| 2000 | Linear Modeling of Genetic Networks from Experimental Data. | Eugene P. van Someren, Lodewyk F. A. Wessels, Marcel J. T. Reinders |
| 2000 | A Statistical Method for Finding Transcription Factor Binding Sites. | Saurabh Sinha, Martin Tompa |
| 2000 | Alignment of Flexible Protein Structures. | Maxim Shatsky, Zipora Y. Fligelman, Ruth Nussinov, Haim J. Wolfson |
| 2000 | Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis. | Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski |
| 2000 | Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. | Roded Sharan, Ron Shamir |
| 2000 | Genomic Fold Assignment and Rational Modeling of Proteins of Biological Interest. | J. Michael Sauder, Roland L. Dunbrack Jr. |
| 2000 | Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains. | Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, Russ B. Altman |
| 2000 | A Pragmatic Information Extraction Strategy for Gathering Data on Genetic Interactions. | Denys Proux, Franois Rechenmann, Laurent Julliard |
| 2000 | Combinatorial Approaches to Finding Subtle Signals in DNA Sequences. | Pavel A. Pevzner, Sing-Hoi Sze |
| 2000 | Spectrum Alignment: Efficient Resequencing by Hybridization. | Itsik Pe'er, Ron Shamir |
| 2000 | Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images. | Robert F. Murphy, Michael V. Boland, Meel Velliste |
| 2000 | An Evaluation of Ontology Exchange Languages for Bioinformatics. | Robin McEntire, Peter D. Karp, Neil F. Abernethy, David Benton, Gregg Helt, Matt DeJongh, Robert Kent, Anthony Kosky, Suzanna Lewis, Dan Hodnett, Eric P. Neumann, Frank Olken, Dhiraj K. Pathak, Peter Tarczy-Hornoch, Luca Toldo, Thodoros Topaloglou |
| 2000 | Computation and Visualization of Degenerate Repeats in Complete Genomes. | Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich |
| 2000 | UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences. | Zhengyan Kan, Warren Gish, Eric C. Rouchka, Jarret Glasscock, David J. States |
| 2000 | Search for a New Description of Protein Topology and Local Structure. | Lukasz Jaroszewski, Adam Godzik |
| 2000 | Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data. | Ian Holmes, William J. Bruno |
| 2000 | Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods. | Steven Hampson, Pierre Baldi, Dennis F. Kibler, Suzanne B. Sandmeyer |
| 2000 | A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations. | Dan Gusfield |
| 2000 | Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization. | Vanathi Gopalakrishnan, Bruce G. Buchanan, John M. Rosenberg |
| 2000 | Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold. | Iddo Friedberg, Tommy Kaplan, Hanah Margalit |
| 2000 | Integrative Analysis of Protein Interaction Data. | Matthias Fellenberg, Kaj Albermann, Alfred Zollner, Hans-Werner Mewes, Jean Hani |
| 2000 | Prediction of the Number of Residue Contacts in Proteins. | Piero Fariselli, Rita Casadio |
| 2000 | Protein Family Classification Using Sparse Markov Transducers. | Eleazar Eskin, William Noble Grundy, Yoram Singer |
| 2000 | Accelerating Protein Classification Using Suffix Trees. | Bogdan Dorohonceanu, Craig G. Nevill-Manning |
| 2000 | A Probabilistic Learning Approach to Whole-Genome Operon Prediction. | Mark W. Craven, David Page, Jude W. Shavlik, Joseph Bockhorst, Jeremy D. Glasner |