9. BIBE 2009: Taichung, Taiwan, ROC

Regular Papers

Algorithms, Modeling and Simulation of Bio-Sets (I)

• Bernard Chen, Sinan Kockara:
  Mining Positional Association Super-Rules on Fixed-Size Protein Sequence Motifs. 1-8
  
• Ikno Kim, Junzo Watada, Jui-Yu Wu, Yu-Yi Chu:
  A Novel Biological Computation Method for Deriving and Resolving Discernibility Relations. 9-14
  
• Min Su Lee, Je-Keun Rhee, Byoung-Hee Kim, Byoung-Tak Zhang:
  AESNB: Active Example Selection with Naive Bayes Classifier for Learning from Imbalanced Biomedical Data. 15-21
  
• Yi-Ming Sun, Wei-Li Liao, Hsien-Da Huang, Baw-Jhiune Liu, Cheng-Wei Chang, Jorng-Tzong Horng, Li-Ching Wu:
  A Human DNA Methylation Site Predictor Based on SVM. 22-29
  

Bio-Imaging

• Natsumi Abe, Jun Sese:
  Constructing Yeast Phenotypic Gene Network Using Morphological Inclusion Relations. 30-37
  
• Jonghyun Park, Wanhyun Cho, Soon-Young Park, Junsik Lim, Soo-Hyung Kim, Gueesang Lee:
  A Generic Framework of Integrating Segmentation and Registration. 38-44
  
• Tansel Halic, Sinan Kockara, Coskun Bayrak, Richard Rowe, Bernard Chen:
  Soft Tissue Deformation and Optimized Data Structures for Mass Spring Methods. 45-52
  

Biomedical Image Analysis and Biomaterials

• DongHo Hong, Wallapak Tavanapong, Johnny Wong, Jung-Hwan Oh, Piet C. de Groen:
  3D Reconstruction of Colon Segments from Colonoscopy Images. 53-60
  
• Chii-Jen Chen, Ruey-Feng Chang, Dar-Ren Chen:
  Automatic Tumor Diagnosis for Breast Ultrasound Using 3D Sub-volume Registration. 61-68
  
• Hussain Fatakdawala, Ajay Basavanhally, Jun Xu, Gyan Bhanot, Shridar Ganesan, Michael D. Feldman, John Tomaszewski, Anant Madabhushi:
  Expectation Maximization driven Geodesic Active Contour with Overlap Resolution (EMaGACOR): Application to Lymphocyte Segmentation on Breast Cancer Histopathology. 69-76
  
• Chao-Chin Chung, Tzou-Chi Huang, Ho-Hsien Chen:
  The Optimization of Monascus Fermentation Process for Pigments Increment and Citrinin Reduction. 77-83
  

Gene Expression Analysis

• Xuan Vinh Nguyen, Julien Epps:
  A Novel Approach for Automatic Number of Clusters Detection in Microarray Data Based on Consensus Clustering. 84-91
  
• Yinyin Yuan, Chang-Tsun Li:
  Inferring Causal Relations from Multivariate Time Series: A Fast Method for Large-Scale Gene Expression Data. 92-99
  
• Li-Yeh Chuang, Kuo-Chuan Wu, Cheng-Hong Yang:
  A Hybrid Feature Selection Method Using Gene Expression Data. 100-106
  
• Marco Tagliasacchi, Marco Masseroli:
  Anomaly-free Prediction of Gene Ontology Annotations Using Bayesian Networks. 107-114
  

Identification and Classification of Genes

• Hasan M. Jamil, J. Jesmin:
  Online Discovery and Refinement of Novel Genes Using GeneScope. 115-122
  
• Yongjin Li, Jagdish Chandra Patra, Jiabao Sun:
  A New Method to Combine Heterogeneous Data Sources for Candidate Gene Prioritization. 123-129
  
• Ritesh Krishna, Chang-Tsun Li, Vicky Buchanan-Wollaston:
  Interaction Based Functional Clustering of Genomic Data. 130-137
  
• Victor C. Liang, Vincent T. Y. Ng:
  Alternative Feature Mapping for Heterogeneous Gene Data Classification. 138-145
  

Protein Structure Prediction and Molecular Simulation

• Qiwen Dong, Xin Geng, Shuigeng Zhou, Jihong Guan:
  Empirical Probability Functions Derived from Dihedral Angles for Protein Structure Prediction. 146-152
  
• Yu-Feng Huang, Chia-Jui Yang, Yi-Wei Yang, Chien-Kang Huang:
  Spatial Encoding Scheme for Protein Supporting Structure Discovery. 153-160
  
• Rao M. Kotamarti, Douglas W. Raiford, Michael L. Raymer, Margaret H. Dunham:
  A Data Mining Approach to Predicting Phylum for Microbial Organisms Using Genome-Wide Sequence Data. 161-167
  
• Jieyue He, Robert W. Harrison, Phang C. Tai, Yi Pan:
  Tri-Cluster-Tri-Scheme-Training: Exploiting Unlabeled Data for Transmembrane Segments Prediction. 168-175
  

Structural and Functional Analysis

• Chan-Shuo Wu, Guan-Shieng Huang:
  A Practical Edit-Distance Model for RNA Secondary-Structure Comparison. 176-183
  
• Peter Clote, Evangelos Kranakis, Danny Krizanc:
  Asymptotics of Canonical RNA Secondary Structures. 184-191
  
• Atthawut Chanthaphan, Santitham Prom-on, Asawin Meechai, Jonathan Hoyin Chan:
  Identifying Functional Modules Using MST-Based Weighted Gene Co-Expression Networks. 192-199
  
• Changyong Yu, Guoren Wang, Yuhai Zhao, Keming Mao, Junjie Wu, Wendan Zhai:
  Generating Peptide Sequence Tags for Peptide Identification via Tandem Mass Spectrometry. 200-207
  

Systems Biology

• Darby Tien-Hao Chang, Jung-Hsin Lin, Chih-Hung Hsieh, Yen-Jen Oyang:
  On the Design of Optimization Algorithms for Prediction of Molecular Interactions. 208-215
  
• Jyh-Jong Tsay, Bo-Liang Wu, Chien-Wen Chen:
  Data Matching for Physical Integration of Biochemical Pathway Databases. 216-220
  
• Carla Claudia da Rocha Rego Monteiro, Kátia Silva Guimaraes:
  Logistic Biclustering Models for Protein Network Inference. 221-227
  
• Peng-Gang Sun, Lin Gao:
  Algorithms Based on Density and Shared Neighbors for Functional Modules Identification in PPI Networks. 228-235
  

Short Papers

Algorithms, Modeling and Simulation of Bio-Sets (II)

• Vincent Rodin, Gabriel Querrec, Pascal Ballet, François-Regis Bataille, Gireg Desmeulles, Jean François Abgrall, Jacques Tisseau:
  Multi-Agents System to Model Cell Signalling by Using Fuzzy Cognitive Maps. Application to Computer Simulation of Multiple Myeloma. 236-241
  
• Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, Hsueh-Wei Chang:
  Genetic Algorithm for the Design of Confronting Two-Pair Primers. 242-247
  
• Vamsi Kundeti, Sanguthevar Rajasekaran:
  On the Hardness of the Border Length Minimization Problem. 248-253
  
• Sung-huai Hsieh, Sheau-Ling Hsieh, Chia-Ping Shen, Wei-Hsin Chen, Po-Hsun Cheng, Kai-Ping Hsu, Chi-Huang Chen, Feipei Lai:
  Web Services Based Bio-signal System Leveraging Support Vector Machines. 254-259
  
• Tzu-Hao Chang, Li-Ching Wu, Chi-Ta Yeh, Cheng-Wei Chang, Baw-Jhiune Liu, Hsien-Da Huang, Jorng-Tzong Horng:
  RiboSW . 260-265
  
• Myungjin Moon, Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Sanghyun Park, Jeehee Yoon:
  A Computational Approach to Detect CNVs Using High-throughput Sequencing. 266-271
  

Algorithms, Modeling and Simulation of Bio-Sets (III)

• Mei-Li You, Hsiao-Ying Chen, Shu-Peng Liu, Kun-Li Wen:
  Applied GM(0, N) Model in the Study of Influence Factor in Preterm Neonates. 272-277
  
• Chih-Chuan Chen, Chao-Chin Hsu, Yi-Chung Cheng, Sheng-Tun Li:
  Knowledge Discovery on In Vitro Fertilization Clinical Data Using Particle Swarm Optimization. 278-283
  
• Po-Yuan Chen, Wei-Tse Hsu, Mien-De Jhuo, Tzu-Hurng Cheng:
  Exploring the Receptor-Based Virtual Screening Study of the Aromatic Substituents for the Hepatitis C Virus NS5B Polymerase by Docking and Scoring. 284-289
  
• Shahriyar Hossain, Cherie Southwood, Hasan M. Jamil, Alexander Gow:
  ArrayQ: Querying Microarray Expressions for Relevant Pathways. 290-294
  
• Gabriele Giarratana, Marco Pizzera, Marco Masseroli, Enzo Medico, Pier Luca Lanzi:
  Data Mining Techniques for the Identification of Genes with Expression Levels Related to Breast Cancer Prognosis. 295-300
  
• Dariusz Mrozek, Bozena Malysiak-Mrozek, Stanislaw Kozielski, Andrzej Swierniak:
  The Energy Distribution Data Bank: Collecting Energy Features of Protein Molecular Structures. 301-306
  
• Wen-Tsai Sung:
  Efficiency Enhancement of Protein Folding for Complete Molecular Simulation via Hardware Computing. 307-312
  

Biomedical Image Processing and Analysis

• Kai-Shung Lin, Chia-Ling Tsai, Michal Sofka, Chih-Hsiangng Tsai, Shih-Jen Chen, Wei-Yang Lin:
  Vascular Tree Construction with Anatomical Realism for Retinal Images. 313-318
  
• Nima Hemmati, Mohammad Djavad Abolhassani:
  Simulation of Ultrasound Propagation in Cancellous Bone by Solving Elastic Wave Equation Using Finite Difference Time Domain Method. 319-323
  
• Yaw-Jiunn Chiou, Hsian-Min Chen, Jyh Wen Chai, Clayton Chi-Chang Chen, Yen Chieh Ouyang, Wu-Chung Su, Ching-Wen Yang, San-Kan Lee, Chein-I Chang:
  Brain Tissue Classification Using Independent Vector Analysis (IVA) for Magnetic Resonance Image. 324-329
  
• Gaixia Xu, Junle Qu, Stefan Jäger, Qingfeng Song, Su-Shing Chen:
  Tracking the Intracellular Dynamics of Transferrin-labeled QDs in Living Panc-1 Cells. 330-334
  
• Joerg Meyer, Ash Pahwa, Peter Saveliev:
  Image Analysis for High Content Screening with cellAnalyst. 335-340
  

Poster Papers

Biomedical Data Engineering

• Zong-Xian Yin:
  Learning Scaling Coefficient in Possibilistic Latent Variable Algorithm from Complex Diagnosis Data. 341-343
  
• Sung-huai Hsieh, Yin-Hsiu Chien, Chia-Ping Shen, Wei-Hsin Chen, Po-Hao Chen, Sheau-Ling Hsieh, Po-Hsun Cheng, Feipei Lai:
  Newborn Screening System Based on Adaptive Feature Selection and Support Vector Machines. 344-347
  
• Ta-Cheng Chen, Jiunn-I Shieh, Kuei-Jen Lee, Jing-Doo Wang, Pei-Chun Chang, Hsiang-Chuan Liu:
  Nonlinear Dynamic Indications in Time Series of Epilepsy Electroencephalogram. 348-351
  
• Taeju Lee, Hyekyung Jeong, Desok Kim, Byung-Do Lee:
  Quantitative Analysis of Endodontic Treatment for Periapical Lesions in Intraoral Radiographs. 352-355
  
• Ming-Chih Shih, Shou-Hsuan Stephen Huang, Chung-Che Jeff Chang:
  A Multidimensional Flow Cytometry Data Classification. 356-359
  

Biomedical Image Processing and Analysis

• Chia-Ling Tsai, Su-Ching Liang, William Warger, Charles DiMarzio:
  Multi-Modal Registration of Embryonic Images for In Vitro Fertilization. 360-363
  
• Jen-Jie Chieh, Chi-How Chen, Shieh-Yueh Yang, Herng-Er Horng, Chin-Yih Hong, Hong-Chang Yang:
  Immunomagnetical Reduction Using High Tc Superconducting Quantum Interference Device (SQUID). 364-365
  
• Myung-Eun Lee, Soo-Hyung Kim, Wan Hyun Cho, Soon-Young Park, Junsik Lim:
  Segmentation of Brain MR Images Using an Ant Colony Optimization Algorithm. 366-369
  

Drug Discovery

• Po-Yuan Chen, Mien-De Jhuo, Wei-Tse Hsu, Tzu-Ching Shih, Tzu-Hurng Cheng:
  The MAPK Signal Pathway Research and New Drug Discovery. 370-373
  

Molecular Evolution and Phylogeny

• Alan C. H. Chen, Han C. W. Hsiao, Jeffrey J. P. Tsai:
  Phylogenetic Analysis Using Nuclear-Encoded Mitochondrial Proteins. 374-377
  
• Rong-Ming Chen, M. T. Hou, Jeffrey J. P. Tsai:
  A Novel Approach for Motif Identification in Unaligned Molecular Sequences. 378-381
  
• Wei-Chen Liao, Nai-Kuei Huang:
  Profiling the Nanoparticles Associated Protein-protein Interactions. 382-385
  
• Chia-Wei Weng, Chang-Chih Chiang, Chien-Hung Huang, Ka-Lok Ng:
  A Platform for Identifying MicroRNA Targeting Genes. 386-387
  
• Chalothorn Liamwirat, Supapon Cheevadthanarak, Asawin Meechai, Sakarindr Bhumiratana:
  Enzyme Relational Network Reveals Target Enzymes within Metabolic Submodules. 388-391
  

Special Session: Bioinformatics & Information Fusion

• Kang-Ping Liu, Lu-Shian Chang, Jinn-Moon Yang:
  ATRIPPI: An Atom-residue Preference Scoring Function for Protein-protein Interactions. 392-399
  
• Christina Schweikert, Yanjun Li, David Dayya, David Yens, Martin Torrents, D. Frank Hsu:
  Analysis of Autism Prevalence and Neurotoxins Using Combinatorial Fusion and Association Rule Mining. 400-404
  
• Tse-Yi Wang, Kuang-Chi Chen, D. Frank Hsu, Cheng-Yan Kao:
  Combining Agent-Based Models with Stochastic Differential Equations for Gene Regulatory Networks. 405-409
  
• Cameron McMunn-Coffran, Christina Schweikert, D. Frank Hsu:
  Microarray Gene Expression Analysis Using Combinatorial Fusion. 410-414
  

Workshop: Biomedical Informatics & Engineering

• Chung C. Chang, Hsueh-Ming Lu:
  Integration of Heterogeneous Medical Decision Support Systems Based on Web Services. 415-422
  
• Mei-Ying Wang, P. H. Tsai, J. W. S. Liu, John K. Zao:
  Wedjat: A Mobile Phone Based Medicine In-take Reminder and Monitor. 423-430
  
• I-Tzu Chen, Yong-Sheng Chen, Li-Fen Chen:
  Beamformer-Based Spatiotemporal Imaging of Correlated Brain Activities. 431-434
  
• Chin-Teng Lin, Fu-Shu Yang, Te-Chung Chiou, Li-Wei Ko, Jeng-Ren Duann, Klaus Gramann:
  EEG-Based Spatial Navigation Estimation in a Virtual Reality Driving Environment. 435-438
  
• Yu-Hsun Lee, Yong-Sheng Chen, Li-Fen Chen:
  Automated Sleep Staging Using Single EEG Channel for REM Sleep Deprivation. 439-442
  
• Yao-Wen Chung, Yu-Sheng Lo, Wen-Sen Lee, Min-Huei Hsu, Chien-Tsai Liu:
  Faster and Active Surveillance of Hospital-Acquired Infections: A Model for Settings with High Sensitivity Predictors. 443-448
  

Workshop: Semantic Biomedical Computing

• David A. Hecht, Phillip C.-Y. Sheu, Jeffrey J. P. Tsai:
  SCDL Applications to Drug Discovery. 449-454
  
• Charles C. N. Wang, David A. Hecht, Han C. W. Hsiao, Phillip C.-Y. Sheu, Jeffrey J. P. Tsai:
  Describing Dynamic Biological Systems in SPDL and SCDL. 455-460
  
• Chih-Hsuan Wei, I-Chin Huang, Yi-Yu Hsu, Hung-Yu Kao:
  Normalizing Biomedical Name Entities by Similarity-Based Inference Network and De-ambiguity Mining. 461-466
  
• Jong-Waye Ou, Rouh-Mei Hu, Rong-Ming Chen, C. Y. Tang, Jeffrey J. P. Tsai:
  An Integrative Tool for Gene Regulatory Network Reconstruction Based on Microarray Data. 467-470
  

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