| 2005 | EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. | Marshall W. Bern, David Goldberg |
| 2005 | Avoiding Local Optima in Single Particle Reconstruction. | Marshall W. Bern, Jindong Chen, Hao Chi Wong |
| 2005 | On Sorting by Translocations. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2005 | Improved Duplication Models for Proteome Network Evolution. | Grkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Sleyman Cenk Sahinalp |
| 2005 | Mapping Molecular Landscapes Inside Cells. | Wolfgang Baumeister |
| 2005 | Consensus Folding of Unaligned RNA Sequences Revisited. | Vineet Bafna, Haixu Tang, Shaojie Zhang |
| 2005 | Improved Recombination Lower Bounds for Haplotype Data. | Vineet Bafna, Vikas Bansal |
| 2005 | Lower Bounds for Maximum Parsimony with Gene Order Data. | Abraham Bachrach, Kevin C. Chen, Chris Harrelson, Radu Mihaescu, Satish Rao, Apurva Shah |
| 2005 | Human Genome Sequence Variation and the Inherited Basis of Common Disease. | David Altshuler |
| 2005 | RNA-RNA Interaction Prediction and Antisense RNA Target Search. | Can Alkan, Emre Karako, Joseph H. Nadeau, Sleyman Cenk Sahinalp, Kaizhong Zhang |
| 2004 | Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs. | Chaya Ben-Zaken Zilberstein, Eleazar Eskin, Zohar Yakhini |
| 2004 | Finding short DNA motifs using permuted markov models. | Xiaoyue Zhao, Haiyan Huang, Terence P. Speed |
| 2004 | Stochastic models inspired by hybridization theory for short oligonucleotide arrays. | Zhijin Wu, Rafael A. Irizarry |
| 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 | Finding approximate tandem repeats in genomic sequences. | Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger |
| 2004 | Faster genome annotation of non-coding RNA families without loss of accuracy. | Zasha Weinberg, Walter L. Ruzzo |
| 2004 | Using motion planning to study RNA folding kinetics. | Xinyu Tang, Bonnie Kirkpatrick, Shawna L. Thomas, Guang Song, Nancy M. Amato |
| 2004 | Databases for Comparative Analysis of Human-Mouse Orthologous Alternative Splicing. | Bahar Taneri, Alexey Novoradovsky, Ben Snyder, Terry Gaasterland |
| 2004 | Designing multiple simultaneous seeds for DNA similarity search. | Yanni Sun, Jeremy Buhler |
| 2004 | Computational identification of evolutionarily conserved exons. | Adam C. Siepel, David Haussler |
| 2004 | PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information. | Rahul Siddharthan, Erik van Nimwegen, Eric D. Siggia |
| 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 | A discriminative model for identifying spatial cis-regulatory modules. | Eran Segal, Roded Sharan |
| 2004 | Chromosomal breakpoint re-use in the inference of genome sequence rearrangement. | David Sankoff, Phil Trinh |
| 2004 | Estimators of Translocations and Inversions in Comparative Maps. | David Sankoff, Matthew Mazowita |