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

Cerberus, an ensemble of eight models over 786 kb of input, is evaluated on GTEx v11 fine-mapped eQTL, sQTL, and paQTL benchmarks with negatives matched on allele frequency, gene expression, and phenotype-specific positional annotations to reduce confounding by these properties.

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