Computational Biology group: Publications

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@article{Kar2016,
  title = "Control of NFAT Isoform Activation and NFAT-Dependent Gene Expression through Two Coincident and Spatially Segregated Intracellular Ca2+ Signals",
  author = "P Kar and GR Mirams and HC Christian and AB Parekh",
  year = "2016",
  journal = "Molecular Cell",
  number = "4",
  pages = "746-759",
  url = "http://www.sciencedirect.com/science/article/pii/S1097276516307195",
  volume = "64",
  doi = "10.1016/j.molcel.2016.11.011",
}

@article{Johnstone2016,
  title = "Hierarchical Bayesian inference for ion channel screening dose-response data",
  author = "RH Johnstone and R Bardenet and DJ Gavaghan and GR Mirams",
  year = "2016",
  journal = "Wellcome Open Research",
  pages = "6",
  publisher = "Wellcome Trust",
  url = "https://wellcomeopenresearch.org/articles/1-6/v1",
  volume = "1",
  doi = "10.12688/wellcomeopenres.9945.1",
}

@article{Mirams2016,
  title = "White Paper: Uncertainty and variability in computational and mathematical models of cardiac physiology",
  author = "GR Mirams and P Pathmanathan and RA Gray and P Challenor and RH Clayton",
  year = "2016",
  journal = "Journal of Physiology",
  doi = "10.1113/JP271671",
}

@article{Mahoney2016,
  title = "Connexin 43 contributes to electrotonic conduction across scar tissue in the intact heart",
  author = "VM Mahoney and V Mezzano and GR Mirams and K Maass and Z Li and M Cerrone and C Vasquez and A Bapat and M Delmar and GE Morley",
  year = "2016",
  journal = "Scientific Reports",
  pages = "26744",
  publisher = "Nature Publishing Group",
  volume = "6",
  doi = "10.1038/srep26744",
}

@article{Hill2016,
  title = "White Paper: Computational Cardiology and Risk Stratification for Sudden Cardiac Death: One of the Grand Challenges for Cardiology in the 21st Century.",
  author = "AP Hill and MD Perry and N Abi-Gerges and J-P Couderc and B Fermini and JC Hancox and BC Knollmann and GR Mirams and J Skinner and W Zareba and JI Vandenberg",
  year = "2016",
  journal = "Journal of Physiology",
  doi = "10.1113/JP272015",
}

@article{Davies2016,
  title = "Recent developments in using mechanistic cardiac modelling for drug safety evaluation",
  author = "MR Davies and K Wang and GR Mirams and A Caruso and D Noble and A Walz and T Lavé and F Schuler and T Singer and L Polonchuk",
  year = "2016",
  journal = "Drug Discovery Today",
  number = "6",
  pages = "924–938",
  volume = "21",
  doi = "10.1016/j.drudis.2016.02.003",
}

@article{CooperWebLab2016,
  title = "The Cardiac Electrophysiology Web Lab",
  author = "Cooper, Jonathan and Scharm, Martin and Mirams, Gary",
  year = "2016",
  journal = "Biophysical Journal",
  number = "2",
  pages = "292-300",
  volume = "110",
  doi = "10.1016/j.bpj.2015.12.012",
}

@article{Johnstone2016,
  title = "Uncertainty and variability in models of the cardiac action potential: can we build trustworthy models?",
  author = "RH Johnstone and ET Chang and R Bardenet and TP de Boer and DJ Gavaghan and P Pathmanathan and RH Clayton and GR Mirams",
  year = "2016",
  journal = "Journal of Molecular and Cellular Cardiology",
  pages = "49-62",
  volume = "96",
  doi = "10.1016/j.yjmcc.2015.11.018",
}

@article{cooper2015cce,
  title = "Cellular cardiac electrophysiology modelling with Chaste and CellML",
  author = "Jonathan Cooper and Raymond Spiteri and Gary Mirams",
  year = "2015",
  journal = "Frontiers in Physiology",
  month = "January",
  pages = "511",
  url = "http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00511",
  volume = "5",
  doi = "10.3389/fphys.2014.00511",
}

@article{Samanta2015,
  title = "Ca2+ Channel Re-localization to Plasma-Membrane Microdomains Strengthens Activation of Ca2+-Dependent Nuclear Gene Expression",
  author = "Krishna Samanta and Pulak Kar and Gary R. Mirams and Anant B. Parekh",
  year = "2015",
  journal = "Cell Reports",
  number = "2",
  pages = "203-216",
  url = "http://dx.doi.org/10.1016/j.celrep.2015.06.018",
  volume = "12",
  doi = "10.1016/j.celrep.2015.06.018",
}

@article{Capel2015,
  title = "Hydroxychloroquine reduces heart rate by modulating the hyperpolarisation activated current ‘If’: Novel electrophysiological insights and therapeutic potential",
  author = "R.A. Capel and N Herring and M Kalla and A Yavari and G.R. Mirams and G. Douglas and G. Bub and K. Channon and D.J. Paterson and D. Terrar and R-A Burton",
  year = "2015",
  journal = "Heart Rhythm",
  number = "10",
  pages = "2186–2194",
  url = "http://dx.doi.org/10.1016/j.hrthm.2015.05.027",
  volume = "12",
  doi = "10.1016/j.hrthm.2015.05.027",
}

@article{Wang2015,
  title = "Cardiac Tissue Slices: Preparation, Handling, and Successful Optical Mapping",
  author = "K Wang and P Lee and GR Mirams and P Sarathchandra and T Borg and DJ Gavaghan and P Kohl and C Bollensdorff",
  year = "2015",
  journal = "American Journal of Physiology: Heart and Circulatory Physiology",
  pages = "H1112-H1125",
  url = "http://ajpheart.physiology.org/content/308/9/H1112",
  volume = "308",
  doi = "10.1152/ajpheart.00556.2014",
}

@article{williams2015,
  title = "A web portal for in-silico action potential predictions",
  author = "Geoff Williams and Gary Mirams",
  year = "2015",
  journal = "Journal of Pharmacological and Toxicological Methods",
  pages = "10-16",
  url = "http://dx.doi.org/10.1016/j.vascn.2015.05.002",
  volume = "75",
  doi = "10.1016/j.vascn.2015.05.002",
}

@article{PlosOne2014,
  title = "Optimising cell aggregate expansion in a perfused hollow fibre bioreactor via mathematical modelling",
  author = "L.A.C.\ Chapman and R.J.\ Shipley and J.P.\ Whiteley and M.J.\ Ellis and H.M.\ Byrne and S.L.\ Waters",
  year = "2014",
  journal = "PLoS ONE",
  pages = "e105813",
  url = "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0105813",
  volume = "9",
  doi = "10.1371/journal.pone.0105813",
}

@article{Mirams2014,
  title = "Prediction of Thorough QT study results using action potential simulations based on ion channel screens",
  author = "GR Mirams and MR Davies and SJ Brough and MH Bridgland-Taylor and Y Cui and DJ Gavaghan and N Abi-Gerges",
  year = "2014",
  journal = "Journal of Pharmacological & Toxicological Methods",
  number = "3",
  pages = "246-254",
  volume = "70",
  doi = "10.1016/j.vascn.2014.07.002",
}

@article{Osborne2014TenSimple,
  title = "Ten simple rules for effective computational research",
  author = "Osborne, J.M. and Bernabeu, M.O. and Bruna, M. and Calderhead, B. and Cooper, J. and Dalchau, N. and Dunn, S-J. and Fletcher, A.G. and Freeman, R. and Groen, D. and Knapp, B. and McInerny, G.J. and Mirams, G.R. and Pitt-Francis, J. and Sengupta, B. and Wright, D.W. and Yates, C.A. and Gavaghan D.J. and Emmott, S. and Deane, C.",
  year = "2014",
  journal = "PLoS Computational Biology",
  number = "3",
  pages = "e1003506",
  volume = "10",
  doi = "10.1371/journal.pcbi.1003506",
}

@article{Davit2013Homogenization,
  title = "{Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare?}",
  author = "Davit, Yohan and Bell, Christopher G. and Byrne, Helen M. and Chapman, Lloyd A. C. and Kimpton, Laura S. and Lang, Georgina E. and Leonard, Katherine H. L. and Oliver, James M. and Pearson, Natalie C. and Shipley, Rebecca J. and Waters, Sarah L. and Whiteley, Jonathan P. and Wood, Brian D. and Quintard, Michel",
  year = "2013",
  issn = "03091708",
  journal = "Advances in Water Resources",
  keywords = "publications",
  month = "dec",
  pages = "178--206",
  url = "http://dx.doi.org/10.1016/j.advwatres.2013.09.006",
  volume = "62",
  doi = "10.1016/j.advwatres.2013.09.006",
}

@article{Walmsley2013,
  title = "mRNA expression levels in failing human hearts predict cellular electrophysiological remodelling: A population-based simulation study",
  author = "Walmsley, J. and  Rodriguez, J.F. and Mirams, G.R. and Burrage, K. and Efimov, I.R. and Rodriguez, B.",
  year = "2013",
  journal = "PLoS ONE",
  number = "2",
  pages = "e56359",
  volume = "8",
  doi = "10.1371/journal.pone.0056359",
}

@article{Beattie2013,
  title = "Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge",
  author = "Kylie A. Beattie and Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J. Gavaghan and Yi Cui and Gary R. Mirams",
  year = "2013",
  journal = "Journal of Pharmacological and Toxicological Methods",
  number = "1",
  pages = "88-96",
  url = "http://www.sciencedirect.com/science/article/pii/S105687191300244X",
  volume = "68",
  doi = "10.1016/j.vascn.2013.04.004",
}

@article{Elkins2013,
  title = "Variability in high-throughput ion channel screening data and consequences for cardiac safety assessment",
  author = "Ryan C. Elkins and Mark R. Davies and Stephen J. Brough and David J. Gavaghan and Yi Cui and Najah Abi-Gerges and Gary R. Mirams",
  year = "2013",
  journal = "Journal of Pharmacological and Toxicological Methods",
  keywords = "high-throughput, compound screening, variability, uncertainty, cardiac safety, action potential, mathematical model",
  number = "1",
  pages = "112-122",
  volume = "68",
  doi = "10.1016/j.vascn.2013.04.007",
}

@article{MiramsChaste2013,
  title = "Chaste: an open source C++ library for computational physiology and biology",
  author = "G.R. Mirams and C.J. Arthurs and M.O. Bernabeu and R. Bordas and J. Cooper and A. Corrias and Y. Davit and S-J. Dunn and A.G. Fletcher and D.G. Harvey and M.E. Marsh and J. M. Osborne and P. Pathmanathan and J. Pitt-Francis and J. Southern and N. Zemzemi and D.J. Gavaghan",
  year = "2013",
  journal = "PLoS Computational Biology",
  number = "3",
  pages = "e1002970",
  url = "http://dx.plos.org/10.1371/journal.pcbi.1002970",
  volume = "9",
  doi = "10.1371/journal.pcbi.1002970",
}

@article{f20eb73a440003b,
  title = "Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk",
  author = "Mirams, G. R. and Cui, Y. and Sher, A. and Fink, M. and Cooper, J. and Heath, B. M. and McMahon, N. C. and Gavaghan, D. J. and Noble, D.",
  year = "2011",
  issn = "00086363",
  journal = "Cardiovascular Research",
  number = "1",
  pages = "53--61",
  url = "http://dx.doi.org/10.1093/cvr/cvr044",
  volume = "91",
  doi = "10.1093/cvr/cvr044",
}

@article{CooperMiramsNiederer2011,
  title = "High-throughput functional curation of cellular electrophysiology models",
  author = "Cooper J., Mirams G.R., Niederer S.A.",
  year = "2011",
  editor = "Denis Noble",
  journal = "Progress in Biophysics and Molecular Biology",
  pages = "11 - 20",
  volume = "107",
  doi = "10.1016/j.pbiomolbio.2011.06.003",
}

@article{ChasteCPC09,
  title = "Chaste: A test-driven approach to software development for biological modelling",
  author = "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, D.J.a c",
  year = "2009",
  affiliation = "Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, United Kingdom; Mathematical Institute, 24-29 St. Giles, Oxford, OX1 3LB, United Kingdom; Oxford Centre for Integrative Systems Biology, South Parks Road, Oxford, OX1 3QU, United Kingdom; Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford, OX1 3PT, United Kingdom; Department of Surgery, Molecular Oncology Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, United Kingdom; School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom",
  journal = "Computer Physics Communications",
  note = "cited By 102",
  number = "12",
  pages = "2452-2471",
  url = "http://www.scopus.com/inward/record.url?eid=2-s2.0-70350588995&partnerID=40&md5=6bf349702a12bd2e867fe8148a17d9bb",
  volume = "180",
  doi = "10.1016/j.cpc.2009.07.019",
}

@inproceedings{GeometricSNP,
  title = "A Geometrical Model for the SNP Motif Identification Problem",
  author = "Gaofeng Huang and Peter Jeavons",
  year = "2007",
  booktitle = "Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2007",
  isbn = "978-1-4244-1509-0 ",
  pages = "395-402",
  url = "http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=4375593",
  doi = "10.1109/BIBE.2007.4375593",
}

@inproceedings{ExactHeuristicSNP,
  title = "Exact and Heuristic Approaches for Identifying Disease-Associated SNP Motifs",
  author = "Gaofeng Huang and Peter Jeavons and Dominic Kwiatkowski",
  year = "2007",
  booktitle = "Proceedings of 5th Asia-Pacific Bioinformatics Conference, APBC 2007",
  isbn = "978-1-86094-783-4",
  pages = "175-184",
  publisher = "Imperial College Press",
  series = "Advances in Bioinformatics and Computational Biology",
  volume = "5",
}

@article{EnhancingBindingSitePrediction,
  title = "Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations",
  author = "S. Gunewardena, P. Jeavons, Z. Zhang",
  year = "2006",
  journal = "Journal of Computational Biology",
  number = "4",
  pages = "929-945",
  url = "http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.929",
  volume = "13",
  doi = "10.1089/cmb.2006.13.929",
}

@article{OperonMycobacteriumBovis,
  title = "Characterization of the putative operon containing arylamine N-acetyltransferase (nat) in Mycobacterium bovis BCG",
  author = "M. Anderton, S. Bhakta, G. Besra, P. Jeavons, L. Eltis, E. Sim",
  year = "2006",
  journal = "Molecular Microbiology",
  number = "1",
  pages = "181-192",
  url = "http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2958.2005.04945.x",
  volume = "59",
  doi = "10.1111/j.1365-2958.2005.04945.x",
}

@techreport{RR-04-24,
  title = "Information categorisation in biological sequence alignments",
  author = "Sumedha Gunewardena and Peter Jeavons",
  year = "2004",
  institution = "Oxford University Computing Laboratory",
  month = "November",
  number = "RR-04-24",
}

@techreport{RR-03-21,
  title = "Finding transcription factor binding sites in DNA Sequences: A template based approach",
  author = "Sumedha Gunewardena and Peter Jeavons",
  year = "2003",
  institution = "Oxford University Computing Laboratory",
  month = "October",
  number = "RR-03-21",
}

@article{AgaroseGelImage,
  title = "Automatic analysis of agarose gel images",
  author = "P. S. Umesh Adiga, A. Bhomra, M. G. Turri, A. Nicod, S. R. Datta, Peter Jeavons, Richard Mott, Jonathan Flint",
  year = "2001",
  journal = "Bioinformatics",
  number = "11",
  pages = "1084-1089",
  url = "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/11/1084",
  volume = "17",
}