| 2000 | Notung: dating gene duplications using gene family trees. | Kevin C. Chen, Dannie Durand, Martin Farach-Colton |
| 2000 | An analytic approach to significance assessment in local sequence alignment with gaps. | Ralf Bundschuh |
| 2000 | Comprehensive statistical method for protein fold recognition. | Jadwiga R. Bienkowska, Lihua Yu, Sophia Zarakhovich, Robert G. Rogers, Temple F. Smith |
| 2000 | Universal DNA tag systems: a combinatorial design scheme. | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Zohar Yakhini |
| 2000 | Tissue classification with gene expression profiles. | Amir Ben-Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michl Schummer, Zohar Yakhini |
| 2000 | Human and mouse gene structure: comparative analysis and application to exon prediction. | Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander |
| 2000 | Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). | Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander |
| 2000 | The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. | Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald |
| 2000 | Optimal amnesic probabilistic automata or how to learn and classify proteins in linear time and space. | Alberto Apostolico, Gill Bejerano |
| 2000 | A combinatorial approach to protein docking with flexible side-chains. | Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Mller |
| 2000 | Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. | Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara |
| 2000 | On approximation algorithms for local multiple alignment. | Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono |
| 1999 | Trends in computational biology. | John C. Wooley |
| 1999 | Derivation of sensitive discrimination potential for virtual ligand screening. | Maxim Totrov, Ruben Abagyan |
| 1999 | Genome sequences and protein structures. | Sarah A. Teichmann, Jong-Chan Park, Cyrus Chothia |
| 1999 | DNA microarrays - the how and the why. | Ed Southern |
| 1999 | Comparison of complete genomes: Organization and evolution (abstract). | Piotr P. Slonimski |
| 1999 | Probability models for genome rearrangement and linear invariants for phylogenetic inference. | David Sankoff, Mathieu Blanchette |
| 1999 | On the power of universal bases in sequencing by hybridization. | Franco P. Preparata, Alan M. Frieze, Eli Upfal |
| 1999 | A dictionary based approach for gene annotation. | Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman |
| 1999 | Progress toward the whole-genome shotgun sequencing of Drosophila. | Gene Myers |
| 1999 | The past, present and future of protein structure prediction (abstract). | John Moult |
| 1999 | Coupled optimization in protein docking. | Julie C. Mitchell, J. Ben Rosen, Andrew T. Phillips, Lynn F. Ten Eyck |
| 1999 | Construction of physical maps from oligonucleotide fingerprints data. | Guy Mayraz, Ron Shamir |
| 1999 | Internal loops in RNA secondary structure prediction. | Rune B. Lyngs, Michael Zuker, Christian N. S. Pedersen |