| 1998 | Assessment of ab initio protein structure prediction. | Arthur M. Lesk |
| 1998 | A polyhedral approach to RNA sequence structure alignment. | Hans-Peter Lenhof, Knut Reinert, Martin Vingron |
| 1998 | Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo. | Jae Kyu Lee, Vlado Danck, Michael S. Waterman |
| 1998 | Beyond mutation matrices: physical-chemistry based evolutionary models. | Jeffrey M. Koshi, David P. Mindell, Richard A. Goldstein |
| 1998 | Genome analysis using clusters of orthologous groups (COGs). | Eugene V. Koonin, Roman L. Tatusov, Michael Y. Galperin, Michael N. Rosanov |
| 1998 | The ordinal quartet method. | Paul E. Kearney |
| 1998 | Algorithms for optical mapping. | Richard M. Karp, Ron Shamir |
| 1998 | Optimal detection of sequence similarity by local alignment. | Terence Hwa, Michael Lssig |
| 1998 | Dynamic programming alignment accuracy. | Ian Holmes, Richard Durbin |
| 1998 | Evolutionary drug discovery (abstract). | Klaus Gubernator |
| 1998 | Family-based homology detection via pairwise sequence comparison. | William Noble Grundy |
| 1998 | Algorithmic determination of core positions in the | Israel M. Gelfand, Alexander Kister, Casimir A. Kulikowski, Ognyan Stoyanov |
| 1998 | A formally exact method to numerically analyze local denaturation in superhelical DNA. | Richard M. Fye, Craig J. Benham |
| 1998 | How fast a protein chain can fold to its most stable structure? | Alexei V. Finkelstein, Azat Ya. Badretdinov |
| 1998 | Constructing maps using the span and inclusion relations. | Daniel P. Fasulo, Tao Jiang, Richard M. Karp, Nitin Sharma |
| 1998 | On the complexity of protein folding (abstract). | Pierluigi Crescenzi, Deborah Goldman, Christos H. Papadimitriou, Antonio Piccolboni, Mihalis Yannakakis |
| 1998 | The human genetic variation (abstract): oligonucleotide chips and human disease. | David R. Cox |
| 1998 | The hierarchical organization of molecular structure computations. | Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman |
| 1998 | Enhancements in sequence analysis with DNA arrays (abstract). | Charles R. Cantor |
| 1998 | Better methods for solving parsimony and compatibility. | Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph |
| 1998 | Protein folding in the hydrophobic-hydrophilic ( | Bonnie Berger, Frank Thomson Leighton |
| 1998 | An algorithm for finding tandem repeats of unspecified pattern size. | Gary Benson |
| 1998 | From four-taxon trees to phylogenies (preliminary report): the case of mammalian evolution. | Amir Ben-Dor, Benny Chor, Dan Graur, Ron Ophir, Dan Pelleg |
| 1998 | Detecting non-adjoining correlations with signals in DNA. | Pankaj Agarwal, Vineet Bafna |
| 1998 | Challenges of biomolecular structure prediction (abstract). | Ruben Abagyan |