Understanding systems-level properties: timely stories from the study of clocks

scientific article published on 10 May 2011

Understanding systems-level properties: timely stories from the study of clocks is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

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P356DOI10.1038/NRG2972
P698PubMed publication ID21556016
P5875ResearchGate publication ID51111195

P2093author name stringJohn B Hogenesch
Hiroki R Ueda
P2860cites workNetwork features of the mammalian circadian clockQ21563545
Disruption of retinoid-related orphan receptor beta changes circadian behavior, causes retinal degeneration and leads to vacillans phenotype in miceQ24533269
Circadian clocks in human red blood cellsQ24620753
CLOCK and NPAS2 have overlapping roles in the suprachiasmatic circadian clockQ24650981
The in vitro real-time oscillation monitoring system identifies potential entrainment factors for circadian clocks.Q25256792
Functional profiling of the Saccharomyces cerevisiae genomeQ27860544
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysisQ27860815
CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clockQ27865241
The VPAC(2) receptor is essential for circadian function in the mouse suprachiasmatic nucleiQ28207565
The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillatorQ28216502
A clock shock: mouse CLOCK is not required for circadian oscillator functionQ28238302
A predictive model of the oxygen and heme regulatory network in yeastQ28473966
A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteriaQ28485565
Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitroQ28485571
Differential functions of mPer1, mPer2, and mPer3 in the SCN circadian clockQ28509438
Delay in feedback repression by cryptochrome 1 is required for circadian clock functionQ28512076
Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythmsQ28584936
Altered patterns of sleep and behavioral adaptability in NPAS2-deficient miceQ28588185
Mop3 is an essential component of the master circadian pacemaker in mammalsQ28591939
Circadian rhythms and memory: not so simple as cogs and gearsQ28752225
A synthetic oscillatory network of transcriptional regulatorsQ29547344
A functional genomics strategy reveals Rora as a component of the mammalian circadian clockQ29616297
The meter of metabolismQ29619740
Intercellular coupling confers robustness against mutations in the SCN circadian clock networkQ30543329
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).Q30806988
Targeted disruption of the mPer3 gene: subtle effects on circadian clock functionQ30901003
Advancing post-genome data and system integration through machine learningQ31162613
Characterization of unknown adult stem cell samples by large scale data integration and artificial neural networks.Q33408220
Network-free inference of knockout effects in yeastQ33523272
Discovering transcriptional modules by Bayesian data integrationQ33597293
The molecular clockwork of a protein-based circadian oscillatorQ33604973
Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteriaQ33885396
Molecular mechanism of temperature sensing by the circadian clock of Neurospora crassaQ33942697
Temperature as a universal resetting cue for mammalian circadian oscillatorsQ34143703
Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiCQ34194360
KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system.Q34194369
No transcription-translation feedback in circadian rhythm of KaiC phosphorylationQ34369194
A detailed predictive model of the mammalian circadian clockQ34385605
Thermally regulated translational control of FRQ mediates aspects of temperature responses in the neurospora circadian clockQ34426048
Signal processing in cellular clocksQ34693749
ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteriaQ34694770
Long and short isoforms of Neurospora clock protein FRQ support temperature-compensated circadian rhythmsQ34718029
Altered behavioral rhythms and clock gene expression in mice with a targeted mutation in the Period1 geneQ34729382
A circadian clock in Neurospora: how genes and proteins cooperate to produce a sustained, entrainable, and compensated biological oscillator with a period of about a dayQ34784363
Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: temperature compensation and damping.Q34795619
The regulatory utilization of genetic redundancy through responsive backup circuitsQ34805700
Structural insights into a circadian oscillatorQ34869684
How a cyanobacterium tells timeQ34872329
A role for casein kinase 2 in the mechanism underlying circadian temperature compensationQ34981570
Estimation of mean body temperature from mean skin and core temperatureQ35546741
Small-scale copy number variation and large-scale changes in gene expression.Q36954927
A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3betaQ37023129
Complexity of the Neurospora crassa circadian clock system: multiple loops and oscillators.Q37141048
Circadian clock genes and sleep homeostasis.Q37497516
Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942.Q37535587
Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analysesQ37535591
A time to fast, a time to feast: the crosstalk between metabolism and the circadian clockQ37588515
Metabolism and circadian rhythms--implications for obesityQ37621141
ON THE MECHANISM OF TEMPERATURE INDEPENDENCE IN A BIOLOGICAL CLOCK.Q37689932
Mammalian Per-Arnt-Sim proteins in environmental adaptationQ37690733
Ordered phosphorylation governs oscillation of a three-protein circadian clockQ39144220
Autonomous synchronization of the circadian KaiC phosphorylation rhythmQ39274167
Quantitative genome-wide analysis of yeast deletion strain sensitivities to oxidative and chemical stress.Q39776817
Synchronization of circadian oscillation of phosphorylation level of KaiC in vitro.Q40778160
Circadian gating of the cell cycle revealed in single cyanobacterial cellsQ41849818
Transcription control reprogramming in genetic backup circuitsQ42648483
Temperature Compensation of Circadian Period Length in Clock Mutants of Neurospora crassaQ46666304
Natural selection favors a newly derived timeless allele in Drosophila melanogasterQ47070309
How temperature changes reset a circadian oscillatorQ47725740
The mPer2 gene encodes a functional component of the mammalian circadian clockQ47946668
Circadian clocks: genes, sleep, and cognitionQ48224921
Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments.Q50893618
Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models.Q51920734
A generalized model of the repressilator.Q51934061
A simpler model of the human circadian pacemaker.Q52082705
A model for circadian oscillations in the Drosophila period protein (PER).Q52329422
Natural variation in a Drosophila clock gene and temperature compensation.Q52560702
Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro.Q53610012
Peripheral circadian oscillators require CLOCKQ59102208
Chemical Oscillations, Waves, and TurbulenceQ60608903
Linkage disequilibrium, mutational analysis and natural selection in the repetitive region of the clock gene, period, in Drosophila melanogasterQ77225350
P433issue6
P304page(s)407-416
P577publication date2011-05-10
P1433published inNature Reviews GeneticsQ1071824
P1476titleUnderstanding systems-level properties: timely stories from the study of clocks
P478volume12

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cites work (P2860)
Q42578914A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators
Q34203771A mammalian circadian clock model incorporating daytime expression elements
Q91874661A mobile ELF4 delivers circadian temperature information from shoots to roots
Q54253935A quantitative study of the diversity of stripe-forming processes in an arthropod cell-based field undergoing axis formation and growth.
Q37556701CGDB: a database of circadian genes in eukaryotes
Q48384545CHRONO integrates behavioral stress and epigenetic control of metabolism
Q28541855Cell type-specific functions of period genes revealed by novel adipocyte and hepatocyte circadian clock models
Q29616556Central and peripheral circadian clocks in mammals
Q47147580CirGRDB: a database for the genome-wide deciphering circadian genes and regulators
Q55221813Circadian Regulation of Horticultural Traits: Integration of Environmental Signals
Q33687817Circadian redox and metabolic oscillations in mammalian systems
Q26830079Circadian rhythms and mood: opportunities for multi-level analyses in genomics and neuroscience: circadian rhythm dysregulation in mood disorders provides clues to the brain's organizing principles, and a touchstone for genomics and neuroscience
Q26796457Circadian systems biology: When time matters
Q27324401Clk post-transcriptional control denoises circadian transcription both temporally and spatially
Q31053995Complex dynamics of transcription regulation
Q36506747DNA methylation changes induced by long and short photoperiods in Nasonia.
Q42774778Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification
Q47644252Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks
Q42013940Development of a configurable growth chamber with a computer vision system to study circadian rhythm in plants
Q35197952Dynamic fluctuations lubricate the circadian clock
Q31161489Expressions of tight junction proteins Occludin and Claudin-1 are under the circadian control in the mouse large intestine: implications in intestinal permeability and susceptibility to colitis
Q34447664Gene and genome parameters of mammalian liver circadian genes (LCGs).
Q36281998Heat shock antagonizes UVA-induced responses in murine melanocytes and melanoma cells: an unexpected interaction
Q64263896Heat the Clock: Entrainment and Compensation in Circadian Rhythms
Q34831729Hepatocyte circadian clock controls acetaminophen bioactivation through NADPH-cytochrome P450 oxidoreductase
Q36567973Histone methyltransferase MLL3 contributes to genome-scale circadian transcription
Q21563355Hsp70-Hsp40 chaperone complex functions in controlling polarized growth by repressing Hsf1-driven heat stress-associated transcription
Q92332181Human Circadian Molecular Oscillation Development Using Induced Pluripotent Stem Cells
Q47113700Integration of omics sciences to advance biology and medicine.
Q27302139Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus
Q41269902Involvement of posttranscriptional regulation of Clock in the emergence of circadian clock oscillation during mouse development.
Q36184574It is time to take timing seriously in clinical genetics
Q28080813Manipulating the circadian and sleep cycles to protect against metabolic disease
Q26822588Mathematical models light up plant signaling
Q41468335Metabolic compensation of the Neurospora clock by a glucose-dependent feedback of the circadian repressor CSP1 on the core oscillator
Q35843886Mining for novel candidate clock genes in the circadian regulatory network
Q35646078Minireview: NAD+, a circadian metabolite with an epigenetic twist
Q34340587Molecular components of the Mammalian circadian clock
Q45900104Nuclear magnetic resonance spectroscopy of the circadian clock of cyanobacteria.
Q57819256Ocular Clocks: Adapting Mechanisms for Eye Functions and Health
Q37978338Paradoxical and bidirectional drug effects
Q37245968Photoreceptor phagocytosis is mediated by phosphoinositide signaling
Q34525869Prevalence of cycling genes and drug targets calls for prospective chronotherapeutics
Q41845617Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules
Q35926212Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways.
Q36342514Rhythmic ring-ring stacking drives the circadian oscillator clockwise
Q36267822Robust network topologies for generating oscillations with temperature-independent periods
Q28542772Role for circadian clock genes in seasonal timing: testing the Bünning hypothesis
Q35672364Suppressing the Neurospora crassa circadian clock while maintaining light responsiveness in continuous stirred tank reactors
Q92783475Synchronization of the Normal Human Peripheral Immune System: A Comprehensive Circadian Systems Immunology Analysis
Q34551665Systems Biology-Derived Discoveries of Intrinsic Clocks
Q26745770TRP channels: a missing bond in the entrainment mechanism of peripheral clocks throughout evolution
Q36455066The Circadian Clock Gene Period1 Connects the Molecular Clock to Neural Activity in the Suprachiasmatic Nucleus
Q92702982The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)
Q24602082The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops
Q38055661The clock shop: coupled circadian oscillators.
Q41958218The free energy cost of accurate biochemical oscillations
Q47282821Thermodynamic Aspects and Reprogramming Cellular Energy Metabolism during the Fibrosis Process
Q34168506Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG) proteins
Q29616252Transcriptional architecture and chromatin landscape of the core circadian clock in mammals
Q33875579Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis
Q52798114[Clock and molecular genetics in Drosophila].