Publications

2018

Brown, L.V., Gaffney, E.A., Wagg, J., Coles, M.C. (2018) An in silico model of cytotoxic T-lymphocyte activation in the lymph node following short peptide vaccinationJournal of The Royal Society Interface, vol. 15, issue 140, doi: 10.1098/rsif.2018.0041

Aldeghi M., Bluck J.P., Biggin P.C. (2018) Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner’s Guide. In: Gore M., Jagtap U. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 1762. Humana Press, New York, NY doi: 10.1007/978-1-4939-7756-7_11

Stefaniak, J., Lewis, A.M., Conole, D., Galan, S.R.G., Bataille, C.J.R., Wynne, G.M., Castaldi, M.P., Lundbäck, T., Russell, A.J., Huber, K. (2018) Chemical Instability and Promiscuity of Arylmethylidenepyrazolinone-Based MDMX InhibitorsACS Chemical Biology. 13. doi: 10.1021/acschembio.8b00665

Knapp B,. Alcala M., Zhang H., West C.E., van der Merwe P.A., Deane C.M. (2018) pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactionsBioinformatics, Vol. 34, Issue 11, 1941–1943, doi: https://doi.org/10.1093/bioinformatics/btx842

Lewin, T.D., Maini, P.K., Moros, E.G., Enderling, H., Byrne, H.M. (2018) The Evolution of Tumour Composition During Fractionated Radiotherapy: Implications for Outcome, Bulletin of Mathematical Biology 80: 1207. doi: https://doi.org/10.1007/s11538-018-0391-9

 

Rukat, T., Holmes, C., Yau, C., (2018) Probabilistic Boolean Tensor DecompositionProceedings of Machine Learning Research, 80:4413-4422 

 

Brown, L.V., Gaffney, E.A., Wagg, J., Coles, M.C. (2018) Applications of Mechanistic Modelling to Clinical and Experimental Immunology: An emerging technology to accelerate immunotherapeutic discovery and development, Journal of Clinical and Experimental Immunology193(3):284-292. doi: 10.1111/cei.13182

 

Raybould, M., Marks, C., Krawczyk, K., Taddese, B., Nowak, J., Lewis, A.P., Bujotzek, A., Shi, J., Deane, C.M. (2018) The Therapeutic Antibody Profiler (TAP): Five Computational Developability GuidelinesProceedings of the National Academy of Sciences USAdoi: https://doi.org/10.1101/359141

Jennings, L.E., Schiedel, M., Hewings, D.S., Picaud, S., Laurin, C.M.C., Bruno, P.A., Bluck, J.P., Scorah, A.R., See, L., Reynolds, J.K., Moroglu, M., Mistry, I.N., Hicks, A., Guzanov, P., Clayton, J., Evans, C.N.G., Stazi, G., Biggin, P.C., Mapp, A.K., Hammond, E.M., Humphreys, P.G., Filippakopoulos, P., Conway, S.J. (2018) BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stabilityBioorganic and Medicinal Chemistry, vol. 26, issue 11, 2937-2957, doi: https://doi.org/10.1016/j.bmc.2018.05.003

Lei, C.L., Kellard, J.A., Hara, M., Johnson, J.D., Rodriguez, B., Briant, L.J.B. (2018) Beta-cell hubs maintain Ca2+ oscillations in human and mouse islet simulationsIslets, 10(4), 151-167doi: 10.1080/19382014.2018.1493316

Papadopoulos, L., Blinder, P., Ronellenfitsch, H., Klimm, F., Katifori, E., Kleinfeld, D., Bassett, D.S. (2018) Comparing two classes of biological distribution systems using network analysisPLoS Computational Biology, 14(9), doi:https://doi.org/10.1371/journal.pcbi.1006428

 

2017

Gavaghan, D.J., Cooper, J., Daly, A.C., Gill, C., Gillow, K., Robinson, M., Simonov, A., Zhang. J., Bond, A.M. (2017) Use of Bayesian Inference for Parameter Recovery in DC and AC Voltammetry, ChemElectroChem, vol. 5, issue 6, 917-935, doi: https://doi.org/10.1002/celc.201700678

Saeed-Vafa, D., Bravo, R., Dean, J.A., El-Kenawi, A., Mon Père, N., Strobl, M., Daniels, C., Stringfield, O., Damaghi, M., Tunali, I., Brown, L., Curtin, L., Nichol, D., Peck, H. Gillies, R., Gallaher, J. (2017) Combining radiomics and mathematical modeling to elucidate mechanisms of resistance to immune checkpoint blockade in non-small cell lung cancerBioRxivdoi: https://doi.org/10.1101/190561

Rukat, T., Holmes, C.C., Titsias, M.K., Yau, C. (2017) Bayesian Boolean Matrix FactorisationProceedings of Machine Learning Research

Ardaseva, A., Rimmer, P. B., Waldmann, I., Rocchetto, M., Yurchenko, S. N., Helling, C., Tennyson, J. (2017) Lightning Chemistry on Earth-Like ExoplanetsMonthly Notices of the Royal Astronomical Society, vol 470, no. 1, stx1012, pp. 187-196. DOI: 10.1093/mnras/stx1012

Haworth, N. L., Wang, Q., Coote, M. L. (2017) Modelling flexible molecules in Solution: A pKa Case StudyThe Journal Physical Chemistry A, 121 (27): 5217–5225. DOI: 10.1021/acs.jpca.7b04133

Langley, G. W., Brinkø, A., Munzel, M., Walport, L. J., Schofield, C. J., Hopkinson, R. J. (2017) Probing the Charge and Conformational Requirements of JmjC DemethylasesThe FASEB Journal, vol. 31 no. 1, Supplement 767.1

Lei, C. L., Wang, K., Clerx, M., Johnstone, R.H, Hortigon-Vinagre, M. P., Zamora, V., Allan, A., Smith, G. L., Gavaghan, D. J., Mirams, G. R., Polonchuck, L. (2017) Tailoring Mathematical Models to Stem-Cell Derived Cardiomyocyte Lines Can Improve Predictions of Drug-Induced Changes to Their ElectrophysiologyFrontiers in Physiology, 8, Article: 986. DOI: https://doi.org/10.3389/fphys.2017.00986

Marks, C.Nowak, J., Klostermann, S., Georges, G., Dunbar, J., Shi, J., Kelm, S., Deane, C. M., (2017) Sphinx: Merging Knowledge-Based and Ab Initio Approaches to Improve Protein Loop PredictionBioinformatics, 33: 1346-1353. DOI: 10.1093/bioinformatics/btw823

Mazer, N. A., Hutton-Smith, L. A., Byrne, H. M., Gaffney, E. A., Maini, P. K., Gadkar, K. (2017) What Determines the Retinal Concentration of an Intravitreally Injected Antibody? New Insights Using a 3-Compartment Semi Mechanistic Pharmacokinetic Model, Conference Publication, ARVO Annual Meeting Abstract, Vol. 58, No. 8.

Parks, T., Mirabel, M. M., Kado, J., Auckland, K., Nowak, J., Rautanen, A., Mentzer, A. J., Marijon, E., Jouven, X., Perman, M. L., Cua, T., Kauwe, J. K., Allen, J. B., Taylor, H., Robson, K. J., Deane, C. M., Steer, A. C., Hill, A. V. S. (2017) Association between a Common Immunoglobulin Heavy Chain Allele and Rheumatic Heart Disease Risk in OceaniaNature Communications, 8, 14946. DOI: 10.1038/ncomms14946

Regep, C., Georges, G., Shi, J., Popovic, B. & Deane, C. M. (2017) The H3 Loop of Antibodies Shows Unique Structural CharacteristicsProteins Structure Function and Bioinformatics, 85(7):1311-1318, DOI: 10.1002/prot.25291

Schuller, M., Höfner, G., Wanner, K. T. (2017) Simultaneous Multiple MS Binding Assays addressing D1 and D2 Dopamine receptorsChemMedChem, 12(19):1585-1594. DOI: 10.1002/cmdc.201700369

Schuller, M., Riedel, K., Gibbs-Seymour, I., Uth, K., Sieg, C., Gehring, A. P., Ahel, I., Bracher, F., Kessler, B. M., Elkins, J. M., Knapp, S. (2017) Discovery of a Selective Allosteric Inhibitor Targeting Macrodomain 2 of Poly-Adenosine-Diphosphate-Ribose Polymerase 14ACS Chemical Biology, 2(11):2866-2874. DOI: 10.1021/acschembio.7b00445

Stolz, B. J., Harrington, H. A., Porter, M. A., Persistent Homology of Time-Dependant Functional Networks Constructed from Coupled Time SeriesChaos, 27, 047410. DOI: https://doi.org/10.1063/1.4978997

Zheng, X., Renslow, R.S., Makola, M.M., Webb, I.K., Deng, L., Thomas, D.G., Govind, N., Ibrahim, Y.M., Kabanda, M.M., Dubery, I.A., Heyman, H.M. (2017) Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass SpectrometryThe Journal of Physical Chemistry Letters, 8: 1381-1388, DOI: 10.1021/acs.jpclett.6b03015

Hutton-Smith, L. A., Gaffney, E. A., Byrne, H. M., Maini, P. K., Gadkar, K., Mazer, N. A. (2017) Ocular Pharmacokinetics of Therapeutic Antibodies Given by Intravitreal Injection: Estimation of Retinal Permeabilities Using a 3 Compartment Semi-Mechanistic Model, Molecular Pharmaceutics, 14(8):2690-2696. DOI: 10.1021/acs.molpharmaceut.7b00164

 

 

2016

Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., Biggin, P. C. (2016) Accurate Calculation of the Absolute Free Energy of Binding for Drug MoleculesChemical Science, 7(1):207-218. DOI: 10.1039/C5SC02678D

Cox, O., Krojer, T., Collins, P., Monteiro, O., Talon, R., Bradley, A., Fedorov, O., Amin, J., Marsden, B., Spencer, J., von Delft, F., Brennan, P. (2016) A Poised Fragment Library Enables Rapid Synthetic Expansion Yielding the First Reported Inhibitors Of PHIP(2), an Atypical BromodomainChemical Science, 7:2322-2330. DOI: 10.1039/C5SC03115J

Dunbar, J.Krawczyk, K.Leem, J.Marks, C.Nowak, J.Regep, C., Georges, G., Kelm, L., Popovic, B., Deane, C. M. (2016). Sabpred: A Structure-Based Antibody Prediction ServerNucleic Acids Research, 44(W1):W474-8. DOI: 10.1093/nar/gkw361

Heifetz, A., Chudyk, E., Gleave, L., Aldeghi, M., Cherezov, V., Fedorov, D., Biggin, P., Bodkin, M. (2016) The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand InteractionsJournal of Chemical Information and Modeling, 25;56(1):159-72. DOI: 10.1021/acs.jcim.5b00644

Heifetz, A., Storer, R., McMurray, G., James, T., Morao, I., Aldeghi, M., Bodkin, M., Biggin, P. (2016) Application of an Integrated GPCR SAR-Modelling Platform to Explain the Activation Selectivity of Human 5-HT2C over 5-HT2BACS Chemical Biology, 11(5):1372-82. DOI: 10.1021/acschembio.5b01045

Hutchinson, L. G., Gaffney, E. A., Maini, P. K., Wagg, J., Phipps, A., Byrne, H. M. (2016) Vascular Phenotype Identification and Anti-Angiogenic Treatment Recommendation: A Pseudo-Multiscale Mathematical Model of AngiogenesisJournal of Theoretical Biology, 398: 162-180. DOI: 10.1016/j.jtbi.2016.03.002

Hutton-Smith, L. A., Gaffney, E. A., Byrne, H. M., Maini, P. K., Schwab, D., Mazer, N. A. (2016) A Mechanistic Model of the Intravitreal Pharmacokinetics of Large Molecules and the Pharmacodynamic Suppression of Ocular VEGF Levels by Ranibizumab in Patients with Neovascular Age-Related Macular DegenerationMolecular Pharmaceutics, Vol. 13, 9, p. 2931-2950. DOI: 10.1021/acs.molpharmaceut.5b00849

Johnstone, R. H., Bardenet, R., Gavaghan, D. J., Mirams, G. R. (2016) Hierarchical Bayesian Inference for Ion Channel Screening Dose-Response DataWellcome Open Research, 1:6, DOI:  10.12688/wellcomeopenres.9945.2

Johnstone, R. H., Chang, E., Bardenet, R., de Boer, T., Gavaghan, D., Pathmanathan, P., Clayton, R., Mirams, G. (2015) Uncertainty and Variability in Models of the Cardiac Action Potential: Can We Build Trustworthy Models?Journal of Molecular and Cellular Cardiology, Volume 96, July 2016, Pages 49-62. DOI: 10.1016/j.yjmcc.2015.11.018

Law, E. C., Wilman, H. R., Kelm, S., Shi, J., Deane, C. M. (2016) Examining the Conservation of Kinks in Alpha HelicesPLoS ONE, 11(6): e0157553. DOI: https://doi.org/10.1371/journal.pone.0157553

Leem, J., Dunbar, J., Georges, G., Shi, J., Deane, C. M. (2016) ABodyBuilder: Automated Antibody Structure Prediction with Data-Driven Accuracy EstimationMAbs, 8:1-10. DOI: 10.1080/19420862.2016.1205773

Lewin, T., Kim, J., Latifi, K., Poleszczuk, J., Bull, J., Byrne, H., Torres-Roca, J., Moros, E., Gatenby, R., Harrison, L., Heukelom, J., Mohamed, A., Rosenthal, D., Fuller, C., Caudell, J., Enderling, H. (2016) Proliferation Saturation Index Predicts Oropharyngeal Squamous Cell Cancer Gross Tumor Volume Reduction to Prospectively Identify Patients for Adaptive Radiation TherapyInternational Journal of Radiation Oncology Biology Physics, 94, 903. DOI: 10.1016/j.ijrobp.2015.12.116

Makola, M. M., Steenkamp, P. A., Dubery, I. A., Kabanda, M. M., Madala, N. E., (2016) Preferential Alkali Metal Adduct Formation by Cis Geometrical Isomers of Dicaffeoylquinic Acids Allows for Efficient Discrimination from their Trans Isomers During Ultra‐High‐Performance Liquid Chromatography/Quadrupole Time‐Of‐Flight Mass SpectrometryRapid Communications in Mass Spectrometry, 2016, 30: 1011-1018, DOI: 10.1002/rcm.7526

Mazer, N. A., Schwab, D., Hutton-Smith, L. A., Byrne, H. M., Gaffney, E. A., Maini, P. K., Hartmann, G., Moelleken, J., Gassner, C., Regula, J. T. (2016) What is the biologically relevant KD for VEGF binding to ranibizumab in the eye? A comparison of in-vivo and in-vitro estimates, Conference Publication, ARVO Annual Meeting Abstract, Vol. 57, No. 12.

Nowak, J., Baker, T., Georges, G., Kelm, S., Klostermann, S., Shi, J., Sridharan, S., Deane, C. M. (2016) Length-Independent Structural Similarities Enrich the Antibody CDR Canonical Class ModelMAbs, 8(4):751-60. DOI: 10.1080/19420862.2016.1158370

 

2015

Atwell, K., Qin, Z., Gavaghan, D., Kugler, H., Hubbard, E., Osborne, J. (2015) Mechano-Logical Model of C. Elegans Germ Line Suggests Feedback on the Cell CycleDevelopment, 142(22):3902-11. DOI: 10.1242/dev.126359

Fedorov, O., Castex, J., Tallant, C., Owen, D., Martin, S., Aldeghi, M., Monteiro, O., Filippakopoulos, P., Picaud, S., Trzupek, J., Gerstenberger, B., Bountra, C., Willmann, D., Wells, C., Philpott, M., Rogers, C., Biggin, P., Brennan, P., Bunnage, M., Schule, R., Gunther, T., Knapp, S., Muller, S. (2015) Selective Targeting of the BRG/PB1 Bromodomains Impairs Embryonic and Trophoblast Stem Cell MaintenanceScience Advances, 1(10): e1500723. DOI: 10.1126/sciadv.1500723

Froese, D., Kopec, J., Fitzpatrick, F., Schuller, M., McCorvie, T. J., Chalk, R., Plessl, T., Fettelschoss, V., Fowler, B., Baumgartner, M. R., Yue, W. W. (2015) Structural Insights into the MMACHC-MMADHC Protein Complex Involved in Vitamin B12 TraffickingJournal of Biological Chemistry, 290(49): 29167-77. DOI: 10.1074/jbc.M115.683268

Khotavivattana, T., Verhoog, S., Tredwell, M., Pfeifer, L., Calderwood, S., Wheelhouse, K., Lee Collier, T., Gouverneur, V. (2015) 18F-Labeling of Aryl-SCF3, -OCF3 and -OCHF2 with [18F] FluorideAngewandte Chemie International Edition, 54: 9991–9995. DOI: 10.1002/anie.201504665

Langley, G. W., Brinkø, A., Münzel, M., Walport, L. J., Schofield, C. J., Hopkinson, R. J. (2015) Analysis of JmjC Demethylase-Catalyzed Demethylation Using Geometrically-Constrained Lysine AnaloguesACS Chemical Biology, 11(3):755-62. DOI: 10.1021/acschembio.5b00738

Nazarov, I. B., Schofield, C. J., Terrar, D. A. (2015) Contributions of Cardiac "Funny" (F) Channels and Sarcoplasmic Reticulum Ca2+ In Regulating Beating Rate of Mouse and Guinea Pig Sinoatrial NodePhysiological Reports, 3(12): e12561, DOI: 10.14814/phy2.12561

Taylor-King, J. P., van Loon, E. E., Rosser, G. et Chapman, S. J. (2015) From Birds to Bacteria: Generalised Velocity Jump Processes with Resting StatesBulletin of Mathematical Biology, 77: 1213. DOI: https://doi.org/10.1007/s11538-015-0083-7

Verhoog, S., Pfeifer, L., Khotavivattana, T., Calderwood, S., Collier, T., Wheelhouse, K., Tredwell, M., Gouverneur, V. (2015) Silver-Mediated 18F-Labeling of Aryl-CF3 and Aryl-CHF2 with 18F-FluorideSynlett, 27(01): 25-28. DOI: 10.1055/s-0035-1560592

 

2014

Dunbar, J., Krawczyk, K., Leem, J., Baker, T., Fuchs, A., Georges, G., Shi J. and Deane, C. M. (2014) SAbDab: the Structural Antibody DatabaseNucleic Acids Research, 42, D1140-D1146. DOI: 10.1093/nar/gkt1043

Dunbar, J., Knapp, B. and Deane, C. M. (2014) Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation StudyPLOS Computational Biology, 10(8), e1003748. DOI: https://doi.org/10.1371/journal.pcbi.1003748

Dunbar, J., Knapp, B., Fuchs, A., Shi J. and Deane, C. M. (2014) Examining Variable Domain Orientations In Antigen Receptors Gives Insight Into TCR-Like Antibody DesignPLOS Computational Biology, 10(9), e1003852. DOI: https://doi.org/10.1371/journal.pcbi.1003852

Jennings, L. E., Measures, A. R., Wilson, B. G., Conway, S. J. (2014) Phenotypic Screening and Fragment-Based Approaches to the Discovery of Small-Molecule Bromodomain LigandsFuture Medicinal Chemistry, 6, 179–204. DOI: 10.4155/fmc.13.197

Jiao, J., Searle, G.E., Tziortzi, A.C., Salinas, C.A., Gunn, R.N., Schnabel, J.A. (2014) Spatio-Temporal Pharmacokinetic Model Based Registration of 4D Brain PET Neuroimaging DataNeuroimage, 84:225-35. DOI: 10.1016/j.neuroimage.2013.08.031

Patel, H. J., Blackley, C. L., Cornish, S. L., Hutson, J. M. (2014) Feshbach resonances, molecular bound states and prospects of ultracold molecule formation in mixtures of ultracold K and CsPhysical Review A 90, 032716/1-10. DOI: https://doi.org/10.1103/PhysRevA.90.032716

Schiller, R., Scozzafava, G., Tumber, A., Wickens, J. R., Bush, J. T., Rai, G., Lejeune, C., Choi, H., Yeh, T.-L., Chan, M. C., Mott, B. T., McCullagh, J. S. O., Maloney, D. J., Schofield, C. J., Kawamura, A. (2014) A Cell-Permeable Ester Derivative of the Jmjc Histone Demethylase Inhibitor IOX1ChemMedChem, 9, 566–71. DOI: 10.1002/cmdc.201300428

Wilman, H. R., Shi, J. and Deane, C. M. (2014), Helix Kinks are Equally Prevalent in Soluble and Membrane ProteinsProteins: Structure, Function, and Bioinformatics, 82: 1960–1970. DOI: 10.1002/prot.24550

Wilman, H. R., Ebejer, J.P., Shi, J., Deane, C. M., Knapp, B. (2014), Crowdsourcing Yields a New Standard for Kinks in Protein HelicesJournal of Chemical Information and Modeling, 54 (9): 2585-2593. DOI: 10.1021/ci500403a

 

2013

Beattie, K. A., Luscombe, C., Williams, G., Munoz-Muriedas, J., Gavaghan, D.J., Cui, Y., Mirams, G. R. (2013) Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular WedgeJournal of Pharmacological and Toxicological Methods, 68(1), 88-96. DOI: http://dx.doi.org/10.1016/j.vascn.2013.04.004

Cazares-Körner, C., Pires, I. M., Swallow, I. D., Grayer, S. C., O'Connor, L. J., Olcina, M. M., Christlieb, M., Conway, S.J., Hammond, E. M. (2013) CH-01 is a Hypoxia-Activated Prodrug That Sensitizes Cells to Hypoxia/Reoxygenation Through Inhibition of Chk1 and Aurora AACS Chemical Biology, 8(7):1451-9. DOI: 10.1021/cb4001537

Dunbar, J., Fuchs, A., Shi, J., Deane, D. M., Bangle, A. (2013) Characterising The VH-VL Orientation in AntibodiesProtein Engineering, Design & Selection, 26(10), 611-620. DOI: 10.1093/protein/gzt020

Helie, J., Milletti, F., Lelimousin, M., Deane, C., Sansom, M., (2013) Interactions of Two Amphipathic Cell-Penetrating Peptides with Complex Model Membranes: Insights From Molecular Dynamics SimulationsBiophysical Journal, Volume 104 , Issue 2 , 600a. DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.3332

Jiao, J., Schnabel, J.A., Gunn, R.N. (2013) A Generalised Spatio-Temporal Registration Framework for Dynamic PET Data: Application to Neuroreceptor Imaging Medical Image Computing and Computer-Assisted InterventionMICCAI 2013: 16th International Conference, Proceedings, Part I,pp.211-8. DOI 10.1007/978-3-642-40811-3_27

Jiao, J., Searle, G.E., Schnabel, J.A., G.E., Gunn, R.N. (2013) Pharmacokinetic Model Based Groupwise Image Registration of 4D Brain PET Data and its Impact on Clinical Occupancy Studies with [11C]-(+)-PHNOInternational Symposium on Cerebral Blood Flow, Metabolism and Function.

Le Page, L. M., Ball, D. R., Ball, V., Mansor, L. S., Heather, L. C., Tyler, D. J. (2013) Assessment of Real-Time Cardiac and Hepatic Glucose Metabolism in the Diabetic Rat Using Hyperpolarised C-13 PyruvateConference Paper, Vol. 30, 42-42.

Lori, C., Lantella, A., Pasquo, A., Alexander, L. T., Knapp, S., Chiaraluce, R. and Consalvi, V. (2013) Effect of Single Amino Acid Substitution Observed in Cancer on Pim-1 Kinase Thermodynamic Stability and StructurePLOS ONE, 8(6): e64824. DOI: https://doi.org/10.1371/journal.pone.0064824

McKeever, S., Gill, M., Connor, A. J., Johnson, D. (2013) Abstraction in Physiological Modelling Languages (pp. 1–8), Presented at the 3rd International Workshop on Model-driven Approaches for Simulation Engineering.

Mizuta, S., Engle, K. M., Verhoog, S., Galicia-López, O., O’Duill, M., Médebielle, M., Wheelhouse, K., Rassias, G., Thompson, A. L., Gouverneur, V. (2013) Trifluoromethylation of Allylsilanes under Photoredox CatalysisOrganic Letters, 15, 1250-1253. DOI: 10.1021/ol400184t

Mizuta, S., Verhoog, S., Engle, K. M., Khotavivattana, T., O’Duill, M., Wheelhouse, K., Rassias, G., Médebielle, M., Gouverneur, V. (2013) Catalytic Hydrotrifluoromethylation of Unactivated AlkenesJournal of the American Chemical Society, 135, 2505-2508. DOI: 10.1021/ja401022x

Mizuta, S., Verhoog, S., Wang, X., Shibata, N., Gouverneur, V., Madebielle, M. (2013) Redox chemistry of trifluoromethyl sulfonium salts as CF3 radical sources, Journal of Fluorine ChemistryJournal of Fluorine Chemistry, 155, 124-131. DOI: 10.1016/j.jfluchem.2013.07.006

 

2012

Bavro, V. N., De Zorzi, R., Schmidt, M. R., Muniz, J.R., Zubcevic, L., Sansom, M. S., Vénien-Bryan, C., Tucker, S. J. (2012) Structure of a KirBac Potassium Channel with an Open Bundle-Crossing Indicates a Mechanism of Channel GatingNature Structural and Molecular Biology, 19(2):158-63. DOI: 10.1038/nsmb.2208.

Connor, A., Cooper, J., Byrne, H., Maini, P., McKeever, S. (2012) Object-Oriented Paradigms for Modelling Vascular Tumour Growth: A Case Study, Proceedings of SIMUL 2012, The Fourth International Conference on Advances in System Simulation, 18.

Dodd, M. S., Ball, D. R., Schroeder, M. A., Le Page, L. M., Atherton, H. J., Heather, L. C., Seymour, A-M., Ashrafian, H., Watkins, H., Clarke, K. and Tyler, D. J. (2012) In Vivo Alterations in Cardiac Metabolism and Function in the Spontaneously Hypertensive Rat HeartCardiovascular Research, Volume 95, Issue 1, 1 July 2012, Pages 69–76. DOI: https://doi.org/10.1093/cvr/cvs164

Gao, Z., Lim, Y. H., Tredwell, M., Li, L., Verhoog, S., Hopkinson, M., Kaluza, W., Collier, T. L., Passchier, J., Huiban, M. and Gouverneur, V. (2012) Metal-Free Oxidative Fluorination of Phenols with [18F]FluorideAngewandte Chemie International Edition, 51: 6733–6737. DOI: 10.1002/anie.201201502

Hewings, D. S., Rooney, T. P. C., Jennings, L. E., Hay, D., Schofield, C. J., Brennan, P. E., Knapp, S. and Conway, S. J. (2012) Progress in the Development and Application of Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine InteractionsJournal of Medicinal Chemistry, 55:9393.  DOI: 10.1021/jm300915b

Jiao, J., Salinas, C.A., Searle, G.E., Gunn, R.N., Schnabel, J.A. (2012) Joint Estimation of Subject Motion and Tracer Kinetic Parameters of Dynamic PET Data in an EM FrameworkProceedings, Volume 8314, Medical Imaging: Image Processing; 83140A. DOI: 10.1117/12.911497

Johnson, D., Connor, A. J., McKeever, S. (2012) Modular Markup for Simulating Vascular Tumour GrowthProceedings of the 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (5th IARWISOCI) - The TUMOR Workshop

Johnson, A., Dunkley, N. C., Mayaud, L., Tsanas, A., Kramer, A., Clifford, G. (2012) Patient-specific Predictions in the Intensive Care Unit using a Bayesian EnsembleComputing in Cardiology Challenge.

Mizuta, S., Galicia-López, O., Engle, K. M., Verhoog, S., Wheelhouse, K., Rassias, G. and Gouverneur, V. (2012) Trifluoromethylation of Allylsilanes under Copper CatalysisChemistry – A European Journal, 18: 8583–8587. doi:10.1002/chem.201201707

Rapedius, M., Schmidt, M. R., Sharma, C., Stansfeld, P. J., Sansom, M. S. P., Baukrowitz, T., Tucker, S. J (2012) State-Independent Intracellular Access of Quaternary Ammonium Blockers to the Pore of TREK-1Channels (Austin), Nov-Dec, 6(6):473-8. DOI: 10.4161/chan.22153

Ross, G. A., Morris, G. M., Biggin, P. C. (2012) Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding SitesPLoS ONE, 7(3): e32036. DOI: https://doi.org/10.1371/journal.pone.0032036

Schmidt, M.R., Stansfeld, P. J., Tucker, J. S. and Sansom, M. S. P. (2012) Simulation-Based Prediction of Phosphatidylinositol 4,5-Bisphosphate Binding to an Ion Channel, Biochemistry, 52 (2), 279-281. DOI: 10.1021/bi301350s