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El. knyga: Proceedings Of The 4th Asia-pacific Bioinformatics Conference

Edited by (Univ Of California, Riverside, Usa), Edited by (Nus, S'pore), Edited by (Deakin Univ, Australia), Edited by (Nat'l Yang-ming Univ, Taiwan)
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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 genomic 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.
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
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