End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. - Samantha Petti; Nicholas Bhattacharya; Roshan Rao; Justas Dauparas; Neil Thomas; Juannan Zhou; Alexander M. Rush; Peter K. Koo; Sergey Ovchinnikov 001 (Bioinform., 2023)

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)