| 2002 | Combinatorial Use of Short Probes for Differential Gene Expression Profiling. | Liling L. Warren, Ben Hui Liu |
| 2002 | Genome Rearrangement Phylogeny Using Weighbor. | Li-San Wang |
| 2002 | Finding Founder Sequences from a Set of Recombinants. | Esko Ukkonen |
| 2002 | Restricting SBH Ambiguity via Restriction Enzymes. | Steven Skiena, Sagi Snir |
| 2002 | MultiProt - A Multiple Protein Structural Alignment Algorithm. | Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson |
| 2002 | Invited Lecture - Molecule as Computation: Towards an Abstraction of Biomolecular Systems. | Ehud Shapiro |
| 2002 | Methods for Inferring Block-Wise Ancestral History from Haploid Sequences. | Russell Schwartz, Andrew G. Clark, Sorin Istrail |
| 2002 | A Hybrid Scoring Function for Protein Multiple Alignment. | Emily Rocke |
| 2002 | Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem. | Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia |
| 2002 | Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks. | Martin Reczko, Petko Fiziev, Eike Staub, Artemis G. Hatzigeorgiou |
| 2002 | Rapid Large-Scale Oligonucleotide Selection for Microarrays. | Sven Rahmann |
| 2002 | A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding. | Mihaela Pertea, Steven Salzberg |
| 2002 | Comparative Methods for Gene Structure Prediction in Homologous Sequences. | Christian N. S. Pedersen, Tejs Scharling |
| 2002 | Modified Mincut Supertrees. | Roderic D. M. Page |
| 2002 | Estimating the Deviation from a Molecular Clock. | Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow |
| 2002 | Invited Lecture - Accelerating Smith-Waterman Searches. | Gene Myers, Richard Durbin |
| 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 | Sequence-Length Requirements for Phylogenetic Methods. | Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow |
| 2002 | FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures. | Mariusz Milik, Sndor Szalma, Krzysztof A. Olszewski |
| 2002 | Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome. | Doron Lipson, Peter Webb, Zohar Yakhini |
| 2002 | On the Control of Hybridization Noise in DNA Sequencing-by-Hybridization. | Hon Wai Leong, Franco P. Preparata, Wing-Kin Sung, Hugo Willy |
| 2002 | Border Length Minimization in DNA Array Design. | Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky |
| 2002 | Segment Match Refinement and Applications. | Aaron L. Halpern, Daniel H. Huson, Knut Reinert |
| 2002 | Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces. | L. R. Grate, Chiranjib Bhattacharyya, Michael I. Jordan, I. Saira Mian |
| 2002 | Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics. | Michael H. Goldwasser, Ming-Yang Kao, Hsueh-I Lu |