271-7 [Journal] [PubMed]
Ko CH, Yamada YR, Welsh DK, Buhr ED, Liu AC, Zhang EE, Ralph MR, Kay SA, Forger DB, Takahashi JS (2010) Emergence of noise-induced oscillations in the central circadian pacemaker. PLoS Biol 8:e1000513 [Journal] [PubMed]
Kondratov RV, Kondratova AA, Lee C, Gorbacheva VY, Chernov MV, Antoch MP (2006) Post-translational regulation of circadian transcriptional CLOCK(NPAS2)/BMAL1 complex by CRYPTOCHROMES. Cell Cycle 5:890-5 [Journal] [PubMed]
Kronauer RE, Forger DB, Jewett ME (1999) Quantifying human circadian pacemaker response to brief, extended, and repeated light stimuli over the phototopic range. J Biol Rhythms 14:500-15 [PubMed]
Kwon I, Lee J, Chang SH, Jung NC, Lee BJ, Son GH, Kim K, Lee KH (2006) BMAL1 shuttling controls transactivation and degradation of the CLOCK/BMAL1 heterodimer. Mol Cell Biol 26:7318-30 [Journal] [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 Mol Biol 9:41 [Journal] [PubMed]
Lee C, Etchegaray JP, Cagampang FR, Loudon AS, Reppert SM (2001) Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107:855-67 [PubMed]
Lee H, Chen R, Lee Y, Yoo S, Lee C (2009) Essential roles of CKIdelta and CKIepsilon in the mammalian circadian clock. Proc Natl Acad Sci U S A 106:21359-64 [Journal] [PubMed]
Lee Y, Chen R, Lee HM, Lee C (2011) Stoichiometric relationship among clock proteins determines robustness of circadian rhythms. J Biol Chem 286:7033-42 [Journal] [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:e33334 [Journal] [PubMed]
Leloup JC, Goldbeter A (2003) Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci U S A 100:7051-6 [Journal] [PubMed]
Leloup JC, Goldbeter A (2004) Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms. J Theor Biol 230:541-62 [Journal] [PubMed]
Li D, Li C (2008) Noise-induced dynamics in the mixed-feedback-loop network motif. Phys Rev E Stat Nonlin Soft Matter Phys 77:011903 [Journal] [PubMed]
Liu AC, Tran HG, Zhang EE, Priest AA, Welsh DK, Kay SA (2008) Redundant function of REV-ERBalpha and beta and non-essential role for Bmal1 cycling in transcriptional regulation of intracellular circadian rhythms. PLoS Genet 4:e1000023 [Journal] [PubMed]
Liu AC, Welsh DK, Ko CH, Tran HG, Zhang EE, Priest AA, Buhr ED, Singer O, Meeker K, Verma IM, Doyle FJ, Takahashi JS, Kay SA (2007) Intercellular coupling confers robustness against mutations in the SCN circadian clock network. Cell 129:605-16 [Journal] [PubMed]
Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U (2009) Computational modeling of biochemical networks using COPASI. Methods Mol Biol 500:17-59 [Journal] [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 Dev 24:358-67 [Journal] [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. Neurobiol Aging 10:683-90 [PubMed]
Mirsky HP, Liu AC, Welsh DK, Kay SA, Doyle FJ (2009) A model of the cell-autonomous mammalian circadian clock. Proc Natl Acad Sci U S A 106:11107-12 [Journal] [PubMed]
Novák B, Tyson JJ (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9:981-91 [Journal] [PubMed]
Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ (2012) The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol 8:574 [Journal] [PubMed]
Preitner N, Damiola F, Lopez-Molina L, Zakany J, Duboule D, Albrecht U, Schibler U (2002) The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110:251-60 [PubMed]
Relógio A, Westermark PO, Wallach T, Schellenberg K, Kramer A, Herzel H (2011) Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput Biol 7:e1002309 [Journal] [PubMed]
Reppert SM, Weaver DR (2001) Molecular analysis of mammalian circadian rhythms. Annu Rev Physiol 63:647-76 [Journal] [PubMed]
Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK (2007) Ordered phosphorylation governs oscillation of a three-protein circadian clock. Science 318:809-12 [Journal] [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:e8561 [Journal] [PubMed]
Sato TK, Yamada RG, Ukai H, Baggs JE, Miraglia LJ, Kobayashi TJ, Welsh DK, Kay SA, Ueda HR, Hogenesch JB (2006) Feedback repression is required for mammalian circadian clock function. Nat Genet 38:312-9 [Journal] [PubMed]
Schmidt H, Jirstrand M (2006) Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics 22:514-5 [Journal] [PubMed]
Siepka SM, Yoo SH, Park J, Song W, Kumar V, Hu Y, Lee C, Takahashi JS (2007) Circadian mutant Overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression. Cell 129:1011-23 [Journal] [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. Biophys J 83:2349-59 [Journal] [PubMed]
Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456:516-9 [Journal] [PubMed]
Suter DM, Molina N, Gatfield D, Schneider K, Schibler U, Naef F (2011) Mammalian genes are transcribed with widely different bursting kinetics. Science 332:472-4 [Journal] [PubMed]
Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M (2009) A tunable synthetic mammalian oscillator. Nature 457:309-12 [Journal] [PubMed]
Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell JE (2008) Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321:126-9 [Journal] [PubMed]
Ueda HR, Hayashi S, Chen W, Sano M, Machida M, Shigeyoshi Y, Iino M, Hashimoto S (2005) System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat Genet 37:187-92 [Journal] [PubMed]
Ukai-Tadenuma M, Yamada RG, Xu H, Ripperger JA, Liu AC, Ueda HR (2011) Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell 144:268-81 [Journal] [PubMed]
Vitaterna MH, King DP, Chang AM, Kornhauser JM, Lowrey PL, McDonald JD, Dove WF, Pinto LH, Turek FW, Takahashi JS (1994) Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science 264:719-25 [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. Curr Biol 14:2289-95 [Journal] [PubMed]
Wilkins AK, Barton PI, Tidor B (2007) The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS Comput Biol 3:e242 [Journal] [PubMed]
Yamada Y, Forger D (2010) Multiscale complexity in the mammalian circadian clock. Curr Opin Genet Dev 20:626-33 [Journal] [PubMed]
Yamaguchi S, Isejima H, Matsuo T, Okura R, Yagita K, Kobayashi M, Okamura H (2003) Synchronization of cellular clocks in the suprachiasmatic nucleus. Science 302:1408-12 [Journal] [PubMed]
Ye R, Selby CP, Ozturk N, Annayev Y, Sancar A (2011) Biochemical analysis of the canonical model for the mammalian circadian clock. J Biol Chem 286:25891-902 [Journal] [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 311:1002-5 [Journal] [PubMed]
Yoo SH, Ko CH, Lowrey PL, Buhr ED, Song EJ, Chang S, Yoo OJ, Yamazaki S, Lee C, Takahashi JS (2005) A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo. Proc Natl Acad Sci U S A 102:2608-13 [Journal] [PubMed]
DeWoskin D, Myung J, Belle MD, Piggins HD, Takumi T, Forger DB (2015) Distinct roles for GABA across multiple timescales in mammalian circadian timekeeping. Proc Natl Acad Sci U S A 112:E3911-9 [Journal] [PubMed]
   HH model neuron of the Suprachiasmatic Nucleus including a persistent Na+ channel (Paul et al 2016) [Model]
Gleit RD, Diniz Behn CG, Booth V (2013) Modeling interindividual differences in spontaneous internal desynchrony patterns. J Biol Rhythms 28:339-55 [Journal] [PubMed]
   Human sleep-wake regulatory network model (Gleit et al 2013, Booth et al 2017) [Model]
Kim JK, Forger DB, Marconi M, Wood D, Doran A, Wager T, Chang C, Walton KM (2013) Modeling and validating chronic pharmacological manipulation of circadian rhythms CPT: Pharmacometrics & Systems Pharmacology 2(7):1-11 [Journal]
   Circadian clock model in mammals (PK/PD model) (Kim & Forger 2013) [Model]
Paul JR, DeWoskin D, McMeekin LJ, Cowell RM, Forger DB, Gamble KL (2016) Regulation of persistent sodium currents by glycogen synthase kinase 3 encodes daily rhythms of neuronal excitability. Nat Commun 7:13470 [Journal] [PubMed]
   HH model neuron of the Suprachiasmatic Nucleus including a persistent Na+ channel (Paul et al 2016) [Model]
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 7:565-573 [Journal]
(86 refs)