| 2000 | Early eukaryote evolution based on mitochondrial gene order breakpoints. | David Sankoff, David Bryant, Mlanie Deneault, B. Franz Lang, Gertraud Burger |
| 2000 | Sequencing-by-hybridization at the information-theory bound: an optimal algorithm. | Franco P. Preparata, Eli Upfal |
| 2000 | Probabilities for having a new fold on the basis of a map of all protein sequences. | Elon Portugaly, Michal Linial |
| 2000 | Mutation-tolerant protein identification by mass-spectrometry. | Pavel A. Pevzner, Vlado Danck, Chris L. Tang |
| 2000 | Determining contact energy function for continuous state models of globular protein conformations. | Y. Zenmei Ohkubo, Gordon M. Crippen |
| 2000 | Human genome analysis and medicine in the 21st century (abstract only). | Yusuke Nakamura |
| 2000 | Molecular diversity: strategies and concerns (abstract only). | Yvonne C. Martin, Mark G. Bures |
| 2000 | Extracting structured motifs using a suffix tree - algorithms and application to promoter consensus identification. | Laurent Marsan, Marie-France Sagot |
| 2000 | Pseudoknots in RNA secondary structures. | Rune B. Lyngs, Christian N. S. Pedersen |
| 2000 | UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. | Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kazmierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga |
| 2000 | Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. | John D. Kececioglu, Sanjay Shete, Jonathan P. Arnold |
| 2000 | Optimizing for success: a new score function for distantly related protein sequence comparison. | Maricel Kann, Richard A. Goldstein |
| 2000 | Sequence comparison to graph comparison--a new generation of algorithms for network analysis of interacting molecules (abstract only). | Minoru Kanehisa |
| 2000 | DNA sequence variation among humans and apes (abstract only). | Henrik Kaessmann, Ingo Ebersberger, Victor Wiebe, Rikard Erlandsson, Jim F. Wilson, Carsten Schwarz, Michaela Winkler, Svante Pbo |
| 2000 | Computing life and global technologies (abstract only). | Leroy E. Hood |
| 2000 | A data-analysis pipeline for large-scale gene expression analysis. | Steffen Hennig, Ralf Herwig, Matthew Clark, Pia Aanstad, A. Musa, John O'Brien, C. Bull, Uwe Radelof, Georgia Panopoulou, Albert J. Poustka, Hans Lehrach |
| 2000 | Contig selection in physical mapping. | Steffen Heber, Jens Stoye, Jrg D. Hoheisel, Martin Vingron |
| 2000 | Systematic and automated discovery of patterns in PROSITE families. | Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano |
| 2000 | New algorithms for the duplication-loss model. | Michael T. Hallett, Jens Lagergren |
| 2000 | Evolutionary features of genomes as disclosed by comparative analysis of complete genome sequences (abstract only). | Takashi Gojobori, T. Daniel Andrews, Takeshi Itoh |
| 2000 | Invited presentation: introns and modules in ancient conserved genes (abstract only). | Walter Gilbert |
| 2000 | Using Bayesian networks to analyze expression data. | Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe'er |
| 2000 | Tree fitting: an algebraic approach using profile distances. | Richard Desper, Martin Vingron |
| 2000 | Multiple maxima of likelihood in phylogenetic trees: an analytic approach. | Benny Chor, Michael D. Hendy, Barbara R. Holland, David Penny |
| 2000 | A compression algorithm for DNA sequences and its applications in genome comparison. | Xin Chen, Sam Kwong, Ming Li |