| 2001 | (1+epsilon)-Approximation of Sorting by Reversals and Transpositions. Niklas Eriksen |
| 2001 | A Chemical-Distance-Based Test for Positive Darwinian Selection. Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur |
| 2001 | A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites. Yoseph Barash, Gill Bejerano, Nir Friedman |
| 2001 | Algorithms for Finding Gene Clusters. Steffen Heber, Jens Stoye |
| 2001 | Algorithms in Bioinformatics, First International Workshop, WABI 2001, Aarhus, Denmark, August 28-31, 2001, Proceedings Olivier Gascuel, Bernard M. E. Moret |
| 2001 | An Improved Model for Statistical Alignment. István Miklós, Zoltán Toroczkai |
| 2001 | Analytic Solutions for Three-Taxon ML Benny Chor, Michael D. Hendy, David Penny |
| 2001 | Assessing the Statistical Significance of Overrepresented Oligonucleotides. Alain Denise, Mireille Régnier, Mathias Vandenbogaert |
| 2001 | Boosting EM for Radiation Hybrid and Genetic Mapping. Thomas Schiex, Patrick Chabrier, Martin Bouchez, Denis Milan |
| 2001 | Comparing Assemblies Using Fragments and Mate-Pairs. Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton |
| 2001 | Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar. Arun K. Jagota, Rune B. Lyngsø, Christian N. S. Pedersen |
| 2001 | Computing Linking Numbers of a Filtration. Herbert Edelsbrunner, Afra Zomorodian |
| 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 | Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes. Li-San Wang |
| 2001 | Experiments in Computing Sequences of Reversals. Anne Bergeron, François Strasbourg |
| 2001 | False Positives in Genomic Map Assembly and Sequence Validation. Thomas S. Anantharaman, Bud Mishra |
| 2001 | Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time. Ganeshkumar Ganapathysaravanabavan, Tandy J. Warnow |
| 2001 | Finding an Optimal Inversion Median: Experimental Results. Adam C. Siepel, Bernard M. E. Moret |
| 2001 | Improving Profile-Profile Alignments via Log Average Scoring. Niklas von Öhsen, Ralf Zimmer |
| 2001 | On the Practical Solution of the Reversal Median Problem. Alberto Caprara |
| 2001 | Pattern Matching and Pattern Discovery Algorithms for Protein Topologies. Juris Viksna, David R. Gilbert |
| 2001 | Placing Probes along the Genome Using Pairwise Distance Data. Will Casey, Bud Mishra, Michael Wigler |
| 2001 | Side Chain-Positioning as an Integer Programming Problem. Olivia Eriksson, Yishao Zhou, Arne Elofsson |
| 2001 | The Performance of Phylogenetic Methods on Trees of Bounded Diameter. Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |