Author

Blazej Banaszewski

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Open access Oct 2026

Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models

Protein design typically generates amino acid sequences first and then translates them into DNA post-hoc limiting control over the nucleotide sequence via codon choice at design time. We introduce NuCaliby, a structure-conditioned model that jointly designs amino acid, mRNA, and DNA sequences of a protein at nucleotide...

Błażej Banaszewski, Lars J. Dornfeld, De-Xiong Chen et al. · bioRxiv · 0 citations

Preprint Aug 2026

Monroe: A Molecular Foundation Model for In-Context Probabilistic Inference

Monroe is presented, a new MFM with several innovations over the existing state of the art: increased scale allowing pre-training on over 81 million molecules from the PM6 quantum chemistry dataset; improved graph representation of stereochemistry; improved training losses including conformer denoising and embedding de...

Błażej Banaszewski, Andrew W. Fitzgibbon · 1 citation