| 2001 | Analysis techniques for microarray time-series data. | Vladimir Filkov, Steven Skiena, Jizu Zhi |
| 2001 | Geometric algorithms for the analysis of 2D-electrophoresis gels. | Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk |
| 2001 | Fast recovery of evolutionary trees with thousands of nodes. | Mikls Csrs |
| 2001 | Hunger for new technologies, metrics, and spatiotemporal models in functional genomic (abstract only). | George M. Church |
| 2001 | Algorithms for identifying protein cross-links via tandem mass spectrometry. | Ting Chen, Jacob D. Jaffe, George M. Church |
| 2001 | Gene-finding via tandem mass spectrometry. | Ting Chen |
| 2001 | Regulatory element detection using correlation with expression (abstract only). | Harmen J. Bussemaker, Hao Li, Eric D. Siggia |
| 2001 | Rapid significance estimation in local sequence alignment with gaps. | Ralf Bundschuh |
| 2001 | Finding motifs using random projections. | Jeremy Buhler, Martin Tompa |
| 2001 | Information processing by cells and biologists (abstract only). | Roger Brent |
| 2001 | Predicting the beta-helix fold from protein sequence data. | Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger |
| 2001 | Algorithms for phylogenetic footprinting. | Mathieu Blanchette |
| 2001 | On the predictive power of sequence similarity in yeast. | Yonatan Bilu, Michal Linial |
| 2001 | Class discovery in gene expression data. | Amir Ben-Dor, Nir Friedman, Zohar Yakhini |
| 2001 | An optimal procedure for gap closing in whole genome shotgun sequencing. | Richard Beigel, Noga Alon, Simon Kasif, Mehmet Serkan Apaydin, Lance Fortnow |
| 2001 | Context-specific Bayesian clustering for gene expression data. | Yoseph Barash, Nir Friedman |
| 2001 | A new approach to sequence comparison: normalized sequence alignment. | Abdullah N. Arslan, mer Egecioglu, Pavel A. Pevzner |
| 2001 | The sequence of the human genome (abstract only). | Mark Adams |
| 2000 | A simple iterative approach to parameter optimization. | Alexander Zien, Ralf Zimmer, Thomas Lengauer |
| 2000 | A unified sequence-structure classification of protein sequences: combining sequence and structure in a map of the protein space. | Golan Yona, Michael Levitt |
| 2000 | Protein structure determination using protein threading and sparse NMR data (extended abstract). | Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu |
| 2000 | The E-CELL project: towards integrative simulation of cellular processes. | Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Yusuke Saito, Tom Shimizu, Yoichi Nakayama |
| 2000 | PDB_ISL: an intermediate sequence library for protein structure assignment. | Sarah A. Teichmann, Cyrus Chothia, George M. Church, Jong-Chan Park |
| 2000 | Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding. | Jon M. Sorenson, Teresa Head-Gordon |
| 2000 | Class prediction and discovery using gene expression data. | Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. Lander |