Publications by Computational Biology and Bioinformatics

Lo, T., Reinert, G. and Zhang, R. (2025) “Isolated vertices in two duplication-divergence models with edge deletion.”

Nissley, D. et al. (2025) “Use of Molecular Simulations to Understand Structural Dynamics of Antibodies”, in Biopharmaceutical Informatics. Taylor & Francis, pp. 201–227.

Quast, N., Deane, C. and Raybould, M. (2025) “STCRpy: a software suite for T cell receptor structure parsing, interaction profiling and machine learning dataset preparation”, bioRxiv.

Ellmen, I. et al. (2025) “Transformers trained on proteins can learn to attend to Euclidean distance”, Transactions on Machine Learning Research, July-2025.

Ellmen, I., Raybould, M. and Deane, C. (2025) “The protein universe in 3D”, Nature Chemical Biology, 21(1), pp. 27–28.

Adams, J. et al. (2025) “Individualised Counterfactual Examples Using Conformal Prediction Intervals”, in Proceedings of Machine Learning Research, pp. 425–444.

Hung, E., Mantziou, A. and Reinert, G. (2024) “A Bayesian mixture model for Poisson network autoregression.”

Mantziou, A. et al. (2024) “GDP nowcasting with large-scale inter-industry payment data in real time -- A network approach”, arXiv.

Erasmus, M. et al. (2024) “AIntibody: an experimentally validated in silico antibody discovery design challenge”, Nature Biotechnology, 42(11).

Limnios, S. et al. (2024) “SaGess: A Sampling Graph Denoising Diffusion Model for Scalable Graph Generation”, in ECAI 2024. IOS Press.