| 1996 | Gene Prediction by Pattern Recognition and Homology Search. | Ying Xu, Edward C. Uberbacher |
| 1996 | Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families. | Thomas D. Wu, Douglas L. Brutlag |
| 1996 | A Knowledge-Based Method for Protein Structure Refinement and Prediction. | Shankar Subramaniam, David K. Tcheng, James M. Fenton |
| 1996 | Compact Encoding Strategies for DNA Sequence Similarity Search. | David J. States, Pankaj Agarwal |
| 1996 | Finding Genes in DNA Using Decision Trees and Dynamic Programming. | Steven Salzberg, Xin Chen, John C. Henderson, Kenneth H. Fasman |
| 1996 | Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming. | Burkhard Rost, Rita Casadio, Piero Fariselli |
| 1996 | Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. | Anders Gorm Pedersen, Pierre Baldi, Sren Brunak, Yves Chauvin |
| 1996 | Genome-Scale DNA Sequence Recognition by Hybridization to Short Oligomers. | Aleksandar Milosavljevic, Suzana Savkovic, Radomir Crkvenjakov, David Salbego, Hope Serrato, Heidi Kreuzer, Anne Gemmell, Shawna Batus, Danica Grujic, Susan Carnahan, Jovanka Tepavcevic |
| 1996 | Applications of GeneMark in Multispecies Environments. | James D. McIninch, William S. Hayes, Mark Borodovsky |
| 1996 | Parameterization Studies for the SAM and HMMER Methods of Hidden Markov Model Generation. | Marcella A. McClure, Chris Smith, Pete Elton |
| 1996 | A Grammar-Based Unification of Several Alignment and Folding Algorithms. | Fabrice Lefebvre |
| 1996 | A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA. | David Kulp, David Haussler, Martin G. Reese, Frank H. Eeckman |
| 1996 | Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing. | Jin Kim, James R. Cole, Eric Torng, Sakti Pramanik |
| 1996 | HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae. | Peter D. Karp, Christos A. Ouzounis, Suzanne M. Paley |
| 1996 | A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. | Paul Horton, Kenta Nakai |
| 1996 | A Top-Down Approach to Whole Genome Visualization. | Klaus Heumann, C. Harris, Hans-Werner Mewes |
| 1996 | Good Maps Are Straight. | Eric Harley, Anthony J. Bonner, Nathan Goodman |
| 1996 | Ontological Foundations for Biology Knowledge Models. | Carole D. Hafner, Natalya Fridman Noy |
| 1996 | GeneFisher-Software Support for the Detection of Postulated Genes. | Robert Giegerich, Folker Meyer, Chris Schleiermacher |
| 1996 | Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. | Mark Gerstein, Michael Levitt |
| 1996 | The Mathematical Model of Subtractive Hybridization and Its Practical Application. | Olga D. Ermolaeva, Sergey A. Lukyanov, Eugene D. Sverdlov |
| 1996 | A Sequence Similarity Search Algorithm Based on a Probabilistic Interpretation of an Alignment Scoring System. | Philipp Bucher, Kay Hofmann |
| 1996 | Discovering Patterns and Subfamilies in Biosequences. | Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo |
| 1996 | From Electron Density and Sequence to Structure: Integrating Protein Image Analysis and Threading for Structure Determination. | Kim Baxter, Evan W. Steeg, Richard H. Lathrop, Janice I. Glasgow, Suzanne Fortier |
| 1996 | The Megaprior Heuristic for Discovering Protein Sequence Patterns. | Timothy L. Bailey, Michael Gribskov |