Computational Biology group: Publications

Journal papers

• [1]

  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

• [2]

  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

• [3]

  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)

• [4]

  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)

• [5]

  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)

• [6]

  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)

• [7]

  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)

• [8]

  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)

• [9]

  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

• [10]

  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

• [11]

  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

• [12]

  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

• [13]

  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

• [14]

  Optimising cell aggregate expansion in a perfused hollow fibre bioreactor via mathematical modelling

  L.A.C. Chapman‚ R.J. Shipley‚ J.P. Whiteley‚ M.J. Ellis‚ H.M. Byrne and S.L. Waters

  In PLoS ONE. Vol. 9. Pages e105813. 2014.

  Details about Optimising cell aggregate expansion in a perfused hollow fibre bioreactor via mathematical modelling | BibTeX data for Optimising cell aggregate expansion in a perfused hollow fibre bioreactor via mathematical modelling | DOI (10.1371/journal.pone.0105813) | Link to Optimising cell aggregate expansion in a perfused hollow fibre bioreactor via mathematical modelling

• [15]

  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)

• [16]

  Ten simple rules for effective computational research

  J.M. Osborne‚ M.O. Bernabeu‚ M. Bruna‚ B. Calderhead‚ J. Cooper‚ N. Dalchau‚ S−J. Dunn‚ A.G. Fletcher‚ R. Freeman‚ D. Groen‚ B. Knapp‚ G.J. McInerny‚ G.R. Mirams‚ J. Pitt−Francis‚ B. Sengupta‚ D.W. Wright‚ C.A. Yates‚ Gavaghan D.J.‚ S. Emmott and C. Deane

  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)

• [17]

  Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare?

  Yohan Davit‚ Christopher G. Bell‚ Helen M. Byrne‚ Lloyd A. C. Chapman‚ Laura S. Kimpton‚ Georgina E. Lang‚ Katherine H. L. Leonard‚ James M. Oliver‚ Natalie C. Pearson‚ Rebecca J. Shipley‚ Sarah L. Waters‚ Jonathan P. Whiteley‚ Brian D. Wood and Michel Quintard

  In Advances in Water Resources. Vol. 62. Pages 178–206. December, 2013.

  Details about Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare? | BibTeX data for Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare? | DOI (10.1016/j.advwatres.2013.09.006) | Link to Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare?

• [18]

  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)

• [19]

  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

• [20]

  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)

• [21]

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

  G.R. Mirams‚ C.J. Arthurs‚ M.O. Bernabeu‚ R. Bordas‚ J. Cooper‚ A. Corrias‚ Y. Davit‚ S−J. Dunn‚ A.G. Fletcher‚ D.G. Harvey‚ M.E. Marsh‚ J. M. Osborne‚ P. Pathmanathan‚ J. Pitt−Francis‚ J. Southern‚ N. Zemzemi and D.J. Gavaghan

  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) | Link to Chaste: an open source C++ library for computational physiology and biology

• [22]

  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

• [23]

  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)

• [24]

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

  D.J.a c Pitt−Francis J.a Pathmanathan P.a Bernabeu M.O.a Bordas R.a Cooper J.a Fletcher A.G.b c Mirams G.R.d Murray P.b Osborne J.M.a c Walter A.b Chapman S.J.b Garny A.d van Leeuwen I.M.M.e Maini P.K.b c Rodríguez B.a Waters S.L.b Whiteley J.P.a b Byrne H.M.f Gavaghan

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

  cited By 102

  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) | Link to Chaste: A test−driven approach to software development for biological modelling

• [25]

  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

• [26]

  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

• [27]

  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

Conference papers

• [1]

  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

• [2]

  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

Technical reports

• [1]

  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

• [2]

  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