{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,28]],"date-time":"2024-05-28T05:53:31Z","timestamp":1716875611586},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9]]},"DOI":"10.1093\/bib\/bbt048","type":"journal-article","created":{"date-parts":[[2013,7,28]],"date-time":"2013-07-28T00:19:40Z","timestamp":1374970780000},"page":"699-709","source":"Crossref","is-referenced-by-count":17,"title":["BioFNet: biological functional network database for analysis and synthesis of biological systems"],"prefix":"10.1093","volume":"15","author":[{"given":"Hiroyuki","family":"Kurata","sequence":"first","affiliation":[]},{"given":"Kazuhiro","family":"Maeda","sequence":"additional","affiliation":[]},{"given":"Toshikazu","family":"Onaka","sequence":"additional","affiliation":[]},{"given":"Takenori","family":"Takata","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2013,7,27]]},"reference":[{"key":"key\n\t\t\t\t20170523193432_bbt048-B1","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/448032a","article-title":"Synthetic biology: designs for life","volume":"448","author":"Ball","year":"2007","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B2","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1101\/gad.1507207","article-title":"Designing biological systems","volume":"21","author":"Drubin","year":"2007","journal-title":"Genes Dev"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B3","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1038\/468889a","article-title":"Build life to understand it","volume":"468","author":"Elowitz","year":"2010","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B4","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1126\/science.1069492","article-title":"Systems biology: a brief overview","volume":"295","author":"Kitano","year":"2002","journal-title":"Science"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B5","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1016\/j.cell.2004.09.008","article-title":"Robustness of cellular functions","volume":"118","author":"Stelling","year":"2004","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B6","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1146\/annurev.biophys.093008.131241","article-title":"Simplified models of biological networks","volume":"39","author":"Sneppen","year":"2010","journal-title":"Annu Rev Biophys"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B7","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1093\/bib\/bbp056","article-title":"BioModels.net Web Services, a free and integrated toolkit for computational modelling software","volume":"11","author":"Li","year":"2010","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B8","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1126\/science.298.5594.824","article-title":"Network motifs: simple building blocks of complex networks","volume":"298","author":"Milo","year":"2002","journal-title":"Science"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B9","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/nrg2102","article-title":"Network motifs: theory and experimental approaches","volume":"8","author":"Alon","year":"2007","journal-title":"Nat Rev Genet"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B10","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1371\/journal.pcbi.0020059","article-title":"Module-based analysis of robustness tradeoffs in the heat shock response system","volume":"2","author":"Kurata","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B11","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1038\/msb4100201","article-title":"Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli","volume":"4","author":"Nishio","year":"2008","journal-title":"Mol Syst Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B12","doi-asserted-by":"crossref","first-page":"2736","DOI":"10.1073\/pnas.0403510102","article-title":"Surviving heat shock: control strategies for robustness and performance","volume":"102","author":"El-Samad","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B13","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/ng881","article-title":"Network motifs in the transcriptional regulation network of Escherichia coli","volume":"31","author":"Shen-Orr","year":"2002","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B14","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.molcel.2013.01.003","article-title":"From systems to structure: bridging networks and mechanism","volume":"49","author":"Fraser","year":"2013","journal-title":"Mol Cell"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B15","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.molcel.2012.12.020","article-title":"Design principles of regulatory networks: searching for the molecular algorithms of the cell","volume":"49","author":"Lim","year":"2013","journal-title":"Mol Cell"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B16","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/S0955-0674(03)00017-6","article-title":"Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell","volume":"15","author":"Tyson","year":"2003","journal-title":"Curr Opin Cell Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B17","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1146\/annurev.physchem.012809.103457","article-title":"Functional motifs in biochemical reaction networks","volume":"61","author":"Tyson","year":"2010","journal-title":"Annu Rev Phys Chem"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B18","doi-asserted-by":"crossref","first-page":"5934","DOI":"10.1073\/pnas.0306752101","article-title":"Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction","volume":"101","author":"Yeger-Lotem","year":"2004","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B19","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1016\/j.cell.2009.06.013","article-title":"Defining network topologies that can achieve biochemical adaptation","volume":"138","author":"Ma","year":"2009","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B20","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/msb.2010.74","article-title":"An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients","volume":"6","author":"Cotterell","year":"2010","journal-title":"Mol Syst Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B21","doi-asserted-by":"crossref","first-page":"e343","DOI":"10.1371\/journal.pbio.0030343","article-title":"Dynamic properties of network motifs contribute to biological network organization","volume":"3","author":"Prill","year":"2005","journal-title":"PLoS Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B22","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1093\/bioinformatics\/btq063","article-title":"Standard virtual biological parts: a repository of modular modeling components for synthetic biology","volume":"26","author":"Cooling","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B23","doi-asserted-by":"crossref","first-page":"e138","DOI":"10.1093\/nar\/gkr616","article-title":"Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors","volume":"39","author":"Rodrigo","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B24","doi-asserted-by":"crossref","first-page":"4071","DOI":"10.1093\/nar\/gkg461","article-title":"CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle","volume":"31","author":"Kurata","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B25","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1101\/gr.3463705","article-title":"CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models","volume":"15","author":"Kurata","year":"2005","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B26","doi-asserted-by":"crossref","first-page":"e1002039","DOI":"10.1371\/journal.pcbi.1002039","article-title":"Emergence of switch-like behavior in a large family of simple biochemical networks","volume":"7","author":"Siegal-Gaskins","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B27","doi-asserted-by":"crossref","first-page":"4238","DOI":"10.1093\/emboj\/17.15.4238","article-title":"Response regulator output in bacterial chemotaxis","volume":"17","author":"Alon","year":"1998","journal-title":"EMBO J"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B28","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/16483","article-title":"Robustness in bacterial chemotaxis","volume":"397","author":"Alon","year":"1999","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B29","doi-asserted-by":"crossref","first-page":"4649","DOI":"10.1073\/pnas.97.9.4649","article-title":"Robust perfect adaptation in bacterial chemotaxis through integral feedback control","volume":"97","author":"Yi","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B30","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1371\/journal.pcbi.0030184","article-title":"Bistability and oscillations in the Huang-Ferrell model of MAPK signaling","volume":"3","author":"Qiao","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B31","doi-asserted-by":"crossref","first-page":"19931","DOI":"10.1073\/pnas.0706792104","article-title":"Input output robustness in simple bacterial signaling systems","volume":"104","author":"Shinar","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B32","doi-asserted-by":"crossref","first-page":"e30","DOI":"10.1371\/journal.pcbi.0020030","article-title":"Dynamical principles of two-component genetic oscillators","volume":"2","author":"Guantes","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B33","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/S1534-5807(03)00292-2","article-title":"Self-enhanced ligand degradation underlies robustness of morphogen gradients","volume":"5","author":"Eldar","year":"2003","journal-title":"Dev Cell"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B34","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.gde.2004.06.009","article-title":"Elucidating mechanisms underlying robustness of morphogen gradients","volume":"14","author":"Eldar","year":"2004","journal-title":"Curr Opin Genet Dev"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B35","doi-asserted-by":"crossref","first-page":"6924","DOI":"10.1073\/pnas.0912734107","article-title":"Scaling of morphogen gradients by an expansion-repression integral feedback control","volume":"107","author":"Ben-Zvi","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B36","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1038\/msb.2012.48","article-title":"A model of spatially restricted transcription in opposing gradients of activators and repressors","volume":"8","author":"White","year":"2012","journal-title":"Mol Syst Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B37","doi-asserted-by":"crossref","first-page":"2703","DOI":"10.1091\/mbc.10.8.2703","article-title":"Molecular interaction map of the mammalian cell cycle control and DNA repair systems","volume":"10","author":"Kohn","year":"1999","journal-title":"Mol. Biol. Cell"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B38","doi-asserted-by":"crossref","first-page":"e134","DOI":"10.1093\/nar\/gkm769","article-title":"Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis","volume":"35","author":"Kurata","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B39","doi-asserted-by":"crossref","first-page":"2005.0006","DOI":"10.1038\/msb4100010","article-title":"A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli","volume":"1","author":"Kalir","year":"2005","journal-title":"Mol Syst Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B40","doi-asserted-by":"crossref","first-page":"15995","DOI":"10.1073\/pnas.1002352107","article-title":"Fold-change detection and scalar symmetry of sensory input fields","volume":"107","author":"Shoval","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B41","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1126\/science.1160617","article-title":"Feedback loops shape cellular signals in space and time","volume":"322","author":"Brandman","year":"2008","journal-title":"Science"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B42","doi-asserted-by":"crossref","first-page":"20815","DOI":"10.1073\/pnas.0706231105","article-title":"Combinatorics of feedback in cellular uptake and metabolism of small molecules","volume":"104","author":"Krishna","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B43","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/S0955-0674(02)00314-9","article-title":"Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability","volume":"14","author":"Ferrell","year":"2002","journal-title":"Curr Opin Cell Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B44","doi-asserted-by":"crossref","first-page":"8697","DOI":"10.1073\/pnas.0602767103","article-title":"Understanding bistability in complex enzyme-driven reaction networks","volume":"103","author":"Craciun","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B45","doi-asserted-by":"crossref","first-page":"R244","DOI":"10.1016\/j.cub.2008.02.035","article-title":"Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses","volume":"18","author":"Ferrell","year":"2008","journal-title":"Curr Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B46","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/35002131","article-title":"Construction of a genetic toggle switch in Escherichia coli","volume":"403","author":"Gardner","year":"2000","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B47","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1126\/science.1113834","article-title":"Interlinked fast and slow positive feedback loops drive reliable cell decisions","volume":"310","author":"Brandman","year":"2005","journal-title":"Science"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B48","doi-asserted-by":"crossref","first-page":"e328","DOI":"10.1371\/journal.pbio.0020328","article-title":"The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis","volume":"2","author":"Eichenberger","year":"2004","journal-title":"PLoS Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B49","doi-asserted-by":"crossref","DOI":"10.1201\/9781420011432","volume-title":"An introduction of systems biology: Design principles of biological circuits","author":"Alon","year":"2006"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B50","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1162\/artl_a_00049","article-title":"Biological design principles of complex feedback modules in the E. coli ammonia assimilation system","volume":"18","author":"Masaki","year":"2012","journal-title":"Artif Life"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B51","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.jmb.2010.06.051","article-title":"Positive autoregulation shapes response timing and intensity in two-component signal transduction systems","volume":"401","author":"Mitrophanov","year":"2010","journal-title":"J Mol Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B52","doi-asserted-by":"crossref","first-page":"e1002331","DOI":"10.1371\/journal.pcbi.1002331","article-title":"A feedback quenched oscillator produces turing patterning with one diffuser","volume":"8","author":"Hsia","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B53","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1073\/pnas.0908647107","article-title":"Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues","volume":"107","author":"Lipshtat","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B54","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/ng869","article-title":"Regulation of noise in the expression of a single gene","volume":"31","author":"Ozbudak","year":"2002","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B55","doi-asserted-by":"crossref","first-page":"11644","DOI":"10.1073\/pnas.0913798107","article-title":"Population robustness arising from cellular heterogeneity","volume":"107","author":"Paszek","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B56","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1073\/pnas.040411297","article-title":"Noise-based switches and amplifiers for gene expression","volume":"97","author":"Hasty","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B57","doi-asserted-by":"crossref","first-page":"225101","DOI":"10.1063\/1.2929841","article-title":"How noise statistics impact models of enzyme cycles","volume":"128","author":"Warmflash","year":"2008","journal-title":"J Chem Phys"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B58","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1073\/pnas.0406841102","article-title":"Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations","volume":"102","author":"Samoilov","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B59","doi-asserted-by":"crossref","first-page":"2183","DOI":"10.1529\/biophysj.107.126185","article-title":"The effects of reversibility and noise on stochastic phosphorylation cycles and cascades","volume":"95","author":"Miller","year":"2008","journal-title":"Biophys J"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B60","doi-asserted-by":"crossref","first-page":"195103","DOI":"10.1063\/1.3264948","article-title":"Stochastic bimodalities in deterministically monostable reversible chemical networks due to network topology reduction","volume":"131","author":"Artyomov","year":"2009","journal-title":"J Chem Phys"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B61","doi-asserted-by":"crossref","first-page":"22096","DOI":"10.1073\/pnas.1008965107","article-title":"Bimodal gene expression in noncooperative regulatory systems","volume":"107","author":"Ochab-Marcinek","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B62","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1007\/s00449-010-0486-7","article-title":"An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks","volume":"34","author":"Maeda","year":"2011","journal-title":"Bioprocess Biosyst Eng"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B63","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/s00449-012-0789-y","article-title":"Flux module decomposition for parameter estimation in a multiple-feedback loop model of biochemical networks","volume":"36","author":"Maeda","year":"2013","journal-title":"Bioprocess Biosyst Eng"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B64","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/nbt0708-771","article-title":"Setting the standard in synthetic biology","volume":"26","author":"Arkin","year":"2008","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170523193432_bbt048-B65","doi-asserted-by":"crossref","first-page":"5988","DOI":"10.1073\/pnas.092133899","article-title":"Mechanisms of noise-resistance in genetic oscillators","volume":"99","author":"Vilar","year":"2002","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/15\/5\/699\/17489382\/bbt048.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,2]],"date-time":"2022-03-02T12:04:25Z","timestamp":1646222665000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article-lookup\/doi\/10.1093\/bib\/bbt048"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,7,27]]},"references-count":65,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2013,7,27]]},"published-print":{"date-parts":[[2014,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbt048","relation":{},"ISSN":["1477-4054","1467-5463"],"issn-type":[{"value":"1477-4054","type":"electronic"},{"value":"1467-5463","type":"print"}],"subject":[],"published":{"date-parts":[[2013,7,27]]}}}