Marc Sturrock
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View article: Bayesian model discovery for reverse-engineering biochemical networks from data
Bayesian model discovery for reverse-engineering biochemical networks from data Open
The reverse engineering of gene regulatory networks based on gene expression data is a challenging inference task. A related problem in computational systems biology lies in identifying signalling networks that perform particular functions…
View article: Data-driven spatio-temporal modelling of glioblastoma
Data-driven spatio-temporal modelling of glioblastoma Open
Mathematical oncology provides unique and invaluable insights into tumour growth on both the microscopic and macroscopic levels. This review presents state-of-the-art modelling techniques and focuses on their role in understanding glioblas…
View article: Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation
Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation Open
Quantitative stochastic models of gene regulatory networks are important tools for studying cellular regulation. Such models can be formulated at many different levels of fidelity. A practical challenge is to determine what model fidelity …
View article: Efficient Bayesian inference for stochastic agent-based models
Efficient Bayesian inference for stochastic agent-based models Open
The modelling of many real-world problems relies on computationally heavy simulations of randomly interacting individuals or agents. However, the values of the parameters that underlie the interactions between agents are typically poorly k…
View article: Data-driven spatio-temporal modelling of glioblastoma
Data-driven spatio-temporal modelling of glioblastoma Open
Mathematical oncology provides unique and invaluable insights into tumour growth on both the microscopic and macroscopic levels. This review presents state-of-the-art modelling techniques and focuses on their role in understanding glioblas…
View article: Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, Apostichopus japonicus
Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, Apostichopus japonicus Open
View article: Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation Open
View article: Emergent expression of fitness-conferring genes by phenotypic selection
Emergent expression of fitness-conferring genes by phenotypic selection Open
Genotypic and phenotypic adaptation is the consequence of ongoing natural selection in populations and is key to predicting and preventing drug resistance. Whereas classic antibiotic persistence is all-or-nothing, here we demonstrate that …
View article: Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation Open
Single cell RNA-sequencing (scRNA-seq) has very rapidly become the new workhorse of modern biology providing an unprecedented global view on cellular diversity and heterogeneity. In particular, the structure of gene-gene expression correla…
View article: Efficient inference for agent-based models of real-world phenomena
Efficient inference for agent-based models of real-world phenomena Open
The modelling of many real-world problems relies on computationally heavy simulations. Since statistical inference rests on repeated simulations to sample the parameter space, the high computational expense of these simulations can become …
View article: A pipeline for systematic comparison of model levels and parameter inference settings applied to negative feedback gene regulation
A pipeline for systematic comparison of model levels and parameter inference settings applied to negative feedback gene regulation Open
Quantitative stochastic models of gene regulatory networks are important tools for studying cellular regulation. Such models can be formulated at many different levels of fidelity. A practical challenge is to determine what model fidelity …
View article: A push-pull system of repressors matches levels of glucose transporters to extracellular glucose in budding yeast
A push-pull system of repressors matches levels of glucose transporters to extracellular glucose in budding yeast Open
Summary A common cellular task is to match gene expression dynamically to a range of concentrations of a regulatory molecule. Studying glucose transport in budding yeast, we determine mechanistically how such matching occurs for seven hexo…
View article: The influence of methylation status on a stochastic model of MGMT dynamics in glioblastoma: Phenotypic selection can occur with and without a downshift in promoter methylation status
The influence of methylation status on a stochastic model of MGMT dynamics in glioblastoma: Phenotypic selection can occur with and without a downshift in promoter methylation status Open
View article: Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics
Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics Open
Glioblastoma (GBM) is the most aggressive malignant primary brain tumour with a median overall survival of 15 months. To treat GBM, patients currently undergo a surgical resection followed by exposure to radiotherapy and concurrent and adj…
View article: growth data.xlsx from Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics
growth data.xlsx from Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics Open
Growth data
View article: cell viability data.xlsx from Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics
cell viability data.xlsx from Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics Open
Cell viability data
View article: Supplementary material from "Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics"
Supplementary material from "Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics" Open
Glioblastoma (GBM) is the most aggressive malignant primary brain tumour with a median overall survival of 15 months. To treat GBM, patients currently undergo a surgical resection followed by exposure to radiotherapy and concurrent and adj…
View article: Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform
Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform Open
Ligand binding to death receptors activates apoptosis in cancer cells. Stimulation of death receptors results in the formation of intracellular multiprotein platforms that either activate the apoptotic initiator Caspase-8 to trigger cell d…
View article: Author Correction: Anti-angiogenic drug scheduling optimisation with application to colorectal cancer
Author Correction: Anti-angiogenic drug scheduling optimisation with application to colorectal cancer Open
View article: Anti-angiogenic drug scheduling optimisation with application to colorectal cancer
Anti-angiogenic drug scheduling optimisation with application to colorectal cancer Open
View article: Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis
Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis Open
Nonlinear responses to signals are widespread natural phenomena that affect various cellular processes. Nonlinearity can be a desirable characteristic for engineering living organisms because it can lead to more switch-like responses, simi…
View article: A mathematical model of pre-diagnostic glioma growth
A mathematical model of pre-diagnostic glioma growth Open
View article: Protein abundance may regulate sensitivity to external cues in polarized cells
Protein abundance may regulate sensitivity to external cues in polarized cells Open
Cell polarization is a ubiquitous process which results in cellular constituents being organized into discrete intracellular spatial domains. It occurs in a variety of cell types, including epithelial cells, immune system cells and neurons…