| 2001 | A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes. | Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouz, Yves Moreau |
| 2001 | Zinc finger gene clusters and tandem gene duplication. | Mengxiang Tang, Michael S. Waterman, Shibu Yooseph |
| 2001 | Using motion planning to study protein folding pathways. | Guang Song, Nancy M. Amato |
| 2001 | Towards predicting coiled-coil protein interactions. | Mona Singh, Peter S. Kim |
| 2001 | RNA biology and the genome (abstract only). | Phillip A. Sharp |
| 2001 | Large scale sequencing by hybridization. | Ron Shamir, Dekel Tsur |
| 2001 | Imposing specificity by regulated localization (abstract only). | Mark Ptashne |
| 2001 | A new approach to fragment assembly in DNA sequencing. | Pavel A. Pevzner, Haixu Tang, Michael S. Waterman |
| 2001 | Gene functional classification from heterogeneous data. | Paul Pavlidis, Jason Weston, Jinsong Cai, William Noble Grundy |
| 2001 | Applications of generalized pair hidden Markov models to alignment and gene finding problems. | Lior Pachter, Marina Alexandersson, Simon Cawley |
| 2001 | Fast and simple character classes and bounded gaps pattern matching, with application to protein searching. | Gonzalo Navarro, Mathieu Raffinot |
| 2001 | Comparing sequence scaffolds. | Gene Myers |
| 2001 | The role of computational chemistry in translating genomic information into bioactive small molecules (abstract only). | Yvonne C. Martin |
| 2001 | Edit distance between two RNA structures. | Guohui Lin, Bin Ma, Kaizhong Zhang |
| 2001 | Genetics and genemoics: impact on drug discovery and development. | Klaus Lindpaintner |
| 2001 | DNA segmentation as a model selection process. | Wentian Li |
| 2001 | Extracting structural information using time-frequency analysis of protein NMR data. | Christopher James Langmead, Bruce Randall Donald |
| 2001 | Comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only). | B. Franz Lang |
| 2001 | 101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem. | Giuseppe Lancia, Robert D. Carr, Brian Walenz, Sorin Istrail |
| 2001 | A NMR-spectra-based scoring function for protein docking. | Oliver Kohlbacher, Andreas Burchardt, Andreas Moll, Andreas Hildebrandt, Peter Bayer, Hans-Peter Lenhof |
| 2001 | Separtating repeats in DNA sequence assembly. | John D. Kececioglu, Jun Ju |
| 2001 | The greedy path-merging algorithm for sequence assembly. | Daniel H. Huson, Knut Reinert, Eugene W. Myers |
| 2001 | Efficient algorithms for lateral gene transfer problems. | Michael T. Hallett, Jens Lagergren |
| 2001 | Optimal sequencing by hybridization in rounds. | Alan M. Frieze, Bjarni V. Halldrsson |
| 2001 | A structural EM algorithm for phylogenetic inference. | Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko |