| 2007 | Nucleosome Occupancy Information Improves | Leelavati Narlikar, Raluca Gordn, Alexander J. Hartemink |
| 2007 | Network Legos: Building Blocks of Cellular Wiring Diagrams. | T. M. Murali, Corban G. Rivera |
| 2007 | A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. | Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler |
| 2007 | Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. | Yue Lu, Sing-Hoi Sze |
| 2007 | Selecting Genomes for Reconstruction of Ancestral Genomes. | Guoliang Li, Jian Ma, Louxin Zhang |
| 2007 | RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints. | Wah-Heng Lee, Wing-Kin Sung |
| 2007 | Evolution of Tandemly Arrayed Genes in Multiple Species. | Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk |
| 2007 | Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. | Hiroyuki Kuwahara, Chris J. Myers |
| 2007 | Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions. | Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss, William Stafford Noble |
| 2007 | A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements. | Anitha Kannan, Andrew Emili, Brendan J. Frey |
| 2007 | Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation. | Hetunandan Kamisetty, Eric P. Xing, Christopher James Langmead |
| 2007 | Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules. | Yuval Inbar, Dina Schneidman-Duhovny, Oranit Dror, Ruth Nussinov, Haim J. Wolfson |
| 2007 | Beyond Galled Trees - Decomposition and Computation of Galled Networks. | Daniel H. Huson, Tobias H. Klpper |
| 2007 | Comparative Analysis of Spatial Patterns of Gene Expression in | Cyrus L. Harmon, Parvez Ahammad, Ann Hammonds, Richard Weiszmann, Susan E. Celniker, Shankar Sastry, Gerald M. Rubin |
| 2007 | Learning Gene Regulatory Networks via Globally Regularized Risk Minimization. | Yuhong Guo, Dale Schuurmans |
| 2007 | Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking. | Joshua A. Grochow, Manolis Kellis |
| 2007 | Baculovirus Phylogeny Based on Genome Rearrangements. | Daniel B. Goodman, Noah Ollikainen, Chris Sholley |
| 2007 | How to Achieve an Equivalent Simple Permutation in Linear Time. | Simon Gog, Martin Bader |
| 2007 | An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and | Abhishek Garg, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli |
| 2007 | QNet: A Tool for Querying Protein Interaction Networks. | Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan |
| 2007 | Identification of Deletion Polymorphisms from Haplotypes. | Erik Corona, Benjamin J. Raphael, Eleazar Eskin |
| 2007 | Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract). | Cdric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk |
| 2007 | Improved Ranking Functions for Protein and Modification-Site Identifications. | Marshall W. Bern, David Goldberg |
| 2007 | Reconstructing the Topology of Protein Complexes. | Allister Bernard, David S. Vaughn, Alexander J. Hartemink |
| 2007 | Framework for Identifying Common Aberrations in DNA Copy Number Data. | Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael T. Barrett, John N. Weinstein, Anne-Lise Brresen-Dale, Zohar Yakhini |