Publications

Publications

Dissemination (including electronic) of all results must acknowledge EU funding. See below for details.

Marco Viceconti and his team at the Insigneo Institute, part of the University of Sheffield have collated and written a report on the CompBioMed solutions and end-user engagement of our Core Partners. We are currently in the process of extending this to our

2018

  • S. Succi, P. V. Coveney,”Big Data: the End of the Scientific Method?” Phil Trans R Soc (Series A) (in press) arxiv.org/abs/1807.09515
  • M. Skalic, A. Varela-Rial, J. Jimenez, G. Martinez-Rosell, G. De Fabritiis, “LigVoxel: Inpainting binding pockets using 3D-convolutional neural networks” Bioinformatics (2018) DOI: 10.1093/bioinformatics/bty583
  • A. Perez, G. Martinez-Rosell, G. De Fabritiis, “Simulations meet machine learning in structural biology” Current Opinion in Structural Biology (2018) DOI: 10.1016/j.sbi.2018.02.004
  • F. Sacco, B. Pain, O. Lehmkuhl, T.L. Iles, P.A. Iaizzo, G. Houzeaux, M. Vazquez, C. Butakoff, J. Aguado-Sierra, “Left Ventricular Trabeculations Decrease the Wall Shear Stress and Increase the Intra-Ventricular Pressure Drop in CFD Simulations” Frontiers in Physiology (2018) DOI: 10.3389/fphys.2018.00458
  • F. Sacco, B. Pain, O. Lehmkuhl, T.L. Iles, P.A. Iaizzo, G. Houzeaux, M. Vazquez, C. Butakoff, J. Aguado-Sierra, “Evaluating the roles of detailed endocardial structures on right ventricular haemodynamics by means of CFD simulations” International Journal for Numerical Methods in Biomedical Engineering (2018) DOI: 10.1002/cnm.3115
  • D. S. M. Boulanger, R. C. Eccleston, A. Phillips, P. V. Coveney, T. Elliott, N. Dalchau, “A mechanistic model for predicting cell surface presentation of competing peptides by MHC class I molecules” Frontiers Immunology (2018) DOI: 10.3389/fimmu.2018.01538
  • D. Groen, R. A. Richardson, R. Coy, U. D. Schiller, H. Chandrashekar, F. Robertson, P. V. Coveney, “Validation of patient-specific cerebral blood flow simulation using transcranial Doppler measurements”, Frontiers Physiology,(2018) DOI: 10.3389/fphys.2018.00721
  • M. O. Bernabeu, M. L. Jones, R. W. Nash, A. Pezzarossa, P. V. Coveney, H. Gerhardt, and C. A. Franco, “PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling”, Biophysical Journal, 114 (9), 2052-2058 (2018) DOI: 10.1016/j.bpj.2018.03.032
  • A. Bhati, S. Wan, Y. Hu, B. Sherborne, P. V. Coveney, “Uncertainty Quantification in Alchemical Free Energy Methods”, Journal of Chemical Theory and Computation, Just Accepted (2018), DOI: 10.1021/acs.jctc.7b01143
  • Z. Altai, M. Viceconti, A. C. Offiah, X. Li, “Investigating the mechanical response of paediatric bone under bending and torsion using finite element analysis”, Biomechanics and Modeling in Mechanobiology (2018), DOI:10.1007/s10237-018-1008-9
  • A. Patronis, R. A. Richardson, S. Schmieschek, B. J. N. Wylie, R. W. Nash, P. V. Coveney, “Modeling Patient-Specific Magnetic Drug Targeting Within the Intracranial Vasculature”, Frontiers in Physiology (2018), DOI: 10.3389/fphys.2018.00331
  • L. Pérez-Benito, H. Keränen, H. van Vlijmen & G. Tresadern, “Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation”, Scientific Reports, 8, 4833 (2018), DOI: 10.1038/s41598-018-23039-5
  • J. Jimenez, M. Skalic, G. Martinez-Rosell, G. De Fabritiis, “KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks”, J. Chem. Inf. Model., 52(8), 287-296 (2018), DOI: 10.1021/acs.jcim.7b00650
  • A. Heifetz, “Computational Methods for GPCR Drug Discovery”, Springer, 1705 (2018), DOI: 10.1007/978-1-4939-7465-8
  • A. Potterton, A. Heifetz, A. Townsend-Nicholson, “Synergistic Use of GPCR Modeling and SDM Experiments to Understand Ligand Binding”, Methods Mol Biol., 1705, 335-343 (2018), DOI: 10.1007/978-1-4939-7465-8_15
  • B. A. J. Lawson, C. C. Drovandi, N. Cusimano, P. Burrage, B. Rodriguez, K. Burrage, “Unlocking data sets by calibrating populations of model to data density: A study in atrial electrophysiology”, Science Advances, 4(1) (2018) DOI: 10.1126/sciadv.1701676
  • A. Heifetz, M. Southey, I. Morao, A. Townsend-Nicholson, M. Bodkin, “Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery”, Methods Mol Biol., 1705, 375-394 (2018), DOI: 10.1007/978-1-4939-7465-8_19
  • S. Li, J. Latt, B. Chopard, “The application of the screen model for stents in cerebral aneurysms”, Computer Fluids, Accepted (2018)

2017

  • A. Kapoor, G. Martinez-Rosell, D. Provasi, G. Fabritiis, M Filizola “Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity”, Scientific Reports, 7, 11255 (2017), DOI: 10.1038/s41598-017-11483-8
  • S. Li, J. Latt, B. Chopard, “Model for pressure drop and flow deflection in the numerical simulation of stents in aneurysms. International journal for numerical methods in biomedical engineering”, International Journal for Numerical Methods in Biomedical Engineering, Available Online (2017), DOI: 10.1002/cnm.2949
  • R. Dutta, B. Chopard, J. Lätt, F. Dubois, K. Boudjeltia, A. Mira, “Parameter estimation of platelets deposition: Approximate Bayesian computation with high performance computing”, arXiv (2017), https://arxiv.org/abs/1710.01054
  • A. Lyon, A. Michole, J.P.Martinez, P.Laguna, B. Rodriguez, “Computational techniques for ECG analysis and interpretation in light of their contribution to medical advances”, Journal of the Royal Society Interface, 15 (138), 2017, DOI: 10.1098/rsif.2017.0821
  • X. Zhou, A. Bueno-Orovio, B-Rodriguez, “In silicon evaluation of arrhythmia”, Current Opinion in Physiology, 1, 95-103 (2017), DOI: 10.1016/j.cophys.2017.11.003
  • R. Eccleston, P. V. Coveney, and N. Dalchau, “Host genotype and time dependent antigen presentation of viral peptides: predictions from theory”, Scientific Reports, 7 (1), 14367 (2017), DOI: 10.1038/s41598-017-14415-8
  • M. Paci, E. Passini, S. Severi, J. Hyttinen, B. Rodriguez, “Phenotypic variability in LQT3 human induced pluripotent stem cell-derived cardiomyocytes and their response to antiarrhythmic pharmacologic therapy: An in silico approach”, Heart Rhythm, Available Online (2017), DOI: 10.1016/j.hrthm.2017.07.026
  • J. Tomek, B. Rodriguez, G. Bub, J. Heijman, “β-adrenergic receptor stimulation inhibits proarrhythmic alternans in post-infarction border zone cardiomyocytes: a computational analysis”, American Journal of Physiology – Heart and Circulatory Physiology, Available Online (2017), DOI: 10.1152/ajpheart.00094.2017
  • G. Závodszky, B. van Rooij, V. Azizi and A. Hoekstra, “Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells”, Front. Physiol., Available Online (2017), DOI: 10.3389/fphys.2017.00563
  • S. Alowayyed, D. Groen, P. V. Coveney, A. G. Hoekstra, “Multiscale Computing in the Exascale Era”, Journal of Computational Science, In Press (2017), DOI: 10.1016/j.jocs.2017.07.004
  • I. Morao, D. G. Fedorov, R. Robinson, M. Southey, A. Townsend-Nicholson, M. J. Bodkin, A. Heifetz, “Rapid and accurate assessment of GPCR–ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method”, Journal of Computational Chemistry, Available Online (2017), DOI: 10.1002/jcc.24850
  • R. C. Eccleston, S. Wan, N. Dalchau, P. V. Coveney, “The role of multiscale protein dynamics in antigen presentation and T lymphocyte recognition”, Frontiers in Immunology, Available Online
    (2017), DOI: 10.3389/fimmu.2017.00797
  • P. S. Zun, T. Anikina, A. Svitenkov, A. G. Hoekstra, “A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data” Frontiers in Physiology, 8, 1-12 (2017), DOI:10.3389/fphys.2017.00284
  • A. Bueno-Orovio, K. Burrage, “Exact solutions to the fractional time-space Bloch–Torrey
    equation for magnetic resonance imaging”, Commun Nonlinear Sci Numer Simulat., 52, 91-109 (2017), DOI:10.1016/j.cnsns.2017.04.013
  • N. Altwaijry, M. Baron, D. Wright, P. V. Coveney, A. Townsend-Nicholson, “An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics”, Journal of Chemical Theory & Computation, 13 (5), 2254–2270 (2017), DOI: 10.1021/acs.jctc.6b01246
  • S. Wan, A. Bhati, S. Skerratt, K. Omoto, V. Shanmugasundaram, S. Bagal, P. V. Coveney, “Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation”, Journal of Chemical Information and Modelling, 57 (4), 897–909 (2017), DOI: 10.1021/acs.jcim.6b00780
  • P. V. Coveney and R. Highfield, “Opinion: Is big data just big hype?”, Longevity Bulletin: Big data in health, Institute and Faculty of Actuaries, 11-12 (2017), ISSN 2397-7213
  • S. Wan, A. P. Bhati, S. J. Zasada, I. Wall, D. Green, P. Bamborough, and P. V. Coveney, “Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: a Computational Study”, J. Chem. Theory Comput., 13 (2), 784–795 (2017), DOI: 10.1021/acs.jctc.6b00794
  • L. J. B. Briant, Q. Zhang, E. Vergari, J. A. Kellard, B. Rodriguez, F. M. Ashcroft, P. Rorsman, “Functional identification of islet cell types by electrophysiological fingerprinting”, Journal of Royal Society Interface, 14 (128), 1-20 (2017), DOI: 10.1098/rsif.2016.0999
  • C. Shanchez, A. Bueno-Orovio, E. Pueyo, B. Rodriguez, “Atrial Fibrillation Dynamics and Ionic Block Effects in Six Heterogeneous Human 3D Virtual Atria with Distinct Repolarization Dynamics”, Front. Bioeng. Biotechnol., 5, 1-13 (2017), DOI: 10.3389/fbioe.2017.00029
  • A. Bhati, S. Wan, D. Wright, P. V. Coveney, “Rapid, accurate, precise and reliable relative free energy prediction using ensemble based thermodynamic integration”, Journal of Chemical Theory and Computation, 13 (1), 210–222 (2017), DOI: 10.1021/acs.jctc.6b00979

 

Acknowledgements

Dissemination (including electronic) of all results must:

  • Display the EU emblem
  • Include the following text: “This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 675451 (CompBioMed project)”

Any dissemination of results must indicate that it reflects only the author’s view and that the Commission is not responsible for any use that may be made of the information it contains