| 2005 | A Hidden Markov Technique for Haplotype Reconstruction. | Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen |
| 2005 | An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree. | Zeshan Peng, H. F. Ting |
| 2005 | Using Semi-definite Programming to Enhance Supertree Resolvability. | Shlomo Moran, Satish Rao, Sagi Snir |
| 2005 | A Linear Time Biclustering Algorithm for Time Series Gene Expression Data. | Sara C. Madeira, Arlindo L. Oliveira |
| 2005 | Minimum Recombination Histories by Branch and Bound. | Rune B. Lyngs, Yun S. Song, Jotun Hein |
| 2005 | Generalized Planted ( | Henry C. M. Leung, Francis Y. L. Chin |
| 2005 | Rotamer-Pair Energy Calculations Using a Trie Data Structure. | Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink |
| 2005 | Discovery of Protein Substructures in EM Maps. | Keren Lasker, Oranit Dror, Ruth Nussinov, Haim J. Wolfson |
| 2005 | Reaction Motifs in Metabolic Networks. | Vincent Lacroix, Cristina G. Fernandes, Marie-France Sagot |
| 2005 | A New Tight Upper Bound on the Transposition Distance. | Anthony Labarre |
| 2005 | A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds. | Gregory Kucherov, Laurent No, Mikhail A. Roytberg |
| 2005 | The Main Structural Regularities of the Sandwich Proteins. | Alexander Kister |
| 2005 | Pattern Identification in Biogeography. | Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Vijaya Ramachandran, Tandy J. Warnow |
| 2005 | Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity. | Eran Eyal, Dan Halperin |
| 2005 | A 1.375-Approximation Algorithm for Sorting by Transpositions. | Isaac Elias, Tzvika Hartman |
| 2005 | The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity. | Daniel Dalevi, Devdatt P. Dubhashi |
| 2005 | On the Complexity of Several Haplotyping Problems. | Rudi Cilibrasi, Leo van Iersel, Steven Kelk, John Tromp |
| 2005 | Computing the Quartet Distance Between Trees of Arbitrary Degree. | Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers |
| 2005 | Clustering Gene Expression Series with Prior Knowledge. | Laurent Brhlin |
| 2005 | A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance. | Robert S. Boyer, Warren A. Hunt Jr., Serita M. Nelesen |
| 2005 | Perfect Sorting by Reversals Is Not Always Difficult. | Sverine Brard, Anne Bergeron, Cdric Chauve, Christophe Paul |
| 2005 | Multiple Structural RNA Alignment with Lagrangian Relaxation. | Markus Bauer, Gunnar W. Klau, Knut Reinert |
| 2005 | Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons. | Pankaj K. Agarwal, Yonatan Bilu, Rachel Kolodny |
| 2004 | Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding. | Sing-Hoi Sze, Songjian Lu, Jianer Chen |
| 2004 | Chaining Algorithms for Alignment of Draft Sequence. | Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou |