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Flux balance analysis in the era of metabolomics

J. M. Lee
2006 Briefings in Bioinformatics  
Flux balance analysis (FBA) has emerged as an effective means to analyse biological networks in a quantitative manner.  ...  This article reviews recent advances in FBA to meet this need and discusses the utility of FBA as a complement to metabolomics and the expected synergy as a result of combining these two techniques.  ...  Acknowledgement We thank Dr Daniel Segrè for his helpful comments on the manuscript.  ... 
doi:10.1093/bib/bbl007 pmid:16772264 fatcat:jwhnqlcwbvc6liwdww5oco7qn4

Defining the Metabolome: Size, Flux, and Regulation

Nicola Zamboni, Alan Saghatelian, Gary J. Patti
2015 Molecular Cell  
Next, Nicola Zamboni describes the power of metabolic flux analysis and explores its most frequent limitations and pitfalls in "Modern Stable-Isotope Metabolic Flux Analysis".  ...  What are the challenges of metabolic flux analysis? How have each been successfully applied?  ...  analysis of fluxes at a specific metabolic node or reaction, or (iv) determination of cellular balances for redox (i.e., NADPH and NADH) and energy (ATP) carriers.  ... 
doi:10.1016/j.molcel.2015.04.021 pmid:26000853 pmcid:PMC4831058 fatcat:weghp2o4jvbd5dvxbtipk4okcu

Metabolomic biomarkers: search, discovery and validation

Douglas B Kell
2007 Expert Review of Molecular Diagnostics  
Acknowledgements I thank the Biotechnology and Biological Sciences Research Council, Engineering and Physical Sciences Research Council and British Heart Foundation for financial support, the Royal Society  ...  This is a contribution from the Manchester Centre for Integrative Systems Biology (www.mcisb.org).  ...  Flux balance analysis in the era of metabolomics. Brief Bioinform. 7(2), 140-150 (2006). Palsson BØ. Systems Biology: Properties of Reconstructed Networks.  ... 
doi:10.1586/14737159.7.4.329 pmid:17620040 fatcat:el5lnd6ibjfitksrzeq5beuypm

Strategies for Extending Metabolomics Studies with Stable Isotope Labelling and Fluxomics

Anubhav Srivastava, Greg Kowalski, Damien Callahan, Peter Meikle, Darren Creek
2016 Metabolites  
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  ...  This report summarizes the key points raised in the peer session which focused on the advantages of using stable isotopes in modern metabolomics and the challenges in conducting flux analyses.  ...  An indirect measurement however can be obtained using the concept of metabolite balancing or flux balance analysis [25] .  ... 
doi:10.3390/metabo6040032 pmid:27706078 pmcid:PMC5192438 fatcat:yxaggf2hundc5boamgz6incewm

Metabolomics for mitochondrial and cancer studies

Deepak Nagrath, Christine Caneba, Thasni Karedath, Nadege Bellance
2011 Biochimica et Biophysica Acta - Bioenergetics  
The recent developments in the area of metabolic flux analysis may help to close the gap between clinical metabolomics research and the development of cancer metabolome.  ...  In the era of personalized medicine with more and more patient specific targeted therapies being used, we need reliable, dynamic, faster, and yet sensitive biomarkers both to track the disease and to develop  ...  Acknowledgments We thank Srividvatha for illustrations, Aaron Damm for critical reading of manuscript. Funding for this work is provided by Rice University to D.N.  ... 
doi:10.1016/j.bbabio.2011.03.006 pmid:21420931 fatcat:7wsnyzg7nrbpbins3pi6t526pe

Metabolic Pathways as Targets for Drug Screening [chapter]

Wai-Nang Paul, Laszlo G., Vay-Liang W.
2012 Metabolomics  
The relationship among any three "extreme ** A balance of flux analysis requires a steady state or quasi-steady state assumption.  ...  "Extreme pathways" as targets for drug screening The application of phenotypic phase plane (PPP) analysis of balance of flux data from tracerbased metabolomics is a graphical way of presenting experimental  ... 
doi:10.5772/33317 fatcat:jceuetqztbajfbqyrub6prgnqa

Systems metabolomics: from metabolomic snapshots to design principles

Chiara Damiani, Daniela Gaglio, Elena Sacco, Lilia Alberghina, Marco Vanoni
2020 Current Opinion in Biotechnology  
Metabolomics is a rapidly expanding technology that finds increasing application in a variety of fields, form metabolic disorders to cancer, from nutrition and wellness to design and optimization of cell  ...  opportunities for understanding design principles of metabolic (dis)regulation and for the development of precision therapies in multifactorial diseases, such as cancer and neurodegenerative diseases.  ...  Acknowledgements The institutional financial support to SYSBIO.ISBE.IT within the Italian Roadmap for ESFRI Research Infrastructures, the FLAG-ERA grant ITFoC and H2020 grants EpiPredict n. 642691 and  ... 
doi:10.1016/j.copbio.2020.02.013 pmid:32278263 fatcat:mkhebg3ivrhc5p53r2iosbmaum

Page 14 of Biological Reviews Vol. 80, Issue 1 [page]

2005 Biological Reviews  
"C-NMR, MS and metabolite flux balanc- ing in biotechnology research. Quarterly Review of Biophysics 31, t1—106. reER Kuite, B. H. & Wesreruorr, H.  ...  Metabolomics in systems biology. Annual Review of Plant Biology 54, 669-689. WECKWERTH, W. & FIEHN, O. (2002). Can we discover novel pathways using metabolomic analysis?  ... 

Metabolomics and systems biology: making sense of the soup

D KELL
2004 Current Opinion in Microbiology  
Such data require proper storage in suitably configured databases, which then permit one to establish the size of microbial metabolomes (hundreds of major metabolites) and allow the nature, organisation  ...  MCA metabolic control analysis  ...  ; many colleagues for very useful and stimulating discussions; and the BBSRC, EPSRC and NERC for financial support.  ... 
doi:10.1016/j.mib.2004.04.012 pmid:15196499 fatcat:5id3b5houzhdpjsnx4ztzgegju

The Plant Subcellular Metabolome: Current State and Advances

Bibhu P. Parida, Biswapriya B. Misra
2015 Postdoc Journal  
We summarize the recent efforts and progresses made in directions of understanding the plant sub-cellular (organellar) metabolomes.  ...  Dissection of organismal metabolomes into smaller subunits of life holds the potential to unravel the details of operative metabolic pathways and metabolic compartmentation at the sub-cellular level.  ...  The corresponding author acknowledges a Postdoctoral Research Associate Fellowship availed at the University of Florida, Gainesville, USA.  ... 
doi:10.14304/surya.jpr.v3n6.7 fatcat:flou3jkoijhf3nvhkuvxdhjkry

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Tunahan Çakır, Mohammad Jafar Khatibipour
2014 Frontiers in Bioengineering and Biotechnology  
in the post-genomic era.  ...  Flux-Balance Analysis to elucidate the active network.The other approach starts from the condition-specific metabolome data, and processes the data with statistical or optimization-based methods to extract  ...  The only major issue, as it is the case in flux-balance equation, is a proper choice of objective function to solve the equation.  ... 
doi:10.3389/fbioe.2014.00062 pmid:25520953 pmcid:PMC4253960 fatcat:l2tsj6oflretrh2a436hoza32u

Tracer-based metabolomics: Concepts and practices

W-N. Paul Lee, Paulin N. Wahjudi, Jun Xu, Vay Liang Go
2010 Clinical Biochemistry  
isotopes and isotopomer analysis using mass spectrometry; and from the modeling of biochemical reactions using flux analysis to the recent theoretical formulation of the constraint based modeling.  ...  In this review, the development of concepts and practices of tracer-based metabolomics is traced from the early application of radioactive isotopes in metabolic studies to the recent application of stable  ...  Acknowledgments Supported by the Biomedical Mass Spectrometry Laboratory of the GCRC (PHS M01-RR00425) and the Metabolomics Core Laboratory of the UCLA Center of Excellence in Pancreatic Diseases (P01  ... 
doi:10.1016/j.clinbiochem.2010.07.027 pmid:20713038 pmcid:PMC2952699 fatcat:47imjmvfazggfkfdrabjyn36f4

Approaches to Computational Strain Design in the Multiomics Era

Peter C. St. John, Yannick J. Bomble
2019 Frontiers in Microbiology  
In particular, we compare methods augmenting flux balance analysis with additional constraints from fluxomic, genomic, and metabolomic datasets and methods employing kinetic representations of individual  ...  We conclude with a discussion of potential future directions for improving strain design predictions in the omics era and remaining experimental and computational hurdles.  ...  A central technique to COBRA methods is flux balance analysis (FBA), which assumes that metabolite concentrations in the cell reach a pseudo steady-state when compared to the time scales associated with  ... 
doi:10.3389/fmicb.2019.00597 pmid:31024467 pmcid:PMC6461008 fatcat:lxsj2py4kzglrlabn6qdhqt3h4

Progress in NMR-based metabolomics of Catharanthus roseus

Qifang PAN, Jingya ZHAO, Yuliang WANG, Kexuan TANG
2015 Frontiers of Agricultural Science and Engineering  
plants, cross talk between pathways, and diversion of carbon fluxes, with the aim of fully unravelling MIA biosynthesis, its regulation and the function of the alkaloids in the plant from a systems biology  ...  Metabolomics has been rapidly developed as an important field in plant sciences and natural products chemistry.  ...  This article does not contain any studies with human or animal subjects performed by any of the authors.  ... 
doi:10.15302/j-fase-2015063 fatcat:vapigrhlgncddfmajow5vs4gtu

Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era

Abdellah Tebani, Lenaig Abily-Donval, Carlos Afonso, Stéphane Marret, Soumeya Bekri
2016 International Journal of Molecular Sciences  
The function describes how the whole system behaves in space and time with regard to metabolic fluxes and response to stimuli [8] [9] [10] .  ...  in the precision medicine era. disorders are individually rare, they are collectively more common and cause a significant childhood morbidity and mortality.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms17071167 pmid:27447622 pmcid:PMC4964538 fatcat:bgxb5gotyffujacdtq44rvx7iu
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