Erasmus, M.F., Spector, L., Perea-Schmittle, K., Ferrara, F., DiNiro, R., Pettus, C., Carnero, L.A.R., Li, J., Cisneros, A., Fanni, A., Pohl, T.J., Knight, D., Cruz, Z., Molina, E., Wang, W., Tessier, P.M., Richardson, C., Turner, L., Kumar, S., Bedinger, D., Sormanni, P., Fernández-Quintero, M.L., Ward, A.B., Loeffler, J.R., Swanson, O.M., Deane, C.M., Raybould, M.I.J., Evers, A., Sellmann, C., Bachas, S., Ruffolo, J., Nastri, H., Ramesh, K., S\orenson, J., Croasdale-Wood, R., Hijano, O., Shahsavarian, M., Qiu, Y., Marcatili, P., Vernet, E., Akbar, R., Friedenson, S., Hartman, T., Kurella, V.b., Malhotra, S., Kumar, S., Kidger, P., Almagro, J.C., Furfine, E., Stanton, M., Villalba, S.D., Tomszak, F., Dovner, M., D'Angelo, S. & Bradbury, A.R.M. (2024) AIntibody: An experimentally-validated in silico antibody discovery design challenge Nature Biotechnology, 42:1637-1642 |
Durant, G., Boyles, F., Birchall, K. & Deane, C.M. (2024) The future of machine learning for small-molecule drug discovery will be driven by data Nature Computational Science, 4:735-743 |
Raybould, M.I.J., Greenshields-Watson, A., Agarwal, P., Aguilar-Sanjuan, B., Olsen, T.H., Turnbull, O.M., Quast, N.P. & Deane, C.M. (2024) The Observed T cell receptor Space database enables paired-chain repertoire mining, coherence analysis and language modelling Cell Reports, 43(9):114704 |
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 |
McMaster, B., Thorpe, C., Ogg, G., Deane, C.M. & Koohy, H. (2024) Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity? Nature Methods, 21:766-776 |
Éliás, S., Wrzodek, C., Deane, C.M., Tissot, A.C., Klostermann, S. & Ros, F. (2024) Prediction of polyspecificity from antibody sequence data by machine learning Frontiers in Bioinformatics, 3:1286883 |
Jiang, Y., Deane, C.M., Morris, G.M. & O’Brien, E.P. (2024) It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs PLOS Computational Biology, 20(3):1-22 |
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 |
Olsen, T.H., Moal, I.H. & Deane, C.M. (2024) Addressing the antibody germline bias and its effect on language models for improved antibody design Bioinformatics, 40(11):btae618 |
Theorell, J., Harrison, R., Williams, R., Raybould, M.I.J., Zhao, M., Fox, H., Fower, A., Miller, G., Wu, Z., Browne, E., Mgbachi, V., Sun, B., Mopuri, R., Li, Y., Waters, P., Deane, C.M., Handel, A., Makuch, M. & Irani, S.R. (2024) Ultrahigh frequencies of peripherally matured LGI1 & CASPR2-reactive B cells characterise encephalitis patient cerebrospinal fluid Proceedings of the National Academy of Sciences USA, 121(7):e2311049121 |
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 |
Outeiral, C. & Deane, C. (2024) Codon language embeddings provide strong signals for protein engineering Nature Machine Intelligence, 6:170-179 |
Condado-Morales, I., Dingfelder, F., Waibel, I., Turnbull, O.M., Patel, B., Cao, Z., Bjelke, J.R., Grell, S.N., Bennet, A., Hummer, A.M., Raybould, M.I.J., Deane, C.M., Egebjerg, T., Lorenzen, N. & Arosio, P. (2024) A comparative study of the developability of full-length antibodies, fragments, and bispecific formats reveals higher stability risks for engineered constructs mAbs, 16(1):2403156 |
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 |
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 |
Fischer, K., Lulla, A., So, T., Pereyra-Gerber, P., Raybould, M.I.J., Kohler, T.N., Kaminski, T.S., Yam-Puc, J.C., Hughes, R., Leiss-Maier, F., Brear, P., Matheson, N.J., Deane, C.M., Hyvonen, M., Thaventhiran, J. & Hollfelder, F. (2024) Microfluidics-enabled fluorescence-activated cell sorting of single pathogen-specific antibody secreting cells for the rapid discovery of monoclonal antibodies Nature Biotechnology, ():10.1038/s41587-024-02346-5 |
Riccabona, J.R., Spoendlin, F.C., Fischer, A.L.M., Loeffler, J.R., Quoika, P.K., Jenkins, T.P., Ferguson, J.A., Smorodina, E., Laustsen, A.H., Greiff, V., Forli, S., Ward, A.B., Deane, C.M. & Fernández-Quintero, M.L. (2024) Assessing AF2’s ability to predict structural ensembles of proteins Structure |
Chinery, L., Jeliazkov, J.R. & Deane, C.M. (2024) Humatch - fast, gene-specific joint humanisation of antibody heavy and light chains mAbs, 16(1):2434121 |
McMaster, B., Thorpe, C., Rossjohn, J., Deane, C.M. & Koohy, H. (2024) Quantifying conformational changes in the TCR:pMHC-I binding interface Frontiers in Immunology, 15:1491656 |
Turnbull, O.M., Oglic, D., Croasdale-Wood, R. & Deane, C.M. (2024) p-IgGen: A Paired Antibody Generative Language Model Bioinformatics, 40(11):btae659 |
Klarner, L., Rudner, T.G., Morris, G.M., Deane, C.M. & Teh, Y.W. (2024) Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design Proceedings of the 41st International Conference on Machine Learning (ICML 2024) |
Gordon, G.L., Greenshields-Watson, A., Agarwal, P., Wong, A., Boyles, F., Hummer, A.M., Lujan Hernandez, A.G. & Deane, C.M. (2024) PLAbDab-nano: a database of camelid and shark nanobodies from patents and literature Nucleic Acids Research, 53(D1):gkae881 |
Richardson, E., Bibi, S., McLean, F., Schimanski, L., Rijal, P., Ghraichy, M., Von Niederhäusern, V., Truück, J., Clutterbuck, E.A., O'Connor, D., Luhn, K., Townsend, A., Peters, B., Pollard, A., Deane, C.M. & Kelly, D. (2024) Computational mining of B cell receptor repertoires reveals antigen-specific and convergent responses to Ebola vaccination Frontiers in Immunology, 15:1383753 |