Publications
2024
Abanades, B., Olsen, T.H., Raybould, M.I.J., Aguilar-Sanjuan, B., Wong, W.K., Georges, G., Bujotzek, A. & Deane, C.M. (2024) The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures Nucleic Acids Research, 52(D1):D545-D551
Carbery, A., Buttenschoen, M., Skyner, R., von Delft, F. & Deane, C.M. (2024) Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures Journal of Cheminformatics, 16(1):32
Creswell, R., Shepherd KM, Lambert B, Mirams GR, Lei CL, Tavener S, Robinson M and Gavaghan DJ (2024) Understanding the impact of numerical solvers on inference for differential equation models Journal of the Royal Society interface, 21(212):20230369-20230369
Gordon, G.L., Raybould, M.I.J., Wong, A. & Deane, C.M. (2024) Prospects for the computational humanization of antibodies and nanobodies Frontiers in Immunology, 15:1399438
Greenshields-Watson, A., Abanades, B. & Deane, C.M. (2024) Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms Frontiers in Immunology, 15:1352703
Raybould, M.I.J., Turnbull, O.M., Suter, A., Guloglu, B. & Deane, C.M. (2024) Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling Communications Biology, 7:62
2023
Agrawal, A., Wang, K., Polonchuk, L., Cooper, J., Hendrix, M., Gavaghan, DJ.. Mirams, GR., Clerx, MH., Models of the cardiac L‐type calcium current: A quantitative review (2023) Mechanisms of disease, 15(1):e1581
Spoendlin, F.C., Abanades, B., Raybould, M.I.J., Wong, W.K., Georges, G., Deane, C.M. Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope (2023) Frontiers in Molecular Biosciences, 10, art. no. 1237621.
Roibu, A.-C., Adaszewski, S., Schindler, T., Smith, S.M., Namburete, A.I.L., Lange, F.J. Brain Ages Derived from Different MRI Modalities are Associated with Distinct Biological Phenotypes (2023) Proceedings - 2023 10th IEEE Swiss Conference on Data Science, SDS 2023, pp. 17-25.
Gordon, G.L., Capel, H.L., Guloglu, B., Richardson, E., Stafford, R.L., Deane, C.M. A comparison of the binding sites of antibodies and single-domain antibodies (2023) Frontiers in Immunology, 14, art. no. 1231623, .
Mokaya, M., Imrie, F., van Hoorn, W.P., Kalisz, A., Bradley, A.R., Deane, C.M. Testing the limits of SMILES-based de novo molecular generation with curriculum and deep reinforcement learning (2023) Nature Machine Intelligence, 5 (4), pp. 386-394.
Augustin, D., Lambert, B., Wang, K., Walz, A.-C., Robinson, M., Gavaghan, D. Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data (2023) PLoS Computational Biology, 19 (5), art. no. e1011135, .
Wills, S., Sanchez-Garcia, R., Dudgeon, T., Roughley, S.D., Merritt, A., Hubbard, R.E., Davidson, J., Von Delft, F., Deane, C.M. Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search (2023) Journal of Chemical Information and Modeling, 63 (11), pp. 3423-3437.
Olsen, T.H., Abanades, B., Moal, I.H., Deane, C.M. KA-Search, a method for rapid and exhaustive sequence identity search of known antibodies
(2023) Scientific Reports, 13 (1), art. no. 11612.
Abanades, B., Wong, W.K., Boyles, F., Georges, G., Bujotzek, A., Deane, C.M. ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins (2023) Communications Biology, 6 (1), art. no. 575.
2022
Bourigault, E., McGowan, D.R., Mehranian, A., Papież, B.W. Multimodal PET/CT Tumour Segmentation and Prediction of Progression-Free Survival Using a Full-Scale UNet with Attention (2022) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13209 LNCS, pp. 189-201
Olsen, T.H., Boyles, F., Deane, C.M. Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences (2022) Protein Science, 31 (1), pp. 141-146.
Hummer, A.M., Abanades, B., Deane, C.M. Advances in computational structure-based antibody design (2022) Current Opinion in Structural Biology, 74, art. no. 102379, .
Creswell, R., Augustin, D., Bouros, I., Farm, H.J., Miao, S., Ahern, A., Robinson, M., Lemenuel-Diot, A., Gavaghan, D.J., Lambert, B.C., Thompson, R.N. Heterogeneity in the onwards transmission risk between local and imported cases affects practical estimates of the time-dependent reproduction number (2022) Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380 (2233), art. no. 20210308,
Abanades, B., Georges, G., Bujotzek A, Deane CM, Xu J., ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation (2022) Bioinformatics, 38 (7) , pp.1877-1880
2021
Dale-Evans, AR, Robinson, MJ, Lloyd-Laney, HO, Gavaghan, DJ, Bond, AM, Parkin, A. A Voltammetric Perspective of Multi-Electron and Proton Transfer in Protein Redox Chemistry: Insights From Computational Analysis of Escherichia coli HypD Fourier Transformed Alternating Current Voltammetry (2021) Frontiers in Chemistry. 9, 672831.
Robinson SA, Raybould MIJ, Schneider C, Wong WK, Marks C, Deane CM. Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies. PLoS Comput Biol. 2021 ;17(12):e1009675.
2020
Ardaševa , A , Gatenby , R A , Anderson , A R A , Byrne , H M , Maini , P K & Lorenzi , T 2020 , Evolutionary dynamics of competing phenotype-structured populations in periodically fluctuating environments, Journal of Mathematical Biology, vol. 80 , pp. 775–807 .
2019
Chan, L., Hutchison, G.R. & Morris, G.M. Bayesian optimization for conformer generation. J Cheminform 11, 32 (2019).
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 vaccination, Journal 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 Inhibitors. ACS 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 interactions. Bioinformatics , 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 Decomposition, Proceedings 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 Immunology, 193(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 Guidelines, Proceedings of the National Academy of Sciences USA, doi: 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 stability, Bioorganic 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 simulations, Islets, 10(4), 151-167, doi: 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 analysis, PLoS 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 cancer, BioRxiv, doi: https://doi.org/10.1101/190561
Rukat, T. , Holmes, C.C., Titsias, M.K., Yau, C. (2017) Bayesian Boolean Matrix Factorisation, Proceedings 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 Exoplanets, Monthly 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 Study, The 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 Demethylases, The 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 Electrophysiology, Frontiers 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 Prediction, Bioinformatics, 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 Oceania, Nature 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 Characteristics, Proteins 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 receptors, ChemMedChem, 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 14, ACS 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 Series, Chaos, 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 Spectrometry, The 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 Molecules, Chemical 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 Bromodomain, Chemical 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 Server, Nucleic 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 Interactions, Journal 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-HT2B, ACS 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 Angiogenesis, Journal 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 Degeneration, Molecular 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 Data, Wellcome 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 Helices, PLoS 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 Estimation, MAbs, 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 Therapy, International 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 Spectrometry, Rapid 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 Model, MAbs, 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 Cycle, Development, 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 Maintenance, Science 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 Trafficking, Journal 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] Fluoride, Angewandte 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 Analogues, ACS 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 Node, Physiological 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 States, Bulletin 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-Fluoride, Synlett, 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 Database, Nucleic 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 Study, PLOS 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 Design, PLOS 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 Ligands, Future 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 Data, Neuroimage, 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 Cs, Physical 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 IOX1, ChemMedChem, 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 Proteins, Proteins: 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 Helices, Journal 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 Wedge, Journal 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 A, ACS 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 Antibodies, Protein 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 Simulations, Biophysical 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 Intervention, MICCAI 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]-(+)-PHNO, International 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 Pyruvate, Conference 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 Structure, PLOS 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 Catalysis, Organic 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 Alkenes, Journal 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 Chemistry, Journal 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 Gating, Nature 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 Heart, Cardiovascular 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]Fluoride, Angewandte 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 Interactions, Journal 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 Framework, Proceedings, 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 Growth, Proceedings 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 Ensemble, Computing 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 Catalysis, Chemistry – 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-1, Channels (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 Sites, PLoS 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
