3. APBC 2005: Singapore

Yi-Ping Phoebe Chen, Limsoon Wong (Eds.): Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore. Imperial College Press, London 2005, ISBN 1-86094-477-9

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• Yi-Ping Phoebe Chen, Limsoon Wong:
  Preface.
  
• Siu-Ming Yiu, P. Y. Chan, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting, Prudence W. H. Wong:
  Allowing mismatches in anchors for wholw genome alignment: Generation and effectiveness. 1-10
  
• Hon Nian Chua, Wing-Kin Sung:
  A better gap penalty for pairwise SVM. 11-20
  
• Zi Huang, Xiaofang Zhou:
  High dimensional indexing for protein structure matching using bowties. 21-30
  
• Greg Butler, Guang Wang, Yue Wang, Liqian Zou:
  A graph database with visual queries for genomics. 31-40
  
• Kishori M. Konwar, Ion I. Mandoiu, Alexander Russell, Alexander A. Shvartsman:
  Improved algorithms for multiplex PCR primer set selection with amplification length constraints. 41-50
  
• Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu:
  Clique-based algorithms for protein threading with profiles and constraints. 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. 65-72
  
• Jinbo Xu, Libo Yu, Ming Li:
  Consensus fold recognition by predicted model quality. 73-83
  
• Rajkumar Bondugula, Ognen Duzlevski, Dong Xu:
  Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction. 85-94
  
• J. Feng, Laxmi Parida, Ruhong Zhou:
  Protein folding trajectory analysis using patterned clusters. 95-104
  
• Emily W. Xu, Daniel G. Brown, Paul Kearney:
  The use of functional domains to improve transmembrane protein topology prediction. 105-116
  
• Jian Guo, Yuanlie Lin, Zhirong Sun:
  A novel method for protein subcellular localization: Combining residue-couple model and SVM. 117-129
  
• Mikael Bodén, John Hawkins:
  Detecting residues in targeting peptides. 131-140
  
• Stefan Maetschke, Michael Towsey, Mikael Bodén:
  BLOMAP: An encoding of amino acids which improves signal peptide cleavage site prediction. 141-150
  
• Kung-Hao Liang:
  Cells In Silico (CIS): A biomedical simulation framework based on Markov random field. 151-160
  
• Zhuo Zhang, Suisheng Tang, See-Kiong Ng:
  Toward discovering disease-specific gene networks from online literature. 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. 171-180
  
• Jian Liu, Bin Ma, Ming Li:
  PRIME: Peptide robust identification from MS/MS spectra. 181-190
  
• Kaibo Duan, Jagath C. Rajapakse:
  SVM-RFE peak selection for cancer classification with mass spectrometry data. 191-200
  
• Xiu Ying Wang, David Dagan Feng:
  Hybrid registration for two-dimensional gel protein images. 201-210
  
• Chao Shi, Lihui Chen:
  Feature dimension reduction for microarray data analysis using locally linear embedding. 211-217
  
• Li Shen, Eng Chong Tan:
  PLS and SVD based penalized logistic regression for cancer classification using microarray data. 219-228
  
• Tsun-Chen Lin, Ru-Sheng Liu, Shu-Yuan Chen, Chen-Chung Liu, Chien-Yu Chen:
  Genetic algorithms and silhouette measures applied to microarray data classification. 229-238
  
• Sanguthevar Rajasekaran, Sudha Balla, Chun-Hsi Huang, Vishal Thapar, Michael R. Gryk, Mark W. Maciejewski, Martin R. Schiller:
  Exact algorithms for motif search. 239-248
  
• Sanguthevar Rajasekaran, Sudha Balla, Chun-Hsi Huang:
  Exact algorithms for planted motif challenge problems. 249-259
  
• Francis Y. L. Chin, Henry C. M. Leung:
  Voting algorithms for discovering long motifs. 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. 273-282
  
• Rajesh Chowdhary, R. Ayesha Ali, Vladimir B. Bajic:
  Modeling 5' regions of histone genes using Bayesian networks. 283-288
  
• Hao-Teng Chang, Tan-Chi Fan, Margaret Dah-Tsyr Chang, Tun-Wen Pai, Bo-Han Su, Pei-Chih Wu:
  Unique peptide prediction of RNase family sequences based on reinforced merging algorithms. 289-298
  
• Dimitris Papamichail, Steven Skiena, C. Van Der Lelie, S. R. McCorkle:
  Bacterial population assay via k-mer analysis. 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. 309-318
  
• Lei Huang, Yang Dai:
  A support vector machine approach for prediction of T Cell epitopes. 319-328
  
• Gang Wu, Guohui Lin, Jia-Huai You, Xiaomeng Wu:
  Faster solution to the maximum quartet consistency problem with constraint programming. 329-338
  
• Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson, Wing-Kin Sung:
  Inferring phylogenetic relationships avoiding forbidden rooted triplets. 339-348
  
• Lusheng Wang, Daming Zhu, Xiaowen Liu, Shaohan Ma:
  An O(N²) algorithm for signed translocation problem. 349-358
  
• Haruki Nakamura:
  Protein informatics towards integration of data grid and computing grid. 359-362
  
• Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang:
  Computing the Assignment of Orthologous Genes via Genome Rearrangement. 363-378
  
• Sin Lam Tan, Vidhu Choudhary, Alan Christoffels, Byrappa Venkatesh, Vladimir B. Bajic:
  Comparison of core promoters in Fugu rubripes and human. 379
  
• Santosh K. Mishra:
  Trends in bioinformatics research and Singapore's role. 381