Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. - Peyton Greenside; Tyler Shimko; Polly Fordyce; Anshul Kundaje (Bioinform., 2018)

DeCoDe: degenerate codon design for complete protein-coding DNA libraries. - Tyler Shimko; Polly Fordyce; Yaron Orenstein (Bioinform., 2020)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - Peter St. John; Dejun Lin; Polina Binder; Malcolm Greaves; Vega Shah; John St. John; Adrian Lange; Patrick D. Hsu; Rajesh Illango; Arvind Ramanathan; Anima Anandkumar; David H. Brookes; et al. (CoRR, 2024)