5. BIBE 2005: Minneapolis, MN, USA

Introduction

• Chairs Forward.
  
• Committees.
  

Regular Papers

• Kun Yang, Jianzhong Li, Zhipeng Cai, Guohui Lin:
  A Model-Free and Stable Gene Selection in Microarray Data Analysis. 3-10
  
• Henry C. M. Leung, Francis Y. L. Chin:
  An Efficient Algorithm for the Extended (l, d)-Motif Problem with Unknown Number of Binding Sites. 11-18
  
• Usman Roshan, Dennis R. Livesay, David La:
  Improved Phylogenetic Motif Detection Using Parsimony. 19-26
  
• Abhijit Pol, Tamer Kahveci:
  Highly Scalable and Accurate Seeds for Subsequence Alignment. 27-31
  
• Bing Bing Zhou, Monther Tarawneh, Chen Wang, Albert Y. Zomaya, Richard P. Brent:
  A Novel Quartet-Based Method for Phylogenetic Inference. 32-39
  
• In-Yee Lee, Jan-Ming Ho, Ming-Syan Chen:
  GOMIT: A Generic and Adaptive Annotation Algorithm Based on Gene Ontology Term Distributions. 40-48
  
• Keith Marsolo, Srinivasan Parthasarathy, Michael D. Twa, Mark Bullimore:
  Classification of Biomedical Data through Model-Based Spatial Averaging. 49-56
  
• Keith Marsolo, Srinivasan Parthasarathy, Chris H. Q. Ding:
  A Multi-Level Approach to SCOP Fold Recognition. 57-64
  
• Zina Ben-Miled, Malika Mahoui, Mindi Dippold, Ali Farooq, Nianhua Li, Omran A. Bukhres:
  A Wrapper Induction Application with Knowledge Base Support: A Use Case for Initiation and Maintenance of Wrappers. 65-72
  
• Courtney Corley, Armin R. Mikler:
  Predicting Human Papilloma Virus Prevalence and Vaccine Policy Effectiveness in Demographic Strata. 73-80
  
• Tamer Kahveci, Venkatakrishnan Ramaswamy, Han Tao, Tao Li:
  Approximate Global Alignment of Sequences. 81-88
  
• Ilias Tagkopoulos, Nikolai Slavov, Sun-Yuan Kung:
  Multi-Class Biclustering and Classification Based on Modeling of Gene Regulatory Networks. 89-96
  
• Xia Cao, Beng Chin Ooi, HweeHwa Pang, Kian-Lee Tan, Anthony K. H. Tung:
  DSIM: A Distance-Based Indexing Method for Genomic Sequences. 97-104
  
• Jie Zheng, Stefano Lonardi:
  Discovery of Repetitive Patterns in DNA with Accurate Boundaries. 105-112
  
• Ssu-Hua Huang, Ru-Sheng Liu, Chien-Yu Chen, Ya-Ting Chao, Shu-Yuan Chen:
  Prediction of Outer Membrane Proteins by Support Vector Machines Using Combinations of Gapped Amino Acid Pair Compositions. 113-120
  
• Cheryl Chan, Parvin Mousavi:
  Discovery of Gene Expression Patterns across Multiple Cancer Types. 121-128
  
• Duygu Ucar, Srinivasan Parthasarathy, Sitaram Asur, Chao Wang:
  Effective Pre-Processing Strategies for Functional Clustering of a Protein-Protein Interactions Network. 129-136
  
• Jijun Tang, Li-San Wang:
  Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony. 137-144
  
• Konstantinos Kalpakis, Parag Namjoshi:
  Haplotype Phasing Using Semidefinite Programming. 145-152
  
• Yuheng Li, Mario Lauria, Ralf Bundschuh:
  Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches. 153-160
  
• Jung Hun Oh, Jean Gao:
  Peptide Identification by Tandem Mass Spectra: An Efficient Parallel Searching. 161-168
  
• Xuezheng Fu, Hao Wang, William L. Harrison, Robert W. Harrison:
  RNA Pseudoknot Prediction Using Term Rewriting. 169-176
  
• Kaushik Sinha, Xuan Zhang, Ruoming Jin, Gagan Agrawal:
  Using Data Mining Techniques to Learn Layouts of Flat-File Biological Datasets. 177-184
  
• Alex E. Lash, Woei-Jyh Lee, Louiqa Raschid:
  A Methodology to Enhance the Semantics of Links between PubMed Publications and Markers in the Human Genome. 185-192
  
• Tie Wang, Jeffrey W. Touchman, Weiyi Zhang, Edward B. Suh, Guoliang Xue:
  A Parallel Algorithm for Extracting Transcription Regulatory Network Motifs. 193-200
  
• Pengjun Pei, Aidong Zhang:
  A Two-Step Approach for Clustering Proteins Based on Protein Interaction Profile. 201-209
  
• Shigeyuki Oba, Kikuya Kato, Shin Ishii:
  Multi-Scale Clustering for Gene Expression Profiling Data. 210-217
  
• Takashi Takenouchi, Masaru Ushijima, Shinto Eguchi:
  GroupAdaBoost for Selecting Important Genes. 218-221
  
• Nikolaos G. Bourbakis, Despina Kavraki:
  A 2D Vibration Array for Sensing Dynamic Changes and 3D Space for Blinds' Navigation. 222-226
  
• Zhen Zhu, Jin Fei, Ioannis Pavlidis:
  Tracking Human Breath in Infrared Imaging. 227-231
  
• Nikolaos G. Bourbakis:
  Detecting Abnormal Patterns in WCE Images. 232-238
  

Short Papers

• Xian Xu, Aidong Zhang:
  Selecting Informative Genes from Microarray Dataset by Incorporating Gene Ontology. 241-245
  
• Jinyan Li, Huiqing Liu, Ling Li:
  Diagnostic Rules Induced by an Ensemble Method for Childhood Leukemia. 246-249
  
• Yingren Liu, Karuturi R. Krishna Murthy, Wing-Kin Sung:
  ConstrainedMotif: A Periodicity Constraint Based Algorithm to Predict Cell-Cycle Associated Promoter Motifs Using Time-Course Gene Expression Data. 250-257
  
• Dan He, Abdullah N. Arslan:
  A Parallel Algorithm for the Constrained Multiple Sequence Alignment Problem. 258-262
  
• Winnie W. M. Lam, Keith C. C. Chan:
  Structural Data Mining on Secondary Genomic Structure. 263-266
  
• Jianhua Xuan, Eric P. Hoffman, Robert Clarke, Yue Wang:
  Normalization of Microarray Data by Iterative Nonlinear Regression. 267-270
  
• Li Wang, Amutha Ramaswamy, Ilya P. Ioshikhes:
  Global Dynamics of Nucleosome Arrays: Influence of Variant Histone H2A.Z. 271-275
  
• Yi Li, Wing-Kin Sung, Lance D. Miller:
  Multimodality as a Criterion for Feature Selection in Unsupervised Analysis of Gene Expression Data. 276-280
  
• Di Wang, Guoren Wang, Qingquan Wu, Baichen Chen:
  Finding LPRs in DNA Sequence Based on a New Index - SUA. 281-284
  
• Xiaolu Huang, Hesham H. Ali, Anguraj Sadanandam, Rakesh Singh:
  Protein Motif Searching Through Similar Enriched Parikh Vector Identification. 285-289
  
• Yuchun Tang, Yan-Qing Zhang, Zhen Huang, Xiaohua Hu:
  Granular SVM-RFE Gene Selection Algorithm for Reliable Prostate Cancer Classification on Microarray Expression Data. 290-293
  
• Huimin Geng, Xutao Deng, Dhundy Bastola, Hesham H. Ali:
  On Clustering Biological Data Using Unsupervised and Semi-Supervised Message Passing. 294-298
  
• Sergey Bereg, Kathryn Bean:
  Constructing Phylogenetic Networks from Trees. 299-305
  
• Paul E. Anderson, Douglas W. Raiford, Deacon J. Sweeney, Travis E. Doom, Michael L. Raymer:
  Stochastic Model of Protease-Ligand Reactions. 306-310
  
• Chun-Yuan Lin, Ken-Li Lin, Chuen-Der Huang, Hsiu-Ming Chang, Chiao Yun Yang, Chin-Teng Lin, Chuan Yi Tang, D. Frank Hsu:
  Feature Selection and Combination Criteria for Improving Predictive Accuracy in Protein Structure Classification. 311-315
  
• Ching-Tang Hsieh, Guang-Lin Hsieh, Eugene Lai, Zong-Ting Hsieh, Guo-Ming Hong:
  A Holter of Low Complexity Design Using Mixed Signal Processor. 316-319
  
• S. Bereg, Y. Zhang:
  Phylogenetic Networks Based on the Molecular Clock Hypothesis. 320-323
  
• Nikolaos G. Bourbakis, Sokratis Makrogiannis, Despina Kavraki:
  A Neural Network-Based Detection of Bleeding in Sequences of WCE Images. 324-327