| 2007 | Heuristics for the Gene-Duplication Problem: A | Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, Andr Wehe |
| 2007 | Improving Inversion Median Computation Using Commuting Reversals and Cycle Information. | William Arndt, Jijun Tang |
| 2007 | A Pseudo-boolean Programming Approach for Computing the Breakpoint Distance Between Two Genomes with Duplicate Genes. | Sbastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thvenin, Stphane Vialette |
| 2007 | Multi-break Rearrangements: From Circular to Linear Genomes. | Max A. Alekseyev |
| 2006 | Revealing the Proteome Complexity by Mass Spectrometry. | Roman A. Zubarev |
| 2006 | An Outsider's View of the Genome. | Carl Zimmer |
| 2006 | Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. | Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg |
| 2006 | Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes. | Andrew Wei Xu, Chunfang Zheng, David Sankoff |
| 2006 | A Parameterized Algorithm for Protein Structure Alignment. | Jinbo Xu, Feng Jiao, Bonnie Berger |
| 2006 | A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem. | Wei Xie, Nikolaos V. Sahinidis |
| 2006 | A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry. | Yin Wu, Yehia Mechref, Iveta Klouckova, Milos V. Novotny, Haixu Tang |
| 2006 | On Genome Evolution with Accumulated Change and Innovation. | Damian Wjtowicz, Jerzy Tiuryn |
| 2006 | A Study of Accessible Motifs and RNA Folding Complexity. | Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson |
| 2006 | Stan Ulam and Computational Biology. | Michael S. Waterman |
| 2006 | Clustering Short Gene Expression Profiles. | Ling Wang, Marco Ramoni, Paola Sebastiani |
| 2006 | Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. | Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano |
| 2006 | Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization. | Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik |
| 2006 | Simulating Protein Motions with Rigidity Analysis. | Shawna L. Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato |
| 2006 | Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. | Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh |
| 2006 | Integrated Protein Interaction Networks for 11 Microbes. | Balaji S. Srinivasan, Antal F. Novak, Jason Flannick, Serafim Batzoglou, Harley H. McAdams |
| 2006 | Domain Architecture in Homolog Identification. | Nan Song, R. D. Sedgewick, Dannie Durand |
| 2006 | A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast. | Mingzhou (Joe) Song, Z. Lewis Liu |
| 2006 | Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. | Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu |
| 2006 | Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. | Sagi Snir, Lior Pachter |
| 2006 | New Methods for Detecting Lineage-Specific Selection. | Adam C. Siepel, Katherine S. Pollard, David Haussler |