| 2001 | Molecular Fingerprinting on the SIMD Parallel Processor Kestrel. | Eric Rice, Richard Hughey |
| 2001 | A New Algorithm for Analysis of Within-Host HIV-1 Evolution. | Fengrong Ren, Soichi Ogishima, Hiroshi Tanaka |
| 2001 | Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra. | Aviv Regev, William Silverman, Ehud Shapiro |
| 2001 | Collective Reorientational Motion and Nuclear Spin Relaxation in Proteins. | J. J. Prompers, S. F. Lienin, R. Brschweiler |
| 2001 | Promoter Region-Based Classification of Genes. | Paul Pavlidis, Terrence S. Furey, M. Liberto, David Haussler, William Noble Grundy |
| 2001 | A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data. | Peter J. Park, Marcello Pagano, Marco Bonetti |
| 2001 | Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar. | Jong C. Park, Hyun Sook Kim, Jung-Jae Kim |
| 2001 | A New Implmentation and Detailed Study of Breakpoint Analysis. | Bernard M. E. Moret, Stacia K. Wyman, David A. Bader, Tandy J. Warnow, Mi Yan |
| 2001 | A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison. | Wellington Santos Martins, Juan del Cuvillo, F. J. Useche, Kevin B. Theobald, Guang R. Gao |
| 2001 | A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions. | Yael Mandel-Gutfreund, A. Baron, Hanah Margalit |
| 2001 | Development of a System for the Inference of Large Scale Genetic Networks. | Yukihiro Maki, Daisuke Tominaga, Masahiro Okamoto, Shoji Watanabe, Yukihiro Eguchi |
| 2001 | BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. | X. Liu, Douglas L. Brutlag, Jun S. Liu |
| 2001 | Reverse Engineering of Metabolic Pathways from Observed Data Using Genetic Programming. | John R. Koza, William Mydlowec, Guido Lanza, Jessen Yu, Martin A. Keane |
| 2001 | Analyzing Rate Heterogeneity During Protein Evolution. | Jeffrey M. Koshi, Richard A. Goldstein |
| 2001 | Mutual Information Analysis as a Tool to Assess the Role of Aneuploidy in the Generation of Cancer-Associated Differential Gene Expression Patterns. | Gregory T. Klus, Andrew Song, Ari Schick, Mattias Wahde, Zoltan Szallasi |
| 2001 | A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny. | Junhyong Kim, Benjamin A. Salisbury |
| 2001 | Unsupervised Learning from Complex Data: The Matrix Incision Tree Algorithm. | Ju-Han Kim, Lucila Ohno-Machado, Isaac S. Kohane |
| 2001 | Genome, Pathway and Interaction Bioinformatics - Session Introduction. | Peter D. Karp, Eric P. Neumann, Pedro Romero |
| 2001 | TEXTQUEST: Document Clustering of MEDLINE Abstracts For Concept Discovery In Molecular Biology. | Ioannis Iliopoulos, Anton J. Enright, Christos A. Ouzounis |
| 2001 | Predicting Gene Function from Gene Expressions and Ontologies. | Torgeir R. Hvidsten, Henryk Jan Komorowski, Arne K. Sandvik, Astrid Lgreid |
| 2001 | Gene Verification and Discovery by Walking Tree Method. | Tai Hsu, Paul Cull |
| 2001 | An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree. | Jotun Hein |
| 2001 | Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks. | Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young |
| 2001 | A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization. | Chittibabu Guda, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov |
| 2001 | Sequence Analysis With the Kestrel SIMD Parallel Processor. | Leslie Grate, Mark Diekhans, David M. Dahle, Richard Hughey |