| 2005 | Stability of Rearrangement Measures in the Comparison of Genome Sequences. | David Sankoff, Matthew Mazowita |
| 2005 | Power Boosts for Cluster Tests. | David Sankoff, Lani Haque |
| 2005 | Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. | Kim R. Rasmussen, Jens Stoye, Eugene W. Myers |
| 2005 | Individual Gene Cluster Statistics in Noisy Maps. | Narayanan Raghupathy, Dannie Durand |
| 2005 | Graph Theoretical Insights into Evolution of Multidomain Proteins. | Teresa M. Przytycka, George B. Davis, Nan Song, Dannie Durand |
| 2005 | A Regulatory Network Controlling Drosophila Development. | Dmitri A. Papatsenko, Mike Levine |
| 2005 | Motif Discovery Through Predictive Modeling of Gene Regulation. | Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina S. Leslie |
| 2005 | A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism. | Aviv A. Mezer, Eran Bosis, Uri Ashery, Esther Nachliel, Menachem Gutman |
| 2005 | A Partial Solution to the C-Value Paradox. | Jeffrey M. Marcus |
| 2005 | Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels. | Orna Man, Joel L. Sussman, Yitzhak Pilpel |
| 2005 | Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition. | Yan Liu, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan |
| 2005 | Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis. | Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini |
| 2005 | Yeast Cells as a Discovery Platform for Neurodegenerative Disease. | Susan Lindquist, Ernest Fraenkel, Tiago Outeiro, Aaron Gitler, Julie Su, Anil Cashikar, Smitha Jagadish |
| 2005 | Probabilistic | Wolfgang P. Lehrach, Dirk Husmeier, Christopher K. I. Williams |
| 2005 | Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs. | Michal Lapidot, Yitzhak Pilpel |
| 2005 | Biology as Information. | Eric S. Lander |
| 2005 | Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes. | David Kulp, Manjunatha Jagalur |
| 2005 | Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution. | Mehmet Koyutrk, Ananth Grama, Wojciech Szpankowski |
| 2005 | Amino Acid Sequence Control of the Folding of the Parallel beta-Helix, the Simplest beta-Sheet Fold. | Jonathan King, Cammie Haase-Pettingell, Ryan Simkovsky, Peter Weigele |
| 2005 | Improvement of Computing Times in Boolean Networks Using Chi-square Tests. | Haseong Kim, Jae K. Lee, Taesung Park |
| 2005 | Predicting Transcription Factor Binding Sites Using Structural Knowledge. | Tommy Kaplan, Nir Friedman, Hanah Margalit |
| 2005 | A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to | Sudhakar Jonnalagadda, Rajagopalan Srinivasan |
| 2005 | Towards an Integrated Protein-Protein Interaction Network. | Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman |
| 2005 | Constructing a Smallest Refining Galled Phylogenetic Network. | Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung |
| 2005 | Reconstruction of Reticulate Networks from Gene Trees. | Daniel H. Huson, Tobias H. Klpper, Peter J. Lockhart, Mike A. Steel |