Yi-Ping Phoebe Chen and Limsoon Wong, editors. Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore. Imperial College Press, London, January 2005.

Contents

• Yi-Ping Phoebe Chen, Limsoon Wong. Preface. pages v-vi.

• S. M. Yiu, P. Y. Chan, T. W. Lam, W. K. Sung, H. F. Ting, P. W. H. Wong. Allowing mismatches in anchors for wholw genome alignment: Generation and effectiveness. pages 1-10.

• Hon Nian Chua, Wing-Kin Sung. A better gap penalty for pairwise SVM. pages 11-20.

• Zi H. Huang, Xiaofang Zhou. High dimensional indexing for protein structure matching using bowties. pages 21-30.

• Greg Bulter, Guang Wang, Yue Wang, Liqian Zou. A graph database with visual queries for genomics. pages 31-40.

• K. M. Konwar, I. I. Mandoiu, A. C. Russell, A. A. Shvartsman. Improved algorithms for multiplex PCR primer set selection with amplification length constraints. pages 41-50.

• Dukka Bahadur K. C., Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu. Clique-based algorithms for protein threading with profiles and constraints. pages 51-64.

• Shiou-Ling Wang, Chung-Ming Chen, Ming-Jing Hwang. Classification of protein 3D folds by hidden Markov learning on sequences of structural alphabets. pages 65-72.

• Jinbo Xu, Libo Yu, Ming Li. Consensus fold recognition by predicted model quality. pages 73-83.

• Rajkumar Bondugula, Ognen Duzlevski, Dong Xu. Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction. pages 85-94.

• J. Feng, L. Parida, R. Zhou. Protein folding trajectory analysis using patterned clusters. pages 95-104.

• Emily W. Xu, Daniel G. Brown, Paul Kearney. The use of functional domains to improve transmembrane protein topology prediction. pages 105-116.

• Jian Guo, Yuanlie Lin, Zhirong Sun. A novel method for protein subcellular localization: Combining residue-couple model and SVM. pages 117-129.

• Mikael Boden, John Hawkins. Detecting residues in targeting peptides. pages 131-140.

• Stefan Maetschke, Michael Towsey, Mikael Boden. BLOMAP: An encoding of amino acids which improves signal peptide cleavage site prediction. pages 141-150.

• Kung-Hao Liang. Cells In Silico (CIS): A biomedical simulation framework based on Markov random field. pages 151-160.

• Zhou Zhang, Suisheng Tang, See-Kiong Ng. Toward discovering disease-specific gene networks from online literature. pages 161-169.

• Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano. A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. pages 171-180.

• Jian Liu, Bin Ma, Ming Li. PRIME: Peptide robust identification from MS/MS spectra. pages 181-190.

• Kaibo Duan, Jagath C. Rajapakse. SVM-RFE peak selection for cancer classification with mass spectrometry data. pages 191-200.

• Xiuying Wang, David Dagan Feng. Hybrid registration for two-dimensional gel protein images. pages 201-210.

• Chao Shi, Lihui Chen. Feature dimension reduction for microarray data analysis using locally linear embedding. pages 211-217.

• Li Shen, Eng Chong Tan. PLS and SVD based penalized logistic regression for cancer classification using microarray data. pages 219-228.

• Tsun-Chen Lin, Ru-Sheng Liu, Shu-Yuan Chen, Chen-Chung Liu, Chieh-Yu Chen. Genetic algorithms and silhouette measures applied to microarray data classification. pages 229-238.

• S. Rajasekaran, S. Balla, C. Huang, V. Thapar, M. Gryk, M. Maciejewski, M. Schiller. Exact algorithms for motif search. pages 239-248.

• Sanguthevar Rajasekaran, Sudha Balla, Chun-Hsi Huang. Exact algorithms for planted motif challenge problems. pages 249-259.

• Francis Y. L. Chin, Henry C. M. Leung. Voting algorithms for discovering long motifs. pages 261-271.

• Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot. A highly scalable algorithm for the extraction of CIS-regulatory regions. pages 273-282.

• Rajesh Chowdhary, R. Ayesha Ali, Vladimir B. Bajic. Modeling 5' regions of histone genes using Bayesian networks. pages 283-288.

• Hao-Teng Chang, Tan-Chi Fan, Margaret Dah-Tsyr Chang, Tun-Wei Pai, Bo-Han Su, Pei-Chih Wu. Unique peptide prediction of RNase family sequences based on reinforced merging algorithms. pages 289-298.

• D. Papamichail, S. S. Skiena, C. Van Der Lelie, S. R. McCorkle. Bacterial population assay via k-mer analysis. pages 299-308.

• Feng-Mao Lin, Hsien-Da Huang, Yu-Chung Chang, Pak-Leong Chan, Jorng-Tzong Horng, Ming-Tat Ko. A database to aid probe design for virus identification. pages 309-318.

• Lei Huang, Yang Dai. A support vector machine approach for prediction of T Cell epitopes. pages 319-328.

• Gang Wu, Guohui Lin, Jia-Huai You, Xiaomeng Wu. Faster solution to the maximum quartet consistency problem with constraint programming. pages 329-338.

• Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson, Wing-Kin Sung. Inferring phylogenetic relationships avoiding forbidden rooted triplets. pages 339-348.

• Lusheng Wang, Daming Zhu, Xiaowen Liu, Shaohan Ma. An O(N²) algorithm for signed translocation problem. pages 349-358.

• Haruki Nakamura. Protein informatics towards integration of data grid and computing grid. pages 359-362.

• X. Chen, J. Zheng, Z. Fu, P.Nan, Y. Zhong, S. Lonardi, T. Jiang. Computing the assignment of orthologous genes via genome rearrangement. pages 363-378.

• Sin Lam Tan, Vidhu Choudhary, Alan Christoffels, Byrappa Venkatesh, Vladimir B. Bajic. Comparison of core promoters in Fugu rubripes and human. page 379.

• Santosh K. Mishra. Trends in bioinformatics research and Singapore's role. page 381.

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