| 2003 | IJCAI | Gaussian Process Models of Spatial Aggregation Algorithms. | Naren Ramakrishnan, Christopher Bailey-Kellogg |
| 2001 | IJCAI | Ambiguity-Directed Sampling for Qualitative Analysis of Sparse Data from Spatially-Distributed Physical Systems. | Christopher Bailey-Kellogg, Naren Ramakrishnan |
| 2001 | ICRA | Physical Geometric Algorithms for Structural Molecular Biology. | Bruce Randall Donald, Christopher Bailey-Kellogg, Jack Kelley, Ryan H. Lilien |
| 2000 | ISMB | Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. | Christopher Bailey-Kellogg, John J. Kelley, Clifford Stein, Bruce Randall Donald |
| 2000 | RECOMB | The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. | Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald |
| 1999 | AAAI | Influence-Based Model Decomposition. | Christopher Bailey-Kellogg, Feng Zhao |
| 1998 | AAAI | Qualitative Analysis of Distributed Physical Systems with Applications to Control Synthesis. | Christopher Bailey-Kellogg, Feng Zhao |
| 1996 | AAAI | Spatial Aggregation: Language and Applications. | Christopher Bailey-Kellogg, Feng Zhao, Kenneth Yip |