Ronan M.T. Fleming <ronan.mt...@gmail.com>: Dec 05 09:02AM
Hi All,
I'm happy to announce the publication of a new protocol enabling the
generation of context-specific and thermodynamically consistent metabolic
models.
Regards,
Ronan
Preciat, G., Wegrzyn, A. B., Luo, X., Thiele, I., Hankemeier, T., &
Fleming, R. M. T. (2025). XomicsToModel: omics data integration and
generation of thermodynamically consistent metabolic models. Nature
Protocols. https://doi.org/10.1038/s41596-025-01288-9
Abstract
Constraint-based modeling can mechanistically simulate the behavior of a
biochemical system, permitting hypothesis generation, experimental design
and interpretation of experimental data, with numerous applications,
especially the modeling of metabolism. Given a generic model, several
methods have been developed to extract a context-specific, genome-scale
metabolic model by incorporating information used to identify metabolic
processes and gene activities in each context. However, the existing model
extraction algorithms are unable to ensure that a context-specific model is
thermodynamically flux consistent. Here we introduce XomicsToModel, a
semiautomated pipeline that integrates bibliomic, transcriptomic, proteomic
and metabolomic data with a generic genome-scale metabolic reconstruction,
or model, to extract a context-specific, genome-scale metabolic model that
is stoichiometrically, thermodynamically and flux consistent. One of the
key advantages of the XomicsToModel pipeline is its ability to seamlessly
incorporate omics data into metabolic reconstructions, ensuring not only
mechanistic accuracy but also physicochemical consistency. This
functionality enables more accurate metabolic simulations and predictions
across different biological contexts, enhancing its utility in diverse
research fields, including systems biology, drug development and
personalized medicine. The XomicsToModel pipeline is exemplified for
extraction of a specific metabolic model from a generic metabolic model; it
enables omics data integration and extraction of physicochemically
consistent mechanistic models from any generic biochemical network. It can
be implemented by anyone who has basic MATLAB programming skills and the
fundamentals of constraint-based modeling.
--
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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Associate Professor,
Digital Metabolic Twin Center, www.digitalmetabolictwin.org
School of Medicine,
University of Galway.
Ireland.
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Coordinator of the Horizon Europe project "Reconstruction and Computational
Modelling for Inherited Metabolic Diseases" (Recon4IMD
<https://www.recon4imd.org/>)
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Peer-reviewed publications: https://goo.gl/FZPG23
Mobile: +353 852 109 806
Github: @rmtfleming <https://github.com/rmtfleming>
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Robert Giessmann <rgies...@gmail.com>: Dec 05 11:41AM +0100
Hi Ronan,
Thanks for sharing! Great that you all extended the COBRA toolbox and now
provide a protocol & tutorial on how to use it for this case. :)
Best,
Robert
On Fri, Dec 5, 2025 at 10:02 AM Ronan M.T. Fleming < |
