| 2010 | Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. | Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutrk |
| 2010 | Genomic DNA | Benny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham |
| 2010 | Hierarchical Generative Biclustering for MicroRNA Expression Analysis. | Jos Caldas, Samuel Kaski |
| 2010 | On Sorting Genomes with DCJ and Indels. | Marlia D. V. Braga |
| 2010 | Pathway-Based Functional Analysis of Metagenomes. | Sivan Bercovici, Itai Sharon, Ron Y. Pinter, Tomer Shlomi |
| 2010 | Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA. | Sivan Bercovici, Dan Geiger |
| 2010 | A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning. | Jean-Denis Benazet, Mirko Bischofberger, Eva Tiecke, Alexandre Gonalves, James F. Martin, Aime Zuniga, Felix Naef, Rolf Zeller |
| 2010 | Detecting Highways of Horizontal Gene Transfer. | Mukul S. Bansal, J. Peter Gogarten, Ron Shamir |
| 2010 | Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. | Ghada Badr, Krister M. Swenson, David Sankoff |
| 2010 | SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. | Ferhat Ay, Tamer Kahveci |
| 2010 | An Algorithmic Framework for Predicting Side-Effects of Drugs. | Nir Atias, Roded Sharan |
| 2010 | A Simple Measure of the Dynamics of Segmented Genomes: An Application to Influenza. | Stphane Aris-Brosou |
| 2010 | Limited Lifespan of Fragile Regions in Mammalian Evolution. | Max A. Alekseyev, Pavel A. Pevzner |
| 2009 | Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. | Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg |
| 2009 | A Probabilistic Graphical Model for Ab Initio Folding. | Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu |
| 2009 | COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study. | Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang |
| 2009 | Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. | Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel |
| 2009 | Natural Parameter Values for Generalized Gene Adjacency. | Zhenyu Yang, David Sankoff |
| 2009 | DCJ Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions. | Andrew Wei Xu |
| 2009 | Simultaneous Alignment and Folding of Protein Sequences. | Jrme Waldisphl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger |
| 2009 | Reconstructing Histories of Complex Gene Clusters on a Phylogeny. | Toms Vinar, Brona Brejov, Giltae Song, Adam C. Siepel |
| 2009 | Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples. | Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin |
| 2009 | Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods. | Eric Tannier |
| 2009 | Sorting Signed Permutations by Inversions in O(nlogn) Time. | Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret |
| 2009 | A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. | Oliver Stegle, Katherine J. Denby, David L. Wild, Zoubin Ghahramani, Karsten M. Borgwardt |