Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. - Evan Seitz; David M. McCandlish; Justin B. Kinney; Peter K. Koo (Nat. Mac. Intell., 2024)

Gauge fixing for sequence-function relationships. - Anna Posfai; Juannan Zhou; David M. McCandlish; Justin B. Kinney (PLoS Comput. Biol., 2025)

On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing. - Samantha Petti; Carlos Martí-Gómez; Justin B. Kinney; Juannan Zhou; David M. McCandlish (CoRR, 2025)