Alvis Brazma, Satoru Miyano, and Tatsuya Akutsu, editors. Proceedings of 6th Asia-Pacific Bioinformatics Conference, 14-17 January 2008, Kyoto, Japan. Imperial College Press, London, January 2008.

Contents

• Alvis Brazma, Satoru Miyano, Tatsuya Akutsu. Preface, page v-vi.

  Keynote Papers

• Andreas Dress. Recent Progress in Phylogenetic Combinatorics, pages 1-4.

• Minoru Kanehisa. KEGG for Medical and Pharmaceutical Applications, page 5.

• Alfonso Valencia. Protein Interactions Extracted from Genomes and Papers, page 7.

• Xuegong Zhang. Putting More Biology in the Learning Machine. (Not provided in time for inclusion in proceedings.)

  Contributed Papers

• Wen-Yun Yang, Bao-Liang Lu. String Kernels with Feature Selection for SVM Protein Classification, pages 9-18.

• Mikael Boden. Predicting Nucleolar Proteins Using Support-Vector Machines, pages 19-28.

• Johannes Asfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei, Arthur Zimek. Supervised Ensembles of Prediction Methods for Subcellular Localization, pages 29-38.

• Aaron M. Smalter, J. Huan, Gerald H. Lushington. Chemical Compound Classification with Automatically Mined Structure Patterns, pages 39-48.

• Alireza Hadj Khodabakhshi, Jan Manuch, Arash Rafiey, Arvind Gupta. Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers, pages 49-58.

• Alper Kucukural, O. Ugur Sezerman, Aytul Ercil. Discrimination of Native Folds Using Network Properties of Protein Structures, pages 59-68.

• Suryani Lukman, Kelvin Sim, Jinyan Li, Yi-Ping Phoebe Chen. Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein Complexes, pages 69-78.
• Oliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer. Structural Descriptors of Protein-Protein Binding Sites, pages 79-88.

• Thomas Wong, Y. S. Chiu, Tak-Wah Lam, S. M. Yiu. A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots, pages 89-100.

• Ryuichiro Nakato, Osamu Gotoh. A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment, pages 101-110.

• Huzefa Rangwala, George Karypis. fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity, pages 111-122.

• Jialiang Yang, Louxin Zhang. Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds, pages 123-132.

• Bin Ma, Hongyi Yao. Seed Optimization Is No Easier than Optimal Golomb Ruler Design, pages 133-144.

• Melissa J. Davis, Andrew Newman, Imran Khan, Jane Hunter, Mark A. Ragan. Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular Interactions, pages 145-154.

• Yuan-Peng Li, Bao-Liang Lu. Semantic Similarity Definition over Gene Ontology by Further Mining of the Information Content, pages 155-164.

• Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun'ichi Tsujii. From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature, pages 165-176.

• Yang Yang, Bao-Liang Lu, Wen-Yun Yang. Classification of Protein Sequences Based on Word Segmentation Methods, pages 177-186.

• Jiayu Wen, Brian J. Parker, Georg F. Weiller. Analysis of Structural Strand Asymmetry in Non-coding RNAs, pages 187-198.

• Huei-Hun Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo. Finding Non-coding RNAs Through Genome-Scale Clustering, pages 199-210.

• Sebastian Bocker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truss. A Fixed-Parameter Approach for Weighted Cluster Editing, pages 211-220.

• Morihiro Hayashida, Tatsuya Akutsu. Image Compression-based Approach to Measuring the Similarity of Protein Structures, pages 221-230.

• Robert Warren, David Sankoff. Genome Halving with Double Cut and Join , pages 231-240.

• Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret. Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes, pages 241-250.

• Cuong Than, Luay Nakhleh. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions, pages 251-260.

• Mohamed I. Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert. Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach, pages 261-272.

• Yunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders. Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks, pages 273-286.

• Xingming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara. Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks, pages 287-296.

• Satish Tadepalli, Naren Ramakrishnan, Layne T. Watson, Bhubaneshwar Mishra, Richard F. Helm. Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics, pages 297-306.

• Christopher James Langmead, Sumit Kumar Jha. Symbolic Approaches for Finding Control Strategies in Boolean Networks, pages 307-320.

• Dmitry A. Konovalov, Dik Heg. Estimation of Population Allele Frequencies from Small Samples Containing Multiple Generations, pages 321-332.

• Zhixiang Chen, Bin Fu, Robert Schweller, Boting Yang, Zhiyu Zhao, Binhai Zhu. Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments, pages 333-342.

• Francis Y. L. Chin, Henry Chi Ming Leung, M. H. Siu, S. M. Yiu. Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency, pages 343-352.

• Bhaskar DasGupta, Jin Jun, Ion I. Mandoiu. Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP, pages 353-362.

• Tyler S. Alioto, Roderic Guigo, Ernesto Picardi, Graziano Pesole. GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts, pages 363-372.

• Yannick Haudry, Chuang Kee Ong, Laurence Ettwiller, Hugo Berube, Ivica Letunic, Misha Kapushesky, Paul-Daniel Weeber, Xi Wang, Julien Gagneur, Charles Girardot, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen Furlong, Joachim Wittbrodt, Thorsten Henrich. Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress, pages 373-382.

• Juntao Li, Majid Eshaghi, Jianhua Liu, Radha Krishna Murthy Karuturi. Near-sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray Studies, pages 383-392.