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| 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 | A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment. Ryuichiro Nakato, Osamu Gotoh |
| 2008 | Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach. Mohamed Ibrahim Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert |
| 2008 | Analysis of Structural Strand Asymmetry in Non-coding RNAs. Jiayu Wen, Brian J. Parker, Georg F. Weiller |
| 2008 | Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks. Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara |
| 2008 | Chemical Compound Classification with Automatically Mined Structure Patterns. Aaron M. Smalter, Jun Huan, Gerald H. Lushington |
| 2008 | Classification of Protein Sequences Based on Word Segmentation Methods. Yang Yang, Bao-Liang Lu, Wen-Yun Yang |
| 2008 | Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. Yannick Haudry, Chuang Kee Ong, Laurence Ettwiller, Hugo Bérubé, Ivica Letunic, Misha Kapushesky, Paul-Daniel Weeber, Xi Wang, Julien Gagneur, Charles Girardot, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich |
| 2008 | Discrimination of Native Folds Using Network Properties of Protein Structures. Alper Küçükural, Osman Ugur Sezerman, Aytül Erçil |
| 2008 | Estimation of Population Allele Frequencies from Small Samples Containing Multiple Generations. Dmitry A. Konovalov, Dik Heg |
| 2008 | Finding Non-coding RNAs Through Genome-Scale Clustering. Huei-Hun Elizabeth Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo |
| 2008 | From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun'ichi Tsujii |
| 2008 | GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts. Tyler S. Alioto, Roderic Guigó, Ernesto Picardi, Graziano Pesole |
| 2008 | Genome Halving with Double Cut and Join. Robert Warren, David Sankoff |
| 2008 | Image Compression-based Approach to Measuring the Similarity of Protein Structures. Morihiro Hayashida, Tatsuya Akutsu |
| 2008 | Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular Interactions. Melissa J. Davis, Andrew F. Newman, Imran Khan, Jane Hunter, Mark A. Ragan |
| 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 | KEGG for Medical and Pharmaceutical Applications. Minoru Kanehisa |
| 2008 | Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments. Zhixiang Chen, Bin Fu, Robert T. Schweller, Boting Yang, Zhiyu Zhao, Binhai Zhu |
| 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 | 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 | Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency. Francis Y. L. Chin, Henry C. M. Leung, Man-Hung Siu, Siu-Ming Yiu |
| 2008 | Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret |
| 2008 | Predicting Nucleolar Proteins Using Support-Vector Machines. Mikael Bodén |
| 2008 | Preface. Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| 2008 | Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP. Bhaskar DasGupta, Jin Jun, Ion I. Mandoiu |
| 2008 | Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| 2008 | Protein Interactions Extracted from Genomes and Papers. Alfonso Valencia |
| 2008 | Recent Progress in Phylogenetic Combinatorics. Andreas W. M. Dress |
| 2008 | Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds. Jialiang Yang, Louxin Zhang |
| 2008 | SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. Cuong Than, Luay Nakhleh |
| 2008 | Seed Optimization Is No Easier than Optimal Golomb Ruler Design. Bin Ma, Hongyi Yao |
| 2008 | Semantic Similarity Definition over Gene Ontology by Further Mining of the Information Content. Yuan-Peng Li, Bao-Liang Lu |
| 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 | String Kernels with Feature Selection for SVM Protein Classification. Wen-Yun Yang, Bao-Liang Lu |
| 2008 | Structural Descriptors of Protein-Protein Binding Sites. Oliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer |
| 2008 | Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers. Alireza Hadj Khodabakhshi, Ján Manuch, Arash Rafiey, Arvind Gupta |
| 2008 | Supervised Ensembles of Prediction Methods for Subcellular Localization. Johannes Aßfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei, Arthur Zimek |
| 2008 | Symbolic Approaches for Finding Control Strategies in Boolean Networks. Christopher James Langmead, Sumit Kumar Jha |
| 2008 | fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity. Huzefa Rangwala, George Karypis |