IEEE BIBE2009 Technical Program

THE 9TH
IEEE INTERNATIONAL CONFERENCE ON
BIOINFORMATICS AND BIOENGINEERING
(BIBE2009)
TECHNICAL PROGRAM
JUNE 22-24, 2009
THE SPLENDOR HOTEL, TAICHUNG, TAIWAN
ORGANIZED BY
ASIA UNIVERSITY
IEEE Computer Society ▪ Asia University ▪ Biological and AI Society
National Science Council ▪ Academia Sinica ▪ Ministry of Education
Teaching Excellence Project, MOE ▪ China Medical University
National University of Tainan ▪ National Chiao-Tung University
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Advanced Program
Time
Monday, June 22
Splendor II
Fong Lo Room III
07:30-08:20
Registration
Room: Hallway in front of the Splendor Room II
08:20-08:30
Welcome from Honorary Conference Chair & General Co-Chairs
Room: Splendor Room II
Keynote Session
Speaker: Dr. Wen-Hsiung Li
08:30-09:30
Chair: Dr. Jean-Claude Latombe
Room: Splendor Room II
09:30-09:50 Coffee Break
Keynote Session
Speaker: Dr. Yuan-Tsong Chen
09:50-11:50 Speaker: Dr. Li-Huei Tsai
Chair: Dr. Jeffrey J.P. Tsai
Room: Splendor Room II
11:50-13:30 Lunch
13:30-14:50 Parallel Session I-1-1
Parallel Session I-1-2
14:50-15:10 Coffee Break
15:10-16:30 Parallel Session I-2-1
Parallel Session I-2-2
16:30-17:30 Poster Session
Banquet & Keynote Session
18:30-21:00 Speaker: Dr. Peter Chung-Yu Wu
Room: Splendor Room II
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Advanced Program
Time
07:30-08:30
Tuesday, June 23
Splendor II
Fong Lo Room III
Registration
Room: Hallway in front of the Splendor Room II
Keynote Session
Speaker: Dr. Michael S. Waterman
08:30-09:30
Chair: Dr. Satoru Miyano
Room: Splendor Room II
09:30-09:50 Coffee Break
Keynote Session
Speaker: Dr. Jean-Claude Latombe
09:50-11:50 Speaker: Dr. David Harel
Chair: Dr. Phillip C.Y. Sheu
Room: Splendor Room II
11:50-13:30 Lunch
13:30-14:50 ParallelSession II-1-1
Parallel Session II-1-2
14:50-15:10 Coffee Break
15:10-17:30 Parallel Session II-2-1
Parallel Session II-2-2
Banquet & Keynote Session
18:30-21:00 Speaker: Dr. Mien-Chie Hung
Room: Splendor Room II
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Advanced Program
Time
07:30-08:30
Wednesday, June 24
Splendor II
Fong Lo Room III
Registration
Room: Hallway in front of the Splendor Room II
08:30-09:50 Parallel Session III-1-1
Parallel Session III-1-2
09:50-10:10 Coffee Break
10:10-11:30 SPECIAL SESSION
WORKSHOP: SBC
11:30-13:00 Lunch
13:00-15:00 Parallel Session III-2-1
WORKSHOP: BIE
ƒ Conference will provide laptop computer, projector, and internet connection for the presenters in
each conference room.
ƒ If the conference attendees stay in the hotel, the hotel will offer breakfasts for them in the
restaurants of the hotel.
ƒ SBC: Workshop on Semantic Biomedical Computing
ƒ BIE: Workshop on Biomedical Informatics & Engineering
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Detailed Program
Monday, June 22
07:30-08:20 Registration
Room: Hallway in front of the Splendor Room II
08:20-08:30 Welcome from Honorary Conference Chair & General Co-Chairs
Room: Splendor Room II
08:30-09:30 Keynote Session
Identification of Functional Signals in DNA Sequences
Speaker: Dr. Wen-Hsiung Li, University of Chicago, USA
Chair: Dr. Jean-Claude Latombe, Stanford University, USA
Room: Splendor Room II
09:30-09:50 Coffee Break
09:50-11:50 Keynote Session
Genomic Medicine to Improve Patient Care and Safety
Speaker: Dr. Yuan-Tsong Chen, Academia Sinica, Taiwan
Recovery of Learning and Memory by an Epigenetic Mechanism
Speaker: Dr. Li-Huei Tsai, Massachusetts Institute of Technology, USA
Chair: Dr. Jeffrey J.P. Tsai, University of Illinois at Chicago, USA
Room: Splendor Room II
11:50-13:30 Lunch
13:30-14:50 Parallel Session I-1-1: Algorithms, Modeling and Simulation of Bio-Sets (I)
Session Chair: Dr. Bernard Chen, University of Central Arkansas, USA
Room: Splendor Room II
Mining Positional Association Super-Rules on Fixed-Size Protein Sequence Motifs
Bernard Chen, Sinan Kockara
A Novel Biological Computation Method for Deriving and Resolving Discernibility Relations
Ikno Kim, Junzo Watada, Jui-Yu Wu, Yu-Yi Chu
AESNB: Active Example Selection with Naïve Bayes Classifier for Learning from
Imbalanced Biomedical Data
Min Su Lee, Je-Keun Rhee, Byoung-Hee Kim, Byoung-Tak Zhang
A Human DNA methylation site predictor base on SVM
Yi-Ming Sun, Baw-Jhiune Liu, Wei-Li Liao, Cheng-Wei Chang, Hsien-Da Huang, JorngTzong Horng, Li-Ching Wu
13:30-14:50 Parallel Session I-1-2: Bio-Imaging
Session Chair: Dr. Jun Sese, Ochanomizu University, Japan
Room: Fong Lo III
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Constructing Yeast Phenotypic Gene Network Using Morphological Inclusion Relations
Natsumi Abe, Jun Sese
A Generic Framework of Integrating Segmentation and Registration
Jonghyun Park, Wanhyun Cho, Soonyoung Park, Junsik Lim, Soohyung Kim, Gueesang Lee
Soft Tissue Deformation and Optimized Data Structures for Mass Spring Methods
T. Halic, S. Kockara, C. Bayrak, R. Rowe, B. Chen
14:50-15:10 Coffee Break
15:10-16:30 Parallel Session I-2-1: Biomedical Image Analysis and Biomaterials
Session Chair: Dr. Anant Madabhushi, Rutgers The State University of New Jersey, USA
Room: Splendor Room II
3D Reconstruction of Colon Segments from Colonoscopy Images
DongHo Hong, Wallapak Tavanapong, Johnny Wong, JungHwan Oh, Piet C. de Groen
Automatic Tumor Diagnosis for Breast Ultrasound using 3D Sub-volume Registration
Chii-Jen Chen, Ruey-Feng Chang, Dar-Ren Chen
Expectation Maximization driven Geodesic Active Contour with Overlap Resolution
(EMaGACOR): Application to Lymphocyte Segmentation on Breast Cancer Histopathology
Hussain Fatakdawala, Ajay Basavanhally, Jun Xu, Gyan Bhanot, Shridar Ganesan, Michael
Feldman, John Tomaszewski, Anant Madabhushi
The Optimization of Monascus Fermentation Process for Pigments Increment and Citrinin
Reduction
Chao-Chin Chung, Tzou-Chi Huang, Ho-Hsien Chen
15:10-16:30 Parallel Session I-2-2: Gene Expression Analysis
Session Chair: Dr. Marco Masseroli, Politecnico di Milano, Italy
Room: Fong Lo III
A Novel Approach for Automatic Number of Clusters Detection in Microarray Data based on
Consensus Clustering
Nguyen Xuan Vinh, Julien Epps
Inferring Causal Relations from Multivariate Time Series: A Fast Method for Large-Scale
Gene Expression Data
Yinyin Yuan, Chang-Tsun Li
A Hybrid Feature Selection Method Using Gene Expression Data
Li-Yeh Chuang, Kuo-Chuan Wu, Cheng-Hong Yang
Anomaly-free Prediction of Gene Ontology Annotations using Bayesian Networks
Marco Tagliasacchi, Marco Masseroli
16:30-17:30 Poster Session
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Biomedical Image Processing and Analysis
Multi-Modal Registration of Embryonic Images for In Vitro Fertilization
Chia-Ling Tsai, Su-Ching Liang, William Warger II, Charles DiMarzio
ImmunoMagnetical Reduction Using High Tc Superconducting Quantum Interference Device
(SQUID)
J.J. Chieh, C.H. Chen, S.Y. Yang, H.E. Horng, H.C. Yang, Chin-Yih Hong
Segmentation of Brain MR Images using an Ant Colony Optimization Algorithm
Myung-Eun Lee, Soo-Hyung Kim, Wan-Hyun Cho, Soon-Young Park, Jun-Sik Lim
Biomedical Data Engineering
Learning Scaling Coefficient in Possibilistic Latent Variable Algorithm from Complex
Diagnosis Data
Zong-Xian Yin
Newborn Screening System Based on Adaptive Feature Selection and Support Vector
Machines
Sung-Huai Hsieh, Yin-Hsiu Chien, Chia-Ping Shen, Wei-Hsin Chen, Po-Hao Chen, SheauLing Hsieh, Po-Hsun Cheng, Feipei Lai
Nonlinear Dynamic Indications in Time Series of Epilepsy Electroencephalogram
Ta-Cheng Chen, Jing-Doo Wang, Jiunn-I Shieh, Pei-Chun Chang, Kuei-Jen Lee, HsiangChuan Liu
Quantitative Analysis of Endodontic Treatment for Periapical Lesions in Intraoral
Radiographs
Taeju Lee, Hyekyung Jeong, Desok Kim, Byung-Do Lee
A Multidimensional Flow Cytometry Data Classification
Ming-Chih Shih, Shou-Hsuan Stephen Huang, Chung-Che Jeff Chang
Drug Discovery
The MAPK Signal Pathway Research and New Drug Discovery
Po-Yuan Chen, Mien-De Jhuo, Wei-Tse Hsu, Tzu-Ching Shih, Tzu-Hurng Cheng
Molecular Evolution and Phylogeny
Phylogenetic Analysis Using Nuclear-Encoded Mitochondrial Proteins
Alan C.H. Chen, Han C.W. Hsiao, Jeffrey J.P. Tsai
A Novel Approach for Motif Identification in Unaligned Molecular Sequences
Rong-Ming Chen, M.T. Hou, Jeffrey J.P. Tsai
Profiling the Nanoparticles Associated Protein-protein Interactions
Wei-Chen Liao, Nai-Kuei Huang
A platform for identifying microRNA targeting genes
Chia-Wei Weng, ChangChih Chiang, Ka-Lok Ng, Chien-Hung Huang
Enzyme Relational Network Reveals Target Enzymes within Metabolic Submodules
Chalothorn Liamwirat, Supapon Cheevadthanarak, Asawin Meechai, Sakarindr Bhumiratana
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18:30-21:00 Banquet & Keynote Session
Implantable Biomedical Devices for Visual Prosthesis and Deep Brain Stimulation
Speaker: Dr. Peter Chung-Yu Wu, National Chiao-Tung University, Taiwan
Room: Splendor Room II
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Detailed Program
Tuesday, June 23
07:30-08:30 Registration
Room: Hallway in front of the Splendor Room II
08:30-09:30 Keynote Session
Sequence Comparison Using Word Counts
Speaker: Dr. Michael S. Waterman, University of Southern California USA
Chair: Dr. Satoru Miyano, University of Tokyo, Japan
Room: Splendor Room II
09:30-09:50 Coffee Break
09:50-11:50 Keynote Session
Computational Tools to Study Protein Low-Frequency Motions
Speaker: Dr. Jean-Claude Latombe, Stanford University USA
Can We Computerize an Elephant?
Speaker: Dr. David Harel, The Weizman Institute of Science, Israel
Chair: Dr. Phillip C.Y. Sheu, University of California, Irvine, USA
Room: Splendor Room II
11:50-13:30 Lunch
13:30-14:50 ParallelSession II-1-1: Identification and Classification of Genes
Session Chair: Dr. Vincent T.Y. Ng, The Hong Kong Polytechnic University, China
Room: Splendor Room II
Online Discovery and Refinement of Novel Genes using GeneScope
Hasan Jamil, Jesmin
A New Method to Combine Heterogeneous Data Sources for Candidate Gene
Prioritization
Yongjin Li, Jagdish C. Patra, Jiabao Sun
Interaction Based Functional Clustering of Genomic Data
Ritesh Krishna, Chang-Tsun Li, Vicky Buchanan-Wollaston
Alternative Feature Mapping for Heterogeneous Gene Data Classification
Victor C. Liang, Vincent T.Y. Ng
13:30-14:50 Parallel Session II-1-2: Protein Structure Prediction and Molecular Simulation
Session Chair: Han C.W. Hsiao, Asia University, Taiwan
Room: Fong Lo III
Empirical probability functions derived from dihedral angles for protein structure
prediction
Qiwen Dong, Xin Geng, Shuigeng Zhou, Jihong Guan
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Spatial Encoding Scheme for Protein Supporting Structure Discovery
Yu-Feng Huang, Chia-Jui Yang, Yi-Wei Yang, Chien-Kang Huang
A Data Mining Approach to Predicting Phylum for Microbial Organisms using
Genome-Wide Sequence Data
Rao M. Kotamarti, Douglas W. Raiford, Michael L. Raymer, Margaret H. Dunham
Tri-Cluster-Tri-Scheme-Training: Exploiting Unlabeled Data for Transmembrane
Segments Prediction
Jieyue He, R. Harrison, Phang C. Tai, Yi Pan
14:50-15:10 Coffee Break
15:10-17:30 Parallel Session II-2-1: Algorithms, Modeling and Simulation of Bio-Sets (II)
Session Chair: Dr. Chun-Ming Chang, Asia University, Taiwan
Room: Splendor Room II
Multi-Agents System to model cell signalling by using Fuzzy Cognitive Maps.
Application to computer simulation of Multiple Myeloma.
Vincent Rodin, Gabriel Querrec, Pascal Ballet, Franc¸ois–R´egis Bataille, Gireg
Desmeulles, Jean–Franc¸ois Abgrall, Jacques Tisseau
Genetic Algorithm for the Design of Confronting Two-Pair Primers
Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, Hsueh-Wei Chang
On The Hardness of the Border Length Minimization Problem
Vamsi Kundeti, Sanguthevar Rajasekaran
Web Services Based Bio-signal System Leveraging Support Vector Machines
Sung-Huai Hsieh, Sheau-Ling Hsieh, Chia-Ping Shen, Wei-Hsin Chen, Po-Hsun
Cheng, Kai-Ping Hsu, Chi-Huang Chen, Feipei Lai
RiboSW – a web server for identifying RNA riboswitches
Tzu-Hao Chang, Baw-Jhiune Liu, Li-Ching Wu, Hsien-Da Huang, Chi-Ta Yeh, JorngTzong Horng, Cheng-Wei Chang
A Computational Approach to Detect CNVs Using High-throughput Sequencing
Myungjin Moon, Jaegyoon Ahn, Chihyun Park, Sanghyun Park, Youngmi Yoon,
Jeehee Yoon
15:10-17:30 Parallel Session II-2-2: Algorithms, Modeling and Simulation of Bio-Sets (III)
Session Chair: Dr. Po-Yuan Chen, China Medical University, Taiwan
Room: Fong Lo III
Applied GM(0,N) Model in the Study of Influence Factor in Preterm Neonates
Mei-Li You, Hsiao-Ying Chen, Shu-Peng Liu, Kun-Li Wen
Knowledge Discovery on In Vitro Fertilization Clinical Data Using Particle Swarm
Optimization
Chih-Chuan Chen, Yi-Chung Cheng, Chao-Chin Hsu, Sheng-Tun Li
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Exploring the Receptor-baseed Virtual Screening Study of the Aromatic Substituents
for the Hepatitis C Virus NS5B polymerase by Docking and Scoring
Po-Yuan Chen, Wei-Tse Hsu, Mien-De Jhuo, Tzu-Hurng Cheng
ArrayQ: Querying Microarray Expressions for Relevant Pathways
Shahriyar Hossain, Cherie M. Southwood, Hasan Jamil, Alexander Gow
Data Mining Techniques for the Identification of Genes with Expression Levels
Related to Breast Cancer Prognosis
Gabriele Giarratana, Marco Pizzera, Marco Masseroli, Enzo Medico, Pier Luca
Lanzi
The Energy Distribution Data Bank: Collecting Energy Features of Protein Molecular
Structures
Dariusz Mrozek, Bożena Małysiak-Mrozek, Stanisław Kozielski, Andrzej Świerniak
Efficiency Enhancement of Protein Folding for Complete Molecular Simulation via
Hardware Computing
Wen-Tsai Sung
18:30-21:00 Banquet & Keynote Session
Challenge of Bioinformatics and Bioengineering: from Signal Pathway to Network and
Imaging in Cancer Therapy
Speaker: Dr. Mien-Chie Hung, The University of Texas MD Anderson Cancer Center, USA
Room: Splendor Room II
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Detailed Program
Wednesday, June 24
07:30-08:30 Registration
Room: Hallway in front of the Splendor Room II
08:30-09:50 Parallel Session III-1-1: Structural and Functional Analysis
Session Chair: Dr. Rouh-Mei Hu, Asia University, Taiwan
Room: Splendor Room II
A Practical Edit-Distance Model for RNA Secondary-Structure Comparison
Chan-Shuo Wu, Guan-Shieng Huang
Asymptotics of Canonical RNA Secondary Structures
Peter Clote, Evangelos Kranakis, Danny Krizanc
Identifying Functional Modules using MST-based Weighted Gene Co-Expression
Networks
Atthawut Chanthaphan, Santitham Prom-on, Asawin Meechai, Jonathan Chan
Generating Peptide Sequence Tags for Peptide Identification via Tandem Mass
Spectrometry
Changyong Yu, Guoren Wang, Yuhai Zhao, Keming Mao, Junjie Wu, Wendan Zhai
08:30-09:50 Parallel Session III-1-2: Systems Biology
Session Chair: Dr. Ka-Lok Ng, Asia University, Taiwan
Room: Fong Lo III
On the Design of Optimization Algorithms for Prediction of Molecular Interactions
Darby Tien-Hao Chang, Jung-Hsin Lin, Chih-Hung Hsieh, Yen-Jen Oyang
Data Matching for Physical Integration of Biochemical Pathway Databases
Jyh-Jong Tsay, Bo-Liang Wu, Chien-Wen Chen
Logistic Biclustering Models for Protein Network Inference
Carla C.R.R. Monteiro, Katia S. Guimarães
Algorithms based on Density and Shared Neighbors for Functional Modules
Identification in PPI Networks
Peng Gang Sun, Lin Gao
09:50-10:10 Coffee Break
10:10-11:30 Special Session: Bioinformatics & Information Fusion
Session Chair: Dr. Frank Hsu, Fordham University, USA
Room: Splendor Room II
ATRIPPI: An atom-residue preference scoring function for protein-protein
interactions
Kang-Ping Liu, Lu-Shian Chang, Jinn-Moon Yang
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Analysis of Autism Prevalence and Neurotoxins Using Combinatorial Fusion and
Association Rule Mining
Christina Schweikert, Yanjun Li, David Dayya, David Yens, Martin Torrents, D. Frank
Hsu
Combining agent-based models with stochastic differential equations for gene
regulatory networks
Tse-Yi Wang, Kuang-Chi Chen, D. Frank Hsu, Cheng-Yan Kao
Microarray Gene Expression Analysis Using Combinatorial Fusion
Cameron McMunn-Coffran, Christina Schweikert, D. Frank Hsu
10:10-11:30 Workshop: Semantic Biomedical Computing
Session Chair: Dr. Phillip C.Y. Sheu, University of California, Irvine, USA
Room: Fong Lo III
SCDL Applications to Drug Discovery
David A. Hecht, Phillip C.Y. Sheu, Jeffrey J.P. Tsai
Describing Dynamic Biological Systems in SPDL and SCDL
Charles C.N. Wang, David A. Hecht, Han C.W. Hsiao, Phillip C.Y. Sheu, Jeffrey J.P.
Tsai
Normalizing Biomedical Name Entities by Similarity-based Inference Network and
De-ambiguity Mining
Chih-Hsuan Wei, I-Chin Huang, Yi-Yu Hsu, Hung-Yu Kao
An Integrative Tool for Gene Regulatory Network Reconstruction Based on
Microarray Data
J.W. Ou, C.Y. Tang, Rong-Ming Chen, R.M. Hu, Jeffrey J.P. Tsai
11:30-13:00 Lunch
13:00-15:00 Parallel Session III-2-1: Biomedical Image Processing and Analysis
Session Chair: Dr. Chia-Ling Tsai, Iona College, USA
Room: Splendor Room II
Vascular Tree Construction with Anatomical Realism for Retinal Images
Kai-Shung Lin, Chia-Ling Tsai, Michal Sofka, Chih-Hsiangng Tsai, Shih-Jen Chen,
Wei-Yang Lin
Simulation of Ultrasound Propagation in Cancellous Bone by Solving Elastic Wave
Equation using Finite Difference Time Domain Method
Nima Hemmati, Mohammad Djavad Abolhassani
Brain Tissue Classification Using Independent Vector Analysis (IVA) for Magnetic
Resonance Image
Yaw-Jiunn Chiou, Hsiang-Min Chen, Jyh Wen Chai, Clayton Chi-Chang Chen, YenChieh Ouyang, Wu-Chung Su, Ching-Wen Yang, San-Kan Lee, Chein-I Chang
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Tracking the Intracellular Dynamics of Transferrin-labeled QDs in Living Panc-1
Cells
Gaixia Xu, Junle Qu, Stefan Jaeger, Qingfeng Song, Su-Shing Chen
Image Analysis for High Content Screening with cellAnalyst
Joerg Meyer, Ash Pahwa, Peter Saveliev
13:00-15:00 Workshop: Biomedical Informatics & Engineering
Session Chair: Dr. John Kar-Kin Zao, National Chiao-Tung University, Taiwan
Room: Fong Lo III
Integration of Heterogeneous Medical Decision Support Systems Based on Web
Services
Chung C. Chang, Hsueh-Ming Lu
Wedjat: A Mobile Phone Based Medication Reminder and Monitor
Mei-Ying Wang, John K. Zao, P.H. Tsai, J.W.S. Liu
Beamformer-based Spatiotemporal Imaging of Correlated Brain Activities
I-Tzu Chen, Yong-Sheng Chen, Li-Fen Chen
EEG-based Spatial Navigation Estimation in a Virtual Reality Driving Environment
Chin-Teng Lin, Fu-Shu Yang, Te-Chung Chiou, Li-Wei Ko, Jeng-Ren Duann, Klaus
Gramann
Automated Sleep Staging using Single EEG Channel for REM Sleep Deprivation
Yu-Hsun Lee, Yong-Sheng Chen, Li-Fen Chen
Faster and Active Surveillance of Hospital-Acquired Infections: A Model for Settings
with High Sensitivity Predictors
Yaowen Chung, Yu-Sheng Lo, Wen -Sen Lee, Min-Huei Hsu, Chien-Tsai Liu
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