Time Performance Room Conference Room 1
October 20, 2008 (Day 1)
08:00-16:30 Registration
09:30-09:50 Open Ceremony
09:50-10:50 Keynote Speech
Data Assimilation for Systems Biology

Prof. Satoru Miyano
The University of Tokyo
10:50-11:10 Coffee Break
11:10-11:50 Plenary Speech
A Network Approach to the Protein Docking Problem

Prof. Ming-Jing Hwang
Institute of Biomedical Sciences, Academia Sinica, Taiwan
11:50-12:20 Lunch
12:20-13:20 Introduction to APBioNet and ISCB (1st Conference Room)
13:20-14:10 Poster Session: Odd Number Poster Presentation
  Session 1: Network and Systems Biology Session 2: Data Mining
14:10-14:50 Invited Speech 1
Anti-tumor Activity of Reishi Polysaccharides: from Gene Expression to Network

Prof. Hsueh-Fen Juan
National Taiwan University, Taiwan
Invited Speech 2
Alternative Machine Learning Algorithms for Bioinformatics Applications

Prof. Yen-Jen Oyang
National Taiwan University, Taiwan
14:50-16:00 Oral Presentations
  • Orthologs-Based Protein-Protein Interaction Prediction and its Application in Inter-Species Interactions
    Sheng-An Lee, Chen-Hsiung Chan, Chia-Ying Yang, Kun-Mao Chao, Kao Cheng-Yan, Jin-Mei Lai, Feng-Sheng Wang and Chi-Ying F. Huang
  • A Protein Interaction Based Model for Schizophrenia Study
    Pei-chun Hsu, Ueng-Cheng Yang, Kuan-Hui Shih, Hai-Gwo Hwu, Chih-Min Liu and Yu-Li Liu
  • Dynamic Sensitivity Analysis of Biological Systems
    Feng-Sheng Wang, Wu-Hsiung Wu and Maw-Shang Chang
Oral Presentations
  • Extracting Transcription Factor Binding Sites from Unaligned Gene Sequenceswith Statistical Models
    Chung-Chin Lu, Wei-Hao Yuan and Te-Ming Chen
  • Predicting RNA-Binding Sites of Proteins Using Support Vector Machines and Evolutionary Information
    Cheng-Wei Cheng, Emily Chia-Yu Su, Ting-Yi Sung and Wen-Lian Hsu

  • In-silico Insight to Predict and Analyse Putative Metal Binding Sites for Phytoremediation in MAP's
    Ashok Sharma, Sudeep Roy, Kumar Parijat Tripathi, Manoj Mishra, Pratibha Roy, Feroz Khan and Abha Meena
16:00-16:20 Coffee Break
  Session 3: miRNA (I) Highlights & Technology I
16:20-17:00 Invited Speech 3
Bioinformatics Research in MicroRNA Regulation: Databases and Tools

Prof. Hsien-Da Huang
National Chiao Tung University
  • Prediction of Protein Subcellular Localization: Implications for Protein Function and Protein Interaction Network
    Emily Chia-Yu Su, Jia-Ming Chang, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung and Wen-Lian Hsu
  • PredictBias: a Server for the Identification of Genomic and Pathogenicity Islands in Prokaryotes
    Sachin Pundhir, Hemant Vijaywargiya and Anil Kumar


  • A Comprehensive and an Update Antibiotic Database on Essential Features of Antibiotics of Microbial Origin with special Emphasis on Bioinformatics
    Rajarajan Swaminathan, Priya Roosvelt, Indu Purushothaman, Yogambal Muthu and MadhanMohan Thangavel
  • BIOSMILE Web Search: a Web Application for Annotating Biomedical Entities and Relations
    Hong-Jie Dai, Chi-Hsin Huang, Ryan T.K. Lin, Pei-Hsuan Chou, Richard Tzong-Han Tsai and Wen-Lian Hsu
17:00-18:10 Oral Presentations
  • Using a Kernel Density Estimation Based Classifier to Predict Species-Specific microRNA Precursors
    Tien-Hao Chang, Chih-Ching Wang and Jian-Wei Chen
  • Filtering of False Positive microRNA Candidates by a Clustering-Based Approach
    Wing-Sze Leung, Marie Chia-Mi Lin, David W. L. Cheung and SM Yiu
  • Finding microRNA Regulatory Modules in Human Genome Using Rule Induction
    Dang Hung Tran, Kenji Satou and Tu Bao Ho
18:30-20:30 Welcome Reception
L'escargots Fresh Cuisine (at the campus of YMU)
October 21, 2008 (Day 2)
08:30-16:30 Registration
09:30-10:30 Keynote Speech
Translational Medicine: A Grand Challenge for Bioinformatics

Prof. Vladimir Brusic
Cancer Vaccine Center, Dana-Farber Cancer Institute
10:30-10:50 Coffee Break
  Session 4: Immunoinformatics Session 5: Data Mining & Text Mining
10:50-11:30 Invited Speech 4
Machine-learning Mechanisms in Prediction of Anti-psychotic Drug Response with Combined Pharmacogenetic and Clinical Data

Prof. Yu-Chuan Li
National Yang Ming University, Taiwan
Invited Speech 5
Integrating High Dimensional Bi-directional Parsing Models for Gene Mention Tagging

Prof. Chun-Nan Hsu
Academia Sinica, Taiwan
11:30-12:40 Oral Presentations
  • Ab-origin: An Enhanced Tool to Identify the Sourcing Gene Segments in Germline for Rearranged Antibodies
    Wang Xiaojing, Zhiwei Cao, Yixue Li, Di Wu, Siyuan Zheng, Jing Sun and Lin Tao
  • The Value of Position-Specific Scoring Matrics for Assessment of Protein Allergenicity
    Shen Jean Lim, Joo Chuan Tong, Fook Tim Chew and Martti Tammi
  • Evaluation of HLA-II Peptide Binding Prediction Servers: Applications for Vaccine Research
    Hong Huang Lin, Guang Lan Zhang, Songsak Tongchusak, Ellis Reinherz and Vladimir Brusic

Oral Presentations
  • Predicted Mouse Peroxisome-targeted Proteins and their Actual Subcellular Locations
    Yumi Mizuno, Igor V. Kurochkin, Marlis Herberth, Yasushi Okazaki and Christian Schoenbach
  • Fast Splice Site Detection Using Information Content and Feature Reduction
    Baten A K M Abdul, Saman Halgamuge and Bill Chang
  • Semi-Automatic Conversion Between Biomedical Predicate Argument Structure Standards
    Richard Tzong-Han Tsai, Hong-Jie Dai, Chi-Hsin Huang and Wen-Lian Hsu
12:40-13:40 Lunch
  Session 6: Proteome Informatics Session 7: Gene Variation
13:40-14:20 Invited Speech 6
New Strategies Towards Rapid and Comprehensive Proteomic Signatures for Biomedical Applications

Prof. Yu-Ju Chen
Academia Sinica, Taiwan
Invited Speech 7
Computational Analysis of Human Influenza A Virus Evolution

Prof. Arthur Chun-Chieh Shih
Academia Sinica, Taiwan
14:20-15:30 Oral Presentations
  • Real value prediction of protein solvent accessibility using enhanced PSSM features
    Tien-Hao Chang, Hsuan-Yu Huang and Yu-Tang Syu
  • Discovering Amino Acid Patterns on Binding Sites in Protein Complexes
    Huang-Cheng Kuo, Ping-Lin Ong, Jung Chang Lin and Jen-Peng Huang
  • Flanking Signal and Mature Peptide Residues Influence Signal Peptide Cleavage
    Khar Heng Choo and Shoba Ranganathan
Oral Presentations
  • VarDetect: a Nucleotide Sequence Variation Exploratory Tool
    Chumpol Ngamphiw, Supasak Kulawonganunchai, Anunchai Assawamakin, Ekachai Jenwitheesuk and Sissades Tongsima
  • FANS: Functional Analysis of Novel SNPs and Mutations in Human and Mouse Genomes
    Chuan-Kun Liu, Yan-Hau Chen, Cheng-Yang Tang, Shu-Chuan Chang, Yi-Jung Lin, Ming-Fang Tsai, Yuan-Tsong Chen and Adam Yao
  • An Integrated Database for Disease, Genetic Variation and Gene
    Jin Ok Yang, Sohyun Hwang, Jong Bhak, Jeongsu Oh and Tae-Kwon Sohn
15:40-16:40  Poster Session: Even Number Poster Presentation
16:50-17:20 Travel to Restaurant
17:30-20:30 Cocktail Party & Banquet
October 22, 2008 (Day 3)
08:30-15:00 Registration
09:30-10:30 Keynote Speech
Needles in the EST haystack: advances in transcriptome analysis of nematode parasites

Prof. Shoba Ranganathan
Macquarie University
10:30-10:50 Coffee Break
  Session 8: Sequence and Structural Analysis Session 9: Database and Data Storage
10:50-11:30 Invited Speech 8
On Finding Short Structural Building Blocks for Constructing 3D structure of Proteins

Prof. Nikhil R. Pal
Indian Statistical Institute, India
Invited Speech 9
Unravelling Monogenic Dispositions in Complex Metabolic Disorders Associated with Familial Combined Hypertriglyceridemia

Prof. Zemin Yao
University of Ottawa, Canada
11:30-12:40 Oral Presentations
  • WSPMaker: Window-Sliding Selection Pressure Plot Maker for Proteins and Domains
    Yong Seok Lee, Tae-Hyung Kim, Tae-Wook Kang, Won-Hyong Chung and Gwang-Sik Shin
  • Use of Sequence Motifs as Barcodes and Secondary Structures of Internal Transcribed Spacer 2 (IT2, rDNA) for Identification of Indian Liver Fluke, Fasciole (Trematoda: Fasciolide) 
    Pramod Prasad, Veena tandon, Devendra Biswal, Lalit Goswami and Anupam Chatterjee
  • Molecular Docking Studies of Dithionitrobenzoic Acid and its Related Compounds to Protein Disulfide Isomerase: Computational Screening of Inhibitors to Prevent HIV-1 Entry
    U Gowthaman, M Jayakanthan and D Sundar
Oral Presentations
  • PEIMAP: a Database of Protein Experimental Interactome Map
    Jea-woon Ryu, Byoung-chul Kim, Daeui Park, seong-Woong Cho, Sungsam Gong, Dan Bolser and Jong Bhak
  • CMKb: a web based prototype for integrating Australian Aboriginal customary medicinal plant knowledge
    Jitendra Gaikwad, Varun Khanna, Subramanyam Vemulpad, Joanne Jamie, Jim Kohen and Shoba Ranganathan
  • An integrated Korea Biodiversity Information Retrieval System
    Jeongheui Lim, Jong Bhak, Hee-Mock Oh, Chang-Bae Kim, Yong-Ha Park and Woon-Kee Paek
12:40-13:10 Lunch
13:10-14:10 APBioNet Open Meeting (1st Conference Room) & Poster Session
  Session 10: miRNA (II) Highlights & Technology II
14:10-14:10 Invited Speech 10
MicroRNA Regulation in Protein Interaction Network

Prof. Hsuan-Cheng Huang
National Yang Ming University
  • Identification of SSR-ESTs Corresponding to Alkaloid, Phenylpropanoid and Terpenoid Biosynthesis in MAP's
    Kumar Parijat Tripathi, Sudeep Roy, Feroz Khan, Ajit Kumar Shasany, Ashok Sharma and S.P.S Khanuja
  • A Pattern Recognition Approach to Infer Time-Lagged Genetic Interactions
    Cheng-Long Chuang, Chih-Hung Jen, Chung-Ming Chen and Grace S. Shieh
  • Signature Evaluation Tool (SET): a Java-Based Tool to Evaluate and Visualize the Sample Discrimination Abilities of Gene Expression signatures
    Chih-Hung Jen, Tsun-Po Yang, Chien-Yi Tung, Shu-Han Su, Chi-Hung Lin, Ming-Ta Hsu and Hsei-Wei Wang
14:50-15:30 Oral Presentations
  • Some High-affinity MicroRNA Recognition Elements (MREs) Are Associated with Alternative Splicing Events
    Cheng-Tao Wu, Chien-Ying Chiou and Ueng-Cheng Yang
  • MiRTif: a Support Vector Machine-Based microRNA Target Interaction Filter
    Yuchen Yang, Yu-Ping Wang and Kuo-Bin Li
15:30-15:50 Coffee Break
15:50-16:50 Keynote Speech
Computational Dissection of Cell Cycle Control Networks
Prof. Terry Gaasterland
16:50-17:00 InCoB2008 Closing Remarks
October 23, 2008 (Day 4)
  1. BioSlax and BioSlax Server: A Complete Freeware Open Source Solution for your Practical Bioinformatics Course
    Justin Choo and Mark De Silva, Singapore
  2. Asian Variome Project (AVP).
    Jong Bhak, KOBIC, Korea.
  3. Information Visualization for High Dimensional Biomedical Data: the Matrix Visualization Approach
    Chun-Houh Chen, Academia Sinica, Taiwan
12:30-14:00 Lunch
  1. Biological Networks: Insight from Interactions
    Prashanth Suravajhala, Roskilde University, Greater Copenhagen
  2. IUBMB-FAOBMB-APBioNet Workshop on Education in Bioinformatics and Computational Biology (WEBCB)
  3. FAOBMB Workshop
    Bioinformatics and systems approaches for disease study
    Ueng-Cheng Yang, National Yang Ming University, Taiwan