| 2004 | The Distribution of Inversion Lengths in Bacteria. | David Sankoff, Jean-Franois Lefebvre, Elisabeth R. M. Tillier, Adrian Maler, Nadia El-Mabrouk |
| 2004 | Parameter Landscape Analysis for Common Motif Discovery Programs. | Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai |
| 2004 | Structured motifs search. | Alberto Policriti, Nicola Vitacolonna, Michele Morgante, Andrea Zuccolo |
| 2004 | Untitled record | Pavel A. Pevzner, Haixu Tang, Glenn Tesler |
| 2004 | Comparing | Hanchuan Peng, Eugene W. Myers |
| 2004 | Somatic evolution of cancer. | Martin Nowak |
| 2004 | Learning Regulatory Network Models that Represent Regulator States and Roles. | Keith Noto, Mark Craven |
| 2004 | SNPing in the human genome. | Deborah A. Nickerson |
| 2004 | Reconstructing reticulate evolution in species: theory and practice. | Luay Nakhleh, Tandy J. Warnow, C. Randal Linder |
| 2004 | Genome Rearrangement in Mitochondria and Its Computational Biology. | Istvn Mikls, Jotun Hein |
| 2004 | Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response. | Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina S. Leslie |
| 2004 | The evolutionary capacity of protein structures. | Leonid Meyerguz, David Kempe, Jon M. Kleinberg, Ron Elber |
| 2004 | Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. | Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen |
| 2004 | Evolutionary change in developmental genetic networks. | William McGinnis |
| 2004 | Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes. | Bob Mau, Aaron E. Darling, Nicole T. Perna |
| 2004 | Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome. | Thomas Manke, Christoph Dieterich, Martin Vingron |
| 2004 | Finding anchors for genomic sequence comparison. | Ross Lippert, Xiaoyue Zhao, Liliana Florea, Clark M. Mobarry, Sorin Istrail |
| 2004 | A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. | Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald |
| 2004 | A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs. | Haifeng Li, Tao Jiang |
| 2004 | An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming. | Jing Li, Tao Jiang |
| 2004 | A structural perspective on genome evolution. | David A. Lee, Alastair Grant, Ian Sillitoe, Mark Dibley, Juan Garcia Ranea, Christine A. Orengo |
| 2004 | Checking homogeneity of motifs' distribution in heterogenous sequences. | Sabrina Ledent, Stphane Robin |
| 2004 | Fishing for Proteins in the Pacific Northwest. | William Krivan |
| 2004 | Maximum likelihood resolution of multi-block genotypes. | Gad Kimmel, Ron Shamir |
| 2004 | Application of Kernel Method to Reveal Subtypes of TF Binding Motifs. | Alexander E. Kel, Yuri Tikunov, Nico Voss, Jrgen Borlak, Edgar Wingender |