| 2009 | RECOMB | Reconstructing Histories of Complex Gene Clusters on a Phylogeny. | Toms Vinar, Brona Brejov, Giltae Song, Adam C. Siepel |
| 2008 | RECOMB | Reconstructing the Evolutionary History of Complex Human Gene Clusters. | Yu Zhang, Giltae Song, Toms Vinar, Eric D. Green, Adam C. Siepel, Webb Miller |
| 2006 | RECOMB | New Methods for Detecting Lineage-Specific Selection. | Adam C. Siepel, Katherine S. Pollard, David Haussler |
| 2004 | ISMB | Efficient approximations for learning phylogenetic HMM models from data. | Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam C. Siepel, David Haussler, David Heckerman |
| 2004 | RECOMB | Computational identification of evolutionarily conserved exons. | Adam C. Siepel, David Haussler |
| 2003 | RECOMB | Combining phylogenetic and hidden Markov models in biosequence analysis. | Adam C. Siepel, David Haussler |
| 2002 | RECOMB | An algorithm to enumerate all sorting reversals. | Adam C. Siepel |
| 2002 | WABI | Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. | Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu |
| 2001 | WABI | Finding an Optimal Inversion Median: Experimental Results. | Adam C. Siepel, Bernard M. E. Moret |