| 2008 | Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks. | Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara |
| 2008 | Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds. | Jialiang Yang, Louxin Zhang |
| 2008 | Classification of Protein Sequences Based on Word Segmentation Methods. | Yang Yang, Bao-Liang Lu, Wen-Yun Yang |
| 2008 | String Kernels with Feature Selection for SVM Protein Classification. | Wen-Yun Yang, Bao-Liang Lu |
| 2008 | A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots. | Thomas K. F. Wong, Y. S. Chiu, Tak Wah Lam, Siu-Ming Yiu |
| 2008 | Analysis of Structural Strand Asymmetry in Non-coding RNAs. | Jiayu Wen, Brian J. Parker, Georg F. Weiller |
| 2008 | Genome Halving with Double Cut and Join. | Robert Warren, David Sankoff |
| 2008 | Protein Interactions Extracted from Genomes and Papers. | Alfonso Valencia |
| 2008 | Finding Non-coding RNAs Through Genome-Scale Clustering. | Huei-Hun Elizabeth Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo |
| 2008 | SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. | Cuong Than, Luay Nakhleh |
| 2008 | Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics. | Satish Tadepalli, Naren Ramakrishnan, Layne T. Watson, Bhubaneswar Mishra, Richard F. Helm |
| 2008 | Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. | Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret |
| 2008 | Chemical Compound Classification with Automatically Mined Structure Patterns. | Aaron M. Smalter, Jun Huan, Gerald H. Lushington |
| 2008 | Structural Descriptors of Protein-Protein Binding Sites. | Oliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer |
| 2008 | fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity. | Huzefa Rangwala, George Karypis |
| 2008 | A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment. | Ryuichiro Nakato, Osamu Gotoh |
| 2008 | Seed Optimization Is No Easier than Optimal Golomb Ruler Design. | Bin Ma, Hongyi Yao |
| 2008 | Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein Complexes. | Suryani Lukman, Kelvin Sim, Jinyan Li, Yi-Ping Phoebe Chen |
| 2008 | Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks. | Yunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders |
| 2008 | Semantic Similarity Definition over Gene Ontology by Further Mining of the Information Content. | Yuan-Peng Li, Bao-Liang Lu |
| 2008 | Near-sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray Studies. | Juntao Li, Majid Eshaghi, Jianhua Liu, Karuturi R. Krishna Murthy |
| 2008 | Symbolic Approaches for Finding Control Strategies in Boolean Networks. | Christopher James Langmead, Sumit Kumar Jha |
| 2008 | Discrimination of Native Folds Using Network Properties of Protein Structures. | Alper Kkural, Osman Ugur Sezerman, Aytl Eril |
| 2008 | Estimation of Population Allele Frequencies from Small Samples Containing Multiple Generations. | Dmitry A. Konovalov, Dik Heg |
| 2008 | From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. | Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun'ichi Tsujii |