| 2002 | A Hybrid Scoring Function for Protein Multiple Alignment. Emily Rocke |
| 2002 | A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants. Raymond Wheeler |
| 2002 | A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding. Mihaela Pertea, Steven Salzberg |
| 2002 | Algorithms in Bioinformatics, Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002, Proceedings Roderic Guigó, Dan Gusfield |
| 2002 | Approximating the Expected Number of Inversions Given the Number of Breakpoints. Niklas Eriksen |
| 2002 | Border Length Minimization in DNA Array Design. Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky |
| 2002 | Combinatorial Use of Short Probes for Differential Gene Expression Profiling. Liling L. Warren, Ben Hui Liu |
| 2002 | Comparative Methods for Gene Structure Prediction in Homologous Sequences. Christian N. S. Pedersen, Tejs Scharling |
| 2002 | Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome. Doron Lipson, Peter Webb, Zohar Yakhini |
| 2002 | Efficient Methods for Inferring Tandem Duplication History. Louxin Zhang, Bin Ma, Lusheng Wang |
| 2002 | Efficient Unbound Docking of Rigid Molecules. Dina Duhovny, Ruth Nussinov, Haim J. Wolfson |
| 2002 | Estimating the Deviation from a Molecular Clock. Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow |
| 2002 | Exploring the Set of All Minimal Sequences of Reversals - An Application to Test the Replication-Directed Reversal Hypothesis. Yasmine Ajana, Jean-François 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 | FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures. Mariusz Milik, Sándor Szalma, Krzysztof A. Olszewski |
| 2002 | Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics. Michael H. Goldwasser, Ming-Yang Kao, Hsueh-I Lu |
| 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 | Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle. Richard Desper, Olivier Gascuel |
| 2002 | Finding Founder Sequences from a Set of Recombinants. Esko Ukkonen |
| 2002 | Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks. Martin Reczko, Petko Fiziev, Eike Staub, Artemis G. Hatzigeorgiou |
| 2002 | Functional Consequences in Metabolic Pathways from Phylogenetic Profiles. Yonatan Bilu, Michal Linial |
| 2002 | Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry. Nathan Edwards, Ross Lippert |
| 2002 | Genome Rearrangement Phylogeny Using Weighbor. Li-San Wang |
| 2002 | Improved Approximation Algorithms for NMR Spectral Peak Assignment. Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Ying Xu |
| 2002 | Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu |
| 2002 | Invited Lecture - Accelerating Smith-Waterman Searches. Gene Myers, Richard Durbin |
| 2002 | Invited Lecture - Molecule as Computation: Towards an Abstraction of Biomolecular Systems. Ehud Shapiro |
| 2002 | K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola, Nathan Srebro |
| 2002 | Methods for Inferring Block-Wise Ancestral History from Haploid Sequences. Russell Schwartz, Andrew G. Clark, Sorin Istrail |
| 2002 | Modified Mincut Supertrees. Roderic D. M. Page |
| 2002 | MultiProt - A Multiple Protein Structural Alignment Algorithm. Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson |
| 2002 | NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. David Bryant, Vincent Moulton |
| 2002 | On the Control of Hybridization Noise in DNA Sequencing-by-Hybridization. Hon Wai Leong, Franco P. Preparata, Wing-Kin Sung, Hugo Willy |
| 2002 | Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design. Miklós Csürös, Aleksandar Milosavljevic |
| 2002 | Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem. Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia |
| 2002 | Rapid Large-Scale Oligonucleotide Selection for Microarrays. Sven Rahmann |
| 2002 | Restricting SBH Ambiguity via Restriction Enzymes. Steven Skiena, Sagi Snir |
| 2002 | Segment Match Refinement and Applications. Aaron L. Halpern, Daniel H. Huson, Knut Reinert |
| 2002 | Sequence-Length Requirements for Phylogenetic Methods. Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow |
| 2002 | Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces. L. R. Grate, Chiranjib Bhattacharyya, Michael I. Jordan, I. Saira Mian |
| 2002 | The Algorithmic of Gene Teams. Anne Bergeron, Sylvie Corteel, Mathieu Raffinot |
| 2002 | The Enhanced Suffix Array and Its Applications to Genome Analysis. Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch |