Tao Jiang, Ueng-Cheng Yang, Phoebe Chen, and Limsoon Wong, editors. Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, Taipei, Taiwan. Imperial College Press, London, February 2006.

Contents

• Tao Jiang, Ueng-cheng Yang, Phoebe Chen, Limsoon Wong. Preface, pages v-vi.

  Keynote Papers

• Wen-Hsiung Li. On the Inference of Regulatory Elements, Circuits, and Modules, pages 1.

• Mark A. Ragan. Automating the Search for Lateral Gene Transfer , pages 3.

• Michael S. Waterman. Whole Genome Optical Mapping, pages 5.

  Contributed Papers

• D.A. Konovalov. Accuracy of Four Heuristics for the Full Sibship Reconstruction Problem in the Presence of Genotype Errors, pages 7-16. ppt with corrigendum.

• P.C.H. Ma and K.C.C. Chan. Inference of Gene Regulatory Networks from Microarray Data: A Fuzzy Logic Approach, pages 17-26.

• C.W. Li, W.C. Chang, and B.S. Chen. System Identification and Robustness Analysis of the Circadian Regulatory Network via Microarray Data in Arabidopsis Thaliana, pages 27-37.

• P. Horton, K.-J. Park, T. Obayashi, and K. Nakai. Protein Subcellular Localisation Prediction with WoLF PSORT, pages 39--48.

• P.-H. Chi and C.-R. Shyu. Predicting Ranked SCOP Domains by Mining Associations of Visual Contents in Distance Matrices, pages 49--58.

• D. Ruths and L. Nakhleh. RECOMP: A Parsimony-Based Method for Detecting Recombination, pages 59--68.

• H.-J. Jin, H.-J. Kim, J.-H. Choi, and H.-G. Cho. AlignScope: A Visual Mining Tool for Gene Team Finding with Whole Genome Alignment, pages 69--78.

• F.Y.L. Chin and H.C.M. Leung. An Efficient Algorithm for String Motif Discovery, pages 79--88.

• Y. Kawada and Y. Sakakibara. Discriminative Detection of Cis-Acting Regulatory Variation From Location Data, pages 89--98.

• T. Akutsu, M. Hayashida, W.-K. Ching, and M.K. Ng. On the Complexity of Finding Control Strategies for Boolean Networks, pages 99--108.

• K.F. Chong, K. Ning, H.W. Leong, and P. Pevzner. Characterization of Multi-Charge Mass Spectra for Peptide Sequencing, pages 109--119.

• Y. Ma, G. Wang, Y. Li, and Y. Zhao. EDAM: An Efficient Clique Discovery Algorithm with Frequency Transformation for Finding Motifs, pages 119--128.

• M.K. Ng. A Recursive Method for Solving Haplotype Frequencies in Multiple Loci Linkage Analysis, pages 129--138.

• S. Das, S. Paul, and C. Dutta. Trends in Codon and Amino Acid Usage in Human Pathogen Tropheryma Whipplei, the only Known Actinobacteria with Reduced Genome, pages 139--148.

• S. Paul, S. Das, and C. Dutta. Consequences of Mutation, Selection, and Physico-Chemical Properties of Encoded Proteins on Synonymous Codon Usage in Adenoviruses, pages 149--158.

• Z. Cai, M. Heydari, and G. Lin. Microarray Missing Value Imputation by Iterated Local Least Squares, pages 159--168.

• S. Thorvaldsen, E. Ytterstad, and T. Fla. Property-Dependent Analysis of Aligned Proteins from Two Or More Populations, pages 169--178.

• L. Shen and E.C. Tan. A Generalized Output-Coding Scheme with SVM for Multiclass Microarray Classification, pages 179--186.

• D. Ruths and L. Nakhleh. Techniques for Assessing Phylogenetic Branch Support: A Performance Study, pages 187--196.

• Y.-P.P. Chen and Q. Chen. Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databases, pages 197--206.

• C. Sinoquet. A Novel Approach for Structured Consensus Motif Inference Under Specificity and Quorum Constraints , pages 207--216.

• C.J. Langmead. A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data, pages 217--226.

• M.J. Arauzo-Bravo, S. Fujii, H. Kono, and A. Sarai. Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach, pages 227--236.

• Z.-R. Xie and M.-J. Hwang. A New Neural Network for B-Turn Prediction: the Effect of Site-Specific Amino Acid Preference, pages 237--246.

• S.-S. Huang, D.L. Fulton, D.J. Arenillas, P. Perco, S.H. Sui, J. Mortimer, and W. Wasserman. Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes, pages 247--256.

• C.-T. Chen, H.-N. Lin, K.-P. Wu, T.-Y. Sung, and W.-L. Hsu. A Knowledge-Based Approach to Protein Local Structure Prediction, pages 257--266.

• L.H. Yang, W. Hsu, M.L. Lee, and L. Wong. Identification of MicroRNA Precursors via SVM, pages 267--276.

• M. Shashikanth, A. Snethalatharani, S.K. Mubarak, and K. Ulaganathan. Genome Wide Computational Analysis of Small Nuclear RNA Genes for Oryza Sativa (Indica and Japonica), pages 277--286.

• X. Han. Resolving the Gene Tree and Species Tree Problem by Phylogenetic Mining, pages 287--296.

• J. Manuch, X. Zhao, L. Stacho, and A. Gupta. Characterization of the Existence of Galled-Tree Networks, pages 297--306.

• J. Assfalg, H.-P. Kriegel, P. Kroeger, P. Kunath, A. Pryakhin, and M. Renz. Semi-Supervised Threshold Queries on Pharmacogenomics Time Sequences, pages 307--316.

• K. Arun and C.J. Langmead. Structure-Based Chemical Shift Prediction Using Random Forests Non-Linear Regression, pages 317--326.

• M. Huang, X. Zhu, S. Ding, H. Yu, and M. Li. ONBRIRES: Ontology-Based Biological Relation Extraction System, pages 327--336.

• P.Y. Chan, T.W. Lam, and S.M. Yiu. A More Accurate and Efficient Whole Genome Phylogeny, pages 337--352.

• D. Pan and F. Wang. Gene Expression Data Clustering Based on Local Similarity Combination, pages 353--362.