Table of Contents

• IUP: Intrinsically Unstructured Protein predictor - A software tool for analyzing polypeptide sequencesMary Qu Yang, Jack Y. Yang. 3-11
• A Language Modeling Text Mining Approach to the Annotation of Protein CommunityXiaodan Zhang, Daniel Duanqing Wu, Xiaohua Zhou, Xiaohua Hu. 12-19
• FIK Model: Novel Efficient Granular Computing Model for Protein Sequence Motifs and Structure Information DiscoveryBernard Chen, Phang C. Tai, Robert W. Harrison, Yi Pan. 20-26
• On Integrating Peptide Sequence Analysis and Relational Distance-Based IndexingWeijia Xu, Rui Mao, Shu Wang, Daniel P. Miranker. 27-34
• Assessing protein function using a combination of supervised and unsupervised learningJack Y. Yang, Mary Qu Yang. 35-44
• Partition Frequency Distance based Filter Method for Finding Approximate Repetitions in DNA SequencesDi Wang, Guoren Wang, Qingquan Wu, Baichen Chen, Changyong Yu, Yi Zhao, Ge Yu. 45-52
• Finding Patterns in Biological Sequences by Longest Common Subsequencesand Shortest Common SupersequencesKang Ning, Hoong Kee Ng, Hon Wai Leong. 53-60
• Mining the Database of Transcription Binding SitesWei Peng, Tao Li, Giri Narasimhan. 61-64
• Extending Pattern Branching to Handle Challenging InstancesJaime Davila, Sanguthevar Rajasekaran. 65-69
• Discovering DNA Motifs with Nucleotide DependencyHenry C. M. Leung, Francis Y. L. Chin. 70-80
• Exploratory Tools for Follow­Up Studies to Microarray ExperimentsKaushik Sinha, Ruoming Jin, Gagan Agrawal, Helen Piontkivska. 81-85
• Mining Positive and Negative Co-regulation Patterns from Microarray DataYuhai Zhao, Guoren Wang, Ying Yin, Ge Yu. 86-93
• Building a Classifier for Integrated Microarray Datasets through Two-Stage ApproachYoungmi Yoon, Jongchan Lee, Sanghyun Park. 94-102
• IntClust: A Software Package for Clustering Replicated Microarray DataWei Peng, Tao Li. 103-109
• Quick Hierarchical Biclustering on Microarray Gene Expression DataLiping Ji, Kenneth Wei-Liang Mock, Kian-Lee Tan. 110-120
• An improved algorithm for the regular expression constrained multiple sequence alignment problemAbdullah N. Arslan, Dan He. 121-126
• Large Grain Size Stochastic Optimization AlignmentPerry Ridge, Hyrum Carroll, Dan Sneddon, Mark J. Clement, Quinn Snell. 127-134
• Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov ModelQiang Xue, James R. Cole, Sakti Pramanik. 135-140
• A Tool for Supporting Integration Across Multiple Flat­File DatasetsXuan Zhang, Gagan Agrawal. 141-148
• Simplicity in RNA Secondary Structure Alignment: Towards biologically plausible alignmentsRimon Mikhaiel, Guohui Lin, Eleni Stroulia. 149-158
• Improving progressive alignment for phylogeny reconstruction using parsimonious guide-treesUsman Roshan, Dennis R. Livesay, Satish Chikkagoudar. 159-164
• Learning the Tree of Phenotypes Using Genomic Data and VISDAYuanjian Feng, Zuyi Wang, Yitan Zhu, Jianhua Xuan, David J. Miller. 165-170
• Visualization of DNA/RNA Structure using Temporal CGRsMargaret H. Dunham, Donya Quick, Yuhang Wang, Monnie McGee, Jim Waddle. 171-178
• Isolation and Visualization of Codon Usage BiasesDouglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer. 179-183
• Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data ExplorationDaniel A. Keim, Daniela Oelke, Royal Truman, Klaus Neuhaus. 183-192
• Evidence of Multiple Maximum Likelihood Points for a Phylogenetic TreeBing Bing Zhou, Monther Tarawneh, Pinghao Wang, Daniel Chu, Chen Wang, Albert Y. Zomaya, Richard P. Brent. 193-200
• A New Kernel Method for RNA ClassificationXiaoming Wu, Jason Tsong-Li Wang, Katherine G. Herbert. 201-208
• RADAR: An InteractiveWeb-Based Toolkit for RNA Data Analysis and ResearchMugdha Khaladkar, Vivian Bellofatto, Jason T. L. Wang, Bin Tian, Kaizhong Zhang. 209-212
• Parsimony approach to test the Evolving Master Gene hypothesis for human Alu repeatsSridhar Ramachandran, Travis E. Doom, Michael L. Raymer, Dan E. Krane. 213-219
• An algorithm for string edit distance allowing substring reversalsAbdullah N. Arslan. 220-226
• Unsupervised Gene Selection For High Dimensional DataYoung Bun Kim, Jean Gao. 227-234
• Using Gene Clustering to Identify Discriminatory Genes with Higher Classification AccuracyZhipeng Cai, Lizhe Xu, Yi Shi, Mohammad R. Salavatipour, Randy Goebel, Guohui Lin. 235-242
• Semi-Supervised Clustering Models for Clinical Risk AssessmentYongyang Huo, Francisco Azuaje, Paul J. McCullagh, Roy Harper. 243-250
• Prediction of Protein Function Using Common-Neighbors in Protein-Protein Interaction NetworksChuan Lin, Daxin Jiang, Aidong Zhang. 251-260
• Determining Molecular Similarity for Drug Discovery using the Wavelet Riemannian MetricElinor Velasquez, Emmanuel R. Yera, Rahul Singh. 261-268
• Assigning Schema Labels Using Ontology And HueristicsXuan Zhang, Ruoming Jin, Gagan Agrawal. 269-280
• Optimal Multi-Objective Control Method for Discrete Genetic Regulatory NetworksOsman Abul, Reda Alhajj, Faruk Polat. 281-284
• Methods for Random Modularization of Biological NetworksZachary M. Saul, Vladimir Filkov. 285-288
• Efficient Modularization of Weighted Protein Interaction Networks using k-Hop Graph ReductionYoung-Rae Cho, Woochang Hwang, Aidong Zhang. 289-298
• A Computational Inference Framework for analyzing Gene Regulation Pathway using Microarray DataDong-Guk Shin, John Bluis, Yoo Ah Kim, Winfried Krueger, Jeffrey Maddox, Ravi Nori, Nathan Viniconis, Hsin-Wei Wang, Alan Wong, David Rowe. 299-306
• The Automation of SIBIOS Workflow CompositionXiang Xiao, Malika Mahoui, Zina Ben-Miled, B. Choudhury. 307-314
• Using MEDLINE as Standard Corpus for Measuring Semantic Similarity in the Biomedical DomainHisham Al-Mubaid, Hoa A. Nguyen. 315-318
• Leveraging Chemical Background Knowledge for the Prediction of Growth InhibitionLothar Richter, Stefan Hechtl, Stefan Kramer. 319-324
• A Supervised Learning Approach to Predicting Coronary Heart Disease Complications in Type 2 Diabetes Mellitus PatientsMarisol Giardina, Francisco Azuaje, Paul J. McCullagh, Roy Harper. 325-331
• Prediction of labor for pregnant women using high-resolution mass spectrometry dataJung Hun Oh, Animesh Nandi, Prem Gurnani, Peter Bryant-Greenwood, Kevin P. Rosenblatt, Jean Gao. 332-339
• Noninvasive Study of the Human Heart using Independent Component AnalysisYi Zhu, Tong Lee Chen, Wanping Zhang, Tzyy-Ping Jung, Jeng-Ren Duann, Scott Makeig, Chung-Kuan Cheng. 340-347
• The Role of Timing in Speech Perception and Speech Production Processes and its Effects on Language Impaired IndividualsAnna Esposito, Nikolaos G. Bourbakis. 348-356
• Analysis of Invariant Meta-features for Learning and Understanding Disable People s Emotional Behavior Related to Their Health Conditions: A Case StudyNikolaos G. Bourbakis, Anna Esposito, Despina Kavraki. 357-369