| Generating functional protein variants with variational autoencoders A Hawkins-Hooker, F Depardieu, S Baur, G Couairon, A Chen, D Bikard PLoS computational biology 17 (2), e1008736, 2021 | 203 | 2021 |
| Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay D Shigaki, O Adato, AN Adhikari, S Dong, A Hawkins‐Hooker, F Inoue, ... Human mutation 40 (9), 1280-1291, 2019 | 52 | 2019 |
| Chainsaw: protein domain segmentation with fully convolutional neural networks J Wells, A Hawkins-Hooker, N Bordin, I Sillitoe, B Paige, C Orengo Bioinformatics 40 (5), btae296, 2024 | 11 | 2024 |
| The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles J Schreiber, C Boix, J wook Lee, H Li, Y Guan, CC Chang, JC Chang, ... Genome biology 24 (1), 79, 2023 | 11 | 2023 |
| MSA-Conditioned Generative Protein Language Models for Fitness Landscape Modelling and Design A Hawkins-Hooker, DT Jones, B Paige Machine Learning in Structural Biology Workshop at NeurIPS, 2021 | 8 | 2021 |
| Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning A Hawkins-Hooker, G Visonà, T Narendra, M Rojas-Carulla, B Schölkopf, ... Nature Communications 14 (1), 4750, 2023 | 7* | 2023 |
| CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods S Jain, C Bakolitsa, SE Brenner, P Radivojac, J Moult, S Repo, ... Genome Biology 25 (1), 2024 | 5 | 2024 |
| Projection layers improve deep learning models of regulatory DNA function A Hawkins-Hooker, H Kenlay, J Reid BioRxiv, 412734, 2018 | 3 | 2018 |
| Moment matching denoising gibbs sampling M Zhang, A Hawkins-Hooker, B Paige, D Barber Advances in Neural Information Processing Systems 36, 2024 | 2 | 2024 |
| Using domain-domain interactions to probe the limitations of MSA pairing strategies A Hawkins-Hooker, DT Jones, B Paige Machine Learning in Structural Biology Workshop at NeurIPS, 2022 | 2 | 2022 |
| PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction A Wenteler, M Occhetta, N Branson, M Huebner, V Curean, W Dee, ... bioRxiv, 2024.10. 02.616248, 2024 | 1 | 2024 |
| Likelihood-based fine-tuning of protein language models for few-shot fitness prediction and design A Hawkins-Hooker, J Kmec, O Bent, P Duckworth bioRxiv, 2024.05. 28.596156, 2024 | 1 | 2024 |
| Preferential Bayesian Optimisation for Protein Design with Ranking-Based Fitness Predictors A Hawkins-Hooker, P Duckworth, O Bent Machine Learning in Structural Biology Workshop at NeurIPS, 2023 | 1 | 2023 |
| MSA Pairing Transfomer: protein interaction partner prediction with few-shot contrastive learning A Hawkins-Hooker, DB Cerigo, U Lupo, D Jones, B Paige ICML 2024 Workshop on Efficient and Accessible Foundation Models for …, 2024 | | 2024 |
| Evaluating Markov Chain Ontology Analysis as a Standalone Enrichment Analysis Method A Hawkins-Hooker | | |
