Author

Claudia L. Driscoll

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#large language models Open access Sep 2026

Coevolutionary mining of prokaryotic non-coding elements with a genome language model

Microbial genomes encode non-coding RNAs (ncRNAs) and nucleic-acid-interacting proteins essential to biology and biotechnology. However, discovery of these systems remains protein-centric and based on similarity to known sequences. Here, we introduce Minerva, a framework for coevolutionary mining that uses genome langu...

David B. Li, G. Brixi, Alexandra S. Kim et al. · bioRxiv · 1 citation

Open access Sep 2026

Forecasting viral evolution from phylogenetic trees

This work introduces antiGen, a machine learning model that forecasts the evolutionary future of viruses by learning from their evolutionary past, and achieves state-of-the-art performance for predicting mutations to the SARS-CoV-2 spike protein.

I. Specht, Soyoon Park, Seyone Chithrananda et al. · bioRxiv · 1 citation

Open access Aug 2026

Aligning protein-generative models to experimental fitness with ProteinDPO

This work demonstrates how to provide task-specific information without losing the general knowledge learned during pretraining by using direct preference optimization to align a structure-conditioned protein language model to preferentially generate stable protein sequences.

Talal Widatalla, Ashir Borah, Samuel H. King et al. · Nature Methods · 3 citations