| 2006 | Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data. | Stefanie Scheid, Rainer Spang |
| 2006 | Statistical Evaluation of Genome Rearrangement. | David Sankoff |
| 2006 | De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis. | Derek A. Ruths, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram |
| 2006 | Identification and Evaluation of Functional Modules in Gene Co-expression Networks. | Jianhua Ruan, Weixiong Zhang |
| 2006 | Inferring Common Origins from mtDNA. | Ajay K. Royyuru, Gabriela Alexe, Daniel E. Platt, Ravi Vijaya Satya, Laxmi Parida, Saharon Rosset, Gyan Bhanot |
| 2006 | An Important Connection Between Network Motifs and Parsimony Models. | Teresa M. Przytycka |
| 2006 | A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. | Nicholas D. Pattengale, Bernard M. E. Moret |
| 2006 | A PQ Framework for Reconstructions of Common Ancestors and Phylogeny. | Laxmi Parida |
| 2006 | Sorting by Translocations Via Reversals Theory. | Michal Ozery-Flato, Ron Shamir |
| 2006 | Alignment Statistics for Long-Range Correlated Genomic Sequences. | Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt |
| 2006 | Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence. | Sauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini, Antonio Rosato |
| 2006 | A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells. | Cline Lefebvre, Wei Keat Lim, Katia Basso, Riccardo Dalla Favera, Andrea Califano |
| 2006 | Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. | Mehmet Koyutrk, Ananth Grama, Wojciech Szpankowski |
| 2006 | Simple and Fast Inverse Alignment. | John D. Kececioglu, Eagu Kim |
| 2006 | A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. | Naftali Kaminski, Ziv Bar-Joseph |
| 2006 | Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. | Hans-Michael Kaltenbach, Sebastian Bcker, Sven Rahmann |
| 2006 | Probabilistic Paths for Protein Complex Inference. | Hailiang Huang, Lan V. Zhang, Frederick P. Roth, Joel S. Bader |
| 2006 | Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. | Jim C. Huang, Quaid Morris, Brendan J. Frey |
| 2006 | Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation. | Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Sleyman Cenk Sahinalp |
| 2006 | Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction. | David Heckerman, Carl Myers Kadie, Jennifer Listgarten |
| 2006 | Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human Genome. | David Haussler |
| 2006 | An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. | Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron |
| 2006 | A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles. | Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald |
| 2006 | Global Interaction Networks Probed by Mass Spectrometry. | Anne-Claude Gavin |
| 2006 | Ordering Partially Assembled Genomes Using Gene Arrangements. | ric Gaul, Mathieu Blanchette |