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Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes

A. Rantanen, T. Mielikainen, J. Rousu, H. Maaheimo, E. Ukkonen
<span title="2006-02-27">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways.  ...  Careful planning of isotopomer measurements is thus needed to maximize the available flux information while minimizing the experimental effort.  ...  ACKNOWLEDGEMENTS The authors thank the reviewers of this paper for many useful comments on the manuscript, Esa Pitkänen and Paula Jouhten for fruitful discussions, and Marina Kurtén for correcting the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btl069">doi:10.1093/bioinformatics/btl069</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16504982">pmid:16504982</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/22grel6g5bfjxkuvvu73oj4zni">fatcat:22grel6g5bfjxkuvvu73oj4zni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170901001002/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/22/10/10.1093/bioinformatics/btl069/2/btl069.pdf?Expires=1504245903&amp;Signature=DzOhsIRXRM0KxUENd8tHkj0z34Kk~EmnjmcGi4UxqvOcVzftdE06ue407~UgLoOn2a06Cj07iX4GlFwPpwcv8s8zREtXAA6ZmwGO1iPiQGzknQJUpvfHvD7OCc6M128-WSm2JLhDNPAS9Dw7zDH4HqgpXM6xrRgcorvgFxfuS7DH6bxqW~M5o8UjU10i81GtwyiMGflv0DDB9RfRx5hAiPwgele8WftWLgBCEMsx1nKwRZcgM6wPg-IZpj7gLVI1zoCWCtHeg8ACdZ88ozB1gZ3fwcPNPTpCUwHHnpn~kIJ~BntjIWdwe2u6UkvOBkXkwNkkXGq31ODWeNt5fwkskQ__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" 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/f9/27/f92713d60f7da0616bcbff3cbfada965541428e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btl069"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
We thank Uwe Sauer and Merja Penttilä for providing the data and for their comments to the work presented in the article; Markus Heinonen, Esa Pitkänen and Arto Åkerlund for the implementation of software  ...  Acknowledgements This research has been supported by Academy of Finland (SYSBIO programme, grant 207436, SYSFYS project).  ...  Estimating the flux distribution of the metabolic network In the main step of our framework for 13 C metabolic flux analysis, the fluxes of the metabolic network are estimated by forming and solving generalized  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-266">doi:10.1186/1471-2105-9-266</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18534038">pmid:18534038</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2430715/">pmcid:PMC2430715</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r6wpaxpi4nfivopysbqp6nficq">fatcat:r6wpaxpi4nfivopysbqp6nficq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501144339/https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/287441/eth-41385-01.pdf;jsessionid=D9FD1CBA277038F5033352F0101A6356?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/41/b4/41b446b73ad5094d0ea910d159afa7c427c03167.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-266"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430715" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

Lake-Ee Quek, Christoph Wittmann, Lars K Nielsen, Jens O Krömer
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6trk66ozdzflxoepgut5p574ca" style="color: black;">Microbial Cell Factories</a> </i> &nbsp;
Exemplified for a microbial flux study with 71 reactions, 8 free flux parameters and mass isotopomer distribution of 10 metabolites, OpenFLUX allowed to automatically compile the EMU-based model from an  ...  Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic  ...  We also thank the University of Queensland and the Australian Institute for Bioengineering and Nanotechnology for financial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1475-2859-8-25">doi:10.1186/1475-2859-8-25</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19409084">pmid:19409084</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2689189/">pmcid:PMC2689189</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7gyikjbvhrc7ngorf6tppgn2py">fatcat:7gyikjbvhrc7ngorf6tppgn2py</a> </span>
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Evidence for transketolase-like TKTL1 flux in CHO cells based on parallel labeling experiments and 13 C-metabolic flux analysis

Woo Suk Ahn, Scott B. Crown, Maciek R. Antoniewicz
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p47wd2skxvdwbanewzmokbss3a" style="color: black;">Metabolic Engineering</a> </i> &nbsp;
In this work, we have applied state-of-the-art techniques in 13 C metabolic flux analysis ( 13 C-MFA) based on parallel labeling experiments and integrated flux fitting to estimate the TKTL1 flux in CHO  ...  to measure 13 C-labeling of fructose 6-phosphate by GC-MS that allows intuitive interpretation of mass isotopomer distributions to determine key fluxes in the model, including glycolysis, oxidative PPP  ...  Metabolic fluxes were estimated by minimizing the variance-weighted sum of squared residuals (SSR) between the experimentally measured and model predicted mass isotopomer distributions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymben.2016.05.005">doi:10.1016/j.ymben.2016.05.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27174718">pmid:27174718</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6053631/">pmcid:PMC6053631</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/awstnmncqvcrdh5jthp3xprjty">fatcat:awstnmncqvcrdh5jthp3xprjty</a> </span>
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OpenFLUX2: 13 C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments

Mikhail S Shupletsov, Lyubov I Golubeva, Svetlana S Rubina, Dmitry A Podvyaznikov, Shintaro Iwatani, Sergey V Mashko
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6trk66ozdzflxoepgut5p574ca" style="color: black;">Microbial Cell Factories</a> </i> &nbsp;
Steady-state 13 C-based metabolic flux analysis ( 13 C-MFA) is the most powerful method available for the quantification of intracellular fluxes.  ...  adequacy, (iv) drawing conclusions concerning the identifiability of fluxes and construction of a contribution matrix reflecting the relative contribution of the measurement variances to the flux variances  ...  E Heinzle, M Reuss, and C Wittmann for their supervision and their excellent introduction to the basic problems of metabolic flux analysis in the 2012 Braundwald Course on Biosystems Engineering -Bioreactors  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/preaccept-1256381938128538">doi:10.1186/preaccept-1256381938128538</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25408234">pmid:25408234</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4263107/">pmcid:PMC4263107</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q7rlwpqstrbfrj4mmuypeccuwq">fatcat:q7rlwpqstrbfrj4mmuypeccuwq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830080644/https://microbialcellfactories.biomedcentral.com/track/pdf/10.1186/s12934-014-0152-x?site=http://microbialcellfactories.biomedcentral.com" 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/0f/ed/0fed622c6d1b2889b79a5d78524af7ebb99bb11e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/preaccept-1256381938128538"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263107" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

OpenFLUX2: 13C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments

Mikhail S Shupletsov, Lyubov I Golubeva, Svetlana S Rubina, Dmitry A Podvyaznikov, Shintaro Iwatani, Sergey V Mashko
<span title="2014-11-19">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6trk66ozdzflxoepgut5p574ca" style="color: black;">Microbial Cell Factories</a> </i> &nbsp;
Steady-state 13 C-based metabolic flux analysis ( 13 C-MFA) is the most powerful method available for the quantification of intracellular fluxes.  ...  adequacy, (iv) drawing conclusions concerning the identifiability of fluxes and construction of a contribution matrix reflecting the relative contribution of the measurement variances to the flux variances  ...  in the metabolic model of the L-lysine-producing C. glutamicum strain applied in the present study, and plans were made to obtain another set of measurements [19] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12934-014-0152-x">doi:10.1186/s12934-014-0152-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25408234">pmid:25408234</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4263107/">pmcid:PMC4263107</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uzwrzsrftfav7dpukwj62pty4y">fatcat:uzwrzsrftfav7dpukwj62pty4y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830080644/https://microbialcellfactories.biomedcentral.com/track/pdf/10.1186/s12934-014-0152-x?site=http://microbialcellfactories.biomedcentral.com" 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/0f/ed/0fed622c6d1b2889b79a5d78524af7ebb99bb11e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12934-014-0152-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263107" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A guide to 13C metabolic flux analysis for the cancer biologist

Maciek R. Antoniewicz
<span title="">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/f2k53wjmkvat3nug46wehytnp4" style="color: black;">Experimental and Molecular Medicine</a> </i> &nbsp;
In particular, 13 C metabolic flux analysis ( 13 C-MFA) has emerged as the primary technique for quantifying intracellular fluxes in cancer cells.  ...  Cancer metabolism is significantly altered from normal cellular metabolism allowing cancer cells to adapt to changing microenvironments and maintain high rates of proliferation.  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s12276-018-0060-y">doi:10.1038/s12276-018-0060-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29657327">pmid:29657327</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5938039/">pmcid:PMC5938039</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l6u2b4o3wvdbhbmrwsgfhar6qm">fatcat:l6u2b4o3wvdbhbmrwsgfhar6qm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210055613/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5938039&amp;blobtype=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/91/6b/916b18664f5f6eb26ee2df1d23f94c2517df21e4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s12276-018-0060-y"> <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/PMC5938039" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for 13 C metabolic flux analysis

Jennifer Au, Jungik Choi, Shawn W. Jones, Keerthi P. Venkataramanan, Maciek R. Antoniewicz
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p47wd2skxvdwbanewzmokbss3a" style="color: black;">Metabolic Engineering</a> </i> &nbsp;
The validated metabolic network model established in this study can be used in future investigations for unbiased 13 C-flux measurements in C. acetobutylicum.  ...  The flux results provided valuable new insights into the metabolism of C. acetobutylicum.  ...  ACKNOWLEDGEMENTS The work was supported by the genomic science grant from Department of Energy DE-SC0007092. The authors declare that they have no competing interests.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymben.2014.08.002">doi:10.1016/j.ymben.2014.08.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25183671">pmid:25183671</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ff7tpnzetnbfjgxo6yvukih2qm">fatcat:ff7tpnzetnbfjgxo6yvukih2qm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723184322/https://manuscript.elsevier.com/S1096717614001050/pdf/S1096717614001050.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/d9/80/d980660115768321ed72b27bd9b97276252009ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymben.2014.08.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Flux analysis shows that hypoxia-inducible-factor-1-alpha minimally affects intracellular metabolism in tumor spheroids

Byoung-jin Kim, Neil S. Forbes
<span title="">2007</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l4g6h6fddrdf3anaug2ej6psh4" style="color: black;">Biotechnology and Bioengineering</a> </i> &nbsp;
Isotope labeling and metabolic flux analysis were also used to quantify the intracellular metabolism of wild-type and HIF-1a-null spheroids.  ...  Hypoxia-inducible-factor-1a (HIF-1a) is a transcription factor that responds to low-oxygen environments by upregulating genes for cell survival and metabolism.  ...  The algorithm was initiated with estimated values for the independent fluxes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/bit.21205">doi:10.1002/bit.21205</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17009333">pmid:17009333</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fi6lwvntjzcnhk72kulpw6g4qu">fatcat:fi6lwvntjzcnhk72kulpw6g4qu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809075435/http://www.ecs.umass.edu/~forbes/Papers/Kim_07.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/95/6a/956a1e328a23c6ec60a55c1d5980c88e000b68bf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/bit.21205"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

A comprehensive analysis of myocardial substrate preference emphasizes the need for a synchronized fluxomic/metabolomic research design

Mukundan Ragavan, Alexander Kirpich, Xiaorong Fu, Shawn C. Burgess, Lauren M. McIntyre, Matthew E. Merritt
<span title="">2017</span> <i title="American Physiological Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yji4wqi55zhhlmsszkszvwwnnu" style="color: black;">American Journal of Physiology. Heart and Circulatory Physiology</a> </i> &nbsp;
Propionate at 1 mM was sufficient to achieve significant increases in pyruvate dehydrogenase flux (3ϫ), and anaplerosis (6ϫ), as measured by isotopomer analysis.  ...  In this report, the optimal concentration of propionate for the activation of glucose oxidation was measured in mouse hearts perfused in Langendorff mode.  ...  ACKNOWLEDGMENTS Authors thank James Rocca, Nicholas Carpenter and Xiaodong Wen for excellent technical assistance. GRANTS  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1152/ajpheart.00016.2017">doi:10.1152/ajpheart.00016.2017</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28411229">pmid:28411229</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5495932/">pmcid:PMC5495932</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/co2lrjbqf5gcvlej2rwgvliram">fatcat:co2lrjbqf5gcvlej2rwgvliram</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200309124743/https://journals.physiology.org/doi/pdf/10.1152/ajpheart.00016.2017" 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/9a/0a/9a0aceb8d981c8ebd95a96f3e7a67d655c4170af.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1152/ajpheart.00016.2017"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495932" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Optimization of Experiment Design for Mass Spectrometric Isotopic Labeling Kinetics [article]

Shefali Lathwal, Raaisa Raaisa, Tiago C. Alves, Richard G. Kibbey, Abhishek K. Jha, Graeme F. Mason
<span title="2018-05-27">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Determination of metabolic fluxes by measurement of time-dependent sampling of isotopic enrichments during the administration of labeled substrates provides rich information.  ...  The correlation analyses can be used to consider what orthogonal measurements might be beneficial for further improvement of measurements.  ...  Such kinetic isotopic measurements have the benefit of yielding absolute rates of metabolism, especially when combined with isotopomeric analysis of stable isotopes (Alves et al., 2015; Chance et al.,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/331520">doi:10.1101/331520</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7pv52qsybzatxaczi3lvk342ly">fatcat:7pv52qsybzatxaczi3lvk342ly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426094912/https://www.biorxiv.org/content/biorxiv/early/2018/05/27/331520.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/e3/75/e37555a66b214dee644a50be1d8d727e41c914db.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/331520"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

'Isotopo' a database application for facile analysis and management of mass isotopomer data

Z. Ahmed, S. Zeeshan, C. Huber, M. Hensel, D. Schomburg, R. Munch, E. Eylert, W. Eisenreich, T. Dandekar
<span title="2014-09-09">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Abstract The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes.  ...  'Isotopo' a database application for facile analysis and management of mass isotopomer data.  ...  Funding for open access charge: DFG and the University of Wuerzburg. Conflict of interest. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau077">doi:10.1093/database/bau077</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25204646">pmid:25204646</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4158277/">pmcid:PMC4158277</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dfxht2y6vnacblbhkcdcbwpcje">fatcat:dfxht2y6vnacblbhkcdcbwpcje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721025044/https://opus.bibliothek.uni-wuerzburg.de/opus4-wuerzburg/frontdoor/deliver/index/docId/12010/file/076_Ahmed_Database.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/e2/92/e292f6559f4f6ec6c1752cc2a55f085761da5600.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau077"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158277" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Strategies for Extending Metabolomics Studies with Stable Isotope Labelling and Fluxomics

Anubhav Srivastava, Greg Kowalski, Damien Callahan, Peter Meikle, Darren Creek
<span title="2016-10-01">2016</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ie7tehbfsfhs5pdyyt2rrdmnpm" style="color: black;">Metabolites</a> </i> &nbsp;
of metabolic pathways.  ...  The advantages and disadvantages of different approaches of fluxomics analyses including flux balance analysis, metabolic flux analysis and kinetic flux profiling were also discussed along with the use  ...  It uses dynamic isotopomer distribution data in order to estimate absolute flux along metabolic pathways.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo6040032">doi:10.3390/metabo6040032</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27706078">pmid:27706078</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5192438/">pmcid:PMC5192438</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yxaggf2hundc5boamgz6incewm">fatcat:yxaggf2hundc5boamgz6incewm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723061839/https://res.mdpi.com/def5020048a004bf07a336856f3c8c366d5012fdfdc8c1d519d2e6aab7db3a643b051ea70f5a2d18299d403a014926f9a322a1af333443bd0f1271cfae73e8bbb5fa9b49b8e406f96a4c94d9949409c2ebbb15382fbb87ad981455218ad5885b856db1d91a7e8befba04a5b33e9b9e1a0a40dea07df2ba658a15cfeeff634514a4050dc1500ee75e8893481f9167143babd43f59298bd41d9c90645c?filename=&amp;attachment=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/46/f5/46f5d5d690e96751ea2f71ff32fe64cd9d56d330.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo6040032"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192438" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis

Martin Beyß, Salah Azzouzi, Michael Weitzel, Wolfgang Wiechert, Katharina Nöh
<span title="2019-05-24">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/67anf6qgandy5adz4rakospiuq" style="color: black;">Frontiers in Microbiology</a> </i> &nbsp;
13C metabolic flux analysis (MFA) is the method of choice when a detailed inference of intracellular metabolic fluxes in living organisms under metabolic quasi-steady state conditions is desired.  ...  , i.e., the metabolic fluxes.  ...  ACKNOWLEDGMENTS The authors thank Peter Droste for insightful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2019.01022">doi:10.3389/fmicb.2019.01022</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31178829">pmid:31178829</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6543931/">pmcid:PMC6543931</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ayaug7q5bfcwvou327gieyjslq">fatcat:ayaug7q5bfcwvou327gieyjslq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200213224942/https://fjfsdata01prod.blob.core.windows.net/articles/files/431106/pubmed-zip/.versions/2/.package-entries/fmicb-10-01022-r1/fmicb-10-01022.pdf?sv=2015-12-11&amp;sr=b&amp;sig=ly%2FRLUXKUW%2B17GFFNojt2jBhSvKxR5M0%2Big9Yz8i7gc%3D&amp;se=2020-02-13T22%3A50%3A12Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fmicb-10-01022.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/56/96/5696b7dea3d185b8ea2bc0fec3db79d5ff07ef92.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2019.01022"> <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/PMC6543931" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis

Esa Pitkänen, Arto Åkerlund, Ari Rantanen, Paula Jouhten, Esko Ukkonen
<span title="2008-06-01">2008</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
Thus, ReMatch provides a common repository for metabolic network models with carbon mappings for the needs of metabolic flux analysis community.  ...  ReMatch is a web-based, user-friendly tool that constructs stoichiometric network models for metabolic flux analysis, integrating user-developed models into a database collected from several comprehensive  ...  Acknowledgments The authors would like to thank the Biomine project, Petteri Hintsanen, Kimmo Kulovesi and Hannu Toivonen at the Department of Computer Science, University of Helsinki, for the BMVis network  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2008-102">doi:10.1515/jib-2008-102</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/omxf2liuubhx5ijtdhydv6w6vq">fatcat:omxf2liuubhx5ijtdhydv6w6vq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705060030/http://biecoll.ub.uni-bielefeld.de/volltexte/2008/296/pdf/jib-102.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/68/51/68519bde29222c9d4f9e7e8d88861d85770d8fde.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2008-102"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> degruyter.com </button> </a>
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