{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T00:52:31Z","timestamp":1775263951985,"version":"3.50.1"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T00:00:00Z","timestamp":1318464000000},"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.1002203","type":"journal-article","created":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T21:01:58Z","timestamp":1318539718000},"page":"e1002203","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":57,"title":["The Dynamics of Supply and Demand in mRNA Translation"],"prefix":"10.1371","volume":"7","author":[{"given":"Chris A.","family":"Brackley","sequence":"first","affiliation":[]},{"given":"M. Carmen","family":"Romano","sequence":"additional","affiliation":[]},{"given":"Marco","family":"Thiel","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,10,13]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1371\/journal.pcbi.0030057","article-title":"Posttranscriptional expression regulation: What determines translation rates?","volume":"3","author":"R Brockmann","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1677\/joe.0.1570361","article-title":"Post-transcriptional gene regulatory mechanisms in eukaryotes: an overview.","volume":"157","author":"D Day","year":"1998","journal-title":"J Endocrinol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/0022-2836(89)90260-X","article-title":"Codon usage determines translation rate in escherichia coli.","volume":"207","author":"MA S\u00f8rensen","year":"1989","journal-title":"J Mol Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1126\/science.1083811","article-title":"Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage.","volume":"300","author":"J Elf","year":"2003","journal-title":"Science"},{"key":"ref5","article-title":"Molecular Biology of the Cell","author":"B Alberts","year":"2008"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"6663","DOI":"10.1093\/nar\/12.17.6663","article-title":"Codon usage can affect efficiency of translation of genes in escherichia coli.","volume":"12","author":"M Robinson","year":"1984","journal-title":"Nucl Acids Res"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"031142","DOI":"10.1103\/PhysRevE.80.031142","article-title":"Competition between multiple totally asymmetric simple exclusion processes for a finite pool of resources.","volume":"80","author":"LJ Cook","year":"2009","journal-title":"Phys Rev E"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.","volume":"324","author":"NT Ingolia","year":"2009","journal-title":"Science"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1007\/BF01050430","article-title":"An exact solution of a one-dimensional asymmetric exclusion model with open boundaries.","volume":"69","author":"B Derrida","year":"1992","journal-title":"J Stat Phys"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1007\/BF01048050","article-title":"Phase transitions in an exactly soluble one-dimensional exclusion process.","volume":"72","author":"G Sch\u00fctz","year":"1993","journal-title":"J Stat Phys"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"016108","DOI":"10.1103\/PhysRevE.70.016108","article-title":"Disordered asymmetric simple exclusion process: Mean-field treatment.","volume":"70","author":"RJ Harris","year":"2004","journal-title":"Phys Rev E"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"078102","DOI":"10.1103\/PhysRevLett.105.078102","article-title":"Limited resources in a driven diffusion process.","volume":"105","author":"CA Brackley","year":"2010","journal-title":"Phys Rev Lett"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"021901","DOI":"10.1103\/PhysRevE.70.021901","article-title":"Mean-field approaches to the totally asymmetric exclusion process with quenched disorder and large particles.","volume":"70","author":"LB Shaw","year":"2004","journal-title":"Phys Rev E"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1529\/biophysj.106.087825","article-title":"A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates.","volume":"92","author":"H Zouridis","year":"2007","journal-title":"Biophys J"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"198104","DOI":"10.1103\/PhysRevLett.102.198104","article-title":"Queueing phase transition: Theory of translation.","volume":"102","author":"MC Romano","year":"2009","journal-title":"Phys Rev Lett"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"3645","DOI":"10.1073\/pnas.0909910107","article-title":"Translation efficiency is determined by both codon bias and folding energy.","volume":"107","author":"T Tuller","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"3889","DOI":"10.1073\/pnas.0635171100","article-title":"Genome-wide analysis of mrna translation profiles in saccharomyces cerevisiae.","volume":"100","author":"Y Arava","year":"2003","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref18","doi-asserted-by":"crossref","DOI":"10.1201\/9781420011432","article-title":"An Introduction to Systems Biology: Design Principles of Biological Circuits","author":"U Alon","year":"2006"},{"key":"ref19","article-title":"Fundamentals of Enzyme Kinetics","author":"A Cornish-Bowden","year":"2004"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"051920","DOI":"10.1103\/PhysRevE.82.051920","article-title":"Slow sites in an exclusion process with limited resources.","volume":"82","author":"CA Brackley","year":"2010","journal-title":"Phys Rev E"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2027","DOI":"10.1088\/0305-4470\/36\/8\/302","article-title":"Totally asymmetric exclusion processes with particles of arbitrary size.","volume":"36","author":"G Lakatos","year":"2003","journal-title":"J Phys A"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"021910","DOI":"10.1103\/PhysRevE.68.021910","article-title":"Totally asymmetric exclusion process with extended objects: A model for protein synthesis.","volume":"68","author":"LB Shaw","year":"2003","journal-title":"Phys Rev E"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.1088\/0305-4470\/37\/6\/010","article-title":"Local inhomogeneity in asymmetric simple exclusion processes with extended objects.","volume":"37","author":"LB Shaw","year":"2004","journal-title":"J Phys A"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1088\/0305-4470\/31\/4\/006","article-title":"Asymmetric simple exclusion model with local inhomogeneity.","volume":"31","author":"AB Kolomeisky","year":"1998","journal-title":"J Phys A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"056122","DOI":"10.1103\/PhysRevE.68.056122","article-title":"Queuing transitions in the asymmetric simple exclusion process.","volume":"68","author":"M Ha","year":"2003","journal-title":"Phys Rev E"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1911","DOI":"10.1103\/PhysRevE.58.1911","article-title":"Driven lattice gases with quenched disorder: Exact results and different macroscopic regimes.","volume":"58","author":"G Tripathy","year":"1998","journal-title":"Phys Rev E"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"051113","DOI":"10.1103\/PhysRevE.76.051113","article-title":"Inhomogeneous exclusion processes with extended objects: The effect of defect locations.","volume":"76","author":"JJ Dong","year":"2007","journal-title":"Phys Rev E"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/0021-9991(75)90060-1","article-title":"A new algorithm for monte carlo simulation of ising spin systems.","volume":"17","author":"AB Bortz","year":"1975","journal-title":"J of Comput Phys"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1074\/mcp.M400099-MCP200","article-title":"Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale.","volume":"3","author":"A Beyer","year":"2004","journal-title":"Mol Cell Proteomics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1128\/JB.122.3.855-865.1975","article-title":"Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast.","volume":"122","author":"C Waldron","year":"1975","journal-title":"J Bacteriol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1006\/jmbi.1997.0942","article-title":"Transfer rna gene redundancy and translational selection in saccharomyces cerevisiae.","volume":"268","author":"R Percudani","year":"1997","journal-title":"J Mol Biol"},{"key":"ref32","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/22.15.2963","article-title":"Seryl-trna synthetase from escherichia col: implication of its n-termspecificity.","volume":"22","author":"F Borel","year":"1994","journal-title":"Nucl Acids Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1093\/nar\/23.1.165","article-title":"Molecular recognition of trnapro by Escherichia coli proline trna synthetase in vitro.","volume":"23","author":"H Liu","year":"1995","journal-title":"Nucl Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1074\/jbc.272.2.1136","article-title":"Defining the active site of yeast seryl-trna synthetase.","volume":"272","author":"B Lenhard","year":"1997","journal-title":"J Biol Chem"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1006\/jmbi.1998.1902","article-title":"Catalytic defect in mutants of class ii histidyl-trna synthetase from salmonella typhimurium previously linked to decreased control of histidine biosynthesis regulation.","volume":"280","author":"C Francklyn","year":"1998","journal-title":"J Mol Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/S0167-4838(98)00115-0","article-title":"The role of tryptophan residues in escherichia coli arginyl-trna synthetase.","volume":"1387","author":"Qs Zhang","year":"1998","journal-title":"Biochimica et Biophysica Acta"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/1752-0509-2-87","article-title":"A quantitative estimation of the global translational activity in logarithmically growing yeast cells.","volume":"2","author":"T von der Haar","year":"2008","journal-title":"BMC Sys Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1002\/j.1460-2075.1988.tb03233.x","article-title":"Ribosome pausing and stacking during translation of a eukaryotic mrna.","volume":"7","author":"SL Wolin","year":"1988","journal-title":"EMBO J"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"198101","DOI":"10.1103\/PhysRevLett.93.198101","article-title":"Clustered bottlenecks in mrna translation and protein synthesis.","volume":"93","author":"T Chou","year":"2004","journal-title":"Phys Rev Lett"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"031106","DOI":"10.1103\/PhysRevE.78.031106","article-title":"Nonequilibrium processes: Driven lattice gases, interface dynamics, and quenched-disorder effects on density profiles and currents.","volume":"78","author":"SLA de Queiroz","year":"2008","journal-title":"Phys Rev E"},{"key":"ref41","article-title":"The Cell Cycle, Principles of Control","author":"DO Morgan","year":"2007"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","article-title":"The codon adaptation index\u2013a measure of directional synonymous codon usage bias, and its potential applications.","volume":"15","author":"P Sharp","year":"1987","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1126\/science.1115791","article-title":"Movement of Eukaryotic mRNAs Between Polysomes and Cytoplasmic Processing Bodies.","volume":"310","author":"M Brengues","year":"2005","journal-title":"Science"},{"key":"ref44","first-page":"M109.000877","article-title":"Genome-wide analysis of trna charging and activation of the eif2 kinase gcn2p.","author":"JM Zaborske","year":"2009","journal-title":"J Biol Chem"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"4242","DOI":"10.1073\/pnas.85.12.4242","article-title":"Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer rna binding to ribosomes in vitro.","volume":"85","author":"LK Thomas","year":"1988","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.jtbi.2005.08.007","article-title":"A model of protein translation including codon bias, nonsense errors, and ribosome recycling.","volume":"239","author":"MA Gilchrist","year":"2006","journal-title":"J Theor Biol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"051904","DOI":"10.1103\/PhysRevE.81.051904","article-title":"Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mrna translation.","volume":"81","author":"L Ciandrini","year":"2010","journal-title":"Phys Rev E"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1529\/biophysj.104.051383","article-title":"Near-critical behavior of aminoacyl-trna pools in e. coli at rate-limiting supply of amino acids.","volume":"88","author":"J Elf","year":"2005","journal-title":"Biophys J"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.jmb.2005.08.076","article-title":"Over expression of a trnaleu isoacceptor changes charging pattern of leucine trnas and reveals new codon reading.","volume":"354","author":"MA S\u00f8rensen","year":"2005","journal-title":"J Mol Biol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1038\/nature04530","article-title":"Endonucleolytic cleavage of eukaryotic mrnas with stalls in translation elongation.","volume":"440","author":"MK Doma","year":"2006","journal-title":"Nature"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1042\/BC20070037","article-title":"Halting a cellular production line: responses to ribosomal pausing during translation.","volume":"099","author":"JR Buchan","year":"2007","journal-title":"Biology of the Cell"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002203","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,10]],"date-time":"2021-12-10T20:41:58Z","timestamp":1639168918000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002203"}},"subtitle":[],"editor":[{"given":"Beate","family":"Schmittmann","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,10,13]]},"references-count":51,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2011,10,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002203","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,13]]}}}