APBC2004 Accepted papers

              The Second Asia-Pacific Bioinformatics Conference

                    (35 full papers accepted plus 13 short papers accepted from 118 submissions)

Session Title

Title of Paper

Author

 

 

 

 

 

Keynote Speaker 1: 

The Future of Bioinformatics

Philip E. Bourne

 

Keynote Speaker 2:

Molecular Imaging and Biomedical Process Modeling

David Dagan Feng

 
S1. RNA Secondary Structure

RNA secondary structure prediction with simple pseudoknots

Jitender S. Deogun, Ruben Donis, Olga Komina, Fangrui Ma

  

Filtering of Ineffective siRNAs and Improved siRNA Design Tool

Prudence WH Wong, TW Lam, YC Mui, SM Yiu, Marie Lin

  

Exact Pattern Matching for RNA Secondary Structures

Ying Xu, Lusheng Wang, Xiaotie Deng

  

 

 

 

 

S2.Recognition Sequences

 

 

Recognition Sequences in the Restriction Endonucleases.

Jan C. Biro, Josephine M.K. Biro

 

Multiple Sequence Alignment using Tabu Search

Tariq Riaz, Yi Wang, Kuo-Bin Li

 

Structure-Function Relationship in DNA sequence Recognition by Transcription Factors

Akinori Sarai, Samuel Selvaraj, Michael M. Gromiha, Hidetoshi Kono

 

 

 

 

S3. Genome Analysis

 

 

Constructing Genome Scale Suffix Trees

A.L. Brown

 

EMAGEN: An Efficient Approach to Multiple Whole Genome Alignment

Jitender S. Deogun, Jingyi Yang, Fangrui Ma

 

Whole-Genome Functional Classification of Genes by Latent Semantic Analysis on Microarray Data

See-Kiong Ng, Sanjay Padmakar Khadayate, Yew-Soon Ong

 

 

 

 

 

S4.Protein Structures and Functions

Protein Side-chain Packing: A maximum edge- weight Clique Algorithmic Approach

Dukka Bahadur K.C., Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki

 

 

THEMATICS is Effective for Active Site Prediction in Comparative Model Structures

Ihsan A. Shehadi, Alper Uzun, Leonel F. Murga, Valentin Ilyin, Mary Jo Ondrechen

 

 

Informative 3D Visualization of Multiple Protein Structures

Paulo Lai, Warren Kaplan, W. Bret Church, Raymond K. Wong

 

S5. Interactive Approaches

A Dihedral angle database of short sub-sequences for protein structure prediction

Saravanan Dayalan, Savitri Bevinakoppa, Heiko Schroder

 

 

Nonparametric approaches to detecting differentially expressed genes in replicated microarray

Markus Neuhäuser, Fred C. Lam

 

 

 

Mega Weaver: A Simple Iterative Approach for BAC Consensus Assembly

Daolong Wang, Mario Lauria, Bo Yuan, Fred A. Wright

 
   

 

S6. Bio-Pathway and Prediction

Transmembrane Region Prediction with Hydropathy Index/Charge Two-Dimensional Trajectories of Stochastic Dynamical Systems

T. Kaburagi, D. Muramatsu, S. Hashimoto, M. Sasaki, T. Matsumoto

 

 

 

Integrating biopathway databases for large-scale modeling and simulation

Masao Nagasaki, Satoru Miyano, Atushi Doi, Hiroshi Matsuno

 

 

PathwayFinder: Paving the Way Towards Automatic Pathway Extraction

 

Daming Yao, Jingbo Wang, Yanmei Lu, Nathan Noble, Huandong Sun, Xiaoyan Zhu, Nan, Lin, Donald G. Payan, Ming Li, Kunbin Qu

 

 

 

 

 

S7. Virus Analysis

Detecting local symmetry axis in 3-dimensional virus structures

Jing He, Desh Ranjan, Michael F. Schmid, Wah Chiu

 

 

Initial SARS genome data analysis using a bioinformatics platform

Hong Luo, Jianmin Wu, Ge Gao, Yin Sun, Yujia Chen, Jingchu Luo

 
  Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type 1 Peter Meintjes, Allen Rodrigo  

 

 

 

 

S8. Bioinformatics Networks

Representing Experimental Biological Data in Metabolic Networks

Tim Dwyer, Hardy Rolletschek, Falk Schreiber

 

 

A novel method for protein subcellular localization Based on Boosting and Probabilistic Neural Network

Jian Guo, Zhirong Sun, Yuanlie Lin

 

 

BRINet: A BioResource Integration Network

Jason E. Sew Hoy, John R. McDonald, Alan F. McCulloch

 
       
S9. Cancer Data and Detection Support Vector Machine Approach for Cancer Detection using Amplified Fragment Length Polymorphism (AFLP) Screening Method Waiming Kong, Lawrence Tham, Yew Wong, Patrick Tan  
  Use of Built-in Features in the Interpretation of High-dimensional Cancer Diagnosis Data

Jinyan Li, Huiqing Liu, Limsoon Wong

  
  Using Emerging Pattern Based Projected Clustering and Gene Expression Data for Cancer Detection Larry T.H. Yu, Fu-lai Chung, Stephen C.F. Chan  
       
S10. Microarray and Gene Expression An empirical Bayes adjustment to multiple p-values for the detection of differentially expressed genes in microarray experiments Somnath Datta and Susmita Datta  
  A Novel Feature Selection Method to Improve Classification of Gene Expression Data

Liang Goh, Qun Song, Nikola Kasabov

 

  
  On the Simutaneous Use of Clinical and Microarray Expression Data in the Cluster Analysis of Tissue Samples G. J. McLaclan, S. Chang, J. Mar, C. Ambroise  
       
S11. Discovery and Search Algorithm Variable-length Intervals in Homology Search Abhijit Chattaraj, Hugh E. Williams  
  Ladderlike Stepping and Interval Jumping Searching Algorithms for DNA Sequences Tun-Wen Pai, Jia-Han Chu, Wei-Yuan Chang, Margaret Dah-Tsyr Chang, Hsiu Ling Tai  
  A Combined Model and a Varied Gibbs Sampling Algorithm Used for Motif Discovery Xiaoming Wu, Bo Wang, Changxin Song, Jingzhi Cheng  
       
S12-1. Phylogenetic Analysis An Overview of the Phylogentics Analysis Library Matthew Goode, Korbinian Strimmer, Alexei Drummond, Ed Buckler  
  Identifying Character Non-Independence in Phylogenetic Data Using Data Mining Techniques Anne M. Maglia, Jennifer L. Leopold, Venkat Ram Ghatti  
S12-2. Short Papers/Phylogenetic Analysis Phylogenetic Trees: An Information Visualisation Perspective * Savrina Flora Carrizo  
  Phylogenetic tree of prokaryotes based on the complete genomes using fractal and correlation analyses * Zu-Guo Yu, Vo Anh  

 

 

 

 

Short 1. Protein Classification and Pyrosequencing

Dispensation Order Generation for Pyrosequencing *

Mats Carlsson, Nicolas Beldiceanu

 

Classification Comparison of Prediction of Solvent Accessibility from Protein Sequences *

Huiling Chen, Huan-Xiang Zhou, Xiaohua Hu, Illhoi Yoo

 

 

A Pathway Editor for Literature-based Knowledge Curation *

Ken Ichiro Fukuda, Toshihsa Takagi

 

 

Empirical knowledge and genetic algorithms for selection of Amide I frequencies in protein secondary structure prediction *

Joachim A. Hering, Peter R. Innocent, Parvez I. Haris

 

 

Towards a Theory of Protein Adsorption: Predicting the Adsorption of Proteins on Surfaces via a Piecewise Linear Model

Dan V. Nicolau Jr.

 

 

Local prediction approach of protein classification using Probabilistic suffix trees *

Zhaohui Sun, Jitender S. Deogun

 
       

Short 2. Genome Data and Visualization

 A rapid method of whole genome visualisation illustrating features in bothcoding and non-coding regions * R. Hall, L. Stern  
  Evolving Genetic Regulatory Networks Using an Artificial Genome * Jennifer Hallinan, Janet Wiles  
  Cluster Ensemble and Its Applications in Gene Expression Analysis * Xiaohua Hu, Illhoi Yoo  
  Advanced Texturing technigs for the Effective Visualization of Neoroanatomy from Diffusion Tensor Imaging Data * Burkhard Wuensche  

 

Measuring Correlation between Microarray Time-series Data using Dominant Spectrum Component *

Lap Kun Yeung, Hong Yan, Lap Keung Szeto, Alan Wee-Chung Liew, Michael Yang, Richard Kong

 

 

  Any query please check with APBC PC Chair Dr. Phoebe Chen at p.chen@qut.edu.au