Author

Johannes Linder

2 papers indexed here

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Open access Oct 2026

Cerberus: bidirectional state space blocks improve accuracy and efficiency of regulatory sequence models

Sequence-to-function models predict regulatory activity and variant effects from DNA sequence alone, and leading models such as Borzoi compute long-range interactions with self-attention. The reference genome caps unique training sequences, and new assays add labels, not sequences. This constraint favors architectures...

David R. Kelley, Han Yuan, Xing-Fan Huang et al. · bioRxiv · 0 citations

#protein folding Open access Oct 2026

Scalable saturation mutagenesis reveals gene regulatory architecture and rare variant effects

Long-context sequence-to-function models enable nucleotide-resolution prediction of regulatory variant effects, motivating comprehensive mutational interrogation across broad genomic contexts. Yet conventional in silico saturation mutagenesis (ISM) scores mutations one at a time, requiring millions of model evaluations...

Han Yuan, Xing-Fan Huang, Benjamin J. Auerbach et al. · bioRxiv · 0 citations