| 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 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 Rouzé, Yves Moreau |
| 2001 | A NMR-spectra-based scoring function for protein docking. Oliver Kohlbacher, Andreas Burchardt, Andreas Moll, Andreas Hildebrandt, Peter Bayer, Hans-Peter Lenhof |
| 2001 | A new approach to fragment assembly in DNA sequencing. Pavel A. Pevzner, Haixu Tang, Michael S. Waterman |
| 2001 | A new approach to sequence comparison: normalized sequence alignment. Abdullah N. Arslan, Ömer Egecioglu, Pavel A. Pevzner |
| 2001 | A structural EM algorithm for phylogenetic inference. Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko |
| 2001 | Algorithms for identifying protein cross-links via tandem mass spectrometry. Ting Chen, Jacob D. Jaffe, George M. Church |
| 2001 | Algorithms for phylogenetic footprinting. Mathieu Blanchette |
| 2001 | An optimal procedure for gap closing in whole genome shotgun sequencing. Richard Beigel, Noga Alon, Simon Kasif, Mehmet Serkan Apaydin, Lance Fortnow |
| 2001 | Analysis techniques for microarray time-series data. Vladimir Filkov, Steven Skiena, Jizu Zhi |
| 2001 | Applications of generalized pair hidden Markov models to alignment and gene finding problems. Lior Pachter, Marina Alexandersson, Simon Cawley |
| 2001 | Class discovery in gene expression data. Amir Ben-Dor, Nir Friedman, Zohar Yakhini |
| 2001 | Comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only). B. Franz Lang |
| 2001 | Comparing sequence scaffolds. Gene Myers |
| 2001 | Context-specific Bayesian clustering for gene expression data. Yoseph Barash, Nir Friedman |
| 2001 | Creating the backbone for the virtual cell: cell mapping projects on the run (abstract only). Matthias Wilm |
| 2001 | DNA segmentation as a model selection process. Wentian Li |
| 2001 | Edit distance between two RNA structures. Guohui Lin, Bin Ma, Kaizhong Zhang |
| 2001 | Efficient algorithms for lateral gene transfer problems. Michael T. Hallett, Jens Lagergren |
| 2001 | Extracting structural information using time-frequency analysis of protein NMR data. Christopher James Langmead, Bruce Randall Donald |
| 2001 | Fast and simple character classes and bounded gaps pattern matching, with application to protein searching. Gonzalo Navarro, Mathieu Raffinot |
| 2001 | Fast recovery of evolutionary trees with thousands of nodes. Miklós Csürös |
| 2001 | Finding motifs using random projections. Jeremy Buhler, Martin Tompa |
| 2001 | Gene functional classification from heterogeneous data. Paul Pavlidis, Jason Weston, Jinsong Cai, William Noble Grundy |
| 2001 | Gene-finding via tandem mass spectrometry. Ting Chen |
| 2001 | Genetics and genemoics: impact on drug discovery and development. Klaus Lindpaintner |
| 2001 | Geometric algorithms for the analysis of 2D-electrophoresis gels. Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk |
| 2001 | Hunger for new technologies, metrics, and spatiotemporal models in functional genomic (abstract only). George M. Church |
| 2001 | Imposing specificity by regulated localization (abstract only). Mark Ptashne |
| 2001 | Information processing by cells and biologists (abstract only). Roger Brent |
| 2001 | Large scale sequencing by hybridization. Ron Shamir, Dekel Tsur |
| 2001 | On the predictive power of sequence similarity in yeast. Yonatan Bilu, Michal Linial |
| 2001 | Optimal sequencing by hybridization in rounds. Alan M. Frieze, Bjarni V. Halldórsson |
| 2001 | Predicting the beta-helix fold from protein sequence data. Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger |
| 2001 | Proceedings of the Fifth Annual International Conference on Computational Biology, RECOMB 2001, Montréal, Québec, Canada, April 22-25, 2001 Thomas Lengauer |
| 2001 | RNA biology and the genome (abstract only). Phillip A. Sharp |
| 2001 | Rapid significance estimation in local sequence alignment with gaps. Ralf Bundschuh |
| 2001 | Regulatory element detection using correlation with expression (abstract only). Harmen J. Bussemaker, Hao Li, Eric D. Siggia |
| 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 | The role of computational chemistry in translating genomic information into bioactive small molecules (abstract only). Yvonne C. Martin |
| 2001 | The sequence of the human genome (abstract only). Mark Adams |
| 2001 | Towards predicting coiled-coil protein interactions. Mona Singh, Peter S. Kim |
| 2001 | Using motion planning to study protein folding pathways. Guang Song, Nancy M. Amato |
| 2001 | Zinc finger gene clusters and tandem gene duplication. Mengxiang Tang, Michael S. Waterman, Shibu Yooseph |