Alex Hawkins-Hooker
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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
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
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
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
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
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
N Null, S Jain, C Bakolitsa, SE Brenner, P Radivojac, J Moult, S Repo, ...
Genome Biology 25 (1), 1-46, 2024
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
Projection layers improve deep learning models of regulatory DNA function
A Hawkins-Hooker, H Kenlay, J Reid
BioRxiv, 412734, 2018
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
Moment matching denoising gibbs sampling
M Zhang, A Hawkins-Hooker, B Paige, D Barber
Advances in Neural Information Processing Systems 36, 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
Critical assessment of genome interpretation consortium. CAGI, the critical assessment of genome interpretation, establishes progress and pprospects for computational genetic …
S Jain, C Bakolitsa, EB Steven, P Radivojac, J Moult, S Repo, AH Roger, ...
Genome Biology 22 (22; 25 (1): 53.), 1-46, 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
Evaluating Markov Chain Ontology Analysis as a Standalone Enrichment Analysis Method
A Hawkins-Hooker
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