Tao Jiang, Ueng-Cheng Yang, Yi-Ping Phoebe Chen, Limsoon Wong (Eds.): Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, Taipei, Taiwan. Imperial College Press, London 2006, ISBN 1-86094-623-2

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Preface

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  Tao Jiang, Ueng-Cheng Yang, Yi-Ping Phoebe Chen, Limsoon Wong: Preface.

Keynote Papers

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  Wen-Hsiung Li: On the Inference of Regulatory Elements, Circuits, and Modules. 1
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  Mark A. Ragan: Automating the Search for Lateral Gene Transfer. 3
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  Michael S. Waterman: Whole Genome Optical Mapping. 5

Contributed Papers

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  Dmitry A. Konovalov: Accuracy of Four Heuristics for the Full Sibship Reconstruction Problem in the Presence of Genotype Errors. 7-16
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  Patrick C. H. Ma, Keith C. C. Chan: Inference of Gene Regulatory Networks from Microarray Data: A Fuzzy Logic Approach. 17-26
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  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. 27-37
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  Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai: Protein Subcellular Localisation Prediction with WoLF PSORT. 39-48
• 
  Pin-Hao Chi, Chi-Ren Shyu: Predicting Ranked SCOP Domains by Mining Associations of Visual Contents in Distance Matrices. 49-58
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  Derek A. Ruths, Luay Nakhleh: RECOMP: A Parsimony-Based Method for Detecting Recombination. 59-68
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  Hee-Jeong Jin, Hye-Jung Kim, Jeong-Hyeon Choi, Hwan-Gue Cho: AlignScope: A Visual Mining Tool for Gene Team Finding with Whole Genome Alignment. 69-78
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  Francis Y. L. Chin, Henry C. M. Leung: An Efficient Algorithm for String Motif Discovery. 79-88
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  Yuji Kawada, Yasubumi Sakakibara: Discriminative Detection of Cis-Acting Regulatory Variation From Location Data. 89-98
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  Tatsuya Akutsu, Morihiro Hayashida, Wai-Ki Ching, Michael K. Ng: On the Complexity of Finding Control Strategies for Boolean Networks. 99-108
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  Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner: Characterization of Multi-Charge Mass Spectra for Peptide Sequencing. 109-119
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  Yifei Ma, Guoren Wang, Yongguang Li, Yuhai Zhao: EDAM: An Efficient Clique Discovery Algorithm with Frequency Transformation for Finding Motifs. 119-128
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  Michael K. Ng: A Recursive Method for Solving Haplotype Frequencies in Multiple Loci Linkage Analysis. 129-138
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  Sabyasachi Das, Sandip Paul, Chitra Dutta: Trends in Codon and Amino Acid Usage in Human Pathogen Tropheryma Whipplei, the only Known Actinobacteria with Reduced Genome. 139-148
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  Sandip Paul, Sabyasachi Das, Chitra Dutta: Consequences of Mutation, Selection, and Physico-Chemical Properties of Encoded Proteins on Synonymous Codon Usage in Adenoviruses. 149-158
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  Zhipeng Cai, Maysam Heydari, Guohui Lin: Microarray Missing Value Imputation by Iterated Local Least Squares. 159-168
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  Steinar Thorvaldsen, Elinor Ytterstad, Tor Flå: Property-Dependent Analysis of Aligned Proteins from Two Or More Populations. 169-178
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  Li Shen, Eng Chong Tan: A Generalized Output-Coding Scheme with SVM for Multiclass Microarray Classification. 179-186
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  Derek A. Ruths, Luay Nakhleh: Techniques for Assessing Phylogenetic Branch Support: A Performance Study. 187-196
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  Yi-Ping Phoebe Chen, Qingfeng Chen: Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databases. 197-206
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  Christine Sinoquet: A Novel Approach for Structured Consensus Motif Inference Under Specificity and Quorum Constraints. 207-216
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  Christopher James Langmead: A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data. 217-226
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  Marcos J. Araúzo-Bravo, Satoshi Fujii, Hidetoshi Kono, Akinori Sarai: Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach. 227-236
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  Zhong-Ru Xie, Ming-Jing Hwang: A New Neural Network for B-Turn Prediction: the Effect of Site-Specific Amino Acid Preference. 237-246
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  Shao-Shan Huang, Debra L. Fulton, David J. Arenillas, Paul Perco, Shannan J. Ho Sui, James R. Mortimer, Wyeth W. Wasserman: Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes. 247-256
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  Ching-Tai Chen, Hsin-Nan Lin, Kuen-Pin Wu, Ting-Yi Sung, Wen-Lian Hsu: A Knowledge-Based Approach to Protein Local Structure Prediction. 257-266
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  Liang Huai Yang, Wynne Hsu, Mong-Li Lee, Limsoon Wong: Identification of MicroRNA Precursors via SVM. 267-276
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  M. Shashikanth, A. Snethalatharani, S. K. Mubarak, K. Ulaganathan: Genome Wide Computational Analysis of Small Nuclear RNA Genes for Oryza Sativa (Indica and Japonica). 277-286
• 
  Xiaoxu Han: Resolving the Gene Tree and Species Tree Problem by Phylogenetic Mining. 287-296
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  Ján Manuch, Xiaohong Zhao, Ladislav Stacho, Arvind Gupta: Characterization of the Existence of Galled-Tree Networks. 297-306
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  Johannes Aßfalg, Hans-Peter Kriegel, Peer Kröger, Peter Kunath, Alexey Pryakhin, Matthias Renz: Semi-Supervised Threshold Queries on Pharmacogenomics Time Sequences. 307-316
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  K. Arun, Christopher James Langmead: Structure-Based Chemical Shift Prediction Using Random Forests Non-Linear Regression. 317-326
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  Minlie Huang, Xiaoyan Zhu, Shilin Ding, Hao Yu, Ming Li: ONBRIRES: Ontology-Based Biological Relation Extraction System. 327-336
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  P. Y. Chan, Tak Wah Lam, Siu-Ming Yiu: A More Accurate and Efficient Whole Genome Phylogeny. 337-352
• 
  De Pan, Fei Wang: Gene Expression Data Clustering Based on Local Similarity Combination. 353-362

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