Clustering metagenomic sequences with interpolated Markov models. - David R. Kelley; Steven L. Salzberg (BMC Bioinform., 2010)

Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. - David R. Kelley; Carl Kingsford (J. Comput. Biol., 2011)

Cross-species regulatory sequence activity prediction. - David R. Kelley (PLoS Comput. Biol., 2020)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2. - Paulina N. Smaruj; Fahad Kamulegeya; David R. Kelley; Geoffrey Fudenberg (PLoS Comput. Biol., 2025)