| 2004 | Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. | Hernn Dopazo, Javier Santoyo, Joaqun Dopazo |
| 2004 | Functional inference from non-random distributions of conserved predicted transcription factor binding sites. | Christoph Dieterich, Sven Rahmann, Martin Vingron |
| 2004 | Improved techniques for the identification of pseudogenes. | Lachlan James M. Coin, Richard Durbin |
| 2004 | Mining frequent patterns in protein structures: a study of protease families. | Shann-Ching Chen, Ivet Bahar |
| 2004 | Splice site identification by idlBNs. | Robert Castelo, Roderic Guig |
| 2004 | A neural-network-based method for predicting protein stability changes upon single point mutations. | Emidio Capriotti, Piero Fariselli, Rita Casadio |
| 2004 | Selecting biomedical data sources according to user preferences. | Sarah Cohen Boulakia, Sverine Lair, Nicolas Stransky, Stphane Graziani, Franois Radvanyi, Emmanuel Barillot, Christine Froidevaux |
| 2004 | Analysis of domain correlations in yeast protein complexes. | Doron Betel, Ruth Isserlin-Weinberger, Christopher W. V. Hogue |
| 2004 | Automatic Quality Assessment of Peptide Tandem Mass Spectra. | Marshall W. Bern, David Goldberg, W. Hayes McDonald, John R. Yates III |
| 2004 | Into the heart of darkness: large-scale clustering of human non-coding DNA. | Gill Bejerano, David Haussler, Mathieu Blanchette |
| 2004 | A knowledge based approach for representing and reasoning about signaling networks. | Chitta Baral, Karen Chancellor, Tran Hoai Nam, Nhan Tran, Anna M. Joy, Michael E. Berens |
| 2004 | Deconvolving cell cycle expression data with complementary information. | Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld |
| 2004 | Application of a new probabilistic model for recognizing complex patterns in glycans. | Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka |
| 2003 | Extracting synonymous gene and protein terms from biological literature. | Hong Yu, Eugene Agichtein |
| 2003 | Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup. | Alexander S. Yeh, Lynette Hirschman, Alexander A. Morgan |
| 2003 | Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. | Yoshihiro Yamanishi, Jean-Philippe Vert, Akihiro Nakaya, Minoru Kanehisa |
| 2003 | ISMB 2003 Organization. | |
| 2003 | Gene structure-based splice variant deconvolution using a microarry platform. | Hui Wang, Earl Hubbell, Jing-Shan Hu, Gangwu Mei, Melissa S. Cline, Gang Lu, Tyson Clark, Michael A. Siani-Rose, Manuel Ares, David Kulp, David Haussler |
| 2003 | Skew in CG content near the transcription start site in Arabidopsis thaliana. | Tatiana V. Tatarinova, Vyacheslav Brover, Maxim Troukhan, Nickolai Alexandrov |
| 2003 | Scaling up accurate phylogenetic reconstruction from gene-order data. | Jijun Tang, Bernard M. E. Moret |
| 2003 | myGrid: personalised bioinformatics on the information grid. | Robert D. Stevens, Alan J. Robinson, Carole A. Goble |
| 2003 | A probabilistic method to detect regulatory modules. | Saurabh Sinha, Erik van Nimwegen, Eric D. Siggia |
| 2003 | CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. | Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, Richard M. Karp |
| 2003 | Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. | Eran Segal, R. Yelensky, Daphne Koller |
| 2003 | Discovering molecular pathways from protein interaction and gene expression data. | Eran Segal, Haidong Wang, Daphne Koller |