Dynamic Programming Alignment Accuracy. - Ian Holmes; Richard Durbin (J. Comput. Biol., 1998)

Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data. - Ian Holmes; William J. Bruno (ISMB, 2000)

Evolutionary HMMs: a Bayesian approach to multiple alignment. - Ian Holmes; William J. Bruno (Bioinform., 2001)

Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars. - Ian Holmes; Gerald M. Rubin (Pacific Symposium on Biocomputing, 2002)

A web-based editor for multiplayer choice games. - Ian Holmes (FDG, 2014)

Modular non-repeating codes for DNA storage. - Ian Holmes (CoRR, 2016)

The National Cancer Institute's Informatics Technology for Cancer Research Program: Building a Community of Practice in Cancer Informatics. - Simina M. Boca; David Hanauer; Ian Holmes; Despina Kontos; Juli D. Klemm (AMIA, 2019)

Cellular Automata Simulation of RNA Self-Replicators. - Ian Holmes (ALIFE, 2020)

Attention-Based Reward Shaping for Sparse and Delayed Rewards. - Ian Holmes; Min Chi (CoRR, 2025)