| 2010 | PSB | Optimization Methods for Selecting Founder Populations for Captive Breeding of Endangered Species. | Webb Miller, Stephen J. Wright, Yu Zhang, Stephan C. Schuster, Vanessa M. Hayes |
| 2010 | PSB | Session Introduction. | Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff |
| 2009 | PSB | Session Introduction. | Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff |
| 2009 | PSB | Simultaneous History Reconstruction for Complex Gene Clusters in Multiple Species. | Yu Zhang, Giltae Song, Chih-Hao Hsu, Webb Miller |
| 2009 | RECOMB | Aligning Two Genomic Sequences That Contain Duplications. | Minmei Hou, Cathy Riemer, Piotr Berman, Ross C. Hardison, Webb Miller |
| 2009 | RECOMB | Whole-Genome Analysis of Gene Conversion Events. | Chih-Hao Hsu, Yu Zhang, Ross C. Hardison, Webb Miller |
| 2009 | RECOMB | Inferring the Recent Duplication History of a Gene Cluster. | Giltae Song, Louxin Zhang, Toms Vinar, Webb Miller |
| 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 |
| 2007 | RECOMB | A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. | Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler |
| 2007 | SODA | Approximating the spanning star forest problem and its applications to genomic sequence alignment. | C. Thach Nguyen, Jian Shen, Minmei Hou, Li Sheng, Webb Miller, Louxin Zhang |
| 2006 | WABI | Controlling Size When Aligning Multiple Genomic Sequences with Duplications. | Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller |
| 2002 | RECOMB | Significance Of inter-species matches when evolutionary rate varies. | Jia Li, Webb Miller |
| 1999 | RECOMB | Winnowing sequences from a database search. | Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller |
| 1998 | RECOMB | Alignments without low-scoring regions. | Zheng Zhang, Piotr Berman, Webb Miller |
| 1997 | RECOMB | Progressive multiple alignment with constraints. | Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller |
| 1997 | RECOMB | Aligning a DNA sequence with a protein sequence. | Zheng Zhang, William R. Pearson, Webb Miller |
| 1997 | WADS | A Linear-Time Algorithm for the 1-Mismatch Problem. | Nikola Stojanovic, Piotr Berman, Deborah Gumucio, Ross C. Hardison, Webb Miller |
| 1995 | SODA | Chaining Multiple-Alignment Fragments in Sub-Quadratic Time. | Gene Myers, Webb Miller |
| 1994 | CPM | Parametric Recomuting in Alignment Graphs. | Xiaoqiu Huang, Pavel A. Pevzner, Webb Miller |
| 1974 | STOC | Computational Complexity and Numerical Stability | Webb Miller |
| 1973 | STOC | Toward Mechanical Verification of Properties of Roundoff Error Propagation | Webb Miller |