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dc.contributor.authorKuwahara, Hiroyuki
dc.contributor.authorUmarov, Ramzan
dc.contributor.authorAlmasri, Islam
dc.contributor.authorGao, Xin
dc.date.accessioned2017-11-29T11:13:54Z
dc.date.available2017-11-29T11:13:54Z
dc.date.issued2017-03-01
dc.identifier.citationKuwahara H, Umarov R, Almasri I, Gao X (2017) ACRE: Absolute concentration robustness exploration in module-based combinatorial networks. Synthetic Biology 2. Available: http://dx.doi.org/10.1093/synbio/ysx001.
dc.identifier.issn2397-7000
dc.identifier.doi10.1093/synbio/ysx001
dc.identifier.urihttp://hdl.handle.net/10754/626222
dc.description.abstractTo engineer cells for industrial-scale application, a deep understanding of how to design molecular control mechanisms to tightly maintain functional stability under various fluctuations is crucial. Absolute concentration robustness (ACR) is a category of robustness in reaction network models in which the steady-state concentration of a molecular species is guaranteed to be invariant even with perturbations in the other molecular species in the network. Here, we introduce a software tool, absolute concentration robustness explorer (ACRE), which efficiently explores combinatorial biochemical networks for the ACR property. ACRE has a user-friendly interface, and it can facilitate efficient analysis of key structural features that guarantee the presence and the absence of the ACR property from combinatorial networks. Such analysis is expected to be useful in synthetic biology as it can increase our understanding of how to design molecular mechanisms to tightly control the concentration of molecular species. ACRE is freely available at https://github.com/ramzan1990/ACRE.
dc.description.sponsorshipThis study is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No URF/1/ 1976-04. We acknowledge the contribution of Basil Arkasosy to the initial phase of this work.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/synbio/article/2/1/ysx001/3058769
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work properly cited. For commercial re-use, please contact journals.permissions@oup.com
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectbiological design principle
dc.subjectcombinatorial network analysis
dc.subjectconcentration robustness
dc.subjectchemical reaction network theory
dc.titleACRE: Absolute concentration robustness exploration in module-based combinatorial networks
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalSynthetic Biology
dc.eprint.versionPublisher's Version/PDF
kaust.personKuwahara, Hiroyuki
kaust.personUmarov, Ramzan
kaust.personAlmasri, Islam
kaust.personGao, Xin
kaust.grant.numberURF/1/1976-04
dc.relation.issupplementedbygithub:ramzan1990/ACRE
refterms.dateFOA2018-06-14T05:13:32Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Software]</i> <br/> Title: ramzan1990/ACRE: Absolute Concentration Robustness Exploration (ACRE). Publication Date: 2016-12-29. github: <a href="https://github.com/ramzan1990/ACRE" >ramzan1990/ACRE</a> Handle: <a href="http://hdl.handle.net/10754/668071" >10754/668071</a></a></li></ul>
dc.date.published-online2017-03-01
dc.date.published-print2017-01


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This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work properly cited. For commercial re-use, please contact journals.permissions@oup.com
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work properly cited. For commercial re-use, please contact journals.permissions@oup.com