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Metabolic modeling-based drug repurposing in Glioblastoma (2022)
Journal Article
Tomi-Andrino, C., Pandele, A., Winzer, K., King, J., Rahman, R., & Kim, D. (2022). Metabolic modeling-based drug repurposing in Glioblastoma. Scientific Reports, 12, Article 11189. https://doi.org/10.1038/s41598-022-14721-w

The manifestation of intra- and inter-tumor heterogeneity hinders the development of ubiquitous cancer treatments, thus requiring a tailored therapy for each cancer type. Specifically, the reprogramming of cellular metabolism has been identified as a... Read More about Metabolic modeling-based drug repurposing in Glioblastoma.

A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications (2022)
Journal Article
Pearcy, N., Garavaglia, M., Millat, T., Gilbert, J. P., Song, Y., Hartman, H., …Minton, N. P. (2022). A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications. PLoS Computational Biology, 18(5), Article e1010106. https://doi.org/10.1371/journal.pcbi.1010106

Exploiting biological processes to recycle renewable carbon into high value platform chemicals provides a sustainable and greener alternative to current reliance on petrochemicals. In this regard Cupriavidus necator H16 represents a particularly prom... Read More about A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications.

Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions (2021)
Journal Article
Tomi-Andrino, C., Norman, R., Millat, T., Soucaille, P., Winzer, K., Barrett, D. A., …Kim, D. (2021). Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions. PLoS Computational Biology, 17(1), Article e1007694. https://doi.org/10.1371/journal.pcbi.1007694

© 2021 Tomi-Andrino et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source a... Read More about Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions.

Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions (2020)
Working Paper
Tomi-Andrino, C., Norman, R., Millat, T., Soucaille, P., Winzer, K., Barrett, D. A., …Kim, D. Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions

Metabolic engineering in the post-genomic era is characterised by the development of new methods for metabolomics and fluxomics, supported by the integration of genetic engineering tools and mathematical modelling. Particularly, constraint-based stoi... Read More about Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions.

Development of a Corynebacterium glutamicum bio-factory for self-sufficient transaminase reactions (2020)
Journal Article
Grigoriou, S., Kugler, P., Kulcinskaja, E., Walter, F., King, J., Hill, P., …O'Reilly, E. (2020). Development of a Corynebacterium glutamicum bio-factory for self-sufficient transaminase reactions. Green Chemistry, 22(13), 4128-4132. https://doi.org/10.1039/d0gc01432j

The development of biocatalytic routes for the synthesis of chiral amines starting from achiral building blocks is highly desirable. Here, we report a self-sufficient whole-cell system for the conversion of a model ketone to the corresponding cyclic... Read More about Development of a Corynebacterium glutamicum bio-factory for self-sufficient transaminase reactions.

Gsmodutils: A python based framework for test-driven genome scale metabolic model development (2018)
Other
Gilbert, J. P., Pearcy, N., Norman, R., Millat, T., Winzer, K., King, J., …Twycross, J. (2018). Gsmodutils: A python based framework for test-driven genome scale metabolic model development

Motivation Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include tho... Read More about Gsmodutils: A python based framework for test-driven genome scale metabolic model development.

Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake (2018)
Journal Article
Dalwadi, M. P., Wang, Y., King, J. R., & Minton, N. P. (2018). Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake. SIAM Journal on Applied Mathematics, 78(3), 1300-1329. https://doi.org/10.1137/17m1138625

In mathematical models that include nutrient delivery to bacteria, it is prohibitively expensive to include a pointwise nutrient uptake within small bacterial regions over bioreactor length-scales, and so such models often impose an effective uptake... Read More about Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake.

Applying asymptotic methods to synthetic biology: modelling the reaction kinetics of the mevalonate pathway (2017)
Journal Article
Dalwadi, M. P., Garavaglia, M., Webb, J. P., King, J. R., & Minton, N. P. (2018). Applying asymptotic methods to synthetic biology: modelling the reaction kinetics of the mevalonate pathway. Journal of Theoretical Biology, 439, https://doi.org/10.1016/j.jtbi.2017.11.022

The mevalonate pathway is normally found in eukaryotes, and allows for the production of isoprenoids, a useful class of organic compounds. This pathway has been successfully introduced to Escherichia coli, enabling a biosynthetic production route for... Read More about Applying asymptotic methods to synthetic biology: modelling the reaction kinetics of the mevalonate pathway.

Multi-timescale analysis of a metabolic network in synthetic biology: a kinetic model for 3-hydroxypropionic acid production via beta-alanine (2017)
Journal Article
Dalwadi, M. P., King, J. R., & Minton, N. P. (2018). Multi-timescale analysis of a metabolic network in synthetic biology: a kinetic model for 3-hydroxypropionic acid production via beta-alanine. Journal of Mathematical Biology, 77(1), 165-199. https://doi.org/10.1007/s00285-017-1189-3

A biosustainable production route for 3-hydroxypropionic acid (3HP), an important platform chemical, would allow 3HP to be produced without using fossil fuels. We are interested in investigating a potential biochemical route to 3HP from pyruvate thro... Read More about Multi-timescale analysis of a metabolic network in synthetic biology: a kinetic model for 3-hydroxypropionic acid production via beta-alanine.

The putative influence of the agr operon upon survival mechanisms used by Clostridium acetobutylicum (2013)
Journal Article
Jabbari, S., Steiner, E., Heap, J. T., Winzer, K., Minton, N. P., & King, J. R. (2013). The putative influence of the agr operon upon survival mechanisms used by Clostridium acetobutylicum. Mathematical Biosciences, 243(2), https://doi.org/10.1016/j.mbs.2013.03.005

The bacterium Clostridium acetobutylicum produces acids as an energy-yielding process during exponential growth. An acidic environment, however, is toxic to the cells and two survival mechanisms are in place to prevent them from dying. Firstly, durin... Read More about The putative influence of the agr operon upon survival mechanisms used by Clostridium acetobutylicum.