4. BIBE 2004: Taichung, Taiwan, ROC

Keynote Speech

• Wen-Hwa Lee:
  Tumor Suppressor Gene Networks as Molecular Targets for Developing New Cancer Treatments. 1-4
  

Invited Speech

• Zhengchang Su, PhuongAn Dam, Victor Olman, Ying Xu:
  Computational Inference of Transcription Regulation and Response Networks in Synechococcus sp. WH8102. 5-8
  

Bioengineering

• Andreas Schmid:
  Retionomorphic Information Processing for Electrical Epi-Retinal Vision Implant Stimulation. 9-16
  
• Yung-Kang Chen, Hsien-Tsai Wu, Chih-Kai Chi, Wei-Chuan Tsai, Ju-Yi Chen, Ming-Chun Wang:
  A New Dual Channel Pulse Wave Velocity Measurement System. 17-21
  
• Daniele Masotti, Elisa Ficarra, Enrico Macii, Luca Benini:
  Techniques for Enhancing Computation of DNA Curvature Molecules. 22-29
  
• Gloria Y. Yang, Vasudev J. Bailey, Gisela Lin, William C. Tang, Joyce H. Keyak:
  Design of Microfabricated Strain Gauge Array to Monitor Bone Deformation In Vitro and In Vivo. 30-37
  
• Weili Zheng, Aamer Aziz, Ihar Volkov, Xin Ma, F. S. Chau, M. Ang Jr., Wieslaw Lucjan Nowinski:
  Towards Automating an Interventional Radiology Procedure. 38-46
  

Data Integration and Protein Folding

• Ane Tröger, Alvaro A. A. Fernandes:
  A Language for Comprehensively Supporting the In Vitro Experimental Process In Silico. 47-56
  
• Pengyu Hong, Sheng Zhong, Wing Hung Wong:
  Towards Ubiquitous Bio-Information Computing: Data Protocols, Middleware, and Web Services for Heterogeneous Biological Information Integration and Retrieval. 57-64
  
• Zina Ben-Miled, Lingma Lu, Malika Mahoui, Jessica Chen, Omran A. Bukhres, Ning Gao, Yue He:
  A Service Discovery Approach in Support of Web Service Integration. 65-72
  
• Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano:
  Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression. 73-78
  
• Eunice E. Santos, Eugene Santos Jr.:
  Reducing the Computational Load of Energy Evaluations for Protein Folding. 79-88
  

Invited Speech

• W. L. Hsu, J. M. Chang, W. C. Chou, J. B. Chen, K. P. Wu, T. Y. Sung, C. F. Chang, W. J. Wu, T. H. Huang:
  An Iterative Relaxation Technique for the NMR Backbone Assignment Problem. 89-92
  

Medical Image Processing I

• Qingmao Hu, Wieslaw Lucjan Nowinski:
  Knowledge-Driven Extraction of the Four Modified Talairach Cortical Landmarks (A, P, L, and R) from MR Neuroimages. 93-99
  
• Ruey-Feng Chang, Chii-Jen Chen, Ming-Feng Ho, Dar-Ren Chen, Woo Kyung Moon:
  Breast Ultrasound Image Classification Using Fractal Analysis. 100-107
  
• Louise Chuang, Jeng-Yang Hwang, Hen-Chang Chang, I-Chang Jou, Shiang-Bin Jong:
  Quantitative Computer Image Analysis of Serum a-fetoprotein Rapid Gold Immunochromatographic Dipstick Assay. 108-114
  
• Wenlong Qian, Zujun Hou, Qingmao Hu, Aamer Aziz, Wieslaw Lucjan Nowinski:
  Segmentation of the Sylvian Fissure in Brain Mr Images. 115-124
  

Parallel Processing and Primer Design

• Weng-Long Chang, Michael (Shan-Hui) Ho, Minyi Guo:
  Fast Parallel Molecular Algorithms for DNA-based Computation: Factoring Integers. 125-133
  
• Damon Shing-Min Liu, Che-Hao Wu:
  An Effective Approach for Constructing the Phylogenetic Tree on a Grid-Based Architecture. 134-141
  
• Shih-Nung Chen, Jeffrey J. P. Tsai, Chih-Wei Huang, Rong-Ming Chen, Raymond C. K. Lin:
  Using Distributed Computing Platform to Solve High Computing and Huge Data Processing Problems in Bioinformatics. 142-148
  
• K. Rocha, C. Medeiros, M. Monteiro, L. Gonçalves, P. Marinho:
  Design of Specie-Specific Primers for Virus Diagnosis in Plants with PCR. 149-158
  

Medical Image Processing II

• Chien-Chuan Ko, Jyh-Wei Jang:
  Interactive Polyp Biopsy based on Automatic Segmentation of Virtual Colonoscopy. 159-166
  
• Yen-Yu Chen, Shen-Chuan Tai:
  Embedded Medical Image Compression Using DCT Based Subband Decomposition and Modified SPIHT Data Organization. 167-174
  
• Adrian S. Barb, Chi-Ren Shyu, Yash Sethi:
  Semantic Integration and Knowledge Exchange for Diagnostic Medical Image Databases. 175-182
  
• Tang-Kai Yin, Nan-Tsing Chiu:
  Discrimination between Alzheimer's Dementia and Controls by Automated Analysis of Statistical Parametric Maps of {99m}Tc-HMPAO-SPECT Volumes. 183-190
  
• Rania Hussein, Frederic Rick McKenzie, Paul Schellhammer, Jose Diaz:
  Quantitation of Extra-Capsular Prostate Tissue from Reconstructed Tissue Images. 191-198
  

Medical Informatics

• Marco Masseroli, Andrea Stella, Natalia Meani, Myriam Alcalay, Francesco Pinciroli:
  GeneWebEx: Gene Annotation Web Extraction, Aggregation, and Updating from Web-Based Biomolecular Databanks. 199-206
  
• David Pérez-Rey, Victor Maojo, Miguel García-Remesal, R. Alonso-Calvo:
  Biomedical Ontologies in Post-Genomic Information Systems. 207-214
  
• Ferran Sanz, Carlos Díaz, Fernando Martín-Sánchez, Julio Bonis:
  European Support to Biomedical Informatics Development: in Pursue of Genomic Medicine. 215-221
  
• Victoria López-Alonso, J. P. Sanchez, I. Liebana, Isabel Hermosilla, Fernando Martín-Sánchez:
  INBIOMED: a Platform for the Integration and Sharing of Genetic, Clinical and Epidemiological Data Oriented to Biomedical Research. 222-226
  
• Miguel García-Remesal, Victor Maojo, Holger Billhardt, José Crespo, R. Alonso-Calvo, David Pérez-Rey, Fernando Martin, A. Sousa:
  ARMEDA II: Supporting Genomic Medicine through the Integration of Medical and Genetic Databases. 227-236
  

Banquet Speech

• Hiroshi Yamaguchi:
  Accelerating Trans-disciplinary Research to a Knowledge-sharing Infrastracture. 237-240
  

Keynote Speech

• Eva Y.-H. P. Lee:
  Protein Network in DNA Damage Response and Breast Carcinogenesis. 241-244
  

Invited Speech

• Wieslaw Lucjan Nowinski:
  Virtual Reality in Brain Intervention. 245-250
  

Gene Expression

• Xiaohua Hu:
  Integration of Cluster Ensemble and Text Summarization for Gene Expression Analysis. 251-258
  
• Kevin Y. Yip, David W. Cheung, Michael K. Ng, Kei-Hoi Cheung:
  Identifying Projected Clusters from Gene Expression Profiles. 259-266
  
• Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik:
  Model-Based Clustering with Genes Expression Dynamics for Time-Course Gene Expression Data. 267-274
  
• Sungroh Yoon, Christine Nardini, Luca Benini, Giovanni De Micheli:
  Enhanced pClustering and Its Applications to Gene Expression Data. 275-282
  
• Zonghong Zhang, Alvin Teo, Beng Chin Ooi, Kian-Lee Tan:
  Mining Deterministic Biclusters in Gene Expression Data. 283-292
  

Transcriptome and Functional Genomics

• Hsun-Chang Chang, Po-Shun Yu, Tze-Wei Huang, Yaw-Ling Lin, Fang-Rong Hsu:
  The Application of Alternative Splicing Graphs in Quantitative Analysis of Alternative Splicing Form from EST Database. 293-300
  
• Judith Zimmermann, Zsuzsanna Lipták, Scott Hazelhurst:
  A Method for Evaluating the Quality of String Dissimilarity Measures and Clustering Algorithms for EST Clustering. 301-309
  
• Fang-Rong Hsu, Hwan-You Chang, Yaw-Ling Lin, Yin-Te Tsai, Hui-Ling Peng, Ying Tsong Chen, Che Feng Chen, Chia Yang Cheng, Chia-Hung Liu, Min Yao Shih:
  Genome-Wide Alternative Splicing Events Detection through Analysis of Large Scale ESTs. 310-316
  
• Francisco Azuaje, Olivier Bodenreider:
  Incorporating Ontology-Driven Similarity Knowledge into Functional Genomics: An Exploratory Study. 317-324
  
• Jorng-Tzong Horng, Kai-Chih Hu, Li-Cheng Wu, Hsien-Da Huang, Horn-Cheng Lai, Ton-Yuen Chu:
  Identifying the Combination of Genetic Factors that Determine Susceptibility to Cervical Cancer. 325-332
  

Invited Speech

• Y.-W. Deng, C. H. Wei, U.-C. Yang:
  Death Domain Resource: an Integrated Protein Domain Database. 333-336
  

Microarray Data Analysis

• Osman Abul, Reda Alhajj, Faruk Polat:
  Markov Decision Processes Based Optimal Control Policies for Probabilistic Boolean Network. 337-344
  
• Hsieh-Hui Yu, Vincent Shin-Mu Tseng, Jiin-Haur Chuang:
  A Multi-Information based Gene Scoring Model with Applications on Analysis of Hepatocellular Carcinoma. 345-350
  
• Karuturi R. Krishna Murthy, Vinsensius B. Vega:
  Friendly Neighbors Method for Unsupervised Determination of Gene Significance in Time-course Microarray Data. 351-357
  
• Han-Yu Chuang, Hongfang Liu, Stuart Brown, Cameron McMunn-Coffran, Cheng-Yan Kao, D. Frank Hsu:
  Identifying Significant Genes from Microarray Data. 358-365
  
• Selnur Erdal, Ozgur Ozturk, David L. Armbruster, Hakan Ferhatosmanoglu, William C. Ray:
  A Time Series Analysis of Microarray Data. 366-378
  

Homology Search

• Kwok Pui Choi, Fanfan Zeng, Louxin Zhang:
  Good Spaced Seeds For Homology Search. 379-386
  
• Gregory Kucherov, Laurent Noé, Yann Ponty:
  Estimating Seed Sensitivity on Homogeneous Alignments. 387-394
  
• Hsiao Ping Lee, Yin-Te Tsai, Ching Hua Shih, Tzu Fang Sheu, Chuan Yi Tang:
  An IDC-based Algorithm for Efficient Homology Filtration with Guaranteed Seriate Coverage. 395-402
  
• S. Alireza Aghili, Ozgur D. Sahin, Divyakant Agrawal, Amr El Abbadi:
  Efficient Filtration of Sequence Similarity Search Through Singular Value Decomposition. 403-410
  
• I-Hsuan Yang, Sheng-Ho Wang, Yang-Ho Chen, Pao-Hsian Huang, Liang Ye, Xiaoqiu Huang, Kun-Mao Chao:
  Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds. 411-418
  

Proteomics

• Anand Kumar, Barry Smith:
  Towards a Proteomics Meta-Classification. 419-426
  
• Darby Tien-Hao Chang, Chien-Yu Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang:
  An Efficient Mechanism for Prediction of Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures. 427-433
  
• Dong-Soo Han, Hong-Soog Kim, Woo-Hyuk Jang, Sung-Doke Lee:
  Domain Combination Based Protein-Protein Interaction Possibility Ranking Method. 434-441
  
• Saravanan Dayalan, Savitri Bevinakoppa:
  Dihedral Angle Database Based on Disulfide Bonds. 442-450
  

Sequence Analysis

• Paul Hsueh-Min Chang, Von-Wun Soo, Tai-Yu Chen, Wei-Shen Lai, Shiun-Cheng Su, Yu-Ling Huang:
  Automating the Determination of Open Reading Frames in Genomic Sequences Using the Web Service Techniques -- A Case Study using SARS Coronavirus. 451-458
  
• Falcon F. M. Liu, Jeffrey J. P. Tsai, Rong-Ming Chen, S. N. Chen, S. H. Shih:
  FMGA: Finding Motifs by Genetic Algorithm. 459-466
  
• Scott Mann, Yi-Ping Phoebe Chen, Luke Eaton:
  A Computational Framework for Nucleic Acid Sub-Sequence Identification. 467-474
  
• Chia-Hung Chang, Han-Yu Chuang, Yi-Hung Chiang, Chien-Shun Chiou, Hsueh-I Lu, Cheng-Yan Kao:
  Automatically Predicting Possible Loci of Variable Number of Tandem Repeats. 475-482
  
• Xiaoan Dong, Sam Yuan Sung, Wing-Kin Sung, Chew Lim Tan:
  Constraint Based Method for Finding Motifs in DNA Sequences. 483-492
  

Keynote Speech

• Richard C. T. Lee:
  Application of Visual Display Techniques to Solve Some Biological Problems. 493-496
  

Invited Speech

• Atsushi Kitazawa, Masayoshi Yoshimura:
  SemanticObjects and Biomedical Informatics. 497-502
  

Structural Biology

• Elke Moritz, Jörg Meyer:
  Interactive 3D Protein Structure Visualization Using Virtual Reality. 503-507
  
• Zeyar Aung, Kian-Lee Tan:
  Automatic Protein Structure Classification through Structural Fingerprinting. 508-515
  
• In-Yee Lee, Ta-tsen Soong, Jan-Ming Ho, Ming-Jing Hwang:
  Derivation and Analysis of Fragment Libraries of Protein Structures. 516-521
  
• Pin-Hao Chi, Grant J. Scott, Chi-Ren Shyu:
  A Fast Protein Structure Retrieval System Using Image-Based Distance Matrices and Multidimensional Index. 522-532
  

Algorithms

• Chuan-Min Lee, Ling-Ju Hung, Maw-Shang Chang, Chuan Yi Tang:
  An Improved Algorithm for the Maximum Agreement Subtree Problem. 533-536
  
• Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto:
  Protein Threading with Profiles and Constraints. 537-544
  
• Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Prudence W. H. Wong, Siu-Ming Yiu:
  A Mutation-Sensitive Approach for Locating Conserved Gene Pairs between Related Species. 545-552
  
• M. C. Chen, Richard C. T. Lee:
  Sorting by Transpositions Based on the First Increasing Substring Concept. 553-560
  

Protein-Protein Interactions

• Ka-Lok Ng, Chien-Hung Huang:
  A Cross-species Study of the Protein-protein Interaction Networks via the Random Graph Approach. 561-567
  
• Soon-Heng Tan, Wing-Kin Sung, See-Kiong Ng:
  Discovering Novel Interacting Motif Pairs from Large Protein-Protein Interaction Datasets. 568-575
  
• Shinsuke Dohkan, Asako Koike, Toshihisa Takagi:
  Prediction of Protein-Protein Interactions Using Support Vector Machines. 576-586
  

Algorithms and Intelligent Systems

• Gina Cooper, Michael L. Raymer, Travis E. Doom, Don Krane, Natsuhiko Futamura:
  Indexing Genomic Databases. 587-591
  
• Jijun Tang, Bernard M. E. Moret, Liying Cui, Claude W. dePamphilis:
  Phylogenetic Reconstruction from Arbitrary Gene-Order Data. 592-599
  
• Fei Xie, Phillip C.-Y. Sheu, Arthur Lander, Vittorio Cristini:
  Semantic Analysis and Synthesis of Complex Biological Systems. 600-610