6. APBC 2008: Kyoto, Japan

• Alvis Brazma, Satoru Miyano, Tatsuya Akutsu:
  Preface.
  

Keynote Papers

• Andreas W. M. Dress:
  Recent Progress in Phylogenetic Combinatorics. 1-4
  
• Minoru Kanehisa:
  KEGG for Medical and Pharmaceutical Applications. 5
  
• Alfonso Valencia:
  Protein Interactions Extracted from Genomes and Papers. 7
  

Contributed Papers

• Wen-Yun Yang, Bao-Liang Lu:
  String Kernels with Feature Selection for SVM Protein Classification. 9-18
  
• Mikael Bodén:
  Predicting Nucleolar Proteins Using Support-Vector Machines. 19-28
  
• Johannes Aßfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei, Arthur Zimek:
  Supervised Ensembles of Prediction Methods for Subcellular Localization. 29-38
  
• Aaron M. Smalter, Jun Huan, Gerald H. Lushington:
  Chemical Compound Classification with Automatically Mined Structure Patterns. 39-48
  
• Alireza Hadj Khodabakhshi, Ján Manuch, Arash Rafiey, Arvind Gupta:
  Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers. 49-58
  
• Alper Küçükural, Osman Ugur Sezerman, Aytul Ercil:
  Discrimination of Native Folds Using Network Properties of Protein Structures. 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. 69-78
  
• Oliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer:
  Structural Descriptors of Protein-Protein Binding Sites. 79-88
  
• Thomas K. F. Wong, Y. S. Chiu, Tak Wah Lam, Siu-Ming Yiu:
  A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots. 89-100
  
• Ryuichiro Nakato, Osamu Gotoh:
  A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment. 101-110
  
• Huzefa Rangwala, George Karypis:
  fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity. 111-122
  
• Jialiang Yang, Louxin Zhang:
  Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds. 123-132
  
• Bin Ma, Hongyi Yao:
  Seed Optimization Is No Easier than Optimal Golomb Ruler Design. 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. 145-154
  
• Yuan-Peng Li, Bao-Liang Lu:
  Semantic Similarity Definition over Gene Ontology by Further Mining of the Information Content. 155-164
  
• Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun-ichi Tsujii:
  From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. 165-176
  
• Yang Yang, Bao-Liang Lu, Wen-Yun Yang:
  Classification of Protein Sequences Based on Word Segmentation Methods. 177-186
  
• Jiayu Wen, Brian J. Parker, Georg F. Weiller:
  Analysis of Structural Strand Asymmetry in Non-coding RNAs. 187-198
  
• Huei-Hun Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo:
  Finding Non-coding RNAs Through Genome-Scale Clustering. 199-210
  
• Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß:
  A Fixed-Parameter Approach for Weighted Cluster Editing. 211-220
  
• Morihiro Hayashida, Tatsuya Akutsu:
  Image Compression-based Approach to Measuring the Similarity of Protein Structures. 221-230
  
• Robert Warren, David Sankoff:
  Genome Halving with Double Cut and Join. 231-240
  
• Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret:
  Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. 241-250
  
• Cuong Than, Luay Nakhleh:
  SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. 251-260
  
• Mohamed Ibrahim Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert:
  Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach. 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. 273-286
  
• Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara:
  Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks. 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. 297-306
  
• Christopher James Langmead, Sumit Kumar Jha:
  Symbolic Approaches for Finding Control Strategies in Boolean Networks. 307-320
  
• Dmitry A. Konovalov, Dik Heg:
  Estimation of Population Allele Frequencies from Small Samples Containing Multiple Generations. 321-332
  
• Zhixiang Chen, Bin Fu, Robert T. Schweller, Boting Yang, Zhiyu Zhao, Binhai Zhu:
  Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments. 333-342
  
• Francis Y. L. Chin, Henry C. M. Leung, Man-Hung Siu, Siu-Ming Yiu:
  Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency. 343-352
  
• Bhaskar DasGupta, Jin Jun, Ion I. Mandoiu:
  Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP. 353-362
  
• Tyler S. Alioto, Roderic Guigó, Ernesto Picardi, Graziano Pesole:
  GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts. 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 E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich:
  Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. 373-382
  
• Juntao Li, Majid Eshaghi, Jianhua Liu, Karuturi R. Krishna Murthy:
  Near-sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray Studies. 383-392