List of works by David Gavaghan

A Local Sensitivity Analysis Method for Developing Biological Models with Identifiable Parameters: Application to L-type Calcium Channel Modelling

A cell cycle model for somitogenesis: mathematical formulation and numerical simulation.

scientific article published in December 2000

A comparison of fully automated methods of data analysis and computer assisted heuristic methods in an electrode kinetic study of the pathologically variable [Fe(CN)6](3-/4-) process by AC voltammetry

scientific article

A global sensitivity tool for cardiac cell modeling: Application to ionic current balance and hypertrophic signaling

scientific article published on January 2010

A hybrid approach to multi-scale modelling of cancer

scientific article

A mathematical evaluation of the alveolar amplitude response technique.

scientific article published in October 1995

A mathematical evaluation of the multiple breath nitrogen washout (MBNW) technique and the multiple inert gas elimination technique (MIGET).

scientific article published in October 1998

A numerical guide to the solution of the bi-domain equations of cardiac electrophysiology

scientific article published on 27 May 2010

A tidal breathing model of the forced inspired inert gas sinewave technique.

scientific article published in November 1996

A tidal breathing model of the inert gas sinewave technique for inhomogeneous lungs

scientific article published in January 2001

A tidal ventilation model for oxygenation in respiratory failure.

scientific article published in June 2003

A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath

scientific article

AN ITERATIVE METHOD FOR REGISTRATION OF HIGH-RESOLUTION CARDIAC HISTOANATOMICAL AND MRI IMAGES

article published in 2007

Access to enhanced differences in Marcus-Hush and Butler-Volmer electron transfer theories by systematic analysis of higher order AC harmonics

scientific article published on 10 December 2012

Action Potential Duration Maps in Homogeneous Cardiac Ventricular Tissue Slices are Independent of Changes in Stimulation Site

Adaptive finite element methods in electrochemistry

scientific article published on December 2006

An evaluation of homogeneity tests in meta-analyses in pain using simulations of individual patient data

scientific article

An integrative computational model for intestinal tissue renewal.

scientific article published on 20 July 2009

Analysis of HypD Disulfide Redox Chemistry via Optimization of Fourier Transformed ac Voltammetric Data

scientific article

CHASTE: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library

scientific article

Cardiac tissue slices: preparation, handling, and successful optical mapping

scientific article

Cell-specific mathematical models of cardiac electrophysiology

scholarly article by Ross Johnstone et al published September 2016 in Journal of Pharmacological and Toxicological Methods

Chaste: Cancer, Heart and Soft Tissue Environment

scientific article published on 13 March 2020

Chaste: an open source C++ library for computational physiology and biology

scientific article

Chaste: using agile programming techniques to develop computational biology software

scientific article

Colorectal cancer through simulation and experiment

scientific article

Comparing individual-based approaches to modelling the self-organization of multicellular tissues

scientific article

Comparison of Functional Parameter Measured from Tissues Slices and Whole-Heart

Computational modelling of cardiac electrophysiology: explanation of the variability of results from different numerical solvers

scientific article published on 28 February 2012

Computational science. Troubling trends in scientific software use.

scientific article

Conformational Dynamics of a Lipid-Interacting Protein: MD Simulations of Saposin B†

article

Considerations for the use of cellular electrophysiology models within cardiac tissue simulations

scientific article published on 15 June 2011

Contrast-independent curvilinear structure detection in biomedical images

scientific article published on 27 January 2012

Deriving dichotomous outcome measures from continuous data in randomised controlled trials of analgesics

scientific article published on August 1996

Deriving dichotomous outcome measures from continuous data in randomised controlled trials of analgesics: use of pain intensity and visual analogue scales

scientific article published on February 1997

Deriving dichotomous outcome measures from continuous data in randomised controlled trials of analgesics: verification from independent data

scientific article published on January 1997

Development of a functional magnetic resonance imaging simulator for modeling realistic rigid-body motion artifacts.

scientific article published in August 2006

Development of an anatomically detailed MRI-derived rabbit ventricular model and assessment of its impact on simulations of electrophysiological function

scientific article

Early afterdepolarisation tendency as a simulated pro-arrhythmic risk indicator

scientific article published on 14 September 2017

Effects of propofol and thiopentone, and benzodiazepine premedication on heart rate variability measured by spectral analysis.

scientific article published in February 1995

Electrochemical Parameter Optimization Using Scientific Workflows

Electrophysiology of Cardiac Tissue Slices before, during, and after Stretch

Enabling computer models of the heart for high-performance computers and the grid

scientific article published on June 2006

Evaluation of an in silico cardiac safety assay: using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge

scientific article

Evaluation of computational modelling as a preclinical proarrhythmic safety assay

Finite element simulation of electrochemically reversible, quasi-reversible and irreversible linear sweep voltammetry at the wall tube electrode

Functional significance of Na+/Ca2+ exchangers co-localization with ryanodine receptors.

scientific article published in March 2007

Generation of histo-anatomically representative models of the individual heart: tools and application

scientific article

Hierarchical Bayesian inference for ion channel screening dose-response data

scientific article

High Performance Computer Simulations of Cardiac Electrical Function Based on High Resolution MRI Datasets

High-throughput cardiac science on the Grid.

scientific article published in August 2010

Hodgkin-Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods

scientific article

Hydrodynamic dispersion within porous biofilms

scientific article published on 23 January 2013

Hyperpolarized Gas MRI For COPD Assessment – Automated Regional Image Analysis And Computational Simulations

scholarly article published May 2010

Implementing vertex dynamics models of cell populations in biology within a consistent computational framework

scientific article published on 09 October 2013

In silico pro-arrhythmia assessment: Can the results of the thorough QT study be predicted?

scholarly article by Gary R. Mirams et al published November 2014 in Journal of Pharmacological and Toxicological Methods

Inappropriate use of the quasi-reversible electrode kinetic model in simulation-experiment comparisons of voltammetric processes that approach the reversible limit

scientific article published on 31 July 2014

Incorporating Local Ca2 + Dynamics into Single Cell Ventricular Models

Inference of intramural wavefront orientation from optical recordings in realistic whole-heart models

scientific article

Information visualisation for science and policy: engaging users and avoiding bias.

scientific article

Integrated approach for the study of anatomical variability in the cardiac Purkinje system: from high resolution MRI to electrophysiology simulation.

scientific article published in January 2010

Interactions between a voltage sensor and a toxin via multiscale simulations.

scientific article

Introducing Drug Action into Single-Cell Cardiac Models

Leveraging e-Science infrastructure for electrochemical research.

scientific article

Lipid bilayer deformation and the free energy of interaction of a Kv channel gating-modifier toxin.

scientific article published on 11 July 2008

Living cardiac tissue slices: an organotypic pseudo two-dimensional model for cardiac biophysics research

scientific article published on 11 August 2014

Mathematical modelling of oxygen transport to tissue.

scientific article published in June 2002

Mathematical modelling of pulmonary gas transport.

scientific article published in July 2003

Mathematical models in physiology

scientific article

Mechano-logical model of C. elegans germ line suggests feedback on the cell cycle.

scientific article

Metabolic alterations during the growth of tumour spheroids

scientific article published on April 2014

Metabolic changes during carcinogenesis: potential impact on invasiveness.

scientific article published on 16 September 2006

Modelling inert gas exchange in tissue and mixed-venous blood return to the lungs

scientific article published in April 2001

Modelling the role of the basement membrane beneath a growing epithelial monolayer

scientific article

Modelling tissue electrophysiology with multiple cell types: applications of the extended bidomain framework

scientific article published on 05 January 2012

Models for pattern formation in somitogenesis: a marriage of cellular and molecular biology

scientific article

Models of the cardiac L‐type calcium current: A quantitative review

scientific article published in 2022

Modulation of shock-end virtual electrode polarisation as a direct result of 3D fluorescent photon scattering.

scientific article published in January 2006

Modules for Reusable and Collaborative Modelling of Biological Mathematical Systems

Multi-scale computational modelling in biology and physiology

scientific article published on 11 August 2007

Multimodal Imaging Techniques for the Extraction of Detailed Geometrical and Physiological Information for Use in Multi-Scale Models of Colorectal Cancer and Treatment of Individual Patients

Multiparameter Estimation in Voltammetry When an Electron Transfer Process Is Coupled to a Chemical Reaction

scientific article published on 4 April 2016

Multiscale cardiac modelling reveals the origins of notched T waves in long QT syndrome type 2.

scientific article published on 25 September 2014

Multistability property in cardiac ionic models of mammalian and human ventricular cells

scientific article published on 11 February 2010

Non-linear modelling of breast tissue.

scientific article published on 22 September 2007

On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data.

scientific article

On the Secure Sharing and Aggregation of Data to Support Systems Biology Research

Optimizing Peer Review of Software Code--Response

scientific article published in Science

Oral morphine in cancer pain: influences on morphine and metabolite concentration

scientific article published on September 1990

P4-21

P4-23

P4-24

Photon scattering effects in optical mapping of propagation and arrhythmogenesis in the heart

scientific article published on November 2007

Pooling data for number needed to treat: no problems for apples

scientific article

Post-genomic science: cross-disciplinary and large-scale collaborative research and its organizational and technological challenges for the scientific research process

scientific article published on June 2006

Predicting Tumour Location by Simulating Large Deformations of the Breast Using a 3D Finite Element Model and Nonlinear Elasticity

article

Predicting tumor location by modeling the deformation of the breast.

scientific article published in October 2008

Prediction of Thorough QT study results using action potential simulations based on ion channel screens

scientific article

Problems with the Current Approach to the Dissemination of Computational Science Research and Its Implications for Research Integrity

scholarly article by David Gavaghan published 15 October 2018 in Bulletin of Mathematical Biology

Progressive changes in T₁, T₂ and left-ventricular histo-architecture in the fixed and embedded rat heart

scientific article published on 8 December 2010

Pulmonary blood flow measured by inspiratory inert gas concentration forcing oscillations

scientific article

Quiescence as a mechanism for cyclical hypoxia and acidosis.

scientific article published on 3 July 2007

Rabbit-specific ventricular model of cardiac electrophysiological function including specialized conduction system

scientific article

Regionally Optimised Mathematical Models of Cardiac Myocyte Orientation in Rat Hearts

article by Ilyas E. Karadag et al published 2011 in Lecture Notes in Computer Science

Relationship between structural changes and hyperpolarized gas magnetic resonance imaging in chronic obstructive pulmonary disease using computational simulations with realistic alveolar geometry.

scientific article published on June 2009

Reproducible model development in the Cardiac Electrophysiology Web Lab

article

Reproducible model development in the cardiac electrophysiology Web Lab

article

Resistance, capacitance, and electrode kinetic effects in Fourier-transformed large-amplitude sinusoidal voltammetry: emergence of powerful and intuitively obvious tools for recognition of patterns of behavior

scientific article published in November 2004

Review of automatic pulmonary lobe segmentation methods from CT.

scientific article

Room Temperature vs Ice Cold - Temperature Effects on Cardiac Cell Action Potential

SGTx1, a Kv channel gating-modifier toxin, binds to the interfacial region of lipid bilayers

scientific article published on 27 October 2006

Simulated micro-electrode array recordings from stem cell-derived cardiomyocytes

scholarly article by Louise Bowler et al published September 2016 in Journal of Pharmacological and Toxicological Methods

Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium

scientific article

Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk ⬇️

scientific article

Sinusoidal Voltage Protocols For Rapid Characterisation Of Ion Channel Kinetics

Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics.

scientific article published on 24 March 2018

Soft tissue modelling of cardiac fibres for use in coupled mechano-electric simulations.

scientific article published on 24 April 2007

Some factors affecting oxygen uptake by red blood cells in the pulmonary capillaries.

scientific article published in February 2001

Synchronization between arterial blood pressure and cerebral oxyhaemoglobin concentration investigated by wavelet cross-correlation.

scientific article

Synthesis of voltage-sensitive optical signals: application to panoramic optical mapping

scientific article

Ten simple rules for a successful cross-disciplinary collaboration

scientific article (publication date: April 2015)

Ten simple rules for effective computational research

scientific article (publication date: March 2014)

The Dynamics and Pinning of a Spike for a Reaction-Diffusion System

article

The effect of diffusion in the respiratory tree on the alveolar amplitude response technique (AART).

scientific article

The effect of inspired oxygen concentration on the ventilation-perfusion distribution in inhomogeneous lungs.

scientific article published in June 2000

The effect of periodic modulation on the aperiodic current in linear-scan and cyclic voltammetries

The effect of the width of the ventilation-perfusion distribution on arterial blood oxygen content.

scientific article published in December 1999

The effects of ventilation pattern on carbon dioxide transfer in three computer models of the airways.

scientific article published in August 2002

The free energy landscape of dimerization of a membrane protein, NanC.

scientific article published on 9 January 2014

The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.

scientific article published on 9 May 2008

The role of acidity in solid tumour growth and invasion

scientific article (publication date: August 2005)

The role of photon scattering in optical signal distortion during arrhythmia and defibrillation

scientific article

The role of photon scattering in voltage-calcium fluorescent recordings of ventricular fibrillation

scientific article published on July 2011

The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt ⬇️

scientific article

The role of the Na+/Ca2+ exchangers in Ca2+ dynamics in ventricular myocytes

scientific article published on 11 August 2007

The role of transmural ventricular heterogeneities in cardiac vulnerability to electric shocks

scientific article

The systems biology approach to drug development: application to toxicity assessment of cardiac drugs

scientific article published on 02 June 2010

The virtual physiological human: tools and applications I.

scientific article published in May 2009

Theoretical Analysis of the Relative Significance of Thermodynamic and Kinetic Dispersion in the dc and ac Voltammetry of Surface-Confined Molecules

scientific article published on 24 April 2015

Theoretical analysis of the two-electron transfer reaction and experimental studies with surface-confined cytochrome c peroxidase using large-amplitude Fourier transformed AC voltammetry

scientific article

Three-dimensional models of individual cardiac histoanatomy: tools and challenges

scientific article published in October 2006

Towards a Grid infrastructure to support integrative approaches to biological research

scientific article published on August 2005

Transmural electrophysiological heterogeneities in action potential duration increase the upper limit of vulnerability

scientific article published on 01 January 2006

Uncertainty and variability in models of the cardiac action potential: Can we build trustworthy models?

scientific article

Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology

scientific article published on January 2015

Unstructured Spectral Elements applied to the Bidomain Model

Using evidence from different sources: an example using paracetamol 1000 mg plus codeine 60 mg

scientific article

Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues

scientific article published on 30 April 2013

Variability in high-throughput ion-channel screening data and consequences for cardiac safety assessment

scientific article

Variation of venous admixture, SF6 shunt, PaO2, and the PaO2/FIO2 ratio with FIO2.

scientific article published in June 2002

Voltage protocol design for determining hERG channel kinetics

scholarly article by Kylie Beattie et al published September 2015 in Journal of Pharmacological and Toxicological Methods

Vulnerability to electric shocks in the regionally-ischemic ventricles

article

Vulnerability to electric shocks in the regionally-ischemic ventricles

eDiamond: A Grid-Enabled Federated Database of Annotated Mammograms

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