| 2001 | Feature selection for DNA methylation based cancer classification. | Fabian Model, Pter Adorjn, Alexander Olek, Christian Piepenbrock |
| 2001 | Generating protein interaction maps from incomplete data: application to fold assignment. | Michael Lappe, Jong-Chan Park, Oliver Niggemann, Liisa Holm |
| 2001 | Integrating genomic homology into gene structure prediction. | Ian Korf, Paul Flicek, Daniel Duan, Michael R. Brent |
| 2001 | Design of a compartmentalized shotgun assembler for the human genome. | Daniel H. Huson, Knut Reinert, Saul A. Kravitz, Karin A. Remington, Arthur L. Delcher, Ian M. Dew, Michael Flanigan, Aaron L. Halpern, Zhongwu Lai, Clark M. Mobarry, Granger G. Sutton, Eugene W. Myers |
| 2001 | Probabilistic divergence measures for detecting interspecies recombination. | Dirk Husmeier, Frank Wright |
| 2001 | GEST: a gene expression search tool based on a novel Bayesian similarity metric. | Lawrence Hunter, Ronald C. Taylor, Sonia M. Leach, Richard Simon |
| 2001 | Identifying splits with clear separation: a new class discovery method for gene expression data. | Anja von Heydebreck, Wolfgang Huber, Annemarie Poustka, Martin Vingron |
| 2001 | Disambiguating proteins, genes, and RNA in text: a machine learning approach. | Vasileios Hatzivassiloglou, Pablo Ariel Dubou, Andrey Rzhetsky |
| 2001 | Promoter prediction in the human genome. | Sridhar Hannenhalli, Samuel Levy |
| 2001 | GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. | Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, Andrey Rzhetsky |
| 2001 | Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences. | Eleazar Eskin, William Noble Grundy, Yoram Singer |
| 2001 | Gene recognition based on DAG shortest paths. | John S. Chuang, Dan Roth |
| 2001 | Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. | Derek Y. Chiang, Patrick O. Brown, Michael B. Eisen |
| 2001 | ISMB 2001. | Sren Brunak, Anders Krogh |
| 2001 | Probe selection algorithms with applications in the analysis of microbial communities. | James Borneman, Marek Chrobak, Gianluca Della Vedova, Andres Figueroa, Tao Jiang |
| 2001 | Separating real motifs from their artifacts. | Mathieu Blanchette, Saurabh Sinha |
| 2001 | Fast optimal leaf ordering for hierarchical clustering. | Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola |
| 2001 | SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. | Vineet Bafna, Nathan Edwards |
| 2001 | An insight into domain combinations. | Gordana Apic, Julian Gough, Sarah A. Teichmann |
| 2001 | An efficient algorithm for finding short approximate non-tandem repeats. | Ezekiel F. Adebiyi, Tao Jiang, Michael Kaufmann |
| 2000 | Analysis of Gene Expression Data with Pathway Scores. | Alexander Zien, Robert Kffner, Ralf Zimmer, Thomas Lengauer |
| 2000 | Towards a Complete Map of the Protein Space Based on a Unified Sequence and Structure Analysis of All Known Proteins. | Golan Yona, Michael Levitt |
| 2000 | Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. | Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan J. Robinson, Esko Ukkonen |
| 2000 | A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy. | Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto |
| 2000 | Sequence Database Search Using Jumping Alignments. | Rainer Spang, Marc Rehmsmeier, Jens Stoye |