CSDL - Proceedings B

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Committees (PDF)

pp. x-xi

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Regular Papers

A Model-Free and Stable Gene Selection in Microarray Data Analysis (Abstract)

Kun Yang, Harbin Institute of Technology

Jianzhong Li, Harbin Institute of Technology

Zhipeng Cai, University of Alberta

Guohui Lin, University of Alberta

pp. 3-10

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An Efficient Algorithm for the Extended (l, d)-Motif Problem with Unknown Number of Binding Sites (Abstract)

Henry C. M. Leung, University of Hong Kong

Francis Y. L. Chin, University of Hong Kong

pp. 11-18

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Improved Phylogenetic Motif Detection Using Parsimony (Abstract)

Usman Roshan, New Jersey Institute of Technology

Dennis R. Livesay, California State Polytechnic University at Pomona

David La, California State Polytechnic University at Pomona

pp. 19-26

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Highly Scalable and Accurate Seeds for Subsequence Alignment (Abstract)

Abhijit Pol, University of Florida

Tamer Kahveci, University of Florida

pp. 27-31

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A Novel Quartet-Based Method for Phylogenetic Inference (Abstract)

B. B. Zhou, University of Sydney

M. Tarawneh, University of Sydney

C. Wang, University of Sydney

A. Y. Zomaya, University of Sydney

R. P. Brent, Australian National University

pp. 32-39

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GOMIT: A Generic and Adaptive Annotation Algorithm Based on Gene Ontology Term Distributions (Abstract)

In-Yee Lee, National Taiwan University and Academia Sinica

Jan-Ming Ho, Academia Sinica

Ming-Syan Chen, National Taiwan University

pp. 40-48

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Classification of Biomedical Data through Model-Based Spatial Averaging (Abstract)

Keith Marsolo, Ohio State University

Srinivasan Parthasarathy, Ohio State University

Michael Twa, Ohio State University

Mark A. Bullimore, Ohio State University

pp. 49-56

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A Multi-Level Approach to SCOP Fold Recognition (Abstract)

Keith Marsolo, Ohio State University

Srinivasan Parthasarathy, Ohio State University

Chris Ding, Lawrence Berkeley National Laboratory

pp. 57-64

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A Wrapper Induction Application with Knowledge Base Support: A Use Case for Initiation and Maintenance of Wrappers (Abstract)

Zina Ben Miled, IUPUI

Malika Mahoui, IUPUI

Mindi Dippold, IUPUI

Ali Farooq, IUPUI

Nianhua Li, IUPUI

Omran Bukhres, IUPUI

pp. 65-72

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Predicting Human Papilloma Virus Prevalence and Vaccine Policy Effectiveness in Demographic Strata (Abstract)

Courtney Corley, University of North Texas

Armin R. Mikler, University of North Texas

pp. 73-80

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Approximate Global Alignment of Sequences (Abstract)

Tamer Kahveci, University of Florida

Venkatakrishnan Ramaswamy, University of Florida

Han Tao, University of Florida

Tao Li, University of Florida

pp. 81-88

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Multi-Class Biclustering and Classification Based on Modeling of Gene Regulatory Networks (Abstract)

Ilias Tagkopoulos, Princeton University

Nikolai Slavov, Princeton University

S. Y. Kung, Princeton University

pp. 89-96

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DSIM: A Distance-Based Indexing Method for Genomic Sequences (Abstract)

Xia Cao, National University of Singapore

Beng Chin Ooi, National University of Singapore

Hwee Hwa Pang, Institute of Infocommunication Research

Kian-Lee Tan, National University of Singapore

Anthony K. H. Tung, National University of Singapore

pp. 97-104

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Discovery of Repetitive Patterns in DNA with Accurate Boundaries (Abstract)

Jie Zheng, University of California at Riverside

Stefano Lonardi, University of California at Riverside

pp. 105-112

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Prediction of Outer Membrane Proteins by Support Vector Machines Using Combinations of Gapped Amino Acid Pair Compositions (Abstract)

Ssu-Hua Huang, Yuan Ze University

Ru-Sheng Liu, Yuan Ze University

Chien-Yu Chen, Yuan Ze University

Ya-Ting Chao, Yuan Ze University

Shu-Yuan Chen, Yuan Ze University

pp. 113-120

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Discovery of Gene Expression Patterns across Multiple Cancer Types (Abstract)

Cheryl Chan, Queen?s University

Parvin Mousavi, Queen?s University

pp. 121-128

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Effective Pre-Processing Strategies for Functional Clustering of a Protein-Protein Interactions Network (Abstract)

Duygu Ucar, Ohio State University

Srinivasan Parthasarathy, Ohio State University

Sitaram Asur, Ohio State University

Chao Wang, Ohio State University

pp. 129-136

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Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony (Abstract)

Jijun Tang, University of South Carolina

Li-San Wang, University of Pennsylvania

pp. 137-144

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Haplotype Phasing Using Semidefinite Programming (Abstract)

Konstantinos Kalpakis, University of Maryland at Baltimore County

Parag Namjoshi, University of Maryland at Baltimore County

pp. 145-152

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Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches (Abstract)

Yuheng Li, Ohio State University

Mario Lauria, Ohio State University

Ralf Bundschuh, Ohio State University

pp. 153-160

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Peptide Identification by Tandem Mass Spectra: An Efficient Parallel Searching (Abstract)

Jung Hun Oh, University of Texas

Jean Gao, University of Texas

pp. 161-168

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RNA Pseudoknot Prediction Using Term Rewriting (Abstract)

X. Z. Fu, Georgia State University

H. Wang, Georgia State University

W. Harrison, University of Missouri

R. Harrison, Georgia State University

pp. 169-176

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Using Data Mining Techniques to Learn Layouts of Flat-File Biological Datasets (Abstract)

Kaushik Sinha, Ohio State University

Xuan Zhang, Ohio State University

Ruoming Jin, Ohio State University

Gagan Agrawal, Ohio State University

pp. 177-184

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A Methodology to Enhance the Semantics of Links between PubMed Publications and Markers in the Human Genome (Abstract)

Alex Lash, Memorial Sloan-Kettering Cancer Center

Woei-Jyh Lee, University of Maryland at College Park

Louiqa Raschid, University of Maryland at College Park

pp. 185-192

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A Parallel Algorithm for Extracting Transcription Regulatory Network Motifs (Abstract)

Tie Wang, Arizona State University

Jeffrey W. Touchman, Arizona State University and Translational Genomics Research Institute

Weiyi Zhang, Arizona State University

Edward B. Suh, Translational Genomics Research Institute

Guoliang Xue, Arizona State University

pp. 193-200

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A Two-Step Approach for Clustering Proteins Based on Protein Interaction Profile (Abstract)

Pengjun Pei, State University of New York at Buffalo

Aidong Zhang, State University of New York at Buffalo

pp. 201-209

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Multi-Scale Clustering for Gene Expression Profiling Data (Abstract)

Shigeyuki Oba, Nara Institute of Science and Technology

Kikuya Kato, Osaka Medical Center for Cancer and Cardiovascular Diseases

Shin Ishii, Nara Institute of Science and Technology

pp. 210-217

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GroupAdaBoost for Selecting Important Genes (Abstract)

Takashi Takenouchi, Nara Institute of Science and Technology

Masaru Ushijima, Japanese Foundation for Cancer Research

Shinto Eguchi, The Institute of Statistical Mathematics

pp. 218-221

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A 2D Vibration Array for Sensing Dynamic Changes and 3D Space for Blinds' Navigation (Abstract)

N. Bourbakis, Wright State University

D. Kavraki, AIIS Inc.

pp. 222-226

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Tracking Human Breath in Infrared Imaging (Abstract)

Zhen Zhu, University of Houston

Jin Fei, University of Houston

Ioannis Pavlidis, University of Houston

pp. 227-231

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Detecting Abnormal Patterns in WCE Images (Abstract)

N. Bourbakis, Wayne State University and AIIS Inc.

pp. 232-238

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Short Papers

Selecting Informative Genes from Microarray Dataset by Incorporating Gene Ontology (Abstract)

Xian Xu, State University of New York at Buffalo

Aidong Zhang, State University of New York at Buffalo

pp. 241-245

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Diagnostic Rules Induced by an Ensemble Method for Childhood Leukemia (Abstract)

Jinyan Li, Institute for Infocomm Research

Huiqing Liu, Institute for Infocomm Research

Ling Li, Institute for Infocomm Research

pp. 246-249

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ConstrainedMotif: A Periodicity Constraint Based Algorithm to Predict Cell-Cycle Associated Promoter Motifs Using Time-Course Gene Expression Data (Abstract)

Yingren Liu, National University of Singapore

Karuturi R. Krishna Murthy, Genome Institute of Singapore

Wing-Kin Sung, Genome Institute of Singapore and National University of Singapore

pp. 250-257

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A Parallel Algorithm for the Constrained Multiple Sequence Alignment Problem (Abstract)

Dan He, University of Vermont

Abdullah N. Arslan, University of Vermont

pp. 258-262

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Structural Data Mining on Secondary Genomic Structure (Abstract)

Winnie W. M. Lam, Hong Kong Polytechnic University

Keith C. C. Chan, Hong Kong Polytechnic University

pp. 263-266

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Normalization of Microarray Data by Iterative Nonlinear Regression (Abstract)

Jianhua Xuan, The Catholic University of America

Eric Hoffman, Children's National Medical Center

Robert Clarke, Georgetown University

Yue Wang, Virginia Polytechnic Institute and State University

pp. 267-270

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Global Dynamics of Nucleosome Arrays: Influence of Variant Histone H2A.Z (Abstract)

Li Wang, Ohio State University

Amutha Ramaswamy, Ohio State University

Ilya Ioshikhes, Ohio State University

pp. 271-275

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Multimodality as a Criterion for Feature Selection in Unsupervised Analysis of Gene Expression Data (Abstract)

Yi Li, Genome Institute of Singapore

Wing-Kin Sung, Genome Institute of Singapore

Lance D. Miller, Genome Institute of Singapore

pp. 276-280

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Finding LPRs in DNA Sequence Based on a New Index — SUA (Abstract)

Di Wang, Northeastern University

Guoren Wang, Northeastern University

Qingquan Wu, Northeastern University and Shanghai Baosight Ltd.

Baichen Chen, Northeastern University

pp. 281-284

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Protein Motif Searching Through Similar Enriched Parikh Vector Identification (Abstract)

Xiaolu Huang, University of Nebraska at Omaha

Hesham Ali, University of Nebraska at Omaha

Anguraj Sadanandam, University of Nebraska Medical Center

Rakesh Singh, University of Nebraska Medical Center

pp. 285-289

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Granular SVM-RFE Gene Selection Algorithm for Reliable Prostate Cancer Classification on Microarray Expression Data (Abstract)

Yuchun Tang, Georgia State University

Yan-Qing Zhang, Georgia State University

Zhen Huang, Georgia State University

Xiaohua Hu, Drexel University

pp. 290-293

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On Clustering Biological Data Using Unsupervised and Semi-Supervised Message Passing (Abstract)

Huimin Geng, University of Nebraska Medical Center

Xutao Deng, University of Nebraska at Omaha

Dhundy Bastola, University of Nebraska Medical Center

Hesham Ali, University of Nebraska at Omaha

pp. 294-298

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Constructing Phylogenetic Networks from Trees (Abstract)

Sergey Bereg, University of Texas at Dallas

Kathryn Bean, University of Texas at Dallas

pp. 299-305

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Stochastic Model of Protease-Ligand Reactions (Abstract)

Paul Anderson, Wright State University

Douglas Raiford, Wright State University

Deacon Sweeney, Wright State University

Travis Doom, Wright State University

Michael Raymer, Wright State University

pp. 306-310

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Feature Selection and Combination Criteria for Improving Predictive Accuracy in Protein Structure Classification (Abstract)

Chun Yuan Lin, National Tsing Hua University

Ken-Li Lin, National Chiao Tung University and Chung Hua University

Chuen-Der Huang, Hsiuping Institute of Technology

Hsiu-Ming Chang, National Tsing Hua University

Chiao Yun Yang, National Tsing Hua University

Chin-Teng Lin, National Chiao Tung University

Chuan Yi Tang, National Tsing Hua University

D. Frank Hsu, Fordham University

pp. 311-315

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A Holter of Low Complexity Design Using Mixed Signal Processor (Abstract)

Chin-Tang Hsieh, TamKang University

Guang-Lin Hsieh, TamKang University

Eugene Lai, TamKang University

Zong-Ting Hsieh, TamKang University

Guo-Ming Hong, TamKang University

pp. 316-319

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Phylogenetic Networks Based on the Molecular Clock Hypothesis (Abstract)

S. Bereg, University of Texas at Dallas

Y. Zhang, University of Texas at Dallas

pp. 320-323

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A Neural Network-Based Detection of Bleeding in Sequences of WCE Images (Abstract)

N. Bourbakis, AIIS Inc. and Wright State University

S. Makrogiannis, Wright State University

D. Kavraki, AIIS Inc.

pp. 324-327

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Author Index

Author Index (PDF)

pp. 328-329