| 1999 | Clustering gene expression patterns. | Amir Ben-Dor, Zohar Yakhini |
| 1999 | Modeling protein families using probabilistic suffix trees. | Gill Bejerano, Golan Yona |
| 1999 | Computational analysis of molecular diversity for drug discovery. | Martin J. Bayley, Valerie J. Gillet, Peter Willett, John Bradshaw, Darren V. S. Green |
| 1999 | Classifying proteins by family using the product of correlated | Timothy L. Bailey, William Noble Grundy |
| 1999 | Algorithms for whole genome shotgun sequencing. | Eric L. Anson, Eugene W. Myers |
| 1998 | Alignments without low-scoring regions. | Zheng Zhang, Piotr Berman, Webb Miller |
| 1998 | Mass spectrometry and the proteome (abstract). | John R. Yates III |
| 1998 | A new method for modeling and solving the protein fold recognition problem (extended abstract). | Ying Xu, Dong Xu, Edward C. Uberbacher |
| 1998 | Regression analysis of multiple protein structures. | Thomas D. Wu, Trevor Hastie, Scott C. Schmidler, Douglas L. Brutlag |
| 1998 | The theoretical limits of DNA sequence discrimination of polyamides. | Wynn L. Walker, David S. Goodsell, Elliot M. Landaw |
| 1998 | Maxwell demon and topology simplification by type II topoisomerases. | Alexander Vologodskii |
| 1998 | Analysis of the position dependent amino acid probabilities and its application to the search for remote homologues. | Shamil R. Sunyaev, Igor V. Rodchenkov, Frank Eisenhaber, Eugene N. Kuznetsov |
| 1998 | Modeling DNA shuffling. | Fengzhu Sun |
| 1998 | New approaches to genomic analysis using single molecules. | David C. Schwartz, Thomas S. Anantharaman, C. Aston, Bud Mishra, V. Clarke, D. Gebauer, S. Delobette, E. Dimalanta, J. Edington, J. Evenzehav, J. Giacalone, C. Hiort, E. Huff, J. Jing, Z. Lai, E. Lee, J. Lin, B. Porter, R. Qi, Y. Skiadis |
| 1998 | Multiple genome rearrangements. | David Sankoff, Mathieu Blanchette |
| 1998 | Identifying satellites in nucleic acid sequences. | Marie-France Sagot, Eugene W. Myers |
| 1998 | An algorithm for finding novel gapped motifs in DNA sequences. | Emily Rocke, Martin Tompa |
| 1998 | Motif discovery without alignment or enumeration (extended abstract). | Isidore Rigoutsos, Aris Floratos |
| 1998 | A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. | Boris A. Reva, Alexei V. Finkelstein, Jeffrey Skolnick |
| 1998 | A unified approach to word statistics. | Mireille Rgnier |
| 1998 | Estimation of allele frequencies from color-multiplexed electropherograms. | David G. Politte, David R. Maffitt, David J. States |
| 1998 | Partitioning | Laxmi Parida, Bud Mishra |
| 1998 | On reconstructing species trees from gene trees in term of duplications and losses. | Bin Ma, Ming Li, Louxin Zhang |
| 1998 | A structure based similarity measure for nucleic acid sequence comparison. | Rongxiang Liu, Thomas W. Blackwell, David J. States |
| 1998 | Bridging the gap between sequence and structure (abstract). | M. Levitt |