| 2002 | Approximating the Expected Number of Inversions Given the Number of Breakpoints. | Niklas Eriksen |
| 2002 | Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry. | Nathan Edwards, Ross Lippert |
| 2002 | Efficient Unbound Docking of Rigid Molecules. | Dina Duhovny, Ruth Nussinov, Haim J. Wolfson |
| 2002 | Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle. | Richard Desper, Olivier Gascuel |
| 2002 | Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design. | Mikls Csrs, Aleksandar Milosavljevic |
| 2002 | Improved Approximation Algorithms for NMR Spectral Peak Assignment. | Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Ying Xu |
| 2002 | NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. | David Bryant, Vincent Moulton |
| 2002 | Functional Consequences in Metabolic Pathways from Phylogenetic Profiles. | Yonatan Bilu, Michal Linial |
| 2002 | Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. | Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder |
| 2002 | The Algorithmic of Gene Teams. | Anne Bergeron, Sylvie Corteel, Mathieu Raffinot |
| 2002 | K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. | Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angle M. Hamel, Tommi S. Jaakkola, Nathan Srebro |
| 2002 | Exploring the Set of All Minimal Sequences of Reversals - An Application to Test the Replication-Directed Reversal Hypothesis. | Yasmine Ajana, Jean-Franois Lefebvre, Elisabeth R. M. Tillier, Nadia El-Mabrouk |
| 2002 | Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation. | Ezekiel F. Adebiyi, Michael Kaufmann |
| 2002 | The Enhanced Suffix Array and Its Applications to Genome Analysis. | Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch |
| 2001 | Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes. | Li-San Wang |
| 2001 | Pattern Matching and Pattern Discovery Algorithms for Protein Topologies. | Juris Viksna, David R. Gilbert |
| 2001 | Determination of Binding Amino Acids Based on Random Peptide Array Screening Data. | Peter J. van der Veen, Lodewyk F. A. Wessels, J. W. Slootstra, R. H. Meloen, Marcel J. T. Reinders, Johannes Hellendoorn |
| 2001 | Finding an Optimal Inversion Median: Experimental Results. | Adam C. Siepel, Bernard M. E. Moret |
| 2001 | Boosting EM for Radiation Hybrid and Genetic Mapping. | Thomas Schiex, Patrick Chabrier, Martin Bouchez, Denis Milan |
| 2001 | A Chemical-Distance-Based Test for Positive Darwinian Selection. | Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur |
| 2001 | Improving Profile-Profile Alignments via Log Average Scoring. | Niklas von hsen, Ralf Zimmer |
| 2001 | The Performance of Phylogenetic Methods on Trees of Bounded Diameter. | Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |
| 2001 | An Improved Model for Statistical Alignment. | Istvn Mikls, Zoltn Toroczkai |
| 2001 | Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar. | Arun K. Jagota, Rune B. Lyngs, Christian N. S. Pedersen |
| 2001 | Comparing Assemblies Using Fragments and Mate-Pairs. | Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton |