The Fourth Asia Pacific Bioinformatics Conference
13-16 Feb, 2006, Taiwan


About Taiwan
AASBi symposium
Important dates
Keynote speakers
Accepted papers
Accepted posters
Visa application
Chairs & committee
Call for papers
Call for poster
Call for tutorial
Previous meetings


download apbc2006_program.pdf

Sunday, 12 February 2006

11:30-13:30  AASBi Board meeting
14:00-17:00  AASBi symposium
14.30–20.30 APBC Registration
Main entry of the activity center
18.30–20.30 APBC & AASBi Reception The Plato Hall

Monday, 13 February 2006

8.30–16.30 Registration Main entry of the activity center
9.00–9.15 Opening Session The Alexander Hall
9.15–10.00 Keynote 1 The Alexander Hall (chair: Tao Jiang,Univ of California - Riverside)
Whole Genome Optical Mapping. Prof. Michael Waterman (Univ of Southern California)

10.00–10.30 Tea Break Lobby

10.30–11.30 Algorithm The Alexander Hall (chair: Michael Waterman, Univ of Southern California)
1.            Property-dependent Analysis of Aligned Proteins from Two or More Populations,   Steinar Thorvaldsen, Elinor Ytterstad, Tor Fla
2.            Alignscope : A Visual Mining Tool for Gene Team Finding with Whole Genome Alignment, Hee-Jeong Jin, Hye-Jung Kim, Jeong-Hyeon Choi, Hwan-Gue Cho
3.            A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data, Christopher Langmead

11.30–13.00 Lunch Break (The Alexander Hall) & Poster Session 1 (The Locke Hall)

13.00 – 14.00 Structure classification and prediction The Alexander Hall (chair: Chris Langmead, Carnegie Mellon Univ)
1.            Predicting Ranked SCOP Domains by Mining Associations of Visual Contents in Distance Matrices, Pin-Hao Chi, Chi-Ren Shyu
2.            A New Neural Network for Beta-turn Prediction: The Effect of Site-specific Amino Acid Preference, Zhong-ru Xie, Ming-jing Hwang
3.            A Knowledge-Based Approach to Protein Local Structure Prediction, Ching-Tai Chen, Hsin-Nan Lin, Kuen-Pin Wu, Ting-Yi Sung, Wen-Lian Hsu

14.00–15.00 Microarray data analysis The Alexander Hall (chair: Ping-Chiang Lyu, Nat’l Tsing-Hua Univ)

1.            Microarray Missing Value Imputation by Iterated Local Least Squares, Zhipeng Cai, Maysam Heydari, Guohui Lin
2.            A generalized output-coding scheme with SVM for multiclass microarray classification, Li Shen, Eng Chong Tan
3.            Gene Expression Data Clustering Based on Local Similarity Combination, De Pan, Fei Wang, Jiankui Guo

15.00–16.00 Tea Break (Lobby) & Poster Session 1  (The Locke Hall)

16.00–17.00 Genome rearrangement The Alexander Hall  (chair: Kun-Mao Chao,Nat’l  Taiwan Univ)

1.            RECOMP: A Parsimony-based Method for Detecting Recombination, Derek Ruths, Luay Nakhleh
2.            Accuracy of four heuristics for the full sibship reconstruction problem in the presence of genotype error, Dmitry Konovalov
3.            A Recursive Method for Solving Haplotype Frequencies in Multiple Loci Linkage Analysis, Michael Ng

19.00–21.00 Conference Banquet

Tuesday, 14 February 2006

8.30–16.30 Registration Lobby (information desk)
9.15–10.00 Keynote 2 The Alexander Hall  (chair: Phoebe Chen, Deakin Univ)
Automating the Search for Lateral Gene Transfer. Prof. Mark Ragan (Univ. of Queensland)

10.00–10.30 Tea Break Lobby

10.30–11.30 Phylogenetics  The Alexander Hall  (chair: Mark Ragan, Univ. of Queensland)
1.            Resoving gene tree and species tree problem by phylogenetic mining, Xiaoxu Han
2.            Techniques for assessing phylogenetic branch support, Derek Ruths, Luay Nakhleh
3.            A More Accurate and Efficient Whole Genome Phylogeny, P.Y. Chan, T.W. Lam, Siu-Ming Yiu

11.30–13.00 Lunch Break  (The Alexander Hall) & Poster Session 2  (The Locke Hall)

13.00–14.00 Gene variation and mutation The Alexander Hall  (chair: Hsueh-Feng Juan, Nat’l TaiwanUniv)
1.            Discriminative Detection of Cis-Acting Regulatory Variation from Location Data, Yuji Kawada, Yasubumi Sakakibara
2.            Trends in codon and amino acid usage in human pathogen Tropheryma whipplei, the only known actinobacteria with reduced genome, Sabyasachi Das, Sandip Paul, Chitra Dutta
3.            Consequences of mutation, selection and physico-chemical properties of encoded proteins on synonymous codon usage in adenoviruses, Sandip Paul, Sabyasachi Das, Chitra Dutta

14.00–14.40 Database The Alexander Hall  (chair: Wen-Lian Hsu, Academia Sinica)
1.            Analyzing inconsistency toward enhancing integration of biological molecular databases, Phoebe Chen, Qingfeng Chen
2.            ONBIRES: ONtology-based BIological Relation Extraction System, Minlie Huang, Xiaoyan Zhu, Shilin Ding, Hao Yu, Ming Li

 14.40–15.40 Tea Break (Lobby) & Poster Session 2  (The Locke Hall)

15.40–16.40 Structure analysis The Alexander Hall   (chair:Ming-Jing Hwang, Academia Sinica)
1.            Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach, Marcos J. Arauzo-Bravo, Satoshi Fujii, Hidetoshi Kono, Akinori Sarai
2.            Characterization of Multi-Charge Mass Spectra for Peptide Sequencing, Ket Fah Chong, Kang Ning, Hon Wai Leong
3.            Structure Based Chemical Shift Prediction Using Random Forests Non-Linear Regression, Christopher Langmead, K Arun

 16.40–17.15 Invited Talk The Alexander Hall  (chair: Limsoon Wong, Institute for Infocomm Research)
Advances in transcriptome analysis. Shoba Ranganathan (McQuarrie Univ) 

Wednesday, 15 February 2006

8.30–16.30 Registration Lobby (information desk)
9.15–10.00 Keynote 3 The Alexander Hall  (chair: Ueng-Cheng Yang,Nat’l Yang-Ming Univ)
On the Inference of Regulatory Elements, Circuits and Modules. Wen-Hsiung Li (Academia Sinica & U. of Chicago)

10.00–10.30 Tea Break Lobby

10.30–11.30 Systems biology and gene network (I) The Alexander Hall   (chair:Hoong-Chien Lee, Nat’l
Central Univ )
1.            Inference of gene regulatory networks from microarray data: a fuzzy logic approach, Ma Chi Hung, Chan Chun Chung
2.            System identification and robustness analysis of the circadian regulatory network via microarray data in arabidopsis thaliana, Bor-Sen Chen
3.            On the Complexity of Finding Control Strategies for Boolean Networks, Tatsuya Akutsu, Morihiro Hayashida, Wai-Ki Ching, Michael Ng

11.30–13.00 Lunch Break (The Alexander Hall) & Poster Session 3 (The Locke Hall)

13.00–14.00 Systems biology and gene network (II) The Alexander Hall   (chair: Christian Schoenbach, RIKEN )
1.            Identification of Over-represented Combinations of Transcription Factor Binding Sites in Sets of Co-expressed Genes, Shao-shan Huang, Debra Fulton, David Arenillas, Paul Perco, Shannan Ho Sui, James Mortimer, Wyeth Wasserman
2.            Characterization of the existence of galled-tree networks, Jan Manuch, Xiaohong Zhao, Ladislav Stacho, Arvind Gupta
3.            Semi-Supervised Threshold Queries on Pharmacogenomics Time Sequences, Johannes Assfalg, Hans-Peter Kriegel, Peer Kroeger, Peter Kunath, A. Pryakhin, & Matthias Renz,

14.00–15.00 Motif analysis The Alexander Hall  (chair: Francis Chin, Hong-Kong Univ)
1.            An efficient algorithm for string motif discovery, Francis Chin, Henry Leung
2.            EDAM An Efficient Clique Discovery Algorithm with Frequency Transformation for Finding Motifs, Guoren Wang, Yifei Ma
3.            A novel approach for structured consensus motif inference under specificity and quorum constraints, Christine Sinoquet

15.00–16.00 Tea Break (Lobby) & Poster Session 3 (The Locke Hall)

16.00–17.00 Analysis of biological molecules The Alexander Hall  (chair: Shoba Ranganathan McQuarrie Univ)
1.            SVM-based Identification of microRNA precursors, Liang Huai Yang, Wynne Hsu, Mong Li Lee, Limsoon Wong
2.            Genome-wide computational analysis of small nuclear RNA genes of Oryza sativa (Indica and Japonica), M.Shashikanth, A.Snehalatharani, Sk. Mubarak, K.Ulaganathan
3.            Protein Subcellular Localization Prediction with wolf PSORT, Horton Paul, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai

17.00–17.15 Closing Session The Alexander Hall

Closing Remarks by General Co-chair, Dr. Wen-Hsiung Li (Academia Sinica & U. of Chicago)
Closing Remarks by PC Co-chair, Dr. Ueng-Cheng Yang (National Yang-Ming Univ)

Thursday, 16 February 2006

8.30–17.30 Registration Classroom I & II (map will be available on the information desk) 

9.00–12.00            Classroom I at NTU
Biostatistical and Bioinformatics Approaches in High Dimensional Data Derived from High Throughput Assays: A Consumer Guide
Prof. Yu Shyr
Vanderbilt University, USA

9.00–12.00            Classroom II at NTU
Systems biology
Prof. Hsuan-Cheng Huang
NationalYang-Ming University, Taiwan, R.O.C.

13.30–16.30          Classroom I at NTU
Matrix visualization and information mining
Dr. Han-Ming Wu & Prof. Chun-Houh Chen
Institute of Statistical Science, Academia Sinica, Taiwan, R.O.C.

13.30–16.30          Classroom II at NTU
Gene Ontology Browsing Utility
Dr. Wen-Dar Lin & Prof. Jan-Ming Ho
Institute of Information Science, Academia Sinica, Taiwan, R.O.C.

Poster session

Posters should be posted before 9:00, presented during the afternoon tea break, and taken off before 17:15.


Session 1 (No. 1-28): Feb. 13

Session 2 (No. 29-56): Feb. 14

Session 3 (No. 57-80): Feb. 15