| 2008 | AVI | Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment. | Clifton Forlines, Ryan H. Lilien |
| 2006 | ISMB | Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. | Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald |
| 2006 | RECOMB | A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles. | Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald |
| 2005 | ISMB | High-throughput inference of protein-protein interfaces from unassigned NMR data. | Ramgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald |
| 2004 | RECOMB | A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. | Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald |
| 2003 | RECOMB | Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. | Christopher James Langmead, Anthony K. Yan, Ryan H. Lilien, Lincong Wang, Bruce Randall Donald |
| 2001 | ICRA | Physical Geometric Algorithms for Structural Molecular Biology. | Bruce Randall Donald, Christopher Bailey-Kellogg, Jack Kelley, Ryan H. Lilien |
| 1996 | ECCV | Object Recognition Using Subspace Methods. | Daniel P. Huttenlocher, Ryan H. Lilien, Clark F. Olson |