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Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends

Bulletin of mathematical biology, 2017-07, Vol.79 (7), p.1449-1486

2017

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Modelling negative feedback networks for activating transcription factor 3 predicts a dominant role for miRNAs in immediate early gene regulation

PLoS computational biology, 2014-05, Vol.10 (5), p.e1003597-e1003597

2014

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Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach

PLoS computational biology, 2015-11, Vol.11 (11), p.e1004589-e1004589

2015

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A mathematical model of the role of aggregation in sonic hedgehog signalling

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008562-e1008562

2021

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A multiscale mathematical model describing the growth and development of bambara groundnut

Journal of theoretical biology, 2023-03, Vol.560, p.111373, Article 111373

2023

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A mathematical model of the mevalonate cholesterol biosynthesis pathway

Journal of theoretical biology, 2018-04, Vol.443, p.157-176

2018

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A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data

Scientific reports, 2020-08, Vol.10 (1), p.13244-13244, Article 13244

2020

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Mathematical Analysis of the Escherichia coli Chemotaxis Signalling Pathway

Bulletin of mathematical biology, 2018-04, Vol.80 (4), p.758-787

2018

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Physiologically-based pharmacokinetic and toxicokinetic models for estimating human exposure to five toxic elements through oral ingestion

Environmental toxicology and pharmacology, 2018-01, Vol.57, p.104-114

2018

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A combined model reduction algorithm for controlled biochemical systems

BMC systems biology, 2017-02, Vol.11 (1), p.17-17, Article 17

2017

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An Integrated Mathematical Model of Cellular Cholesterol Biosynthesis and Lipoprotein Metabolism

Processes, 2018-08, Vol.6 (8), p.134

2018

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Model reduction in mathematical pharmacology: Integration, reduction and linking of PBPK and systems biology models

Journal of pharmacokinetics and pharmacodynamics, 2018-08, Vol.45 (4), p.537-555

2018

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Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network

CPT: pharmacometrics and systems pharmacology, 2019-05, Vol.8 (5), p.259-272

2019

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A mathematical model of the sterol regulatory element binding protein 2 cholesterol biosynthesis pathway

Journal of theoretical biology, 2014-05, Vol.349 (100), p.150-162

2014

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Model reduction in mathematical pharmacology

Journal of pharmacokinetics and pharmacodynamics, 2018-08, Vol.45 (4), p.537-555

2018

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Feedback regulation by Atf3 in the endothelin-1-responsive transcriptome of cardiomyocytes: Egr1 is a principal Atf3 target

Biochemical journal, 2012-06, Vol.444 (2), p.343-355

2012

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Modeling chemotaxis reveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase

PLoS computational biology, 2010-08, Vol.6 (8), p.e1000896

2010

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Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias

iScience, 2021-05, Vol.24 (5), p.102484-102484, Article 102484

2021

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Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease

NPJ systems biology and applications, 2018-08, Vol.4 (1), p.33-10, Article 33

2018

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Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005329-e1005329

2017

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Response kinetics in the complex chemotaxis signalling pathway of Rhodobacter sphaeroides

Journal of the Royal Society interface, 2013-04, Vol.10 (81), p.20121001

2013

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Investigating Flavonoids as Molecular Templates for the Design of Small-Molecule Inhibitors of Cell Signaling

Journal of food science, 2013-12, Vol.78 (12), p.N1921-N1928

2013

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Understanding the link between single cell and population scale responses of Escherichia coli in differing ligand gradients

Computational and structural biotechnology journal, 2015-01, Vol.13 (C), p.528-538

2015

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Fold-Change Detection in a Whole-Pathway Model of Escherichia coli chemotaxis

Bulletin of mathematical biology, 2014-06, Vol.76 (6), p.1376-1395

2014

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Modelling acidosis and the cell cycle in multicellular tumour spheroids

Journal of theoretical biology, 2012-04, Vol.298, p.107-115

2012

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Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends

Modelling negative feedback networks for activating transcription factor 3 predicts a dominant role for miRNAs in immediate early gene regulation

Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach

A mathematical model of the role of aggregation in sonic hedgehog signalling

A multiscale mathematical model describing the growth and development of bambara groundnut

A mathematical model of the mevalonate cholesterol biosynthesis pathway

A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data

Mathematical Analysis of the Escherichia coli Chemotaxis Signalling Pathway

Physiologically-based pharmacokinetic and toxicokinetic models for estimating human exposure to five toxic elements through oral ingestion

A combined model reduction algorithm for controlled biochemical systems

An Integrated Mathematical Model of Cellular Cholesterol Biosynthesis and Lipoprotein Metabolism

Model reduction in mathematical pharmacology: Integration, reduction and linking of PBPK and systems biology models

Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network

A mathematical model of the sterol regulatory element binding protein 2 cholesterol biosynthesis pathway

Model reduction in mathematical pharmacology

Feedback regulation by Atf3 in the endothelin-1-responsive transcriptome of cardiomyocytes: Egr1 is a principal Atf3 target

Modeling chemotaxis reveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase

Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias

Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease

Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients

Response kinetics in the complex chemotaxis signalling pathway of Rhodobacter sphaeroides

Investigating Flavonoids as Molecular Templates for the Design of Small-Molecule Inhibitors of Cell Signaling

Understanding the link between single cell and population scale responses of Escherichia coli in differing ligand gradients

Fold-Change Detection in a Whole-Pathway Model of Escherichia coli chemotaxis

Modelling acidosis and the cell cycle in multicellular tumour spheroids

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