Publications

Control of NFAT Isoform Activation and NFAT−Dependent Gene Expression through Two Coincident and Spatially Segregated Intracellular Ca2+ Signals

P Kar‚ GR Mirams‚ HC Christian and AB Parekh

In Molecular Cell. Vol. 64. No. 4. Pages 746−759. 2016.

Details about Control of NFAT Isoform Activation and NFAT−Dependent Gene Expression through Two Coincident and Spatially Segregated Intracellular Ca2+ Signals | BibTeX data for Control of NFAT Isoform Activation and NFAT−Dependent Gene Expression through Two Coincident and Spatially Segregated Intracellular Ca2+ Signals | DOI (10.1016/j.molcel.2016.11.011) | Link to Control of NFAT Isoform Activation and NFAT−Dependent Gene Expression through Two Coincident and Spatially Segregated Intracellular Ca2+ Signals

Hierarchical Bayesian inference for ion channel screening dose−response data

RH Johnstone‚ R Bardenet‚ DJ Gavaghan and GR Mirams

In Wellcome Open Research. Vol. 1. Pages 6. 2016.

Details about Hierarchical Bayesian inference for ion channel screening dose−response data | BibTeX data for Hierarchical Bayesian inference for ion channel screening dose−response data | DOI (10.12688/wellcomeopenres.9945.1) | Link to Hierarchical Bayesian inference for ion channel screening dose−response data

White Paper: Uncertainty and variability in computational and mathematical models of cardiac physiology

GR Mirams‚ P Pathmanathan‚ RA Gray‚ P Challenor and RH Clayton

In Journal of Physiology. 2016.

Details about White Paper: Uncertainty and variability in computational and mathematical models of cardiac physiology | BibTeX data for White Paper: Uncertainty and variability in computational and mathematical models of cardiac physiology | DOI (10.1113/JP271671)

Connexin 43 contributes to electrotonic conduction across scar tissue in the intact heart

VM Mahoney‚ V Mezzano‚ GR Mirams‚ K Maass‚ Z Li‚ M Cerrone‚ C Vasquez‚ A Bapat‚ M Delmar and GE Morley

In Scientific Reports. Vol. 6. Pages 26744. 2016.

Details about Connexin 43 contributes to electrotonic conduction across scar tissue in the intact heart | BibTeX data for Connexin 43 contributes to electrotonic conduction across scar tissue in the intact heart | DOI (10.1038/srep26744)

White Paper: Computational Cardiology and Risk Stratification for Sudden Cardiac Death: One of the Grand Challenges for Cardiology in the 21st Century.

AP Hill‚ MD Perry‚ N Abi−Gerges‚ J−P Couderc‚ B Fermini‚ JC Hancox‚ BC Knollmann‚ GR Mirams‚ J Skinner‚ W Zareba and JI Vandenberg

In Journal of Physiology. 2016.

Details about White Paper: Computational Cardiology and Risk Stratification for Sudden Cardiac Death: One of the Grand Challenges for Cardiology in the 21st Century. | BibTeX data for White Paper: Computational Cardiology and Risk Stratification for Sudden Cardiac Death: One of the Grand Challenges for Cardiology in the 21st Century. | DOI (10.1113/JP272015)

Recent developments in using mechanistic cardiac modelling for drug safety evaluation

MR Davies‚ K Wang‚ GR Mirams‚ A Caruso‚ D Noble‚ A Walz‚ T Lavé‚ F Schuler‚ T Singer and L Polonchuk

In Drug Discovery Today. Vol. 21. No. 6. Pages 924–938. 2016.

Details about Recent developments in using mechanistic cardiac modelling for drug safety evaluation | BibTeX data for Recent developments in using mechanistic cardiac modelling for drug safety evaluation | DOI (10.1016/j.drudis.2016.02.003)

The Cardiac Electrophysiology Web Lab

Jonathan Cooper‚ Martin Scharm and Gary Mirams

In Biophysical Journal. Vol. 110. No. 2. Pages 292−300. 2016.

Details about The Cardiac Electrophysiology Web Lab | BibTeX data for The Cardiac Electrophysiology Web Lab | DOI (10.1016/j.bpj.2015.12.012)

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

RH Johnstone‚ ET Chang‚ R Bardenet‚ TP de Boer‚ DJ Gavaghan‚ P Pathmanathan‚ RH Clayton and GR Mirams

In Journal of Molecular and Cellular Cardiology. Vol. 96. Pages 49−62. 2016.

Details about Uncertainty and variability in models of the cardiac action potential: can we build trustworthy models? | BibTeX data for Uncertainty and variability in models of the cardiac action potential: can we build trustworthy models? | DOI (10.1016/j.yjmcc.2015.11.018)

Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance

Daniel Nichol‚ Peter Jeavons‚ Alexander G. Fletcher‚ Robert A. Bonomo‚ Philip K. Maini‚ Jerome L. Paul‚ Robert A. Gatenby‚ Alexander R.A. Anderson and Jacob G. Scott

In PLoS Computational Biology. 2015.

Details about Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance | BibTeX data for Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance | DOI (10.1371/journal.pcbi.1004493)

Hydroxychloroquine reduces heart rate by modulating the hyperpolarisation activated current ‘If’: Novel electrophysiological insights and therapeutic potential

R.A. Capel‚ N Herring‚ M Kalla‚ A Yavari‚ G.R. Mirams‚ G. Douglas‚ G. Bub‚ K. Channon‚ D.J. Paterson‚ D. Terrar and R−A Burton

In Heart Rhythm. Vol. 12. No. 10. Pages 2186–2194. 2015.

Details about Hydroxychloroquine reduces heart rate by modulating the hyperpolarisation activated current ‘If’: Novel electrophysiological insights and therapeutic potential | BibTeX data for Hydroxychloroquine reduces heart rate by modulating the hyperpolarisation activated current ‘If’: Novel electrophysiological insights and therapeutic potential | DOI (10.1016/j.hrthm.2015.05.027) | Link to Hydroxychloroquine reduces heart rate by modulating the hyperpolarisation activated current ‘If’: Novel electrophysiological insights and therapeutic potential

Ca2+ Channel Re−localization to Plasma−Membrane Microdomains Strengthens Activation of Ca2+−Dependent Nuclear Gene Expression

Krishna Samanta‚ Pulak Kar‚ Gary R. Mirams and Anant B. Parekh

In Cell Reports. Vol. 12. No. 2. Pages 203−216. 2015.

Details about Ca2+ Channel Re−localization to Plasma−Membrane Microdomains Strengthens Activation of Ca2+−Dependent Nuclear Gene Expression | BibTeX data for Ca2+ Channel Re−localization to Plasma−Membrane Microdomains Strengthens Activation of Ca2+−Dependent Nuclear Gene Expression | DOI (10.1016/j.celrep.2015.06.018) | Link to Ca2+ Channel Re−localization to Plasma−Membrane Microdomains Strengthens Activation of Ca2+−Dependent Nuclear Gene Expression

Cardiac Tissue Slices: Preparation‚ Handling‚ and Successful Optical Mapping

K Wang‚ P Lee‚ GR Mirams‚ P Sarathchandra‚ T Borg‚ DJ Gavaghan‚ P Kohl and C Bollensdorff

In American Journal of Physiology: Heart and Circulatory Physiology. Vol. 308. Pages H1112−H1125. 2015.

Details about Cardiac Tissue Slices: Preparation‚ Handling‚ and Successful Optical Mapping | BibTeX data for Cardiac Tissue Slices: Preparation‚ Handling‚ and Successful Optical Mapping | DOI (10.1152/ajpheart.00556.2014) | Link to Cardiac Tissue Slices: Preparation‚ Handling‚ and Successful Optical Mapping

A web portal for in−silico action potential predictions

Geoff Williams and Gary Mirams

In Journal of Pharmacological and Toxicological Methods. Vol. 75. Pages 10−16. 2015.

Details about A web portal for in−silico action potential predictions | BibTeX data for A web portal for in−silico action potential predictions | DOI (10.1016/j.vascn.2015.05.002) | Link to A web portal for in−silico action potential predictions

Cellular cardiac electrophysiology modelling with Chaste and CellML

Jonathan Cooper‚ Raymond Spiteri and Gary Mirams

In Frontiers in Physiology. Vol. 5. Pages 511. January, 2015.

Details about Cellular cardiac electrophysiology modelling with Chaste and CellML | BibTeX data for Cellular cardiac electrophysiology modelling with Chaste and CellML | DOI (10.3389/fphys.2014.00511) | Link to Cellular cardiac electrophysiology modelling with Chaste and CellML

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

GR Mirams‚ MR Davies‚ SJ Brough‚ MH Bridgland−Taylor‚ Y Cui‚ DJ Gavaghan and N Abi−Gerges

In Journal of Pharmacological & Toxicological Methods. Vol. 70. No. 3. Pages 246−254. 2014.

Details about Prediction of Thorough QT study results using action potential simulations based on ion channel screens | BibTeX data for Prediction of Thorough QT study results using action potential simulations based on ion channel screens | DOI (10.1016/j.vascn.2014.07.002)

Ten simple rules for effective computational research

James M Osborne‚ Miguel O Bernabeu‚ Maria Bruna‚ Ben Calderhead‚ Jonathan Cooper‚ Neil Dalchau‚ Sara−Jane Dunn‚ Alexander G Fletcher‚ Robin Freeman‚ Derek Groen and others

In PLoS Computational Biology. Vol. 10. No. 3. Pages e1003506. 2014.

Details about Ten simple rules for effective computational research | BibTeX data for Ten simple rules for effective computational research | DOI (10.1371/journal.pcbi.1003506)

mRNA expression levels in failing human hearts predict cellular electrophysiological remodelling: A population−based simulation study

J. Walmsley‚ J.F. Rodriguez‚ G.R. Mirams‚ K. Burrage‚ I.R. Efimov and B. Rodriguez

In PLoS ONE. Vol. 8. No. 2. Pages e56359. 2013.

Details about mRNA expression levels in failing human hearts predict cellular electrophysiological remodelling: A population−based simulation study | BibTeX data for mRNA expression levels in failing human hearts predict cellular electrophysiological remodelling: A population−based simulation study | DOI (10.1371/journal.pone.0056359)

Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge

Kylie A. Beattie‚ Chris Luscombe‚ Geoff Williams‚ Jordi Munoz−Muriedas‚ David J. Gavaghan‚ Yi Cui and Gary R. Mirams

In Journal of Pharmacological and Toxicological Methods. Vol. 68. No. 1. Pages 88−96. 2013.

Details about Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge | BibTeX data for Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge | DOI (10.1016/j.vascn.2013.04.004) | Link to Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge

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

Ryan C. Elkins‚ Mark R. Davies‚ Stephen J. Brough‚ David J. Gavaghan‚ Yi Cui‚ Najah Abi−Gerges and Gary R. Mirams

In Journal of Pharmacological and Toxicological Methods. Vol. 68. No. 1. Pages 112−122. 2013.

Details about Variability in high−throughput ion channel screening data and consequences for cardiac safety assessment | BibTeX data for Variability in high−throughput ion channel screening data and consequences for cardiac safety assessment | DOI (10.1016/j.vascn.2013.04.007)

Estimation of conductivity tensors from human ventricular optical mapping recordings

J. Walmsley‚ G.R. Mirams‚ I.R. Efimov‚ K. Burrage and B. Rodriguez

In Functional Imaging and Modeling of the Heart. Vol. 7495. Pages 224–231. 2013.

Details about Estimation of conductivity tensors from human ventricular optical mapping recordings | BibTeX data for Estimation of conductivity tensors from human ventricular optical mapping recordings

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

Gary R Mirams‚ Christopher J Arthurs‚ Miguel O Bernabeu‚ Rafel Bordas‚ Jonathan Cooper‚ Alberto Corrias‚ Yohan Davit‚ Sara−Jane Dunn‚ Alexander G Fletcher‚ Daniel G Harvey and others

In PLoS computational biology. Vol. 9. No. 3. Pages e1002970. 2013.

Details about Chaste: an open source C++ library for computational physiology and biology | BibTeX data for Chaste: an open source C++ library for computational physiology and biology | DOI (10.1371/journal.pcbi.1002970)

Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials

N Zemzemi‚ MO Bernabeu‚ J Saiz‚ J Cooper‚ P Pathmanathan‚ GR Mirams‚ J Pitt−Francis and B Rodriguez

In British Journal of Pharmacology. Vol. 168. No. 3. Pages 718−733. 2013.

Details about Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials | BibTeX data for Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials | DOI (10.1111/j.1476-5381.2012.02200.x)

Machine Learning and Software Engineering in Health Informatics

David A. Clifton‚ Jeremy Gibbons‚ Jim Davies and Lionel Tarassenko

May, 2012.

Details about Machine Learning and Software Engineering in Health Informatics | BibTeX data for Machine Learning and Software Engineering in Health Informatics | DOI (10.1109/RAISE.2012.6227968) | Download (pdf) of Machine Learning and Software Engineering in Health Informatics

Modelling the effect of gap junctions on tissue−level cardiac electrophysiology

Doug Bruce‚ Pras Pathmanathan and Jonathan P. Whiteley

In Ezio Bartocci and Luca Bortolussi, editors, Proceedings First International Workshop on Hybrid Systems and Biology‚ Newcastle Upon Tyne‚ 3rd September 2012. Vol. 92 of Electronic Proceedings in Theoretical Computer Science. Pages 1−15. Open Publishing Association. 2012.

Details about Modelling the effect of gap junctions on tissue−level cardiac electrophysiology | BibTeX data for Modelling the effect of gap junctions on tissue−level cardiac electrophysiology | DOI (10.4204/EPTCS.92.1)

High−throughput functional curation of cellular electrophysiology models

Niederer S.A. Cooper J. Mirams G.R.

In Progress in Biophysics and Molecular Biology. Vol. 107. Pages 11 − 20. 2011.

Details about High−throughput functional curation of cellular electrophysiology models | BibTeX data for High−throughput functional curation of cellular electrophysiology models | DOI (10.1016/j.pbiomolbio.2011.06.003)

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

G. R. Mirams‚ Y. Cui‚ A. Sher‚ M. Fink‚ J. Cooper‚ B. M. Heath‚ N. C. McMahon‚ D. J. Gavaghan and D. Noble

In Cardiovascular Research. Vol. 91. No. 1. Pages 53–61. 2011.

Details about Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk | BibTeX data for Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk | DOI (10.1093/cvr/cvr044) | Link to Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk

Stratagems for Effective Function Evaluation in Computational Chemistry

G.S. Skone

PhD Thesis 2010.

Details about Stratagems for Effective Function Evaluation in Computational Chemistry | BibTeX data for Stratagems for Effective Function Evaluation in Computational Chemistry | Download  (pdf) of Stratagems for Effective Function Evaluation in Computational Chemistry

Chaste: a test−driven approach to software development for biological modelling

Joe Pitt−Francis‚ Pras Pathmanathan‚ Miguel O Bernabeu‚ Rafel Bordas‚ Jonathan Cooper‚ Alexander G Fletcher‚ Gary R Mirams‚ Philip Murray‚ James M Osborne‚ Alex Walter and others

In Computer Physics Communications. Vol. 180. No. 12. Pages 2452–2471. 2009.

Details about Chaste: a test−driven approach to software development for biological modelling | BibTeX data for Chaste: a test−driven approach to software development for biological modelling | DOI (10.1016/j.cpc.2009.07.019)

A computational study of discrete mechanical tissue models

P Pathmanathan‚ J Cooper‚ A Fletcher‚ G Mirams‚ P Murray‚ J Osborne‚ J Pitt−Francis‚ A Walter and S J Chapman

In Physical Biology. Vol. 6. No. 3. 2009.

Details about A computational study of discrete mechanical tissue models | BibTeX data for A computational study of discrete mechanical tissue models | DOI (10.1088/1478-3975/6/3/036001)

Basic Strategies for Molecular Docking with Scoring Functions

Gwyn Skone‚ Stephen Cameron and Irina Voiculescu

In German Conference on Bioinformatics. September, 2008.

Details about Basic Strategies for Molecular Docking with Scoring Functions | BibTeX data for Basic Strategies for Molecular Docking with Scoring Functions

A Geometrical Model for the SNP Motif Identification Problem

Gaofeng Huang and Peter Jeavons

In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering‚ BIBE 2007. Pages 395−402. 2007.

Details about A Geometrical Model for the SNP Motif Identification Problem | BibTeX data for A Geometrical Model for the SNP Motif Identification Problem | DOI (10.1109/BIBE.2007.4375593) | Link to A Geometrical Model for the SNP Motif Identification Problem

Exact and Heuristic Approaches for Identifying Disease−Associated SNP Motifs

Gaofeng Huang‚ Peter Jeavons and Dominic Kwiatkowski

In Proceedings of 5th Asia−Pacific Bioinformatics Conference‚ APBC 2007. Vol. 5 of Advances in Bioinformatics and Computational Biology. Pages 175−184. Imperial College Press. 2007.

Details about Exact and Heuristic Approaches for Identifying Disease−Associated SNP Motifs | BibTeX data for Exact and Heuristic Approaches for Identifying Disease−Associated SNP Motifs

Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations

Z. Zhang S. Gunewardena P. Jeavons

In Journal of Computational Biology. Vol. 13. No. 4. Pages 929−945. 2006.

Details about Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations | BibTeX data for Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations | DOI (10.1089/cmb.2006.13.929) | Link to Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations

Characterization of the putative operon containing arylamine N−acetyltransferase (nat) in Mycobacterium bovis BCG

E. Sim M. Anderton S. Bhakta G. Besra P. Jeavons L. Eltis

In Molecular Microbiology. Vol. 59. No. 1. Pages 181−192. 2006.

Details about Characterization of the putative operon containing arylamine N−acetyltransferase (nat) in Mycobacterium bovis BCG | BibTeX data for Characterization of the putative operon containing arylamine N−acetyltransferase (nat) in Mycobacterium bovis BCG | DOI (10.1111/j.1365-2958.2005.04945.x) | Link to Characterization of the putative operon containing arylamine N−acetyltransferase (nat) in Mycobacterium bovis BCG

Exact and Heuristic Approaches for Identifying Disease−Associated SNP Motifs

Gaofeng Huang‚ Peter Jeavons and Dominic Kwiatkowski

No. RR−05−03. Oxford University Computing Laboratory. July, 2005.

Details about Exact and Heuristic Approaches for Identifying Disease−Associated SNP Motifs | BibTeX data for Exact and Heuristic Approaches for Identifying Disease−Associated SNP Motifs | Download  (ps) of Exact and Heuristic Approaches for Identifying Disease−Associated SNP Motifs

Information categorisation in biological sequence alignments

Sumedha Gunewardena and Peter Jeavons

No. RR−04−24. Oxford University Computing Laboratory. November, 2004.

Details about Information categorisation in biological sequence alignments | BibTeX data for Information categorisation in biological sequence alignments | Download  (ps) of Information categorisation in biological sequence alignments

Finding transcription factor binding sites in DNA Sequences: A template based approach

Sumedha Gunewardena and Peter Jeavons

No. RR−03−21. Oxford University Computing Laboratory. October, 2003.

Details about Finding transcription factor binding sites in DNA Sequences: A template based approach | BibTeX data for Finding transcription factor binding sites in DNA Sequences: A template based approach | Download  (ps) of Finding transcription factor binding sites in DNA Sequences: A template based approach

Automatic analysis of agarose gel images

Jonathan Flint P. S. Umesh Adiga A. Bhomra M. G. Turri A. Nicod S. R. Datta Peter Jeavons Richard Mott

In Bioinformatics. Vol. 17. No. 11. Pages 1084−1089. 2001.

Details about Automatic analysis of agarose gel images | BibTeX data for Automatic analysis of agarose gel images | Link to Automatic analysis of agarose gel images