| 147 | -- | 148 | Thomas Lengauer. Preface: Special RECOMB 2001 Issue |
| 149 | -- | 168 | Nancy M. Amato, Guang Song. Using Motion Planning to Study Protein Folding Pathways |
| 169 | -- | 191 | Yoseph Barash, Nir Friedman. Context-Specific Bayesian Clustering for Gene Expression Data |
| 193 | -- | 210 | Yonatan Bilu, Michal Linial. The Advantage of Functional Prediction Based on Clustering of Yeast Genes and Its Correlation with Non-Sequence Based Classifications |
| 211 | -- | 223 | Mathieu Blanchette, Benno Schwikowski, Martin Tompa. Algorithms for Phylogenetic Footprinting |
| 225 | -- | 242 | Jeremy Buhler, Martin Tompa. Finding Motifs Using Random Projections |
| 243 | -- | 260 | Ralf Bundschuh. Rapid Significance Estimation in Local Sequence Alignment with Gaps |
| 261 | -- | 276 | Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger. Predicting the Beta-Helix Fold from Protein Sequence Data |
| 277 | -- | 297 | Miklós Csürös. Fast Recovery of Evolutionary Trees with Thousands of Nodes |
| 299 | -- | 315 | Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk. Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels |
| 317 | -- | 330 | Vladimir Filkov, Steven Skiena, Jizu Zhi. Analysis Techniques for Microarray Time-Series Data |
| 331 | -- | 353 | Nir Friedman, Matan Ninio, Itsik Pe er, Tal Pupko. A Structural EM Algorithm for Phylogenetic Inference |
| 355 | -- | 369 | Alan M. Frieze, Bjarni V. Halldórsson. Optimal Sequencing by Hybridization in Rounds |
| 371 | -- | 388 | Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang. A General Edit Distance between RNA Structures |
| 389 | -- | 399 | Lior Pachter, Marina Alexandersson, Simon Cawley. Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems |
| 401 | -- | 411 | Paul Pavlidis, Jason Weston, Jinsong Cai, William Stafford Noble. Learning Gene Functional Classifications from Multiple Data Types |
| 413 | -- | 428 | Ron Shamir, Dekel Tsur. Large Scale Sequencing by Hybridization |
| 429 | -- | 446 | Mengxiang Tang, Michael S. Waterman, Shibu Yooseph. Zinc Finger Gene Clusters and Tandem Gene Duplication |
| 447 | -- | 464 | Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau. A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes |