Filters








3,769 Hits in 9.7 sec

Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli [chapter]

Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira
<span title="">2009</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In this work, we present an expansion of the original E. coli dynamic model [1] , which links the acetate metabolism and tricarboxylic acid cycle (TCA) with the phosphotransferase systems, the pentose-phosphate  ...  From an engineering perspective, dynamic mathematical modeling to quantitatively assess intracellular metabolism and predict the complex behavior of living cells is one of the most successful tools to  ...  Costa would like to thank Fundação para a Ciência e Tecnologia for providing the grant SFRH/BD/25506/2005. The authors thank Dr. C. Chassagnole, which provided the experimental data set.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-02481-8_163">doi:10.1007/978-3-642-02481-8_163</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pqnd4c2nubcojcnhwpqh4xzxde">fatcat:pqnd4c2nubcojcnhwpqh4xzxde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170816065022/http://repositorium.sdum.uminho.pt/bitstream/1822/16824/1/2980.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5a/27/5a27314ccc5a4cc47dd335afe7b20eb250949b63.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-02481-8_163"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Editorial: Current Challenges in Modeling Cellular Metabolism

Daniel Machado, Kai H. Zhuang, Nikolaus Sonnenschein, Markus J. Herrgård
<span title="2015-11-26">2015</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tkuhrcyiufdxtkdmjqvay6f2ua" style="color: black;">Frontiers in Bioengineering and Biotechnology</a> </i> &nbsp;
AUTHOR CONTRIBUTIONS All authors have read and revised the manuscript. ACKNOWLEDGMENTS The authors would like to thank the financial support from the Novo Nordisk Foundation.  ...  Machado et al. (2015) use a multi-omics dataset of Escherichia coli to analyze the contribution of allosteric regulation in controlling central carbon metabolism.  ...  The author then provides examples of thermodynamic analysis of small metabolic pathways, highlighting future directions for integration of thermodynamics and large-scale modeling.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00193">doi:10.3389/fbioe.2015.00193</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26636080">pmid:26636080</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4659907/">pmcid:PMC4659907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zug6ge2rvjcdvfksqb55l6ri3u">fatcat:zug6ge2rvjcdvfksqb55l6ri3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303190806/http://pdfs.semanticscholar.org/b1cb/c001128f3009ea9db52fea650be457ffe5e1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b1/cb/b1cbc001128f3009ea9db52fea650be457ffe5e1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00193"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659907" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Transcriptional Regulation in Constraints-based Metabolic Models ofEscherichia coli

Markus W. Covert, Bernhard Ø. Palsson
<span title="2002-05-10">2002</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mryncoafc5cxdicldzfm4vlsze" style="color: black;">Journal of Biological Chemistry</a> </i> &nbsp;
Here we present an in silico model of the central E. coli metabolism that accounts for regulation of gene expression.  ...  and regulatory rules for the E. coli MG1655 in silico central metabolic/regulatory model.  ...  Acknowledgment-We thank Christophe Schilling for assistance in drawing the figures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/jbc.m201691200">doi:10.1074/jbc.m201691200</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12006566">pmid:12006566</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/en3dauw3ebfrvnnv6emfpp67ma">fatcat:en3dauw3ebfrvnnv6emfpp67ma</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723171322/http://www.jbc.org/content/277/31/28058.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f5/03/f5033ecb8fe8e8e8daf7255885397351fe13e4d5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/jbc.m201691200"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Network-level architecture and the evolutionary potential of underground metabolism

R. A. Notebaart, B. Szappanos, B. Kintses, F. Pal, A. Gyorkei, B. Bogos, V. Lazar, R. Spohn, B. Csorg, A. Wagner, E. Ruppin, C. Pal (+1 others)
<span title="2014-07-28">2014</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
Here, we provide a comprehensive computational model of the underground metabolism in Escherichia coli.  ...  analyses at the level of the entire metabolic network.  ...  We thank István Nagy for DNA sequencing, Christoph Kaleta for useful suggestions on elementary flux mode sampling, and Martijn Huynen and Steve Oliver for insightful comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1406102111">doi:10.1073/pnas.1406102111</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25071190">pmid:25071190</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4136603/">pmcid:PMC4136603</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b4ymcmafonhoflu5lslelnaede">fatcat:b4ymcmafonhoflu5lslelnaede</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170316072340/http://www.cs.tau.ac.il/~ruppin/underground_pnas.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/e8/e6e8c9ee5f1a47a18974b6e80104fb0d9b6c4085.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1406102111"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136603" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metabolic systems analysis to advance algal biotechnology

Brian J. Schmidt, Xiefan Lin-Schmidt, Austin Chamberlin, Kourosh Salehi-Ashtiani, Jason A. Papin
<span title="">2010</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xaczoswdiveqdplhgaqdqjtsmq" style="color: black;">Biotechnology Journal</a> </i> &nbsp;
The reconstructed metabolic network model was initially focused on central metabolism.  ...  The ideal selection for de novo metabolic design would be a laboratory model organism, such as Escherichia coli, S. cerevisiae, or C. reinhardtii due to the availability of laboratory techniques for genetic  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/biot.201000129">doi:10.1002/biot.201000129</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20665641">pmid:20665641</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qrqi2dq54rbqziupu3azyh37ca">fatcat:qrqi2dq54rbqziupu3azyh37ca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110331181553/http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2010/Schmidt-etal_BiotechJ_AlgalSysBiol.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/07/3c/073c0c56c27c5a48acdcff9e615ecaa288ebfdbe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/biot.201000129"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Mathematical models of plant metabolism

Hai Shi, Jörg Schwender
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/leca7sevx5fbxol36lihhcvvce" style="color: black;">Current Opinion in Biotechnology</a> </i> &nbsp;
Constraint-Based modeling, the functional analysis of metabolic networks at the whole cell or genome scale, is more difficult to apply to plants than to microbes.  ...  Here we discuss recent developments in Constraint-Based modeling in plants with focus on issues of model reconstruction and flux prediction.  ...  For the E. coli reconstruction iJO1366, 97% of the 1366 genes in the model have annotation of metabolic function based on experimental evidence [39].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2015.10.008">doi:10.1016/j.copbio.2015.10.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26723012">pmid:26723012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eins5c54sjaffjn5unrsq767vu">fatcat:eins5c54sjaffjn5unrsq767vu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724041347/https://manuscript.elsevier.com/S0958166915001615/pdf/S0958166915001615.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/93/88/93886ffac051cb72336310610bc32de809319ef2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2015.10.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Improving prediction fidelity of cellular metabolism with kinetic descriptions

Anupam Chowdhury, Ali Khodayari, Costas D Maranas
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/leca7sevx5fbxol36lihhcvvce" style="color: black;">Current Opinion in Biotechnology</a> </i> &nbsp;
coli 2 Kinetic Model.  ...  In addition to providing a dynamic view of metabolism, kinetic descriptors offer the 43 opportunity of linking together several layers of regulatory events into an integrated framework. 44 Kinetic model  ...  Acknowledgement 31 The authors gratefully acknowledge funding from the DOE (http://www.energy.gov/) grant 32 numbers DE-SC0008091 and DE-SC0012377, and the NSF (http://www.nsf.gov/) award number  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2015.08.011">doi:10.1016/j.copbio.2015.08.011</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26318076">pmid:26318076</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q3owgtvvdfdgziul3ayqgzvgxy">fatcat:q3owgtvvdfdgziul3ayqgzvgxy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719083512/https://manuscript.elsevier.com/S095816691500110X/pdf/S095816691500110X.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9f/46/9f46cf4f851eb6d5a83a351576dcf2b38815517b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2015.08.011"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling

R.S. Costa, I. Rocha, E.C. Ferreira, D. Machado
<span title="2011-05-01">2011</span> <i title="Institution of Engineering and Technology (IET)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ffpmxadwhvduloylhs64zvxkrm" style="color: black;">IET Systems Biology</a> </i> &nbsp;
In this work, we provide a critical overview of specific limitations found during the reconstruction of the central carbon metabolism dynamic model from E. coli (based on kinetic data available).  ...  data into a complete large scale model.  ...  In the course of the reconstruction of the dynamic model for the central carbon metabolism of E. coli we have encountered several problems with the available enzyme kinetic data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1049/iet-syb.2009.0058">doi:10.1049/iet-syb.2009.0058</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21639589">pmid:21639589</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6yuzpbanxbab3jj3plgnkp2oum">fatcat:6yuzpbanxbab3jj3plgnkp2oum</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181101223406/http://repositorium.sdum.uminho.pt/bitstream/1822/16719/1/Final.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/98/8e/988ef3473e21cbc6610f188250e77c77c0a58f69.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1049/iet-syb.2009.0058"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

Radhakrishnan Mahadevan, Michael A. Henson
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
The advent of genome-sequencing technologies and bioinformatics allowed the reconstruction of large-scale metabolic networks in model organisms, which paved the way for the extension of flux balance analysis  ...  These developments allowed the construction of the first genome-scale models of Escherichia coli (10) and Saccharomyces cerevisiae (14) in the early 2000s.  ...  Competing Interests: The authors have declared that no competing interests exist.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5936/csbj.201210008">doi:10.5936/csbj.201210008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24688668">pmid:24688668</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3962185/">pmcid:PMC3962185</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vrgo5rz35rdu3k4q5f7kqdd5tq">fatcat:vrgo5rz35rdu3k4q5f7kqdd5tq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190318130105/https://core.ac.uk/download/pdf/82278849.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/66/b8/66b8f3725779015a0c78de80c08b8c77547851af.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5936/csbj.201210008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962185" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off Between Regulation and Enzymatic Activity

Ed Reznik, Dimitris Christodoulou, Joshua E. Goldford, Emma Briars, Uwe Sauer, Daniel Segrr, Elad Noor
<span title="">2018</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tol7woxlqjeg5bmzadeg6qrg3e" style="color: black;">Social Science Research Network</a> </i> &nbsp;
In Brief Reznik et al. report a computational pipeline for the genome-scale reconstruction of metabolic small molecule regulatory networks.  ...  by EC number to reactions in the most recent genome-scale reconstruction of E. coli, iJO1366.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2139/ssrn.3155788">doi:10.2139/ssrn.3155788</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lcunuafjubb2ha752c7lbpqocu">fatcat:lcunuafjubb2ha752c7lbpqocu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200309164207/https://open.bu.edu/bitstream/handle/2144/24310/Reznik_etal_CellReports_2017.pdf;jsessionid=A27E4980E65A750060BF94341589249F?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/96/8b/968beb00379b82a0b7bfeb370d30bdcaac01b55d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2139/ssrn.3155788"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ssrn.com </button> </a>

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

Ed Reznik, Dimitris Christodoulou, Joshua E. Goldford, Emma Briars, Uwe Sauer, Daniel Segrè, Elad Noor
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5ihveavyobfs3mlzee7cjt7mfe" style="color: black;">Cell Reports</a> </i> &nbsp;
In Brief Reznik et al. report a computational pipeline for the genome-scale reconstruction of metabolic small molecule regulatory networks.  ...  by EC number to reactions in the most recent genome-scale reconstruction of E. coli, iJO1366.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.celrep.2017.08.066">doi:10.1016/j.celrep.2017.08.066</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28903046">pmid:28903046</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5600504/">pmcid:PMC5600504</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pxwwwujiwvazlmomcrmsachguu">fatcat:pxwwwujiwvazlmomcrmsachguu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724175948/https://open.bu.edu/bitstream/handle/2144/24310/Reznik_etal_CellReports_2017.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/42/c842798ae0edac63408ceffa9c0fee99672ae27c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.celrep.2017.08.066"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600504" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli

Pierre Millard, Kieran Smallbone, Pedro Mendes, Costas D. Maranas
<span title="2017-02-10">2017</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
To clarify its role, we developed and validated a detailed kinetic model of Escherichia coli central metabolism that links growth to environment.  ...  These properties have important physiological implications for E. coli and significantly expand the self-regulating capacities of its metabolism.  ...  We are grateful to the IT Research staff of the University of Manchester's Faculty of Engineering and Physical Sciences for help with running the HTCondor pool.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005396">doi:10.1371/journal.pcbi.1005396</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28187134">pmid:28187134</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5328398/">pmcid:PMC5328398</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ilsw55mdrzeclj77vunvpjyjmq">fatcat:ilsw55mdrzeclj77vunvpjyjmq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170620072020/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005396&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/87/d9/87d9db0fdcf15864db7a67fbae3540dfbc0f2872.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005396"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328398" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers

Katsuyuki Yugi, Hiroyuki Kubota, Atsushi Hatano, Shinya Kuroda
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/va62z7g5ofgoday6mzmc4uzqgm" style="color: black;">Trends in Biotechnology</a> </i> &nbsp;
To overcome 7 the lack of comprehensiveness and the information gap regarding interaction across 8 multiple omic layers, an approach for reconstructing molecular networks by connecting 9 multiple omic  ...  We introduce technologies for connecting multi-omic data based on 27 prior knowledge of biochemical interactions and characterize a biochemical trans-omic 28 network by concepts of a static and dynamic  ...  The dynamic signal flow described in this study covers the whole of central 5 carbon metabolism [34].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tibtech.2015.12.013">doi:10.1016/j.tibtech.2015.12.013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26806111">pmid:26806111</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4vfmjxezyzaoloh6n25cgkdchu">fatcat:4vfmjxezyzaoloh6n25cgkdchu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725152158/https://manuscript.elsevier.com/S0167779915002735/pdf/S0167779915002735.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/2e/c62e6e250256692b4d5f33ddef8e9156ec607dd9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tibtech.2015.12.013"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

Eytan Ruppin, Jason A Papin, Luis F de Figueiredo, Stefan Schuster
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/leca7sevx5fbxol36lihhcvvce" style="color: black;">Current Opinion in Biotechnology</a> </i> &nbsp;
Here, we review methods for the reconstruction of metabolic networks, modeling techniques such as flux balance analysis and elementary flux modes and current progress in their development and applications  ...  Computer simulations of the dynamic behavior of such networks are difficult due to a lack of kinetic data and to computational limitations.  ...  The authors thank Christoph Kaleta and Steffen Klamt for helpful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2010.07.002">doi:10.1016/j.copbio.2010.07.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20692823">pmid:20692823</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yiify7d3sze2bdraxqhd7huukm">fatcat:yiify7d3sze2bdraxqhd7huukm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110401065607/http://www.cs.tau.ac.il/~ruppin/curr.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/95/c1/95c14f8d3b0977dc0e0c03e209606a8c82b6d1c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2010.07.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Flux balance analysis of biological systems: applications and challenges

K. Raman, N. Chandra
<span title="2009-03-15">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
FBA has been used to analyse genome-scale reconstructions of several organisms; it has also been used to analyse the effect of perturbations, such as gene deletions or drug inhibitions in silico.  ...  Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation.  ...  They have used this approach, called integrated FBA (iFBA), to create an integrated model of E. coli, which combines a flux-balancebased central carbon metabolic and transcriptional regulatory model [  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbp011">doi:10.1093/bib/bbp011</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19287049">pmid:19287049</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/542cezsctjdmznnpwyfwpkdj3a">fatcat:542cezsctjdmznnpwyfwpkdj3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308161612/http://pdfs.semanticscholar.org/eb2e/0b94172b26efdb2b2e3d1d0bdc0776136d5c.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/eb/2e/eb2e0b94172b26efdb2b2e3d1d0bdc0776136d5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbp011"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 3,769 results