Andrew M. Dickson

MetaBiome integrates agent-based modeling and metabolic networks to simulate spatial regulation in gut microbial communities, revealing how microbes adapt to environmental conditions.

This paper fine-tunes protein embeddings to improve interpretable function prediction, showing that fine-tuned models outperform pre-trained ones in both known and novel function classification.

GO Bench provides a benchmarking hub for evaluating machine learning models in protein function annotation using Gene Ontology terms.

The paper develops function-conditioned generative models to predict functionally important protein residues using Gene Ontology data and protein language models.