| 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 | A method for optimal design of a threading scoring function. Jadwiga R. Bienkowska, Robert G. Rogers, Temple F. Smith |
| 1999 | A solvation potential with improved contact definitions and optimized by extensive threading. Alan A. Dombkowski, Gordon M. Crippen |
| 1999 | Algorithms for choosing differential gene expression experiments. Richard M. Karp, Roland Stoughton, Ka Yee Yeung |
| 1999 | Algorithms for whole genome shotgun sequencing. Eric L. Anson, Eugene W. Myers |
| 1999 | An algorithm for clustering cDNAs for gene expression analysis. Erez Hartuv, Armin O. Schmitt, Jörg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir |
| 1999 | An anytime algorithm for gapped block protein threading with pair interactions. Richard H. Lathrop |
| 1999 | Classifying proteins by family using the product of correlated Timothy L. Bailey, William Noble Grundy |
| 1999 | Clustering gene expression patterns. Amir Ben-Dor, Zohar Yakhini |
| 1999 | Comparing genes and genomes (abstract): from polymorphism to phylogeny. Peer Bork |
| 1999 | Comparison of complete genomes: Organization and evolution (abstract). Piotr P. Slonimski |
| 1999 | Computational analysis of molecular diversity for drug discovery. Martin J. Bayley, Valerie J. Gillet, Peter Willett, John Bradshaw, Darren V. S. Green |
| 1999 | Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut. Thomas Christof, John D. Kececioglu |
| 1999 | Construction of physical maps from oligonucleotide fingerprints data. Guy Mayraz, Ron Shamir |
| 1999 | Coupled optimization in protein docking. Julie C. Mitchell, J. Ben Rosen, Andrew T. Phillips, Lynn F. Ten Eyck |
| 1999 | DNA microarrays - the how and the why. Ed Southern |
| 1999 | De Novo peptide sequencing via tandem mass spectrometry: a graph-theoretical approach. Vlado Dancík, Theresa A. Addona, Karl R. Clauser, James E. Vath |
| 1999 | Derivation of sensitive discrimination potential for virtual ligand screening. Maxim Totrov, Ruben Abagyan |
| 1999 | Efficient algorithms for protein sequence design and the analysis of certain evolutionary fitness landscapes. Jon M. Kleinberg |
| 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 | Evolution of metabolisms: a new method for the comparison of metabolic pathways. Christian V. Forst, Klaus Schulten |
| 1999 | Fast detection of common geometric substructure in proteins. L. Paul Chew, Daniel P. Huttenlocher, Klara Kedem, Jon M. Kleinberg |
| 1999 | Faster reliable phylogenetic analysis. Vincent Berry, David Bryant |
| 1999 | Formulations and hardness of multiple sorting by reversals. Alberto Caprara |
| 1999 | Genome sequences and protein structures. Sarah A. Teichmann, Jong-Chan Park, Cyrus Chothia |
| 1999 | Identifying gene regulatory networks from experimental data. Ting Chen, Vladimir Filkov, Steven Skiena |
| 1999 | Internal loops in RNA secondary structure prediction. Rune B. Lyngsø, Michael Zuker, Christian N. S. Pedersen |
| 1999 | Modeling protein families using probabilistic suffix trees. Gill Bejerano, Golan Yona |
| 1999 | Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. Daniel H. Huson, Scott Nettles, Tandy J. Warnow |
| 1999 | On the power of universal bases in sequencing by hybridization. Franco P. Preparata, Alan M. Frieze, Eli Upfal |
| 1999 | Optimizing combinatorial library construction via split synthesis. Barry Cohen, Steven Skiena |
| 1999 | Probability models for genome rearrangement and linear invariants for phylogenetic inference. David Sankoff, Mathieu Blanchette |
| 1999 | Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, RECOMB 1999, Lyon, France, April 11-14, 1999 Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman |
| 1999 | Progress toward the whole-genome shotgun sequencing of Drosophila. Gene Myers |
| 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 | Reconstructing the pre-doubling genome. Nadia El-Mabrouk, David Bryant, David Sankoff |
| 1999 | Searching gene transfers on Laurent Bize, Florence Muri, Franck Samson, François Rodolphe, S. Dusko Ehrlich, Bernard Prun, Philippe Bessières |
| 1999 | Sequence homology detection through large scale pattern discovery. Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustavo Stolovitzky, Yuan Gao |
| 1999 | Significance testing for genomic mismatch scanning. Gregory R. Grant, R. S. Spielman, Elisabetta Manduchi, Vivian G. Cheung, Warren J. Ewens |
| 1999 | The past, present and future of protein structure prediction (abstract). John Moult |
| 1999 | Trends in computational biology. John C. Wooley |
| 1999 | Whole genome association studies in humans (abstract). Daniel Cohen, Marta Blumenfeld, Ilya Chumakov, Nicholas J. Schork |
| 1999 | Winnowing sequences from a database search. Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller |