Claus O. Wilke

1 week ago | biorxiv.org | Luiz Vieira |Morgan C. Handojo |Claus O. Wilke

AbstractProtein language models (pLMs) can offer deep insights into evolutionary and structural properties of proteins. While larger models, such as the 15 billion parameter model ESM-2, promise to capture more complex patterns in sequence space, they also present practical challenges due to their high dimensionality and high computational cost.

Sep 9, 2024 | biorxiv.org | Brent Allman |Luiz Vieira |Daniel Diaz |Daniel Díaz |Claus O. Wilke

AbstractPredicting the evolutionary patterns of emerging and endemic viruses is key for mitigating their spread in host populations. In particular, it is critical to rapidly identify mutations with the potential for immune escape or increased disease burden (variants of concern). Knowing which circulating mutations are such variants of concern can inform treatment or mitigation strategies such as alternative vaccines or targeted social distancing.

Aug 15, 2024 | oncodaily.com | Luiz Vieira |Claus O. Wilke |Bryan Davies

Samuel Hume, Researcher at the University of Oxford, recently shared on X:“The 10 biggest medical research papers from this week (in my opinion!)1. A blood test for Alzheimer disease, which improved diagnostic accuracy – by dementia specialists – from 73% to 91%. ‘Blood Biomarkers to Detect Alzheimer Disease in Primary Care and Secondary Care‘2.

Nov 15, 2023 | biorxiv.org | Anastasiya V Kulikova |Jennifer Parker |Bryan Davies |Claus O. Wilke

AbstractClass II microcins are antimicrobial peptides that have shown some potential as novel antibiotics. However, to date only ten class II microcins have been described, and discovery of novel microcins has been hampered by their short length and high sequence divergence. Here, we ask if we can use numerical embeddings generated by protein large language models to detect microcins in bacterial genome assemblies and whether this method can outperform sequence-based methods such as BLAST.

Sep 10, 2023 | biorxiv.org | Justin R. Randall |Luiz Vieira |Claus O. Wilke |Bryan Davies

AbstractAntimicrobial peptides commonly act by disrupting bacterial membranes, but also frequently damage mammalian membranes. Deciphering the rules governing membrane selectivity is critical to understanding their function and enabling their therapeutic use. Past attempts to decipher these rules often fail because they cannot interrogate adequate peptide sequence variation.