| 1999 | Efficient database screening for rational drug design using pharmacophore-constrained conformational search. | Steven M. LaValle, Paul W. Finn, Lydia E. Kavraki, Jean-Claude Latombe |
| 1999 | An anytime algorithm for gapped block protein threading with pair interactions. | Richard H. Lathrop |
| 1999 | Efficient algorithms for protein sequence design and the analysis of certain evolutionary fitness landscapes. | Jon M. Kleinberg |
| 1999 | Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM. | Lawrence A. Kelley, Robert M. MacCallum, Michael J. E. Sternberg |
| 1999 | Algorithms for choosing differential gene expression experiments. | Richard M. Karp, Roland Stoughton, Ka Yee Yeung |
| 1999 | Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. | Daniel H. Huson, Scott Nettles, Tandy J. Warnow |
| 1999 | An algorithm for clustering cDNAs for gene expression analysis. | Erez Hartuv, Armin O. Schmitt, Jrg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir |
| 1999 | Significance testing for genomic mismatch scanning. | Gregory R. Grant, R. S. Spielman, Elisabetta Manduchi, Vivian G. Cheung, Warren J. Ewens |
| 1999 | Evolution of metabolisms: a new method for the comparison of metabolic pathways. | Christian V. Forst, Klaus Schulten |
| 1999 | Sequence homology detection through large scale pattern discovery. | Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustavo Stolovitzky, Yuan Gao |
| 1999 | Reconstructing the pre-doubling genome. | Nadia El-Mabrouk, David Bryant, David Sankoff |
| 1999 | A solvation potential with improved contact definitions and optimized by extensive threading. | Alan A. Dombkowski, Gordon M. Crippen |
| 1999 | De Novo peptide sequencing via tandem mass spectrometry: a graph-theoretical approach. | Vlado Danck, Theresa A. Addona, Karl R. Clauser, James E. Vath |
| 1999 | Optimizing combinatorial library construction via split synthesis. | Barry Cohen, Steven Skiena |
| 1999 | Whole genome association studies in humans (abstract). | Daniel Cohen, Marta Blumenfeld, Ilya Chumakov, Nicholas J. Schork |
| 1999 | Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut. | Thomas Christof, John D. Kececioglu |
| 1999 | Fast detection of common geometric substructure in proteins. | L. Paul Chew, Daniel P. Huttenlocher, Klara Kedem, Jon M. Kleinberg |
| 1999 | Identifying gene regulatory networks from experimental data. | Ting Chen, Vladimir Filkov, Steven Skiena |
| 1999 | Formulations and hardness of multiple sorting by reversals. | Alberto Caprara |
| 1999 | Untitled record | Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Eric Rivals, Martin Vingron |
| 1999 | Comparing genes and genomes (abstract): from polymorphism to phylogeny. | Peer Bork |
| 1999 | Searching gene transfers on | Laurent Bize, Florence Muri, Franck Samson, Franois Rodolphe, S. Dusko Ehrlich, Bernard Prun, Philippe Bessires |
| 1999 | A method for optimal design of a threading scoring function. | Jadwiga R. Bienkowska, Robert G. Rogers, Temple F. Smith |
| 1999 | Faster reliable phylogenetic analysis. | Vincent Berry, David Bryant |
| 1999 | Winnowing sequences from a database search. | Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller |