| 2004 | A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs. Haifeng Li, Tao Jiang |
| 2004 | A discriminative model for identifying spatial cis-regulatory modules. Eran Segal, Roded Sharan |
| 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 random graph approach to NMR sequential assignment. Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan |
| 2004 | A structural perspective on genome evolution. David A. Lee, Alastair Grant, Ian Sillitoe, Mark Dibley, Juan Garcia Ranea, Christine A. Orengo |
| 2004 | Algorithms for inferring cis-regulatory structures and protein interaction networks. Richard M. Karp |
| 2004 | Aligning alignments exactly. John D. Kececioglu, Dean Starrett |
| 2004 | An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming. Jing Li, Tao Jiang |
| 2004 | Checking homogeneity of motifs' distribution in heterogenous sequences. Sabrina Ledent, Stéphane Robin |
| 2004 | Chromosomal breakpoint re-use in the inference of genome sequence rearrangement. David Sankoff, Phil Trinh |
| 2004 | Comparing Hanchuan Peng, Eugene W. Myers |
| 2004 | Computational identification of evolutionarily conserved exons. Adam C. Siepel, David Haussler |
| 2004 | Designing multiple simultaneous seeds for DNA similarity search. Yanni Sun, Jeremy Buhler |
| 2004 | Discovering temporal relations in molecular pathways using protein-protein interactions. Martin Farach-Colton, Yang Huang, John L. L. Woolford |
| 2004 | Evolutionary change in developmental genetic networks. William McGinnis |
| 2004 | Faster genome annotation of non-coding RNA families without loss of accuracy. Zasha Weinberg, Walter L. Ruzzo |
| 2004 | Fifty years of sequence analysis: what have we learned? Russell F. Doolittle |
| 2004 | Finding anchors for genomic sequence comparison. Ross Lippert, Xiaoyue Zhao, Liliana Florea, Clark M. Mobarry, Sorin Istrail |
| 2004 | Finding approximate tandem repeats in genomic sequences. Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger |
| 2004 | Finding motifs for insufficient number of sequences with strong binding to transcription facto. Francis Y. L. Chin, Henry C. M. Leung, Siu-Ming Yiu, Tak Wah Lam, Roni Rosenfeld, Wai Wan Tsang, David K. Smith, Y. Jiang |
| 2004 | Finding short DNA motifs using permuted markov models. Xiaoyue Zhao, Haiyan Huang, Terence P. Speed |
| 2004 | From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles. Eleazar Eskin |
| 2004 | Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad |
| 2004 | Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp |
| 2004 | Identifying conserved gene clusters in the presence of orthologous groups. Xin He, Michael H. Goldwasser |
| 2004 | Interface surfaces for protein-protein complexes. Yih-En Andrew Ban, Herbert Edelsbrunner, Johannes Rudolph |
| 2004 | Learning multiple evolutionary pathways from cross-sectional data. Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer |
| 2004 | Maximum likelihood resolution of multi-block genotypes. Gad Kimmel, Ron Shamir |
| 2004 | Mining protein family specific residue packing patterns from protein structure graphs. Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan F. Prins, Alexander Tropsha |
| 2004 | Multiple organism gene finding by collapsed gibbs sampling. Sourav Chatterji, Lior Pachter |
| 2004 | Perfect phylogeny and haplotype assignment. Eran Halperin, Richard M. Karp |
| 2004 | Probabilistic discovery of overlapping cellular processes and their regulation. Alexis J. Battle, Eran Segal, Daphne Koller |
| 2004 | Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004, San Diego, California, USA, March 27-31, 2004 Philip E. Bourne, Dan Gusfield |
| 2004 | Protein similarity from knot theory and geometric convolution. Michael A. Erdmann |
| 2004 | RNAi, genome ultrastructure, and other unexpected tales from the analysis of genetic silencing. Andrew Fire |
| 2004 | Recent advances on the manipulation of single biomolecules. Carlos Bustamante |
| 2004 | Reconciliation problems for duplication, loss and horizontal gene transfer. Pawel Górecki |
| 2004 | Reconstructing reticulate evolution in species: theory and practice. Luay Nakhleh, Tandy J. Warnow, C. Randal Linder |
| 2004 | SNPing in the human genome. Deborah A. Nickerson |
| 2004 | Simultaneous identification of duplications and lateral transfers. Michael T. Hallett, Jens Lagergren, Ali Tofigh |
| 2004 | Somatic evolution of cancer. Martin Nowak |
| 2004 | Stochastic models inspired by hybridization theory for short oligonucleotide arrays. Zhijin Wu, Rafael A. Irizarry |
| 2004 | Structured motifs search. Alberto Policriti, Nicola Vitacolonna, Michele Morgante, Andrea Zuccolo |
| 2004 | Systems biology and malaria. Elizabeth A. Winzeler, Karine G. Le Roch, Yingyao Zhou, Peter L. Blair, Muni Grainger, J. Kathleen Moch, J. David Haynes, Patricia De la Vega, Anthony A. Holder, Serge Batalov, Daniel J. Carucci |
| 2004 | The evolutionary capacity of protein structures. Leonid Meyerguz, David Kempe, Jon M. Kleinberg, Ron Elber |
| 2004 | Using motion planning to study RNA folding kinetics. Xinyu Tang, Bonnie Kirkpatrick, Shawna L. Thomas, Guang Song, Nancy M. Amato |
| 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 |