| 2008 | Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution. | Jin Jun, Paul Ryvkin, Edward Hemphill, Ion I. Mandoiu, Craig E. Nelson |
| 2008 | Constructing Level-2 Phylogenetic Networks from Triplets. | Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout |
| 2008 | The Statistical Power of Phylogenetic Motif Models. | John Hawkins, Timothy L. Bailey |
| 2008 | An Alignment-Free Distance Measure for Closely Related Genomes. | Bernhard Haubold, Mirjana Domazet-Loso, Thomas Wiehe |
| 2008 | A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. | Raluca Gordn, Leelavati Narlikar, Alexander J. Hartemink |
| 2008 | Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. | Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer |
| 2008 | Automatic Parameter Learning for Multiple Network Alignment. | Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou |
| 2008 | Discovering Local Patterns of Co-evolution. | Yifat Felder, Tamir Tuller |
| 2008 | Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information. | Eleazar Eskin |
| 2008 | Constructing Treatment Portfolios Using Affinity Propagation. | Delbert Dueck, Brendan J. Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili, Gabe Musso, Robert Hegele |
| 2008 | Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations. | Jean-Philippe Doyon, Cdric Chauve, Sylvie Hamel |
| 2008 | DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. | Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet |
| 2008 | Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing. | Ritendra Datta, Marshall W. Bern |
| 2008 | Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions. | Mikls Csrs |
| 2008 | Limitations of Pseudogenes in Identifying Gene Losses. | James C. Costello, Mira V. Han, Matthew W. Hahn |
| 2008 | BCL-2: From Translocation to Therapy. | Suzanne Cory |
| 2008 | CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads. | Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai, Jonathan A. Eisen |
| 2008 | Orchestration of DNA Methylation. | Howard Cedar |
| 2008 | Locating Multiple Gene Duplications through Reconciled Trees. | J. Gordon Burleigh, Mukul S. Bansal, Andr Wehe, Oliver Eulenstein |
| 2008 | Computation of Median Gene Clusters. | Sebastian Bcker, Katharina Jahn, Julia Mixtacki, Jens Stoye |
| 2008 | A Phylogenetic Approach to Genetic Map Refinement. | Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk |
| 2008 | An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. | Matthias Bernt, Daniel Merkle, Martin Middendorf |
| 2008 | On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2008 | Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information. | Sivan Bercovici, Dan Geiger, Liran Shlush, Karl Skorecki, Alan A. Templeton |
| 2008 | Perfect DCJ Rearrangement. | Sverine Brard, Annie Chateau, Cdric Chauve, Christophe Paul, Eric Tannier |