Proceedings of the 4th Asia-Pacific Bioinformatics Conference : Taipei, Taiwan 13 - 16 February 2006

by Jiang, Tao; Yang, Ueng-Cheng; Chen, Yi-Ping Phoebe; Wong, Limsoon

• ISBN13: 9781860946233
• ISBN10: 1860946232
• Format: Hardcover
• Copyright: 2006-02-28
• Publisher: World Scientific Pub Co Inc

Summary

High-throughput sequencing and functional genomics technologies have given us a draft human genome sequence and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, and gene expression profiles of normal and diseased tissues in different clinical states are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the annotation of genornic sequences, in the understanding of the interplay between genes and proteins, in the analysis of the genetic variability of species, and so on. This proceedings contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics, by researchers, professionals, and industrial practitioners at the 4th Asia-Pacific Bioinformatics Conference held in Taipei in February 2006.

Table of Contents

Preface	v
APBC 2006 Organization	vii
Keynote Papers
Wen-Hsiung Li.
On the Inference of Regulatory Elements, Circuits and Modules	1	(2)
Mark A. Ragan.
Automating the Search for Lateral Gene Transfer	3	(2)
Michael S. Waterman.
Whole Genome Optical Mapping	5	(2)
Contributed Papers
D.A. Konovalov.
Accuracy of Four Heuristics for the Full Sibship Reconstruction Problem in the Presence of Genotype Errors	7	(10)
P.C.H. Ma & K.C.C. Chan.
Inference of Gene Regulatory Networks from Microarray Data: A Fuzzy Logic Approach	17	(10)
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	(12)
P. Horton, K.-J. Park, T. Obayashi, & K. Nakai.
Protein Subcellular Localization Prediction with WoLF PSORT	39	(10)
P.-H. Chi & C.-R. Shyu.
Predicting Ranked SCOP Domains by Mining Associations of Visual Contents in Distance Matrices	49	(10)
D. Ruths & L. Nakhleh.
RECOMP: A Parsimony-Based Method for Detecting Recombination	59	(10)
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	69	(10)
F.Y.L. Chin & H.C.M. Leung.
An Efficient Algorithm for String Motif Discovery	79	(10)
Y. Kawada & Y. Sakakibara.
Discriminative Detection of Cis-Acting Regulatory Variation from Location Data	89	(10)
T. Akutsu, M. Hayashida, W.-K. Ching, & M.K. Ng.
On the Complexity of Finding Control Strategies for Boolean Networks	99	(10)
K.F. Chong, K. Ning, H.W. Leong, & P. Pevzner.
Characterization of Multi-Charge Mass Spectra for Peptide Sequencing	109	(10)
Y. Ma, G. Wang, Y. Li, & Y. Zhao.
EDAM: An Efficient Clique Discovery Algorithm with Frequency Transformation for Finding Motifs	119	(10)
M.K. Ng, E.S. Fung, W.-K. Ching, & Y.-F. Lee.
A Recursive Method for Solving Haplotype Frequencies in Multiple Loci Linkage Analysis	129	(10)
S. Das, S. Paul, & C. Dutta.
Trends in Codon and Amino Acid Usage in Human Pathogen Tropheryma Whipplei, the Only Known Actinobacteria with Reduced Genome	139	(10)
S. Paul, S. Das, & C. Dutta.
Consequences of Mutation, Selection and Physico-Chemical Properties of Encoded Proteins on Synonymous Codon Usage in Adenoviruses	149	(10)
Z. Cai, M. Heydari, & G. Lin.
Microarray Missing Value Imputation by Iterated Local Least Squares	159	(10)
S. Thorvaldsen, E. Ytterstad, & T. Fla.
Property-Dependent Analysis of Aligned Proteins from Two Or More Populations	169	(10)
L. Shen & E.C. Tan.
A Generalized Output-Coding Scheme with SVM for Multiclass Microarray Classification	179	(8)
D. Ruths & L. Nakhleh.
Techniques for Assessing Phylogenetic Branch Support: A Performance Study	187	(10)
Y.-P.P. Chen & Q. Chen.
Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databases	197	(10)
C. Sinoquet.
A Novel Approach for Structured Consensus Motif Inference Under Specificity and Quorum Constraints	207	(10)
C.J. Langmead.
A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data	217	(10)
M.J. Aralizo-Bravo, S. Fujii, H. Kono, & A. Sarai.
Disentangling the Role of Tetranucleotides in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach	227	(10)
Z.-R. Xie & M.-J. Hwang.
A New Neural Network for B-Turn Prediction: The Effect of Site-Specific Amino Acid Preference	237	(10)
S.-S. Huang, D.L. Fulton, D.J. Arenillas, P. Perco, S.J.H. Sui, J.R. Mortimer, & W.W. Wasserman.
Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes	247	(10)
C.-T. Chen, H.-N. Lin, K.-P. Wu, T.-Y. Sung, & W.-L. Hsu.
A Knowledge-Based Approach to Protein Local Structure Prediction	257	(10)
L.H. Yang, W. Hsu, M.L. Lee, & L. Wong.
Identification of MicroRNA Precursors via SVM	267	(10)
M. Shashikanth, A. Snehalatharani, S.K. Mubarak, & K. Ulaganathan.
Genome-Wide Computational Analysis of Small Nuclear RNA Genes of Oryza Sativa (Indica and Japonica)	277	(10)
X. Han.
Resolving the Gene Tree and Species Tree Problem by Phylogenetic Mining	287	(10)
J. Manuch, X. Zhao, L. Stacho, & A. Gupta.
Characterization of the Existence of Galled-Tree Networks (Extended Abstract)	297	(10)
J. Assfalg, H.-P. Kriegel, P. Kroger, P. Kunath, A. Pryakhin, & M. Renz.
Semi-Supervised Threshold Queries on Pharmacogenomics Time Sequences	307	(10)
K. Arun & C.J. Langmead.
Structure Based Chemical Shift Prediction Using Random Forests Non-Linear Regression	317	(10)
M. Huang, X. Zhu, S. Ding, H. Yu, & M. Li.
ONBIRES: Ontology-Based Biological Relation Extraction System	327	(10)
P.Y. Chan, T.W. Lam, S.M. Yiu, & C.M. Liu.
A More Accurate and Efficient Whole Genome Phylogeny	337	(16)
D. Pan & F. Wang.
Gene Expression Data Clustering Based on Local Similarity Combination	353	(10)
Author Index	363