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Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models

PLoS computational biology, 2023-09, Vol.19 (9), p.e1011515-e1011515

2023

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Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand

PLoS computational biology, 2024-01, Vol.20 (1), p.e1011752-e1011752

2024

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Modelling the dynamics of infection, waning of immunity and re-infection with the Omicron variant of SARS-CoV-2 in Aotearoa New Zealand

Epidemics, 2022-12, Vol.41, p.100657-100657, Article 100657

2022

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Computationally efficient framework for diagnosing, understanding and predicting biphasic population growth

Journal of the Royal Society interface, 2022-12, Vol.19 (197), p.20220560

2022

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Using mechanistic model-based inference to understand and project epidemic dynamics with time-varying contact and vaccination rates

Scientific reports, 2022-11, Vol.12 (1), p.20451-13, Article 20451

2022

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Likelihood-based estimation and prediction for a measles outbreak in Samoa

Infectious disease modelling, 2023-03, Vol.8 (1), p.212-227

2023

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A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005688-e1005688

2017

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Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand

PeerJ (San Francisco, CA), 2022-10, Vol.10, p.e14119-e14119, Article e14119

2022

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Modelling count data with partial differential equation models in biology

Journal of theoretical biology, 2024-03, Vol.580, p.111732-111732, Article 111732

2024

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The impact of Covid-19 vaccination in Aotearoa New Zealand: A modelling study

Vaccine, 2024-02, Vol.42 (6), p.1383-1391

2024

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Practical parameter identifiability for spatio-temporal models of cell invasion

Journal of the Royal Society interface, 2020-03, Vol.17 (164), p.20200055

2020

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Implementing measurement error models with mechanistic mathematical models in a likelihood-based framework for estimation, identifiability analysis and prediction in the life sciences

Journal of the Royal Society interface, 2024-01, Vol.21 (210), p.20230402

2024

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Making Predictions Using Poorly Identified Mathematical Models

Bulletin of mathematical biology, 2024, Vol.86 (7), p.80, Article 80

2024

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Parameter identifiability and model selection for sigmoid population growth models

Journal of theoretical biology, 2022-02, Vol.535, p.110998-110998, Article 110998

2022

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Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models

Journal of theoretical biology, 2022-09, Vol.549, p.111201-111201, Article 111201

2022

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Model-based data analysis of tissue growth in thin 3D printed scaffolds

Journal of theoretical biology, 2021-11, Vol.528, p.110852-110852, Article 110852

2021

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Sensitivity of Reverse Transcription Polymerase Chain Reaction Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Through Time

The Journal of infectious diseases, 2022-12, Vol.227 (1), p.9-17

2022

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Cell proliferation within small intestinal crypts is the principal driving force for cell migration on villi

The FASEB journal, 2017-02, Vol.31 (2), p.636-649

2017

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Generalised likelihood profiles for models with intractable likelihoods

Statistics and computing, 2024-02, Vol.34 (1), Article 50

2024

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Incorporating Posterior‐Informed Approximation Errors Into a Hierarchical Framework to Facilitate Out‐of‐the‐Box MCMC Sampling for Geothermal Inverse Problems and Uncertainty Quantification

Water resources research, 2020-01, Vol.56 (1), p.n/a

2020

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Profile likelihood analysis for a stochastic model of diffusion in heterogeneous media

Proceedings of the Royal Society. A, Mathematical, physical, and engineering sciences, 2021-06, Vol.477 (2250), p.20210214-20210214

2021

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Profile likelihood-based parameter and predictive interval analysis guides model choice for ecological population dynamics

Mathematical biosciences, 2023-01, Vol.355, p.108950-108950, Article 108950

2023

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Randomized Truncated SVD Levenberg‐Marquardt Approach to Geothermal Natural State and History Matching

Water resources research, 2018-03, Vol.54 (3), p.2376-2404

2018

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Case studies of predictive uncertainty quantification for geothermal models

Geothermics, 2021-12, Vol.97, p.102263, Article 102263

2021

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Where next for the reproducibility agenda in computational biology?

BMC systems biology, 2016-07, Vol.10 (1), p.52-52, Article 52

2016

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Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models

Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand

Modelling the dynamics of infection, waning of immunity and re-infection with the Omicron variant of SARS-CoV-2 in Aotearoa New Zealand

Computationally efficient framework for diagnosing, understanding and predicting biphasic population growth

Using mechanistic model-based inference to understand and project epidemic dynamics with time-varying contact and vaccination rates

Likelihood-based estimation and prediction for a measles outbreak in Samoa

A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium

Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand

Modelling count data with partial differential equation models in biology

The impact of Covid-19 vaccination in Aotearoa New Zealand: A modelling study

Practical parameter identifiability for spatio-temporal models of cell invasion

Implementing measurement error models with mechanistic mathematical models in a likelihood-based framework for estimation, identifiability analysis and prediction in the life sciences

Making Predictions Using Poorly Identified Mathematical Models

Parameter identifiability and model selection for sigmoid population growth models

Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models

Model-based data analysis of tissue growth in thin 3D printed scaffolds

Sensitivity of Reverse Transcription Polymerase Chain Reaction Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Through Time

Cell proliferation within small intestinal crypts is the principal driving force for cell migration on villi

Generalised likelihood profiles for models with intractable likelihoods

Incorporating Posterior‐Informed Approximation Errors Into a Hierarchical Framework to Facilitate Out‐of‐the‐Box MCMC Sampling for Geothermal Inverse Problems and Uncertainty Quantification

Profile likelihood analysis for a stochastic model of diffusion in heterogeneous media

Profile likelihood-based parameter and predictive interval analysis guides model choice for ecological population dynamics

Randomized Truncated SVD Levenberg‐Marquardt Approach to Geothermal Natural State and History Matching

Case studies of predictive uncertainty quantification for geothermal models

Where next for the reproducibility agenda in computational biology?

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