{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T19:51:59Z","timestamp":1767383519127},"reference-count":156,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2010,3,26]],"date-time":"2010-03-26T00:00:00Z","timestamp":1269561600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000723","type":"journal-article","created":{"date-parts":[[2010,3,25]],"date-time":"2010-03-25T18:17:37Z","timestamp":1269541057000},"page":"e1000723","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction"],"prefix":"10.1371","volume":"6","author":[{"given":"Hiroyuki","family":"Kuwahara","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris J.","family":"Myers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael S.","family":"Samoilov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2010,3,26]]},"reference":[{"key":"ref1","article-title":"Urologic Diseases in America. US Department of Health and Human Services, PHS, NIH, NIDDK","author":"M Litwin","year":"2007"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"9827","DOI":"10.1073\/pnas.93.18.9827","article-title":"Type 1 fimbrial expression enhances <italic>Escherichia coli<\/italic> virulence for the urinary tract.","volume":"93","author":"H Connell","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1016\/S0891-5520(05)70373-1","article-title":"Diagnosis and treatment of uncomplicated urinary tract infection.","volume":"11","author":"TM Hooton","year":"1997","journal-title":"Infect Dis Clin N Am"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1128\/IAI.01319-06","article-title":"In vivo gene expression analysis identifies genes required for enhanced colonization of the mouse urinary tract by uropathogenic <italic>Escherichia coli<\/italic> strain CFT073 <italic>dsdA<\/italic>.","volume":"75","author":"BJ Haugen","year":"2007","journal-title":"Infect Immun"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"4445","DOI":"10.1128\/JCM.40.12.4445-4449.2002","article-title":"Differences in virulence factors among clinical isolates of <italic>Escherichia coli<\/italic> causing cystitis and pyelonephritis in women and prostatitis in men.","volume":"40","author":"J Ruiz","year":"2002","journal-title":"J Clin Microbiol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"6373","DOI":"10.1128\/IAI.72.11.6373-6381.2004","article-title":"Transcriptome of uropathogenic <italic>Escherichia coli<\/italic> during urinary tract infection.","volume":"72","author":"JA Snyder","year":"2004","journal-title":"Infect Immun"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"7588","DOI":"10.1128\/IAI.73.11.7588-7596.2005","article-title":"Coordinate expression of fimbriae in uropathogenic <italic>Escherichia coli<\/italic>.","volume":"73","author":"JA Snyder","year":"2005","journal-title":"Infect Immun"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1111\/j.1365-2958.1992.tb01518.x","article-title":"A key role for type 1 pili in enterobacterial communicability.","volume":"6","author":"CA Bloch","year":"1992","journal-title":"Mol Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1007\/s10156-007-0506-Y","article-title":"Molecular epidemiology of uropathogenic <italic>Escherichia coli<\/italic>.","volume":"13","author":"S Yamamoto","year":"2007","journal-title":"J Infect Chemother"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1111\/j.2164-0947.1965.tb02342.x","article-title":"The structure, function, synthesis and genetic control of bacterial pili and a molecular model for DNA and RNA transport in gram-negative bacteria.","volume":"27","author":"CC Brinton","year":"1965","journal-title":"Trans N Y Acad Sci"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1073\/pnas.92.6.2081","article-title":"FimH adhesin of type 1 pili is assembled into a fibrillar tip structure in the <italic>Enterobacteriaceae<\/italic>.","volume":"92","author":"C Jones","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2803","DOI":"10.1093\/emboj\/19.12.2803","article-title":"Type 1 pilus-mediated bacterial invasion of bladder epithelial cells.","volume":"19","author":"JJ Martinez","year":"2000","journal-title":"EMBO J"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1126\/science.282.5393.1494","article-title":"Induction and evasion of host defenses by type 1-piliated uropathogenic <italic>Escherichia coli<\/italic>.","volume":"282","author":"MA Mulvey","year":"1998","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1046\/j.1365-2958.1998.01061.x","article-title":"Genetic analysis of <italic>Escherichia coli<\/italic> biofilm formation: roles of flagella, motility, chemotaxis and type I pili.","volume":"30","author":"LA Pratt","year":"1998","journal-title":"Mol Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1128\/IAI.69.3.1322-1328.2001","article-title":"Biofilm formation in a hydrodynamic environment by novel FimH variants and ramifications for virulence.","volume":"69","author":"M Schembri","year":"2001","journal-title":"Infect Immun"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1126\/science.1084550","article-title":"Intracellular bacterial biofilm-like pods in urinary tract infections.","volume":"301","author":"GG Anderson","year":"2003","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2230","DOI":"10.1111\/j.1462-5822.2007.00952.x","article-title":"Development of intracellular bacterial communities of uropathogenic <italic>Escherichia coli<\/italic> depends on type 1 pili.","volume":"9","author":"KJ Wright","year":"2007","journal-title":"Cell Microbiol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"e329","DOI":"10.1371\/journal.pmed.0040329","article-title":"Detection of intracellular bacterial communities in human urinary tract infection.","volume":"4","author":"DA Rosen","year":"2007","journal-title":"PLoS Med"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1126\/science.276.5312.607","article-title":"Prevention of mucosal <italic>Escherichia coli<\/italic> infection by FimH-adhesin-based systemic vaccination.","volume":"276","author":"S Langermann","year":"1997","journal-title":"Science"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"4572","DOI":"10.1128\/IAI.69.7.4572-4579.2001","article-title":"Establishment of a persistent <italic>Escherichia coli<\/italic> reservoir during the acute phase of a bladder infection.","volume":"69","author":"M Mulvey","year":"2001","journal-title":"Infect Immun"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"19884","DOI":"10.1073\/pnas.0606329104","article-title":"Filamentation by <italic>Escherichia coli<\/italic> subverts innate defenses during urinary tract infection.","volume":"103","author":"S Justice","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1056\/NEJMoa011265","article-title":"Widespread distribution of urinary tract infections caused by a multidrug-resistant <italic>Escherichia coli<\/italic> clonal group.","volume":"345","author":"A Manges","year":"2001","journal-title":"N Eng J Med"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1038\/183782a0","article-title":"Non-flagellar appendages of bacteria.","volume":"183","author":"CC Brinton","year":"1959","journal-title":"Nature"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1126\/science.1115109","article-title":"Contact-dependent inhibition of growth in <italic>Escherichia coli<\/italic>.","volume":"309","author":"SK Aoki","year":"2005","journal-title":"Science"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3747","DOI":"10.1128\/JB.01870-07","article-title":"Multiple genes repress motility in uropathogenic <italic>Escherichia coli<\/italic> constitutively expressing type 1 fimbriae.","volume":"190","author":"AN Simms","year":"2008","journal-title":"J Bacteriol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1046\/j.1365-2958.1998.01104.x","article-title":"Role of fimbriae-mediated adherence for neutrophil migration across <italic>Escherichia coli<\/italic>-infected epithelial cell layers.","volume":"30","author":"G Godaly","year":"1998","journal-title":"Mol Microbiol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.4049\/jimmunol.166.2.1148","article-title":"Bacterial invasion augments epithelial cytokine responses to <italic>Escherichia coli<\/italic> through a lipopolysaccharide-dependent mechanism.","volume":"166","author":"J Schilling","year":"2001","journal-title":"J Immunol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"7412","DOI":"10.1074\/jbc.M110560200","article-title":"Molecular regulation of urothelial renewal and host defenses during infection with uropathogenic <italic>Escherichia coli<\/italic>.","volume":"277","author":"IU Mysorekar","year":"2002","journal-title":"J Biol Chem"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"5724","DOI":"10.1073\/pnas.82.17.5724","article-title":"An invertible element of DNA controls phase variation of type 1 fimbriae of <italic>Escherichia coli<\/italic>.","volume":"82","author":"JM Abraham","year":"1985","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"6186","DOI":"10.1128\/jb.175.19.6186-6193.1993","article-title":"Environmental regulation of the <italic>fim<\/italic> switch controlling type 1 fimbrial phase variation in <italic>Escherichia coli<\/italic> K-12: effects of temperature and media.","volume":"175","author":"DL Gally","year":"1993","journal-title":"J Bacteriol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1111\/j.1574-6968.1998.tb12973.x","article-title":"Differential temperature modulation by H-NS of the <italic>fimB<\/italic> and <italic>fimE<\/italic> recombinase genes which control the orientation of the type 1 fimbrial phase switch.","volume":"162","author":"PB Olsen","year":"1998","journal-title":"FEMS Microbiol Lett"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1046\/j.1365-2958.1999.01257.x","article-title":"The molecular basis for the specificity of <italic>fimE<\/italic> in the phase variation of type 1 fimbriae of <italic>Escherichia coli<\/italic> K-12.","volume":"31","author":"H Kulasekara","year":"1999","journal-title":"Mol Microbiol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1128\/IAI.70.3.1391-1402.2002","article-title":"Osmolarity and pH growth conditions regulate <italic>fim<\/italic> gene transcription and type 1 pilus expression in uropathogenic <italic>Escherichia coli<\/italic>.","volume":"70","author":"WR Schwan","year":"2002","journal-title":"Infect Immun"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1046\/j.1365-2958.1999.01555.x","article-title":"Molecular switches \u2013 the ON and OFF of bacterial phase variation.","volume":"33","author":"I Henderson","year":"1999","journal-title":"Mol Microbiol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.jtbi.2004.11.020","article-title":"Diversity in times of adversity: probabilistic strategies in microbial survival games.","volume":"234","author":"DM Wolf","year":"2005","journal-title":"J Theor Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/j.jtbi.2004.11.021","article-title":"A microbial modified prisoner&apos;s dilemma game: how frequency-dependent selection can lead to random phase variation.","volume":"234","author":"DM Wolf","year":"2005","journal-title":"J Theor Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/nature04588","article-title":"An excitable gene regulatory circuit induces transient cellular differentiation.","volume":"440","author":"GM Suel","year":"2006","journal-title":"Nature"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1111\/j.1365-2958.2006.05249.x","article-title":"Bistability in bacteria.","volume":"61","author":"D Dubnau","year":"2006","journal-title":"Mol Microbiol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"re17","DOI":"10.1126\/stke.3662006re17","article-title":"From fluctuations to phenotypes: The physiology of noise.","volume":"2006","author":"MS Samoilov","year":"2006","journal-title":"Sci STKE"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"18958","DOI":"10.1073\/pnas.0706110104","article-title":"Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities.","volume":"104","author":"MN Artyomov","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/ng.110","article-title":"Stochastic switching as a survival strategy in fluctuating environments.","volume":"40","author":"M Acar","year":"2008","journal-title":"Nat Genet"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"e1000518","DOI":"10.1371\/journal.pcbi.1000518","article-title":"Integrating extrinsic and intrinsic cues into a minimal model of lineage commitment for hematopoietic progenitors.","volume":"5","author":"S Palani","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"14091","DOI":"10.1073\/pnas.0905988106","article-title":"Toward a microscopic model of bidirectional synaptic plasticity.","volume":"106","author":"GC Castellani","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"I1","DOI":"10.1186\/1471-2105-10-S12-I1","article-title":"Trends in modeling biomedical complex systems.","volume":"10","author":"L Milanesi","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.6116279","article-title":"Phase variation of type 1 fimbriae in <italic>Escherichia coli<\/italic> is under transcriptional control.","volume":"214","author":"BI Eisenstein","year":"1981","journal-title":"Science"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1128\/CDLI.8.3.489-495.2001","article-title":"Type 1 fimbriation and its phase switching in diarrheagenic <italic>Escherichia coli<\/italic> strains.","volume":"8","author":"KI Iida","year":"2001","journal-title":"Clin Diagn Lab Immunol"},{"key":"ref47","first-page":"169","article-title":"Type-1 fimbriae of <italic>Escherichia coli<\/italic>.","author":"SN Abraham","year":"1997"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1002\/j.1460-2075.1986.tb04372.x","article-title":"Two regulatory <italic>fim<\/italic> genes, <italic>fimB<\/italic> and <italic>fimE<\/italic>, control the phase variation of type 1 fimbriae in <italic>Escherichia coli<\/italic>.","volume":"5","author":"P Klemm","year":"1986","journal-title":"EMBO J"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"5298","DOI":"10.1128\/jb.173.17.5298-5307.1991","article-title":"Type 1 fimbriation and <italic>fimE<\/italic> mutants of <italic>Escherichia coli<\/italic> K-12.","volume":"173","author":"IC Blomfield","year":"1991","journal-title":"J Bacteriol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1128\/jb.175.1.27-36.1993","article-title":"Lrp stimulates phase variation of type 1 fimbriation in <italic>Escherichia coli<\/italic> K-12.","volume":"175","author":"IC Blomfield","year":"1993","journal-title":"J Bacteriol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1046\/j.1365-2958.1998.01049.x","article-title":"Temperature sensing in bacterial gene regulation \u2013 what it all boils down to.","volume":"30","author":"R Hurme","year":"1998","journal-title":"Mol Microbiol"},{"key":"ref52","first-page":"111","article-title":"Adherence and the pathogenesis of urinary tract infection.","author":"H Connell","year":"1997"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1200\/JCO.2001.19.3.676","article-title":"Increased temperature of malignant urinary bladder tumors <italic>in vivo<\/italic>: the application of a new method based on a catheter technique.","volume":"19","author":"C Stefanadis","year":"2001","journal-title":"J Clin Oncol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1038\/nbt1253","article-title":"Deviant effects in molecular reaction pathways.","volume":"24","author":"MS Samoilov","year":"2006","journal-title":"Nature Biotechnology"},{"key":"ref55","article-title":"Markov Processes: An Introduction for Physical Scientists","author":"DT Gillespie","year":"1992"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1016\/0378-4371(92)90283-V","article-title":"A rigorous derivation of the chemical master equation.","volume":"188","author":"DT Gillespie","year":"1992","journal-title":"Physica A"},{"key":"ref57","article-title":"Stochastic Processes in Physics and Chemistry","author":"NG van Kampen","year":"1992"},{"key":"ref58","article-title":"Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences","author":"CW Gardiner","year":"2004"},{"key":"ref59","first-page":"1735","article-title":"Stochastic chemical kinetics.","author":"DT Gillespie","year":"2005"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1716","DOI":"10.1063\/1.1378322","article-title":"Approximate accelerated stochastic simulation of chemically reacting systems.","volume":"115","author":"DT Gillespie","year":"2001","journal-title":"J Chem Phys"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"12784","DOI":"10.1063\/1.1627296","article-title":"Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method.","volume":"119","author":"M Rathinam","year":"2003","journal-title":"J Chem Phys"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1146\/annurev.physchem.58.032806.104637","article-title":"Stochastic simulation of chemical kinetics.","volume":"58","author":"DT Gillespie","year":"2007","journal-title":"Annu Rev Phys Chem"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1007\/11880646_7","article-title":"Automated abstraction methodology for genetic regulatory networks.","volume":"4220","author":"H Kuwahara","year":"2006","journal-title":"Trans on Comput Syst Biol VI LNCS"},{"key":"ref64","article-title":"Model Abstraction and Temporal Behavior Analysis of Genetic Regulatory Networks.","author":"H Kuwahara","year":"2007"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1093\/genetics\/149.4.1633","article-title":"Stochastic kinetic analysis of developmental pathway bifurcation in phage <italic>\u03bb<\/italic>-infected <italic>Escherichia coli<\/italic> cells.","volume":"149","author":"A Arkin","year":"1998","journal-title":"Genetics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1111\/j.1574-6968.1994.tb06681.x","article-title":"Localization of promoters in the <italic>fim<\/italic> gene cluster and the effect of H-NS on the transcription of <italic>fimB<\/italic> and <italic>fimE<\/italic>.","volume":"116","author":"PB Olsen","year":"1994","journal-title":"FEMS Microbiol Lett"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"5665","DOI":"10.1128\/jb.176.18.5665-5672.1994","article-title":"The leucine-responsive regulatory protein binds to the <italic>fim<\/italic> switch to control phase variation of type 1 fimbrial expression in <italic>Escherichia coli<\/italic> K-12.","volume":"176","author":"DL Gally","year":"1994","journal-title":"J Bacteriol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1046\/j.1365-2958.1998.00720.x","article-title":"Leucine alters the interaction of the leucine-responsive regulatory protein (Lrp) with the <italic>fim<\/italic> switch to stimulate site-specific recombination in <italic>Escherichia coli<\/italic>.","volume":"27","author":"PL Roesch","year":"1998","journal-title":"Mol Microbiol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1007\/BF00290342","article-title":"Regulation of <italic>lrp<\/italic> gene expression by H-NS and Lrp proteins in <italic>Escherichia coli<\/italic>: Dominant negative mutations in <italic>lrp<\/italic>.","volume":"247","author":"T Oshima","year":"1995","journal-title":"Mol Gen Genet"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1046\/j.1365-2958.1997.3151679.x","article-title":"H-NS: a modulator of environmentally regulated gene expression.","volume":"24","author":"T Atlung","year":"1997","journal-title":"Mol Microbiol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1046\/j.1365-2958.1997.2241615.x","article-title":"Integration host factor stimulates both FimB- and FimE-mediated site-specific DNA inversion that controls phase variation of type 1 fimbriae expression in <italic>Escherichia coli<\/italic>.","volume":"23","author":"IC Blomfield","year":"1997","journal-title":"Mol Microbiol"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"4299","DOI":"10.1093\/emboj\/18.15.4299","article-title":"Robustness of a gene regulatory circuit.","volume":"18","author":"JW Little","year":"1999","journal-title":"EMBO J"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"10205","DOI":"10.1021\/jp025846z","article-title":"Signal processing by simple chemical systems.","volume":"106","author":"M Samoilov","year":"2002","journal-title":"J Phys Chem A"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"2487","DOI":"10.1371\/journal.pcbi.0030246","article-title":"Operating regimes of signaling cycles: Statics, dynamics, and noise filtering.","volume":"3","author":"C Gomez-Uribe","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1371\/journal.pbio.0050009","article-title":"An HIV feedback resistor: Auto-regulatory circuit deactivator and noise buffer.","volume":"5","author":"LS Weinberger","year":"2007","journal-title":"PLoS Biol"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1529\/biophysj.107.110403","article-title":"Noise-limited frequency signal transmission in gene circuits.","volume":"93","author":"CM Tan","year":"2007","journal-title":"Biophys J"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1752-0509-2-44","article-title":"Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory.","volume":"2","author":"WJ Heuett","year":"2008","journal-title":"BMC Syst Biol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1126\/science.1151582","article-title":"The frequency dependence of osmo-adaptation in <italic>Saccharomyces cerevisiae<\/italic>.","volume":"319","author":"JT Mettetal","year":"2008","journal-title":"Science"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1103\/PhysRevLett.84.2271","article-title":"Pumped biochemical reactions, nonequilibrium circulation, and stochastic resonance.","volume":"84","author":"H Qian","year":"2000","journal-title":"Phys Rev Lett"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"056112","DOI":"10.1103\/PhysRevE.76.056112","article-title":"Response to a temperature modulation as a signature of chemical mechanisms.","volume":"76","author":"H Berthoumieux","year":"2007","journal-title":"Phys Rev E"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"5373","DOI":"10.1073\/pnas.0709903105","article-title":"The thermal impulse response of <italic>Escherichial coli<\/italic>.","volume":"105","author":"E Paster","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"084106","DOI":"10.1063\/1.3206736","article-title":"Determination of the six rate constants of a three-state enzymatic network and a noninvasive test of detailed balance.","volume":"131","author":"H Berthoumieux","year":"2009","journal-title":"J Chem Phys"},{"key":"ref83","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":"M Samoilov","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1146\/annurev.biophys.36.040306.132705","article-title":"Living with noisy genes: How cells function reliably with inherent variability in gene expression.","volume":"36","author":"N Maheshri","year":"2007","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"2350","DOI":"10.1529\/biophysj.106.093781","article-title":"Classical versus stochastic kinetics modeling of biochemical reaction systems.","volume":"92","author":"J Goutsias","year":"2007","journal-title":"Biophys J"},{"key":"ref86","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":"CA Miller","year":"2008","journal-title":"Biophys J"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"058105","DOI":"10.1103\/PhysRevLett.100.058105","article-title":"Noise enhanced persistence in a biochemical regulatory network with feedback control.","volume":"100","author":"M Assaf","year":"2008","journal-title":"Phys Rev Lett"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/msb.2008.31","article-title":"Colored extrinsic fluctuations and stochastic gene expression.","volume":"4","author":"V Shahrezaei","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"4861","DOI":"10.1039\/b900335p","article-title":"Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity.","volume":"11","author":"H Qian","year":"2009","journal-title":"Phys Chem Chem Phys"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1089\/15362310252780852","article-title":"Fifteen minutes of <italic>fim<\/italic>: Control of type 1 pili expression in <italic>E. coli<\/italic>.","volume":"6","author":"DM Wolf","year":"2002","journal-title":"OMICS"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.jtbi.2006.08.016","article-title":"Orientational control is an efficient control mechanism for phase switching in the <italic>E. coli<\/italic> fim system.","volume":"244","author":"D Chu","year":"2007","journal-title":"J Theor Biol"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"8829","DOI":"10.1073\/pnas.97.16.8829","article-title":"Bad bugs and beleaguered bladders: Interplay between uropathogenic <italic>Escherichia coli<\/italic> and innate host defenses.","volume":"97","author":"MA Mulvey","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref93","article-title":"Roitt&apos;s Essential Immunology","author":"P Delves","year":"2006"},{"key":"ref94","first-page":"1301","article-title":"Antibiotics for recurrent urinary tract infections.","volume":"71","author":"M Schooff","year":"2005","journal-title":"Am Fam Physician"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1097\/00003086-200508000-00011","article-title":"Engineering approaches for the detection and control of orthopaedic biofilm infections.","volume":"437","author":"G Ehrlich","year":"2005","journal-title":"Clin Orthop Relat Res"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.284.5418.1318","article-title":"Bacterial biofilms: A common cause of persistent infections.","volume":"284","author":"J Costerton","year":"1999","journal-title":"Science"},{"key":"ref97","first-page":"8","article-title":"Medical milestones of the last millennium.","volume":"34","author":"C Lewis","year":"2000","journal-title":"FDA Consumer"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1126\/science.299.5604.188","article-title":"Asian medicine: The new face of traditional chinese medicine.","volume":"299","author":"D Normile","year":"2003","journal-title":"Science"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1038\/nature04640","article-title":"Production of the antimalarial drug precursor artemisinic acid in engineered yeast.","volume":"440","author":"D Ro","year":"2006","journal-title":"Nature"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1016\/S0895-4356(00)00352-8","article-title":"Urinary tract infection among women aged 40 to 65: Behavioral and sexual risk factors.","volume":"54","author":"B Foxman","year":"2001","journal-title":"J Clin Epidemiol"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"157","DOI":"10.3109\/02813439209014054","article-title":"Symptomatic lower urinary tract infection induced by cooling of the feet: A controlled experimental trial.","volume":"10","author":"A Baerheim","year":"1992","journal-title":"Scand J Prim Health Care"},{"key":"ref102","article-title":"The Patient&apos;s Encyclopaedia of Urinary Tract Infection, Sexual Cystitis and Interstitial Cystitis","author":"A Kilmartin","year":"2004"},{"key":"ref103","article-title":"Cold showers are good for you \u2013 official","author":"O Gillie","year":"1999"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1152\/jappl.1999.87.2.699","article-title":"Immune changes in humans during cold exposure: effects of prior heating and exercise.","volume":"87","author":"I Brenner","year":"1999","journal-title":"J Appl Physiol"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1139\/y98-040","article-title":"Physical exercise as a human model of limited inflammatory response.","volume":"76","author":"P Shek","year":"1998","journal-title":"Can J Physiol Pharmacol"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"16470","DOI":"10.1073\/pnas.182427199","article-title":"Self-perpetuating epigenetic pili switches in bacteria.","volume":"99","author":"A Hernday","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref107","first-page":"145","article-title":"Stochastic modeling of the pap-pili epigenetic switch.","author":"B Munsky","year":"2005"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1046\/j.1365-2958.1998.00872.x","article-title":"Thermoregulation of <italic>Escherichia coli pap<\/italic> transcription: H-NS is a temperature-dependent DNA methylation blocking factor.","volume":"28","author":"C White-Ziegler","year":"1998","journal-title":"Mol Microbiol"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1097\/01.ju.0000134880.55119.cf","article-title":"Cool (TRPM8) and hot (TRPV1) receptors in the bladder and male genital tract.","volume":"172","author":"R Stein","year":"2004","journal-title":"J Urol"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1016\/S0022-5347(05)68062-7","article-title":"The bladder cooling reflex and the use of cooling as stimulus to the lower urinary tract.","volume":"162","author":"G Geirsson","year":"1999","journal-title":"J Urol"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1152\/ajprenal.00467.2004","article-title":"More than just a barrier: urothelium as a drug target for urinary bladder pain.","volume":"289","author":"L Birder","year":"2005","journal-title":"Am J Physiol Renal Physiol"},{"key":"ref112","article-title":"Transient Receptor Potential (TRP) Channels (Handbook of Experimental Pharmacology).","year":"2007"},{"key":"ref113","first-page":"1","article-title":"Dialogue on reverse-engineering assessment and methods: The DREAM of high-throughput pathway inference.","author":"G Stolovitzky","year":"2007"},{"key":"ref114","first-page":"114","article-title":"Network inference by combining biologically motivated regulatory constraints with penalized regression.","author":"F Parisi","year":"2009"},{"key":"ref115","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1038\/nrd2195","article-title":"A robustness-based approach to systems-oriented drug design.","volume":"6","author":"H Kitano","year":"2007","journal-title":"Nat Rev Drug Discov"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"e252","DOI":"10.1371\/journal.pbio.0050252","article-title":"Negative autoregulation by FAS mediates robust fetal erythropoiesis.","volume":"5","author":"M Socolovsky","year":"2007","journal-title":"PLoS Biol"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1752-0509-2-10","article-title":"Identification of gene interactions associated with disease from gene expression data using synergy networks.","volume":"2","author":"J Watkinson","year":"2008","journal-title":"BMC Syst Biol"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"4323","DOI":"10.1073\/pnas.0701722105","article-title":"Network properties of genes harboring inherited disease mutations.","volume":"105","author":"I Feldman","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref119","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1017\/S002190020002547X","article-title":"Stochastic approach to chemical kinetics.","volume":"4","author":"DA McQuarrie","year":"1967","journal-title":"J Appl Probab"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"7983","DOI":"10.1063\/1.468996","article-title":"One-dimensional chemical master equation: Uniqueness and analytical form of certain solutions.","volume":"102","author":"M Samoilov","year":"1995","journal-title":"J Chem Phys"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1109\/MSP.2007.273051","article-title":"Stochastic modeling and simulation of gene networks.","volume":"24","author":"X Cai","year":"2007","journal-title":"IEEE Signal Proc Mag"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1186\/1471-2105-8-480","article-title":"TABASCO: A single molecule, base-pair resolved gene expression simulator.","volume":"8","author":"S Kosuri","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"205101","DOI":"10.1063\/1.2919546","article-title":"A constant-time kinetic monte carlo algorithm for simulation of large biochemical reaction networks.","volume":"128","author":"A Slepoy","year":"2008","journal-title":"J Chem Phys"},{"key":"ref124","doi-asserted-by":"crossref","first-page":"165101","DOI":"10.1063\/1.2987701","article-title":"An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.","volume":"129","author":"H Kuwahara","year":"2008","journal-title":"J Chem Phys"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1752-0509-2-30","article-title":"Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability.","volume":"2","author":"YF Cao","year":"2008","journal-title":"BMC Syst Biol"},{"key":"ref126","doi-asserted-by":"crossref","first-page":"051906","DOI":"10.1103\/PhysRevE.79.051906","article-title":"Quantifying stochastic effects in biochemical reaction networks using partitioned leaping.","volume":"79","author":"LA Harris","year":"2009","journal-title":"Phys Rev E"},{"key":"ref127","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":"J Comp Phys"},{"key":"ref128","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":"J Phys Chem"},{"key":"ref129","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1021\/jp993732q","article-title":"Efficient exact stochastic simulation of chemical systems with many species and many channels.","volume":"104","author":"M Gibson","year":"2000","journal-title":"J Phys Chem A"},{"key":"ref130","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1063\/1.1778376","article-title":"Efficient formulation of the stochastic simulation algorithm for chemically reacting system.","volume":"121","author":"Y Cao","year":"2004","journal-title":"J Chem Phys"},{"key":"ref131","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1073\/pnas.79.4.1129","article-title":"Quantitative model for gene regulation by <italic>\u03bb<\/italic> phage repressor.","volume":"79","author":"GK Ackers","year":"1982","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref132","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1042\/BJ20050453","article-title":"H-NS is a part of a thermally controlled mechanism for bacterial gene regulation.","volume":"391","author":"S Ono","year":"2005","journal-title":"Biochem J"},{"key":"ref133","doi-asserted-by":"crossref","first-page":"041123","DOI":"10.1103\/PhysRevE.78.041123","article-title":"Population extinction in a time-modulated environment.","volume":"78","author":"M Assaf","year":"2008","journal-title":"Phys Rev E"},{"key":"ref134","first-page":"149","article-title":"Trapezoidal tau-leaping formula for the stochastic simulation of biochemical systems.","author":"Y Cao","year":"2005"},{"key":"ref135","doi-asserted-by":"crossref","first-page":"044104","DOI":"10.1063\/1.2145882","article-title":"The finite state projection algorithm for the solution of the chemical master equation.","volume":"124","author":"B Munsky","year":"2006","journal-title":"J Chem Phys"},{"key":"ref136","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1109\/TAC.2007.911361","article-title":"The finite state projection approach for the analysis of stochastic noise in gene networks.","volume":"52","author":"B Munsky","year":"2008","journal-title":"IEEE Trans Automat Contr"},{"key":"ref137","doi-asserted-by":"crossref","first-page":"014116","DOI":"10.1063\/1.1824902","article-title":"The slow-scale stochastic simulation algorithm.","volume":"122","author":"Y Cao","year":"2005","journal-title":"J Chem Phys"},{"key":"ref138","first-page":"125","article-title":"Abstracted stochastic analysis of type 1 pili expression in <italic>E. coli<\/italic>.","author":"H Kuwahara","year":"2006"},{"key":"ref139","first-page":"166","article-title":"Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions.","author":"H Kuwahara","year":"2007"},{"key":"ref140","doi-asserted-by":"crossref","first-page":"333","DOI":"10.2174\/138920206778948718","article-title":"Understanding the dynamic behavior of genetic regulatory networks by functional decomposition.","volume":"7","author":"W Longabaugh","year":"2006","journal-title":"Curr Genomics"},{"key":"ref141","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/gb-2006-7-8-114","article-title":"Fast, cheap and somewhat in control.","volume":"7","author":"A Arkin","year":"2006","journal-title":"Genome Biol"},{"key":"ref142","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1109\/TAC.2007.911346","article-title":"Stochastic modeling and control of biological systems: The lactose regulation system of <italic>Escherichia coli<\/italic>.","volume":"53","author":"AA Julius","year":"2008","journal-title":"IEEE Trans Autom Control"},{"key":"ref143","doi-asserted-by":"crossref","DOI":"10.1007\/b98841","article-title":"Mathematical Physiology","author":"J Keener","year":"1998"},{"key":"ref144","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":"J Phys Chem"},{"key":"ref145","doi-asserted-by":"crossref","first-page":"095105","DOI":"10.1063\/1.2971036","article-title":"Stochastic chemical kinetics and the total quasi-steady-state assumption: Application to the stochastic simulation algorithm and chemical master equation.","volume":"129","author":"S MacNamera","year":"2008","journal-title":"J Chem Phys"},{"key":"ref146","doi-asserted-by":"crossref","DOI":"10.1002\/0471200611","article-title":"Elements of information theory","author":"TM Cover","year":"1991"},{"key":"ref147","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1063\/1.1336499","article-title":"On the deduction of chemical reaction pathways from measurements of time series of concentrations.","volume":"11","author":"M Samoilov","year":"2001","journal-title":"Chaos"},{"key":"ref148","doi-asserted-by":"crossref","first-page":"S231","DOI":"10.1093\/bioinformatics\/18.suppl_2.S231","article-title":"The mutual information: Detecting and evaluating dependencies between variables.","volume":"18","author":"R Steuer","year":"2002","journal-title":"Bioinformatics"},{"key":"ref149","doi-asserted-by":"crossref","first-page":"2539","DOI":"10.1093\/bioinformatics\/btl432","article-title":"Few crucial links assure checkpoint efficiency in the yeast cell-cycle network.","volume":"22","author":"G Stoll","year":"2006","journal-title":"Bioinformatics"},{"key":"ref150","doi-asserted-by":"crossref","first-page":"204104","DOI":"10.1063\/1.2397685","article-title":"Reduction and solution of the chemical master equation using time-scale separation and finite state projection.","volume":"125","author":"S Peles","year":"2006","journal-title":"J Chem Phys"},{"key":"ref151","doi-asserted-by":"crossref","first-page":"58001","DOI":"10.1209\/0295-5075\/77\/58001","article-title":"The Berry phase and the pump flux in stochastic chemical kinetics.","volume":"77","author":"NA Sinitsyn","year":"2007","journal-title":"EPL"},{"key":"ref152","doi-asserted-by":"crossref","first-page":"17256","DOI":"10.1073\/pnas.0803850105","article-title":"Analytical distributions for stochastic gene expression.","volume":"105","author":"V Shahrezaei","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref153","doi-asserted-by":"crossref","first-page":"154114","DOI":"10.1063\/1.2907242","article-title":"Coarse graining of master equations with fast and slow states.","volume":"128","author":"S Pigolotti","year":"2008","journal-title":"J Chem Phys"},{"key":"ref154","doi-asserted-by":"crossref","first-page":"10546","DOI":"10.1073\/pnas.0809340106","article-title":"Adiabatic coarse-graining and simulations of stochastic biochemical networks.","volume":"106","author":"NA Sinitsyn","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref155","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1049\/iet-syb:20070082","article-title":"Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks.","volume":"2","author":"B Munsky","year":"2008","journal-title":"IET Syst Biol"},{"key":"ref156","article-title":"Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions.","author":"A Finney","year":"2003"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000723","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T02:07:10Z","timestamp":1635127630000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000723"}},"subtitle":[],"editor":[{"given":"Mustafa","family":"Khammash","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2010,3,26]]},"references-count":156,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2010,3,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000723","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,3,26]]}}}