| 2009 | Whole-Genome Analysis of Gene Conversion Events. | Chih-Hao Hsu, Yu Zhang, Ross C. Hardison, Webb Miller |
| 2009 | Aligning Two Genomic Sequences That Contain Duplications. | Minmei Hou, Cathy Riemer, Piotr Berman, Ross C. Hardison, Webb Miller |
| 2009 | Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. | Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Sleyman Cenk Sahinalp |
| 2009 | Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. | Zengyou He, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, Weichuan Yu |
| 2009 | Evaluating Between-Pathway Models with Expression Data. | Benjamin J. Hescott, Mark D. M. Leiserson, Lenore Cowen, Donna K. Slonim |
| 2009 | The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. | Dan Gusfield |
| 2009 | Shared Peptides in Mass Spectrometry Based Protein Quantification. | Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna |
| 2009 | Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology. | Alexandre Donz, Gilles Clermont, Axel Legay, Christopher James Langmead |
| 2009 | Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes Using Pseudo-Boolean Optimization. | Joo Delgado, Ins Lynce, Vasco Manquinho |
| 2009 | Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep. | Constantinos Daskalakis, Elchanan Mossel, Sbastien Roch |
| 2009 | Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction. | Cdric Chauve, Utz-Uwe Haus, Tamon Stephen, Vivija P. You |
| 2009 | New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. | Cdric Chauve, Nadia El-Mabrouk |
| 2009 | Topology-Free Querying of Protein Interaction Networks. | Sharon Bruckner, Falk Hffner, Richard M. Karp, Ron Shamir, Roded Sharan |
| 2009 | Counting All DCJ Sorting Scenarios. | Marlia D. V. Braga, Jens Stoye |
| 2009 | Finding Nested Common Intervals Efficiently. | Guillaume Blin, Jens Stoye |
| 2009 | Optimizing PCR Assays for DNA Based Cancer Diagnostics. | Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna |
| 2009 | Pseudo Boolean Programming for Partially Ordered Genomes. | Sbastien Angibaud, Guillaume Fertin, Annelyse Thvenin, Stphane Vialette |
| 2009 | A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances. | Zaky Adam, David Sankoff |
| 2008 | Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. | Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg |
| 2008 | Reconstructing the Evolutionary History of Complex Human Gene Clusters. | Yu Zhang, Giltae Song, Toms Vinar, Eric D. Green, Adam C. Siepel, Webb Miller |
| 2008 | Gene Team Tree: A Compact Representation of All Gene Teams. | Melvin Zhang, Hon Wai Leong |
| 2008 | Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information. | Jing Zhang, Xin Gao, Jinbo Xu, Ming Li |
| 2008 | Sorting Genomes with Insertions, Deletions and Duplications by DCJ. | Sophia Yancopoulos, Richard Friedberg |
| 2008 | A Fast and Exact Algorithm for the Median of Three Problem-A Graph Decomposition Approach. | Andrew Wei Xu |
| 2008 | Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. | Igor Ulitsky, Richard M. Karp, Ron Shamir |