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E-raamat: Proceedings Of The 6th Asia-pacific Bioinformatics Conference

Edited by (Univ Of Tokyo, Japan), Edited by (Kyoto Univ, Japan), Edited by (European Bioinformatics Inst, Uk)
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High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically, and agriculturally important species, thus enabling large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures, metabolic pathways, and gene expression profiles of normal and diseased tissues are rapidly being generated for human and model organisms. Bioinformatics is therefore gaining importance in the annotation of genomic sequences; the understanding of the interplay among and between genes and proteins; the analysis of the genetic variability of species; the identification of pharmacological targets; and the inference of evolutionary origins, mechanisms, and relationships. This proceedings volume contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics by researchers, professionals, and industry practitioners at the 6th Asia-Pacific Bioinformatics Conference held in Kyoto, Japan, in January 2008.
Preface v
APBC 2008 Organization vii
Keynote Papers
Recent Progress in Phylogenetic Combinatorics
1(4)
Andreas Dress
KEGG for Medical and Pharmaceutical Applications
5(2)
Minoru Kanehisa
Protein Interactions Extracted from Genomes and Papers
7(2)
Alfonso Valencia
Contributed Papers
String Kernels with Feature Selection for SVM Protein Classification
9(10)
Wen- Yun Yang
Bao-Liang Lu
Predicting Nucleolar Proteins Using Support-Vector Machines
19(10)
Mikael Boden
Supervised Ensembles of Prediction Methods for Subcellular Localization
29(10)
Johannes Aßfalg
Jing Gong
Hans-Peter Kriegel
Alexey Pryakhin
Tiandi Wei
Arthur Zimek
Chemical Compound Classification with Automatically Mined Structure Patterns
39(10)
Aaron M. Smalter
J. Huan
Gerald H. Lushington
Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers
49(10)
Alireza Hadj Khodabakhshi
Jan Manuch
Arash Rafiey
Arvind Gupta
Discrimination of Native Folds Using Network Properties of Protein Structures
59(10)
Alper Kucukural
O. Ugur Sezerman
Aytul Ercil
Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein Complexes
69(10)
Suryani Lukman
Kelvin Sim
Jinyan Li
Yi-Ping Phoebe Chen
Structural Descriptors of Protein-Protein Binding Sites
79(10)
Oliver Sander
Francisco S. Domingues
Hongbo Zhu
Thomas Lengauer
Ingolf Sommer
A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots
89(12)
Thomas Wong
Y. S. Chiu
Tak- Wah Lam
S. M. Yiu
A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment
101(10)
Ryuichiro Nakato
Osamu Gotoh
fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity
111(12)
Huzefa Rangwala
George Karypis
Run Probability of High-Order Seed Patterns and Its Applications to Finding Good Transition Seeds
123(10)
Jialiang Yang
Louxin Zhang
Seed Optimization Is No Easier than Optimal Golomb Ruler Design
133(12)
Bin Ma
Hongyi Yao
Integrating Hierarchical Controlled Vocabularies with OWL Ontology: A Case Study from the Domain of Molecular Interactions
145(10)
Melissa J. Davis
Andrew Newman
Imran Khan
Jane Hunter
Mark A. Ragan
Semantic Similarity Definition over Gene Ontology by Further Mining of the Information Content
155(10)
Yuan-Peng Li
Bao-Liang Lu
From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature
165(12)
Jin-Dong Kim
Tomoko Ohta
Kanae Oda
Jun'ichi Tsujii
Classification of Protein Sequences Based on Word Segmentation Methods
177(10)
Yang Yang
Bao-Liang Lu
Wen-Yun Yang
Analysis of Structural Strand Asymmetry in Non-coding RNAs
187(12)
Jiayu Wen
Brian J. Parker
Georg F. Weiller
Finding Non-coding RNAs Through Genome-Scale Clustering
199(12)
Huei-Hun Tseng
Zasha Weinberg
Jeremy Gore
Ronald R. Breaker
Walter L. Ruzzo
A Fixed-Parameter Approach for Weighted Cluster Editing
211(10)
Sebastian Bocker
Sebastian Briesemeister
Quang Bao Anh Bui
Anke Truß
Image Compression-based Approach to Measuring the Similarity of Protein Structures
221(10)
Morihiro Hayashida
Tatsuya Akutsu
Genome Halving with Double Cut and Join
231(10)
Robert Warren
David Sankoff
Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes
241(10)
Krister M. Swenson
William Arndt
Jijun Tang
Bernard M. E. Moret
SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions
251(10)
Cuong Than
Luay Nakhleh
Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach
261(12)
Mohamed I. Abouelhoda
Robert Giegerich
Behshad Behzadi
Jean-Marc Steyaert
Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks
273(14)
Yunlei Li
Dick de Ridder
Marco J. L. de Groot
Marcel J. T. Reinders
Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks
287(10)
Xingming Zhao
Rui-Sheng Wang
Luonan Chen
Kazuyuki Aihara
Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics
297(10)
Satish Tadepalli
Naren Ramakrishnan
Layne T. Watson
Bhubaneshwar Mishra
Richard F. Helm
Symbolic Approaches for Finding Control Strategies in Boolean Networks
307(14)
Christopher James Langmead
Sumit Kumar Jha
Estimation of Population Allele Frequencies from Small Samples Containing Multiple Generations
321(12)
Dmitry A. Konovalov
Dik Heg
Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments
333(10)
Zhixiang Chen
Bin Fu
Robert Schweller
Boting Yang
Zhiyu Zhao
Binhai Zhu
Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency
343(10)
Francis Y. L. Chin
Henry Chi Ming Leung
M. H. Siu
S. M. Yiu
Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP
353(10)
Bhaskar DasGupta
Jin Jun
Ion I. Mandoiu
GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments to Predict Alternative Transcripts
363(10)
Tyler S. Alioto
Roderic Guigo
Ernesto Picardi
Graziano Pesole
Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4D Xpress
373(10)
Yannick Haudry
Chuang Kee Ong
Laurence Ettwiller
Hugo Berube
Ivica Letunic
Misha Kapushesky
Paul-Daniel Weeber
Xi Wang
Julien Gagneur
Charles Girardot
Detlev Arendt
Peer Bork
Alvis Brazma
Eileen Furlong
Joachim Wittbrodt
Thorsten Henrich
Near-Sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray Studies
383(10)
Juntao Li
Majid Eshaghi
Jianhua Liu
Radha Krishna Murthy Karuturi
Author Index 393