{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:11:34Z","timestamp":1772172694603,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007740","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,9,16]],"date-time":"2020-09-16T00:00:00Z","timestamp":1600214400000}}],"reference-count":123,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2020,9,3]],"date-time":"2020-09-03T00:00:00Z","timestamp":1599091200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001869","name":"Academia Sinica","doi-asserted-by":"publisher","award":["AS-IA-106-M01"],"award-info":[{"award-number":["AS-IA-106-M01"]}],"id":[{"id":"10.13039\/501100001869","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["MOST 105-2113-M-001 -009 -MY4"],"award-info":[{"award-number":["MOST 105-2113-M-001 -009 -MY4"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007740","type":"journal-article","created":{"date-parts":[[2020,9,3]],"date-time":"2020-09-03T13:53:49Z","timestamp":1599141229000},"page":"e1007740","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9623-4706","authenticated-orcid":true,"given":"Ignasius","family":"Joanito","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9188-0036","authenticated-orcid":true,"given":"Ching-Cher Sanders","family":"Yan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3842-2893","authenticated-orcid":true,"given":"Jhih-Wei","family":"Chu","sequence":"additional","affiliation":[]},{"given":"Shu-Hsing","family":"Wu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7187-427X","authenticated-orcid":true,"given":"Chao-Ping","family":"Hsu","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,9,3]]},"reference":[{"issue":"4","key":"pcbi.1007740.ref001","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1128\/MMBR.00036-15","article-title":"Circadian Rhythms in Cyanobacteria","volume":"79","author":"SE Cohen","year":"2015","journal-title":"Microbiology and molecular biology reviews: MMBR"},{"key":"pcbi.1007740.ref002","first-page":"25","volume-title":"Advances in genetics","author":"C Heintzen","year":"2007"},{"key":"pcbi.1007740.ref003","first-page":"141","volume-title":"Advances in genetics","author":"PE Hardin","year":"2011"},{"key":"pcbi.1007740.ref004","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/B978-0-12-387690-4.00006-4","article-title":"Genetics of circadian rhythms in Mammalian model organisms","volume":"74","author":"PL Lowrey","year":"2011","journal-title":"Advances in genetics"},{"key":"pcbi.1007740.ref005","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1146\/annurev.arplant.52.1.139","article-title":"CIRCADIAN RHYTHMS IN PLANTS","volume":"52","author":"CR McClung","year":"2001","journal-title":"Annual review of plant physiology and plant molecular biology"},{"issue":"2","key":"pcbi.1007740.ref006","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/s10059-009-0113-0","article-title":"A time to fast, a time to feast: the crosstalk between metabolism and the circadian clock","volume":"28","author":"J Kovac","year":"2009","journal-title":"Molecules and cells"},{"issue":"8","key":"pcbi.1007740.ref007","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/nrn2881","article-title":"Circadian rhythms and memory formation","volume":"11","author":"JR Gerstner","year":"2010","journal-title":"Nat Rev Neurosci"},{"issue":"5734","key":"pcbi.1007740.ref008","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1126\/science.1115581","article-title":"Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage","volume":"309","author":"AN Dodd","year":"2005","journal-title":"Science"},{"key":"pcbi.1007740.ref009","first-page":"221","volume-title":"Progress in Molecular Biology and Translational Science","author":"L Fu","year":"2013"},{"issue":"2","key":"pcbi.1007740.ref010","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/ng.520","article-title":"New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk","volume":"42","author":"J Dupuis","year":"2010","journal-title":"Nat Genet"},{"issue":"43","key":"pcbi.1007740.ref011","article-title":"Impact of the Circadian Clock on the Aging Process","volume":"6","author":"SS Fonseca Costa","year":"2015","journal-title":"Frontiers in Neurology"},{"issue":"12","key":"pcbi.1007740.ref012","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nsmb.3327","article-title":"Molecular mechanisms at the core of the plant circadian oscillator","volume":"23","author":"MA Nohales","year":"2016","journal-title":"Nat Struct Mol Biol"},{"issue":"5531","key":"pcbi.1007740.ref013","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1126\/science.1061320","article-title":"Reciprocal regulation between TOC1 and LHY\/CCA1 within the Arabidopsis circadian clock","volume":"293","author":"D Alabadi","year":"2001","journal-title":"Science"},{"issue":"12","key":"pcbi.1007740.ref014","doi-asserted-by":"crossref","first-page":"e0143943","DOI":"10.1371\/journal.pone.0143943","article-title":"Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions","volume":"10","author":"S Adams","year":"2015","journal-title":"PLoS ONE"},{"issue":"3","key":"pcbi.1007740.ref015","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1105\/tpc.15.00737","article-title":"Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock","volume":"28","author":"M Kamioka","year":"2016","journal-title":"Plant Cell"},{"issue":"8","key":"pcbi.1007740.ref016","doi-asserted-by":"crossref","first-page":"3167","DOI":"10.1073\/pnas.1200355109","article-title":"Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor","volume":"109","author":"JM Gendron","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"6077","key":"pcbi.1007740.ref017","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1126\/science.1219075","article-title":"Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator","volume":"336","author":"W Huang","year":"2012","journal-title":"Science"},{"issue":"5","key":"pcbi.1007740.ref018","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1093\/pcp\/pci086","article-title":"PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana","volume":"46","author":"N Nakamichi","year":"2005","journal-title":"Plant & cell physiology"},{"issue":"3","key":"pcbi.1007740.ref019","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1105\/tpc.109.072892","article-title":"PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock","volume":"22","author":"N Nakamichi","year":"2010","journal-title":"Plant Cell"},{"issue":"42","key":"pcbi.1007740.ref020","doi-asserted-by":"crossref","first-page":"17123","DOI":"10.1073\/pnas.1205156109","article-title":"Transcriptional repressor PRR5 directly regulates clock-output pathways","volume":"109","author":"N Nakamichi","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"6767","key":"pcbi.1007740.ref021","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/35002125","article-title":"A synthetic oscillatory network of transcriptional regulators","volume":"403","author":"MB Elowitz","year":"2000","journal-title":"Nature"},{"issue":"7","key":"pcbi.1007740.ref022","doi-asserted-by":"crossref","first-page":"e1003705","DOI":"10.1371\/journal.pcbi.1003705","article-title":"Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock","volume":"10","author":"K Fogelmark","year":"2014","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"pcbi.1007740.ref023","doi-asserted-by":"crossref","first-page":"13944","DOI":"10.1038\/s41598-018-32030-z","article-title":"An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states","volume":"8","author":"I Joanito","year":"2018","journal-title":"Scientific reports"},{"key":"pcbi.1007740.ref024","doi-asserted-by":"crossref","first-page":"74","DOI":"10.3389\/fpls.2016.00074","article-title":"A Compact Model for the Complex Plant Circadian Clock","volume":"7","author":"J De Caluw\u00e9","year":"2016","journal-title":"Frontiers in Plant Science"},{"key":"pcbi.1007740.ref025","doi-asserted-by":"crossref","first-page":"13181","DOI":"10.1038\/ncomms13181","article-title":"LWD\u2013TCP complex activates the morning gene CCA1 in Arabidopsis","volume":"7","author":"J-F Wu","year":"2016","journal-title":"Nature Communications"},{"issue":"7356","key":"pcbi.1007740.ref026","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/nature10182","article-title":"The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth","volume":"475","author":"DA Nusinow","year":"2011","journal-title":"Nature"},{"issue":"11","key":"pcbi.1007740.ref027","doi-asserted-by":"crossref","first-page":"1903","DOI":"10.1038\/emboj.2010.76","article-title":"PRR5 regulates phosphorylation, nuclear import and subnuclear localization of TOC1 in the Arabidopsis circadian clock","volume":"29","author":"L Wang","year":"2010","journal-title":"The EMBO journal"},{"issue":"9","key":"pcbi.1007740.ref028","doi-asserted-by":"crossref","first-page":"3292","DOI":"10.1073\/pnas.0400163101","article-title":"CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis","volume":"101","author":"X Daniel","year":"2004","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"6966","key":"pcbi.1007740.ref029","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/nature02163","article-title":"Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana","volume":"426","author":"P Mas","year":"2003","journal-title":"Nature"},{"issue":"3","key":"pcbi.1007740.ref030","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1105\/tpc.016808","article-title":"The F-Box Protein ZEITLUPE Confers Dosage-Dependent Control on the Circadian Clock, Photomorphogenesis, and Flowering Time","volume":"16","author":"DE Somers","year":"2004","journal-title":"The Plant Cell"},{"key":"pcbi.1007740.ref031","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nrm2688","article-title":"The ubiquitin\u201326S proteasome system at the nexus of plant biology","volume":"10","author":"RD Vierstra","year":"2009","journal-title":"Nature Reviews Molecular Cell Biology"},{"issue":"9","key":"pcbi.1007740.ref032","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1093\/pcp\/pcx071","article-title":"E3 Ubiquitin Ligases: Ubiquitous Actors in Plant Development and Abiotic Stress Responses","volume":"58","author":"K Shu","year":"2017","journal-title":"Plant and Cell Physiology"},{"issue":"3","key":"pcbi.1007740.ref033","doi-asserted-by":"crossref","first-page":"e23206","DOI":"10.4161\/psb.23206","article-title":"Proteasomal regulation of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) stability is part of the complex control of CCA1","volume":"8","author":"S Kangisser","year":"2013","journal-title":"Plant signaling & behavior"},{"issue":"5","key":"pcbi.1007740.ref034","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1007\/s11103-005-3096-z","article-title":"DET1 regulates the proteasomal degradation of LHY, a component of the Arabidopsis circadian clock","volume":"57","author":"HR Song","year":"2005","journal-title":"Plant molecular biology"},{"issue":"2","key":"pcbi.1007740.ref035","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/j.bbrc.2010.06.067","article-title":"Ubiquitination of LHY by SINAT5 regulates flowering time and is inhibited by DET1","volume":"398","author":"BS Park","year":"2010","journal-title":"Biochemical and biophysical research communications"},{"issue":"11","key":"pcbi.1007740.ref036","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1093\/pcp\/pcm122","article-title":"Rhythmic and light-inducible appearance of clock-associated pseudo-response regulator protein PRR9 through programmed degradation in the dark in Arabidopsis thaliana","volume":"48","author":"S Ito","year":"2007","journal-title":"Plant Cell Physiol"},{"issue":"3","key":"pcbi.1007740.ref037","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1111\/j.1365-313X.2007.03258.x","article-title":"PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis","volume":"52","author":"EM Farre","year":"2007","journal-title":"The Plant journal: for cell and molecular biology"},{"issue":"8","key":"pcbi.1007740.ref038","doi-asserted-by":"crossref","first-page":"2516","DOI":"10.1105\/tpc.107.053033","article-title":"Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana","volume":"19","author":"T Kiba","year":"2007","journal-title":"Plant Cell"},{"issue":"5","key":"pcbi.1007740.ref039","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1016\/j.febslet.2006.01.016","article-title":"Arabidopsis GIGANTEA protein is post-transcriptionally regulated by light and dark","volume":"580","author":"KM David","year":"2006","journal-title":"FEBS letters"},{"issue":"5","key":"pcbi.1007740.ref040","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/j.molcel.2008.09.026","article-title":"COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability","volume":"32","author":"JW Yu","year":"2008","journal-title":"Mol Cell"},{"key":"pcbi.1007740.ref041","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1038\/nrg.2016.150","article-title":"Transcriptional architecture of the mammalian circadian clock","volume":"18","author":"JS Takahashi","year":"2016","journal-title":"Nature Reviews Genetics"},{"issue":"5","key":"pcbi.1007740.ref042","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1016\/j.cell.2007.04.030","article-title":"Circadian Mutant Overtime Reveals F-box Protein FBXL3 Regulation of Cryptochrome and Period Gene Expression","volume":"129","author":"SM Siepka","year":"2007","journal-title":"Cell"},{"issue":"5826","key":"pcbi.1007740.ref043","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1126\/science.1141138","article-title":"The After-Hours Mutant Reveals a Role for Fbxl3 in Determining Mammalian Circadian Period","volume":"316","author":"SIH Godinho","year":"2007","journal-title":"Science"},{"issue":"5826","key":"pcbi.1007740.ref044","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1126\/science.1141194","article-title":"SCFFbxl3 Controls the Oscillation of the Circadian Clock by Directing the Degradation of Cryptochrome Proteins","volume":"316","author":"L Busino","year":"2007","journal-title":"Science"},{"issue":"5","key":"pcbi.1007740.ref045","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2013.01.054","article-title":"FBXL21 Regulates Oscillation of the Circadian Clock through Ubiquitination and Stabilization of Cryptochromes","volume":"152","author":"A Hirano","year":"2013","journal-title":"Cell"},{"issue":"5","key":"pcbi.1007740.ref046","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1016\/j.cell.2013.01.055","article-title":"Competing E3 Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm","volume":"152","author":"S-H Yoo","year":"2013","journal-title":"Cell"},{"issue":"22","key":"pcbi.1007740.ref047","doi-asserted-by":"crossref","first-page":"3454","DOI":"10.1016\/j.cub.2017.10.014","article-title":"Stability of Wake-Sleep Cycles Requires Robust Degradation of the PERIOD Protein","volume":"27","author":"M D\u2019Alessandro","year":"2017","journal-title":"Current Biology"},{"key":"pcbi.1007740.ref048","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1038\/msb.2012.6","article-title":"The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops","volume":"8","author":"A Pokhilko","year":"2012","journal-title":"Mol Syst Biol"},{"issue":"12","key":"pcbi.1007740.ref049","doi-asserted-by":"crossref","first-page":"e1005266","DOI":"10.1371\/journal.pcbi.1005266","article-title":"Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator","volume":"12","author":"JP Pett","year":"2016","journal-title":"PLOS Computational Biology"},{"issue":"5885","key":"pcbi.1007740.ref050","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1126\/science.1156951","article-title":"Robust, tunable biological oscillations from interlinked positive and negative feedback loops","volume":"321","author":"TY Tsai","year":"2008","journal-title":"Science"},{"issue":"48","key":"pcbi.1007740.ref051","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1098\/rsif.2009.0487","article-title":"Switchable genetic oscillator operating in quasi-stable mode","volume":"7","author":"N Strelkowa","year":"2010","journal-title":"Journal of The Royal Society Interface"},{"key":"pcbi.1007740.ref052","article-title":"Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors","author":"R Perez-Carrasco","year":"2018","journal-title":"Cell Syst"},{"issue":"4","key":"pcbi.1007740.ref053","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/0021-9991(76)90041-3","article-title":"A general method for numerically simulating the stochastic time evolution of coupled chemical reactions","volume":"22","author":"DT Gillespie","year":"1976","journal-title":"Journal of Computational Physics"},{"issue":"25","key":"pcbi.1007740.ref054","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions","volume":"81","author":"DT Gillespie","year":"1977","journal-title":"The Journal of Physical Chemistry"},{"key":"pcbi.1007740.ref055","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/ncomms1516","article-title":"Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology","volume":"2","author":"B Wang","year":"2011","journal-title":"Nature Communications"},{"key":"pcbi.1007740.ref056","first-page":"175","article-title":"Tight Transcriptional Control Mechanism Ensures Stable High-Level Expression from T7 Promoter-Based Expression Plasmids","volume":"13","author":"N Mertens","year":"1995","journal-title":"Bio\/Technology"},{"issue":"1","key":"pcbi.1007740.ref057","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1754-1611-5-12","article-title":"BglBrick vectors and datasheets: A synthetic biology platform for gene expression","volume":"5","author":"TS Lee","year":"2011","journal-title":"Journal of Biological Engineering"},{"issue":"8","key":"pcbi.1007740.ref058","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1093\/nar\/gkq164","article-title":"Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology","volume":"38","author":"HH Huang","year":"2010","journal-title":"Nucleic acids research"},{"issue":"3","key":"pcbi.1007740.ref059","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.tig.2006.01.006","article-title":"Similar gene expression profiles do not imply similar tissue functions","volume":"22","author":"I Yanai","year":"2006","journal-title":"Trends in Genetics"},{"issue":"1","key":"pcbi.1007740.ref060","doi-asserted-by":"crossref","first-page":"012704","DOI":"10.1103\/PhysRevE.91.012704","article-title":"Transcriptional leakage versus noise: a simple mechanism of conversion between binary and graded response in autoregulated genes","volume":"91","author":"A Ochab-Marcinek","year":"2015","journal-title":"Physical review E, Statistical, nonlinear, and soft matter physics"},{"issue":"1","key":"pcbi.1007740.ref061","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1214\/aoms\/1177729694","article-title":"On Information and Sufficiency","volume":"22","author":"S Kullback","year":"1951","journal-title":"Ann Math Statist"},{"issue":"6767","key":"pcbi.1007740.ref062","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/35002258","article-title":"Biological rhythms: Circadian clocks limited by noise","volume":"403","author":"N Barkai","year":"2000","journal-title":"Nature"},{"issue":"9","key":"pcbi.1007740.ref063","doi-asserted-by":"crossref","first-page":"5988","DOI":"10.1073\/pnas.092133899","article-title":"Mechanisms of noise-resistance in genetic oscillators","volume":"99","author":"JMG Vilar","year":"2002","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pcbi.1007740.ref064","doi-asserted-by":"crossref","first-page":"2605","DOI":"10.1038\/ncomms3605","article-title":"Tuning the range and stability of multiple phenotypic states with coupled positive\u2013negative feedback loops","volume":"4","author":"MS Avenda\u00f1o","year":"2013","journal-title":"Nature Communications"},{"issue":"1","key":"pcbi.1007740.ref065","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1371\/journal.pcbi.0040008","article-title":"Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback","volume":"4","author":"G Hornung","year":"2008","journal-title":"PLOS Computational Biology"},{"issue":"8","key":"pcbi.1007740.ref066","doi-asserted-by":"crossref","first-page":"4933","DOI":"10.1073\/pnas.0736949100","article-title":"Circadian phase-specific degradation of the F-box protein ZTL is mediated by the proteasome","volume":"100","author":"WY Kim","year":"2003","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7160","key":"pcbi.1007740.ref067","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/nature06132","article-title":"ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light","volume":"449","author":"WY Kim","year":"2007","journal-title":"Nature"},{"issue":"D1","key":"pcbi.1007740.ref068","doi-asserted-by":"crossref","first-page":"D1040","DOI":"10.1093\/nar\/gkw982","article-title":"PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants","volume":"45","author":"J Jin","year":"2016","journal-title":"Nucleic acids research"},{"issue":"D1","key":"pcbi.1007740.ref069","doi-asserted-by":"crossref","first-page":"D1155","DOI":"10.1093\/nar\/gky1081","article-title":"PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants","volume":"47","author":"C-N Chow","year":"2018","journal-title":"Nucleic acids research"},{"issue":"1","key":"pcbi.1007740.ref070","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1074\/mcp.M115.054064","article-title":"Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry","volume":"15","author":"H Huang","year":"2016","journal-title":"Molecular & Cellular Proteomics"},{"issue":"6902","key":"pcbi.1007740.ref071","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/nature00955","article-title":"Deficient pheromone responses in mice lacking a cluster of vomeronasal receptor genes","volume":"419","author":"K Del Punta","year":"2002","journal-title":"Nature"},{"issue":"29","key":"pcbi.1007740.ref072","doi-asserted-by":"crossref","first-page":"10387","DOI":"10.1073\/pnas.0503029102","article-title":"LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms","volume":"102","author":"SP Hazen","year":"2005","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"2","key":"pcbi.1007740.ref073","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.cub.2010.12.013","article-title":"Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis","volume":"21","author":"LE Dixon","year":"2011","journal-title":"Current biology: CB"},{"issue":"34","key":"pcbi.1007740.ref074","doi-asserted-by":"crossref","first-page":"E4802","DOI":"10.1073\/pnas.1513609112","article-title":"Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis","volume":"112","author":"DH Nagel","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"3","key":"pcbi.1007740.ref075","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1111\/nph.15415","article-title":"Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets","volume":"220","author":"S Adams","year":"2018","journal-title":"New Phytologist"},{"issue":"1","key":"pcbi.1007740.ref076","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1104\/pp.15.01562","article-title":"A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis","volume":"170","author":"TL Liu","year":"2016","journal-title":"Plant physiology"},{"issue":"2","key":"pcbi.1007740.ref077","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1271\/bbb.69.382","article-title":"Molecular dissection of the promoter of the light-induced and circadian-controlled APRR9 gene encoding a clock-associated component of Arabidopsis thaliana","volume":"69","author":"S Ito","year":"2005","journal-title":"Bioscience, biotechnology, and biochemistry"},{"issue":"3","key":"pcbi.1007740.ref078","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/0092-8674(86)90653-7","article-title":"virA and virG control the plant-induced activation of the T-DNA transfer process of A. tumefaciens","volume":"46","author":"SE Stachel","year":"1986","journal-title":"Cell"},{"issue":"1","key":"pcbi.1007740.ref079","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1007\/BF00326554","article-title":"The promoter proximal region in the virD locus of Agrobacterium tumefaciens is necessary for the plant-inducible circularization of T-DNA","volume":"206","author":"A Yamamoto","year":"1987","journal-title":"Molecular and General Genetics MGG"},{"issue":"8","key":"pcbi.1007740.ref080","doi-asserted-by":"crossref","first-page":"2432","DOI":"10.1128\/JB.185.8.2432-2440.2003","article-title":"Signal Detection and Target Gene Induction by the CpxRA Two-Component System","volume":"185","author":"PA DiGiuseppe","year":"2003","journal-title":"Journal of Bacteriology"},{"issue":"5","key":"pcbi.1007740.ref081","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1016\/j.ymthe.2003.07.005","article-title":"Transcriptional and posttranslational regulation of cre recombinase by ru486 as the basis for an enhanced inducible expression system","volume":"8","author":"S Kyrkanides","year":"2003","journal-title":"Molecular Therapy"},{"key":"pcbi.1007740.ref082","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nature07616","article-title":"A tunable synthetic mammalian oscillator","volume":"457","author":"M Tigges","year":"2009","journal-title":"Nature"},{"key":"pcbi.1007740.ref083","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1038\/nature08753","article-title":"A synchronized quorum of genetic clocks","volume":"463","author":"T Danino","year":"2010","journal-title":"Nature"},{"issue":"2","key":"pcbi.1007740.ref084","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.cell.2007.05.045","article-title":"A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells","volume":"130","author":"TL Deans","year":"2007","journal-title":"Cell"},{"issue":"29","key":"pcbi.1007740.ref085","doi-asserted-by":"crossref","first-page":"10840","DOI":"10.1073\/pnas.0604085103","article-title":"Minimal model of spiky oscillations in NF-\u03baB signaling","volume":"103","author":"S Krishna","year":"2006","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"pcbi.1007740.ref086","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/msb4100172","article-title":"Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator","volume":"3","author":"WW Wong","year":"2007","journal-title":"Molecular Systems Biology"},{"key":"pcbi.1007740.ref087","doi-asserted-by":"crossref","unstructured":"Clamons SE, Murray RM. Modeling Dynamic Transcriptional Circuits with CRISPRi. bioRxiv. 2017.","DOI":"10.1101\/225318"},{"issue":"10","key":"pcbi.1007740.ref088","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.tim.2005.08.006","article-title":"Cell individuality: the bistability of competence development","volume":"13","author":"SV Avery","year":"2005","journal-title":"Trends in Microbiology"},{"issue":"8","key":"pcbi.1007740.ref089","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.cub.2007.03.016","article-title":"Positive-Feedback Loops as a Flexible Biological Module","volume":"17","author":"NT Ingolia","year":"2007","journal-title":"Current Biology"},{"issue":"11","key":"pcbi.1007740.ref090","doi-asserted-by":"crossref","first-page":"4999","DOI":"10.1063\/1.1545446","article-title":"Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm","volume":"118","author":"CV Rao","year":"2003","journal-title":"The Journal of chemical physics"},{"issue":"4","key":"pcbi.1007740.ref091","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1023\/A:1021286607354","article-title":"Deterministic Versus Stochastic Models for Circadian Rhythms","volume":"28","author":"D Gonze","year":"2002","journal-title":"Journal of Biological Physics"},{"key":"pcbi.1007740.ref092","first-page":"171","volume-title":"Methods in Enzymology","author":"D Gonze","year":"2011"},{"issue":"1","key":"pcbi.1007740.ref093","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1049\/iet-syb.2009.0057","article-title":"Legitimacy of the stochastic Michaelis-Menten approximation","volume":"5","author":"KR Sanft","year":"2011","journal-title":"IET systems biology"},{"issue":"15","key":"pcbi.1007740.ref094","doi-asserted-by":"crossref","first-page":"8614","DOI":"10.1073\/pnas.151588598","article-title":"Intrinsic noise in gene regulatory networks","volume":"98","author":"M Thattai","year":"2001","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"5717","key":"pcbi.1007740.ref095","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1126\/science.1109090","article-title":"Noise Propagation in Gene Networks","volume":"307","author":"JM Pedraza","year":"2005","journal-title":"Science"},{"issue":"22","key":"pcbi.1007740.ref096","doi-asserted-by":"crossref","first-page":"8372","DOI":"10.1073\/pnas.0507818103","article-title":"Stochastic models for regulatory networks of the genetic toggle switch","volume":"103","author":"T Tian","year":"2006","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"2","key":"pcbi.1007740.ref097","doi-asserted-by":"crossref","first-page":"026107","DOI":"10.1063\/1.2211787","article-title":"Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks","volume":"16","author":"M Scott","year":"2006","journal-title":"Chaos (Woodbury, NY)"},{"issue":"1","key":"pcbi.1007740.ref098","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1752-0509-6-39","article-title":"The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions","volume":"6","author":"P Thomas","year":"2012","journal-title":"BMC systems biology"},{"issue":"3","key":"pcbi.1007740.ref099","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.bpj.2014.06.012","article-title":"The Validity of Quasi-Steady-State Approximations in Discrete Stochastic Simulations","volume":"107","author":"K Kim Jae","year":"2014","journal-title":"Biophysical Journal"},{"issue":"1","key":"pcbi.1007740.ref100","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12918-015-0218-3","article-title":"The relationship between stochastic and deterministic quasi-steady state approximations","volume":"9","author":"JK Kim","year":"2015","journal-title":"BMC systems biology"},{"issue":"6","key":"pcbi.1007740.ref101","doi-asserted-by":"crossref","first-page":"e1005571","DOI":"10.1371\/journal.pcbi.1005571","article-title":"Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation","volume":"13","author":"JK Kim","year":"2017","journal-title":"PLOS Computational Biology"},{"issue":"3","key":"pcbi.1007740.ref102","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1002\/1439-7641(20020315)3:3<285::AID-CPHC285>3.0.CO;2-A","article-title":"Stochastic resonance in biology. How noise can enhance detection of weak signals and help improve biological information processing","volume":"3","author":"P Hanggi","year":"2002","journal-title":"Chemphyschem: a European journal of chemical physics and physical chemistry"},{"issue":"5","key":"pcbi.1007740.ref103","doi-asserted-by":"crossref","first-page":"e1000348","DOI":"10.1371\/journal.pcbi.1000348","article-title":"What Is Stochastic Resonance? Definitions, Misconceptions, Debates, and Its Relevance to Biology","volume":"5","author":"MD McDonnell","year":"2009","journal-title":"PLOS Computational Biology"},{"issue":"1","key":"pcbi.1007740.ref104","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1063\/1.4756221","article-title":"Stochastic oscillatory dynamics of generalized repressilators","volume":"1479","author":"N Strelkowa","year":"2012","journal-title":"AIP Conference Proceedings"},{"issue":"1","key":"pcbi.1007740.ref105","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1007\/BF01053970","article-title":"Stochastic resonance in neuron models","volume":"70","author":"A Longtin","year":"1993","journal-title":"Journal of Statistical Physics"},{"issue":"64","key":"pcbi.1007740.ref106","article-title":"Stochastic and Deterministic Models of Cellular p53 Regulation","volume":"3","author":"G Leenders","year":"2013","journal-title":"Frontiers in Oncology"},{"issue":"2","key":"pcbi.1007740.ref107","doi-asserted-by":"crossref","first-page":"e52736","DOI":"10.1371\/journal.pone.0052736","article-title":"The Dynamics of Stress p53-Mdm2 Network Regulated by p300 and HDAC1","volume":"8","author":"A Arora","year":"2013","journal-title":"PLOS ONE"},{"issue":"3","key":"pcbi.1007740.ref108","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1016\/j.jtbi.2004.11.038","article-title":"Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana","volume":"234","author":"JC Locke","year":"2005","journal-title":"Journal of theoretical biology"},{"key":"pcbi.1007740.ref109","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/msb4100102","article-title":"Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana","volume":"2","author":"JC Locke","year":"2006","journal-title":"Mol Syst Biol"},{"issue":"1","key":"pcbi.1007740.ref110","article-title":"A mechanism for robust circadian timekeeping via stoichiometric balance","volume":"8","author":"JK Kim","year":"2012","journal-title":"Molecular Systems Biology"},{"issue":"4","key":"pcbi.1007740.ref111","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1049\/iet-syb.2015.0090","article-title":"Protein sequestration versus Hill-type repression in circadian clock models","volume":"10","author":"JK Kim","year":"2016","journal-title":"IET systems biology"},{"key":"pcbi.1007740.ref112","doi-asserted-by":"crossref","DOI":"10.1201\/9781420011432","volume-title":"An Introduction to Systems Biology: Design Principles of Biological Circuits","author":"U Alon","year":"2006"},{"issue":"11","key":"pcbi.1007740.ref113","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1016\/j.tibs.2014.09.003","article-title":"Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback","volume":"39","author":"JE Ferrell","year":"2014","journal-title":"Trends in biochemical sciences"},{"issue":"34","key":"pcbi.1007740.ref114","doi-asserted-by":"crossref","first-page":"23073","DOI":"10.1074\/jbc.M803471200","article-title":"Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins","volume":"283","author":"S Fujiwara","year":"2008","journal-title":"The Journal of biological chemistry"},{"issue":"2","key":"pcbi.1007740.ref115","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1104\/pp.109.137414","article-title":"Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis","volume":"150","author":"E Yakir","year":"2009","journal-title":"Plant physiology"},{"key":"pcbi.1007740.ref116","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1038\/msb.2010.69","article-title":"Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model","volume":"6","author":"A Pokhilko","year":"2010","journal-title":"Mol Syst Biol"},{"issue":"4","key":"pcbi.1007740.ref117","doi-asserted-by":"crossref","first-page":"044109","DOI":"10.1063\/1.2159468","article-title":"Efficient step size selection for the tau-leaping simulation method","volume":"124","author":"Y Cao","year":"2006","journal-title":"The Journal of chemical physics"},{"issue":"6","key":"pcbi.1007740.ref118","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1016\/j.cell.2005.09.031","article-title":"Real-time kinetics of gene activity in individual bacteria","volume":"123","author":"I Golding","year":"2005","journal-title":"Cell"},{"issue":"5767","key":"pcbi.1007740.ref119","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1126\/science.1119623","article-title":"Probing gene expression in live cells, one protein molecule at a time","volume":"311","author":"J Yu","year":"2006","journal-title":"Science"},{"issue":"1","key":"pcbi.1007740.ref120","doi-asserted-by":"crossref","first-page":"16851","DOI":"10.1038\/s41598-017-16835-y","article-title":"Efficient and flexible implementation of Langevin simulation for gene burst production","volume":"7","author":"C-CS Yan","year":"2017","journal-title":"Scientific reports"},{"issue":"1","key":"pcbi.1007740.ref121","doi-asserted-by":"crossref","first-page":"012722","DOI":"10.1103\/PhysRevE.88.012722","article-title":"Generation of oscillating gene regulatory network motifs","volume":"88","author":"M van Dorp","year":"2013","journal-title":"Physical review E, Statistical, nonlinear, and soft matter physics"},{"issue":"12","key":"pcbi.1007740.ref122","doi-asserted-by":"crossref","first-page":"e0166867","DOI":"10.1371\/journal.pone.0166867","article-title":"Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis","volume":"11","author":"I Otero-Muras","year":"2016","journal-title":"PLOS ONE"},{"issue":"5","key":"pcbi.1007740.ref123","doi-asserted-by":"crossref","first-page":"056005","DOI":"10.1088\/1478-3975\/10\/5\/056005","article-title":"Analysis of precision in chemical oscillators: implications for circadian clocks","volume":"10","author":"T d'Eysmond","year":"2013","journal-title":"Physical biology"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007740","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,9,16]],"date-time":"2020-09-16T00:00:00Z","timestamp":1600214400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007740","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,3,30]],"date-time":"2021-03-30T16:52:14Z","timestamp":1617123134000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007740"}},"subtitle":[],"editor":[{"given":"Attila","family":"Csik\u00e1sz-Nagy","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,9,3]]},"references-count":123,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2020,9,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007740","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.02.24.962415","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,9,3]]}}}