CONTENTS -- Preface -- APBC 2006 Organization -- Programme Committee -- Keynote Papers -- Wen-Hsiung Li. On the Inference of Regulatory Elements, Circuits and Modules -- Mark A. Ragan. Automating the Search for Lateral Gene Transfer -- Michael S. Waterman. Whole Genome Optical Mapping -- Contributed Papers -- D.A. Konovalov. Accuracy of Four Heuristics for the Full Sibship Reconstruc- tion Problem in the Presence of Genotype Errors -- 1 Introduction -- 2 Method -- 2.1 Accuracy -- 2.2 Simulations -- 3 Algorithms -- 3.1 The Modified SIMPSON (MS2) Algorithm -- 3.2 The SIMPSON-assisted Descending Ratio (SDR) Algorithm -- 4 Results and Discussion -- Acknowledgments -- References -- P.C.H. Ma & K.C.C. Chan. Inference of Gene Regulatory Networks from Microarray Data: A Fuzzy Logic Approach -- 1 Introduction -- 2 The proposed algorithm -- 2.1. Linguistic variables and linguistic terms representation -- 2.2. Discovering the interesting patterns -- 2.3. Prediction based on the discovered patterns -- 3 Experimental results -- 3.1. Experimental data -- 3.2. Method of evaluating the results -- 3.3. Results -- 3.4. Biological interpretation -- 4 Conclusions -- References -- C.W. Li, W.C. Chang, & B.S. Chen. System Identification and Robustness Analysis of the Circadian Regulatory Network via Microarray Data in Arabidopsis Thaliana -- 1 Introduction -- 2 Dynamic System Description of Circadian Regulatory Model -- 3. Assay of the Model -- 3.1. Assay of ARX System Model -- 3.1.1. Determination of system order -- 3.2. Sensitivity Analysis of Circadian System -- 3.2.1. Circadian clock frequency assay -- 3.2.2. Trans-perturbation assay -- 3.2.2.1. Trans-sensitivity rate Y simulation of gene -- 3.2.2.2 Trans-expression threshold M1 simulation of gene -- 4. Results -- 5. Discussion -- Acknowledgments -- References.

P. Horton, K.-J. Park, T. Obayashi, & K. Nakai. Protein Subcellular Local- ization Prediction with WOLF PSORT -- 1. Introduction -- 2. Methods -- 2.1. Dataset -- 2.1.1. Site Definition -- 2.2. WoLF PSORT system -- 2.3. Classification -- 2.3.1. Candidate Features -- 2.3.2. Classification Algorithm -- 2.3.3. Extensions for Dual Localization Prediction -- 2.3.4. Feature Selection and Weighting -- 2.3.5. Reducing Over-reliance on Sequence Similarity -- 2.3.6. Evaluation of WoLF PSORT Accuracy -- 3. Results -- 3.1. Effect of Feature Weighting -- 3.2. WoLF PSORT Combined with BLAST -- 3.3. WoLF PSORT Server -- 4. Discussion -- 4.1. Interpretable Results -- 4.2. Evaluation in the Presence of Similar Sequences -- 4.3. Predicting Dual Localization -- 5. Conclusion -- 6. Acknowledgement -- References -- P.-H. Chi & C.-R. Shyu. Predicting Ranked SCOP Domains by Mining As- sociations of Visual Contents in Distance Matrices -- 1. Introduction -- 2. Preliminaries -- 3. Method -- 3.1. Space Partition Algorithm Using C4.5 Decision Tree -- 3.2. Mining Training Data and Prediction Model -- 4. Experiment -- 5. Conclusion -- References -- D. Ruths & L. Nakhleh. RECOMP: A Parsimony-Based Method for Detecting Recombination -- 1. Introduction -- 2. Phylogeny-based Recombination Detection -- 3. RECOMP -- 4. Empirical Performance -- 4.1. Data -- 4.2. Results -- 5. Conclusions and Future Work -- References -- H.-J. Jin, H.-J. Kim, J.-H. Choi, & H.-G. Cho. AlignScope: A Visual Mining Tool for Gene Team Finding with Whole Genome Alignment -- 1. Introduction -- 2. Clustering for Gene Pairs -- 2.1. Preliminary -- 2.2. Zoned Hierarchical Clustering -- Effecting Zone of each cluster -- 2.3. Two Density Measures for Level-of-Detail and Detection of Gene Clusters -- 2.4. Spliced Gene Clusters -- 3. Visualization of Gene Pairs -- Data Filtering -- Shape and Color of Alignment pair.

4. Experiment Result -- 5. Conclusion -- Acknowledgments -- References -- F.Y.L. Chin & H.C.M. Leung. An Efficient Algorithm for String Motif Discovery -- 1 Introduction -- 2 The Motif Discovery Problem -- 3 Algorithm -- 4 Experimental Results -- 4.1. Simulated Data -- 4.2. Real Biological Data -- 5 Discussion -- 6.References -- Y. Kawada & Y. Sakakibara. Discriminative Detection of Cis-Acting Regula- tory Variation from Location Data -- 1. Introduction -- 2. Methods -- 2.1. Consensus Tree Construction -- 2.2. Extractions of cis-regulatory elements based on functional annotations -- 3. Experimental Results -- 3.1. Data -- 3.2. Detection of Known Motifs -- 3.3. Putative Cis-Regulatory Variants -- 3.4. Detection of Multiple Motifs of Non-DNA-Binding Cofactors -- 4. Conclusion -- References -- T. Akutsu, M. Hayashida, W.-K. Ching, & M.K. Ng. On the Complexity of Finding Control Strategies for Boolean Networks -- 1. Introduction -- 2. Boolean Network and Its Control -- Definition 2.1. (BN-CONTROL) -- 3. Hardness of Finding Control Strategies -- 4. Algorithms for Trees -- 5. Concluding Remarks -- References -- K.F. Chong, K. Ning, H.W. Leong, & P. Pevzner. Characterization of Multi- Charge Mass Spectra for Peptide Sequencing -- 1 Introduction -- 2 Modeling of Multi-Charge Spectra -- 2.1. Quality Measures for Evaluating Mass Spectra -- 2.2. Experimental Data and Analysis -- 3 A Simple de Novo Algorithm for Multi-Charge Spectra -- 3.1 Strong Tags in the Multi-Charge Spectra -- 3.2 The GBST Algorithm -- 3.3 Experiments on Algorithms -- 4 Conclusion -- Acknowledgements -- References -- Y. Ma, G. Wang, Y. Li, & Y. Zhao. EDAM: An Efficient Clique Discovery Algorithm with Frequency Transformation for Finding Motifs -- 1. Introduction -- 2. Problem Description -- 3. EDAM -- 3.1. Frequency Transformation -- 3.2. MBR-clique Searching -- 3.3. Motif Discovery.

4. Analysis -- 4.1. Space complexity -- 4.2. Time complexity -- 5. Experimental Results -- 6. Conclusions and Discussions -- References -- M.K. Ng, E.S. Fung, W.-K. Ching, & Y.-F. Lee. A Recursive Method for Solving Haplotype Fkequencies in Multiple Loci Linkage Analysis -- 1. Introduction -- 2. The Recombination Matrix An -- 3. Recursive Solvers -- 3.1. Computational Results -- 4. Concluding Remarks -- References -- S. Das, S. Paul, & C. Dutta. Trends in Codon and Amino Acid Usage in Hu- man Pathogen Tropheryma Whipplei, the Only Known Actinobacteria with Reduced Genome -- 1. Introduction -- 2. Methods and Materials -- 2.1 Sequence retrieval -- 2.2 Sequence analysis for identifying trends in codon and amino acid usage -- 3. Results and Discussion -- 3.1 Asymmetrical mutational bias, coupled with replicational-transcriptional selection on synonymous codon usage -- 3.2 Evidences for translational selection in T. whipplei -- 3.3 Major sources of variation in proteome composition -- 3.4 Relation between gene expression, protein conservation and amino acid usage -- References -- S. Paul, S. Das, & C. Dutta. Consequences of Mutation, Selection and PhysicGChemical Properties of Encoded Proteins on Synonymous Codon Usage in Adenoviruses -- 1. Introduction -- 2. Methods and Materials -- 2.1 Retrieval of sequences -- 2.2 Sequence analysis -- 3. Results and Discussion -- 3.1 Inter-and Intra-species variation in compositional constraints on codon usage -- 3.2 Virus-specific synonymous codon usage patterns with no sign of host-specificity -- 3.3 Differential codon usage in structural and nonstructural genes -- 3.4 Correlation between synonymous base compositions and hydropathy of encoded proteins -- References -- Z. Cai, M. Heydari, & G. Lin. Microarray Missing Value Imputation by Iterated Local Least Squares -- 1. Introduction.

2. Iterated Local Least Squares Imputation - ILLsimpute -- 2.1. Local Least Squares Imputation - LLSimpute -- 2.2. Measures of Performance -- 2.3. Nearest Neighboring Gene Determination -- 2.4. Iterated Local Least Squares Imputation - ILLsimpute -- 3. Experimental Results -- 3.1. Datasets -- 3.2. Threshold Determination in ILLsimpute -- 3.3. Number of Iterations Determination in ILLsimpute -- 3.4. Imputation Accuracy Comparison -- 4. Conclusions -- References -- S. Thorvaldsen, E. Ytterstad, & T. Fla. Property-Dependent Analysis of Aligned Proteins from Two Or More Populations -- 1 Introduction -- 2 Materials and Methods -- 2.1 Sequence Data -- 2.2 Comparing Sequence Properties by Statistical Methods -- One-way ANOVA -- Matched-pair tests for step change -- Cumulative Mann-Kendall test for monotonic trend -- Visualization -- 3 Applications and Results -- 3.1 Difference in Physiochemical Properties -- 4 Some Conclusions -- Acknowledgments -- References -- L. Shen & E.C. Tan. A Generalized Output-Coding Scheme with SVM for Multiclass Microarray Classification -- 1 Introduction -- 2 Methods -- 2.1 Output-Coding for Multiclass Classification -- 2.2 Feature Selection -- 3 Results -- 3.1 Datasets and Experimental Setup -- 3.2 Experimental Results -- 4 Conclusions -- References -- D. Ruths & L. Nakhleh. Techniques for Assessing Phylogenetic Branch Support: A Performance Study -- 1. Introduction -- 2. Methods -- 2.1. Phylogeny Estimation Methods -- 2.2. Bootstrap -- 2.3. Consensus Trees & Branch Contraction -- 2.4. Tree Comparison -- 3. Experimental Design -- 4. Results -- 4.1. Selection of Optimal MP Consensus Method -- 4.2. Branch Support vs. Substitution Rate -- 4.3. Effects of Branch Contraction on Accuracy -- 5. Discussion -- 6. Conclusions -- References.

Y.-P.P. Chen & Q. Chen. Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databases.