Outputs (55)

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., Woods, C., Tomi-Andrino, C., Bommareddy, R. R., Cho, B. K., Fell, D. A., Poolman, M., King, J. R., Winzer, K., Twycross, J., & 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.

Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching (2022)
Book Chapter
Pinel, G. D., Horder, J. L., King, J. R., McIntyre, A., Mongan, N. P., López, G. G., & Benest, A. V. (2022). Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching. In A. V. Benest (Ed.), Angiogenesis: Methods and Protocol (369-426). Springer. https://doi.org/10.1007/978-1-0716-2059-5_29

RNA-seq is a common approach used to explore gene expression data between experimental conditions or cell types and ultimately leads to information that can shed light on the biological processes involved and inform further hypotheses. While the prot... Read More about Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching.

Free boundary problems for Stokes flow, with applications to the growth of biological tissues (2021)
Journal Article
King, J., & Venkataraman, C. (2021). Free boundary problems for Stokes flow, with applications to the growth of biological tissues. Interfaces and Free Boundaries, 23(4), 433–458. https://doi.org/10.4171/IFB/459

We formulate, analyse and numerically simulate what are arguably the two simplest Stokes-flow free boundary problems relevant to tissue growth, extending the classical Stokes free boundary problem by incorporating (i) a volumetric source (the nutrien... Read More about Free boundary problems for Stokes flow, with applications to the growth of biological tissues.

Multiscale analysis of nutrient uptake by plant roots with sparse distribution of root hairs: nonstandard scaling (2021)
Journal Article
King, J. R., Köry, J., & Ptashnyk, M. (2021). Multiscale analysis of nutrient uptake by plant roots with sparse distribution of root hairs: nonstandard scaling. SIAM Journal on Applied Mathematics, 81(4), 1361-1388. https://doi.org/10.1137/19M1309626

In this paper we undertake a multiscale analysis of nutrient uptake by plant roots by considering different scale relations between the radius of root hairs and the distance between them. We combine the method of formal asymptotic expansions and rigo... Read More about Multiscale analysis of nutrient uptake by plant roots with sparse distribution of root hairs: nonstandard scaling.

Parameter estimation in fluorescence recovery after photobleaching: Quantitative analysis of protein binding reactions and diffusion (2021)
Journal Article
Williamson, D. E., Sahai, E., Jenkins, R. P., O'Dea, R. D., & King, J. R. (2021). Parameter estimation in fluorescence recovery after photobleaching: Quantitative analysis of protein binding reactions and diffusion. Journal of Mathematical Biology, 83, Article 1. https://doi.org/10.1007/s00285-021-01616-z

Fluorescence recovery after photobleaching (FRAP) is a common experimental method for investigating rates of molecular redistribution in biological systems. Many mathematical models of FRAP have been developed, the purpose of which is usually the est... Read More about Parameter estimation in fluorescence recovery after photobleaching: Quantitative analysis of protein binding reactions and diffusion.

An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling (2021)
Journal Article
Dowbaj, A. M., Jenkins, R. P., Williamson, D., Heddleston, J. M., Ciccarelli, A., Fallesen, T., Hahn, K. M., O'Dea, R. D., King, J. R., Montagner, M., & Sahai, E. (2021). An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling. Journal of Cell Science, 134(13), Article 5520657. https://doi.org/10.1242/jcs.253484

The shuttling of transcription factors and transcriptional regulators into and out of the nucleus is central to the regulation of many biological processes. Here we describe a new method for studying the rates of nuclear entry and exit of transcripti... Read More about An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling.

Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria (2021)
Journal Article
Youlden, G. H., Ricci, V., Wang-Kan, X., Piddock, L. J., Jabbari, S., & King, J. R. (2021). Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria. Journal of Mathematical Biology, 82, Article 31. https://doi.org/10.1007/s00285-021-01576-4

Efflux pumps are a mechanism of intrinsic and evolved resistance in bacteria. If an efflux pump can expel an antibiotic so that its concentration within the cell is below a killing threshold the bacteria are resistant to the antibiotic. Efflux pumps... Read More about Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria.

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., King, J., & Kim, D.-H. (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.

Termination points and homoclinic glueing for a class of inhomogeneous nonlinear ordinary differential equations (2021)
Journal Article
Keeler, J., Blyth, M., & King, J. (2021). Termination points and homoclinic glueing for a class of inhomogeneous nonlinear ordinary differential equations. Nonlinearity, 34(1), 532-561. https://doi.org/10.1088/1361-6544/abb18f

Solutions u(x) to the class of inhomogeneous nonlinear ordinary differential equations taking the form u + u 2 = αf (x) for parameter α are studied. The problem is defined on the x line with decay of both the solution u(x) and the imposed forcing f (... Read More about Termination points and homoclinic glueing for a class of inhomogeneous nonlinear ordinary differential equations.

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