| 2000 | A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. | Mary E. Cosner, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman |
| 2000 | Biclustering of Expression Data. | Yizong Cheng, George M. Church |
| 2000 | Efficient Attractor Analysis Based on Self-Dependent Subsets of Elements An Application to Signal Transduction Studies. | Maura Crdenas-Garca, Jaime Lagunez-Otero, Nikolai A. Korneev |
| 2000 | Analysis of Gene Expression Microarrays for Phenotype Classification. | Andrea Califano, Gustavo Stolovitzky, Yuhai Tu |
| 2000 | Regulatory Element Detection Using a Probabilistic Segmentation Model. | Harmen J. Bussemaker, Hao Li, Eric D. Siggia |
| 2000 | Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars. | Michael P. S. Brown |
| 2000 | Robust Parametric and Semi-Parametric Spot Fitting for Spot Array Images. | Norbert Brndle, Horng-Yang Chen, Horst Bischof, Hilmar Lapp |
| 2000 | An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. | Mathieu Blanchette, Benno Schwikowski, Martin Tompa |
| 2000 | Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. | Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Sren Brunak |
| 2000 | Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. | Christopher Bailey-Kellogg, John J. Kelley, Clifford Stein, Bruce Randall Donald |
| 2000 | The Conserved Exon Method for Gene Finding. | Vineet Bafna, Daniel H. Huson |
| 1999 | Database Search Based on Bayesian Alignment. | Jun Zhu, Roland Lthy, Charles E. Lawrence |
| 1999 | Analysis of Ribosomal RNA Sequences by Combinatorial Clustering. | Poe Xing, Casimir A. Kulikowski, Ilya B. Muchnik, Inna Dubchak, Denise M. Wolf, Sylvia Spengler, Manfred Zorn |
| 1999 | Pharmaceutical Target Discovery Using Guilt-by-Association: Schizophrenia and Parkinson's Disease Genes. | Michael G. Walker, Wayne Volkmuth, Tod M. Klingler |
| 1999 | Seamless Integration of Biological Applications within a Database Framework. | Thodoros Topaloglou, Anthony Kosky, Victor M. Markowitz |
| 1999 | An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem. | Martin Tompa |
| 1999 | A Motion Planning Approach to Flexible Ligand Binding. | Amit Pal Singh, Jean-Claude Latombe, Douglas L. Brutlag |
| 1999 | Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity. | Volker Schnecke, Leslie A. Kuhn |
| 1999 | A Linear Time Algorithm for Finding All Maximal Scoring Subsequences. | Walter L. Ruzzo, Martin Tompa |
| 1999 | Building Dictionaries of 1D and 3D Motifs by Mining the Unaligned 1D Sequences of 17 Archaeal and Bacterial Genomes. | Isidore Rigoutsos, Yuan Gao, Aris Floratos, Laxmi Parida |
| 1999 | Rapid Assessment of Extremal Statistics for Gapped Local Alignment. | Rolf Olsen, Ralf Bundschuh, Terence Hwa |
| 1999 | A Dataset Generator for Whole Genome Shotgun Sequencing. | Gene Myers |
| 1999 | Spatio-Temporal Registration of the Expression Patterns of Drosophila Segmentation Genes. | Ekaterina M. Myasnikova, David Kosman, John Reinitz, Maria Samsonova |
| 1999 | Quantitative, Scalable Discrete-Event Simulation of Metabolic Pathways. | Peter A. Meric, Michael J. Wise |
| 1999 | Metrics and Similarity Measures for Hidden Markov Models. | Rune B. Lyngs, Christian N. S. Pedersen, Henrik Nielsen |