David Sankoff, Lusheng Wang, and Francis Chin, editors. Proceedings of 5th Asia-Pacific Bioinformatics Conference, 15-17 January 2007, Hong Kong. Imperial College Press, London, January 2007.

Contents

• David Sankoff, Lusheng Wang, Francis Chin. Preface. pages v-vi.

• Jennifer A. Marshall Graves. Exploring Genomes of Distantly Related Mammals. page 1.

• Joe Nadeau. Bugs, Guts and Fat---A Systems Approach to the Metabolic 'Axis of Evil'. page 3.

• Pavel Pevzner. Protein Identification via Spectral Networks Analysis. page 5.

• Daniel H. Huson, Alexander F. Auch, Qi Ji, and Stephan C. Schuster. Metagenome Analysis using Megan. pages 7-16.

• Q. Fu, E. Bent, J. Borneman, M. Chrobak, and N. Young. Algorithmic Approaches to Selecting Control Clones in DNA Array Hybridization Experiments. pages 17-26.

• Matteo Comin and Laxmi Parida. Subtle Motif Discovery for Detection of DNA Regulatory Sites. pages 27-36.

• Xudong Xie, Shuanhu Wu, Kin-Man Lam, and Hong Yan. An Effective Promoter Detection Method using the Adaboost Algorithm. pages 37-46.

• Hongya Zhao, Alan W. C. Liew, and Hong Yan. A New Strategy of Geometrical Biclustering for Microarray Data Analysis. pages 47-56.

• V. Choi, Y. Huang, V. Lam, D. Potter, R. Laubenbacher, and K. Duca. Using Formal Concept Analysis for Microarray Data Comparison. pages 57-66.

• Sara C. Madeira and Arlindo L. Oliveira. An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression Data. pages 67-80.

• Zhipeng Cai, Randy Goebel, Mohammad R. Salavatipour, Yi Shi, Lizhe Xu, and Guohui Lin. Selecting Genes with Dissimilar Discrimination Strength for Sample Class Prediction. pages 81-90.

• M. Stissing, T. Mailund, C.N.S. Pedersen, G.S. Brodal, and R. Fagerberg. Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. pages 91-100.

• M. Stissing, C.N.S. Pedersen, T. Mailund, G.S. Brodal, and R. Fagerberg. Computing the Quartet Distance Between Evolutionary Trees of Bounded Degree. pages 101-110.

• P. Wang, B. B. Zhou, M. Taraeneh, D. Chu, C. Wang, A. Y. Zomaya, and R. P. Brent. A Global Maximum Likelihood Super-Quartet Phylogeny Method. pages 111-120.

• Seung-Jin Sul and Tiffani L. Williams. A Randomized Algorithm for Comparing Sets of Phylogenetic Trees. pages 121-130.

• Minghui Jiang, Ying Xu, and Binhai Zhu. Protein Structure-Structure Alignment with Discrete Fr'echet Distance. pages 131-141.

• Yonggang Lu, Jing He, and Charlie E. M. Strauss. Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta. pages 143-151.

• Jan Manuch and Daya Ram Gaur. Fitting Protein Chains to Cubic Lattice is NP-Complete. pages 153-164.

• Tatsuya Akutsu and Daiji Fukagawa. Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments. pages 165-174.

• Gaofeng Huang, Peter Jeavons, and Dominic Kwiatkowski. Exact and Heuristic Approaches for Identifying Disease-Associated SNP Motifs. pages 175-184.

• Young Ju Suh and Wentian Li. Genotype-Based Case-Control Analysis, Violation of Hardy-Weinberg Equilibrium, and Phase Diagrams. pages 185-194.

• B. C. Easton, A. V. Isaev, G. A. Huttley, and P. Maxwell. A Probabilistic Method to Identify Compensatory Substitutions for Pathogenic Mutations. pages 195-204.

• M. Belcaid, A. Bergeron, A. Chateau, C. Chauve, Y. Gingras, G. Poisson, and M. Vendette. Exploring Genome Rearrangements using Virtual Hybridization. pages 205-214.

• Narayanan Raghupathy, Rose Hoberman, and Dannie Durand. Two Plus Two Does not Equal Three: Statistical Tests for Multiple Genome Comparison. pages 215-225.

• Wei Xu. The Distance Between Randomly Constructed Genomes. pages 227-236.

• Zheng Fu and Tao Jiang. Computing the Breakpoint Distance between Partially Ordered Genomes. pages 237-246.

• Jochen Supper, Holger Fr"ohlich, Christian Spieth, Andreas Dr"ager, and Andreas Zell. Inferring Gene Regulatory Networks by Machine Learning Methods. pages 247-256.

• Morihiro Hayashida, Tatsuya Akutsu, and Hiroshi Nagamochi. A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs. pages 257-266.

• Jochen Supper, Holger Fr"ohlich, and Andreas Zell. Gene Regulatory Network Inference via Regression Based Topological Refinement. pages 267-276.

• Falk H"uffner, Sebastian Wernicke, and Thomas Zichner. Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway Detection. pages 277-286.

• Kang Ning, Ket Fah Chong, and Hon Wai Leong. De Novo Peptide Sequencing for Mass Spectra Based on Multi-Charge Strong Tags. pages 287-296.

• Baozhen Shan, Bin Ma, Kaizhong Zhang, and Gilles Lajoie. Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry. pages 297-306.

• Shilin Ding, Minlie Huang, and Xiaoyan Zhu. Semi-supervised Pattern Learning for Extracting Relations from Bioscience Texts. pages 307-316.

• Kinya Okada, Kiyoshi Asai, and Masanori Arita. Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions. pages 317-326.

• Denise Y. F. Mak and Gary Benson. All Hits All The Time: Parameter Free Calculation of Seed Sensitivity. pages 327-340.

• Sung-Hee Park, David Gilbert, and Keun Ho Ryu. Fast Structural Similarity Search Based on Topology String Matching. pages 341-351.

• Sebastian Wernicke and Florian Rasche. Simple and Fast Alignment of Metabolic Pathways by Exploiting Local Diversity. pages 353-362.

• Betty Yee Man Chen, and Jaime G. Carbonell. Combining N-grams and Alignment in G-protein Coupling Specificity Prediction. pages 363-372.