The Community for Technology Leaders
13th IEEE International Conference on BioInformatics and BioEngineering (2005)
Minneapolis, Minnesota
Oct. 19, 2005 to Oct. 21, 2005
ISBN: 0-7695-2476-1
TABLE OF CONTENTS
Introduction

Chairs Forward (PDF)

pp. ix

Committees (PDF)

pp. x-xi
Regular Papers

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

Zhipeng Cai , University of Alberta
Jianzhong Li , Harbin Institute of Technology
Kun Yang , Harbin Institute of Technology
Guohui Lin , University of Alberta
pp. 3-10

Improved Phylogenetic Motif Detection Using Parsimony (Abstract)

David La , California State Polytechnic University at Pomona
Dennis R. Livesay , California State Polytechnic University at Pomona
Usman Roshan , New Jersey Institute of Technology
pp. 19-26

Highly Scalable and Accurate Seeds for Subsequence Alignment (Abstract)

Abhijit Pol , University of Florida
Tamer Kahveci , University of Florida
pp. 27-31

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

B. B. Zhou , University of Sydney
A. Y. Zomaya , University of Sydney
C. Wang , University of Sydney
M. Tarawneh , University of Sydney
R. P. Brent , Australian National University
pp. 32-39

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

Ming-Syan Chen , National Taiwan University
Jan-Ming Ho , Academia Sinica
In-Yee Lee , National Taiwan University and Academia Sinica
pp. 40-48

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

Michael Twa , Ohio State University
Mark A. Bullimore , Ohio State University
Srinivasan Parthasarathy , Ohio State University
Keith Marsolo , Ohio State University
pp. 49-56

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

Approximate Global Alignment of Sequences (Abstract)

Han Tao , University of Florida
Tamer Kahveci , University of Florida
Venkatakrishnan Ramaswamy , University of Florida
Tao Li , University of Florida
pp. 81-88

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

Nikolai Slavov , Princeton University
Ilias Tagkopoulos , Princeton University
S. Y. Kung , Princeton University
pp. 89-96

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

Kian-Lee Tan , National University of Singapore
Xia Cao , National University of Singapore
Beng Chin Ooi , National University of Singapore
Hwee Hwa Pang , Institute of Infocommunication Research
Anthony K. H. Tung , National University of Singapore
pp. 97-104

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

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

Ya-Ting Chao , Yuan Ze University
Shu-Yuan Chen , Yuan Ze University
Ssu-Hua Huang , Yuan Ze University
Ru-Sheng Liu , Yuan Ze University
Chien-Yu Chen , Yuan Ze University
pp. 113-120

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

Parvin Mousavi , Queen?s University
Cheryl Chan , Queen?s University
pp. 121-128

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

Duygu Ucar , Ohio State University
Sitaram Asur , Ohio State University
Srinivasan Parthasarathy , Ohio State University
Chao Wang , Ohio State University
pp. 129-136

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

Jijun Tang , University of South Carolina
Li-San Wang , University of Pennsylvania
pp. 137-144

Haplotype Phasing Using Semidefinite Programming (Abstract)

Parag Namjoshi , University of Maryland at Baltimore County
Konstantinos Kalpakis , University of Maryland at Baltimore County
pp. 145-152

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

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

RNA Pseudoknot Prediction Using Term Rewriting (Abstract)

W. Harrison , University of Missouri
H. Wang , Georgia State University
X. Z. Fu , Georgia State University
R. Harrison , Georgia State University
pp. 169-176

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

Ruoming Jin , Ohio State University
Kaushik Sinha , Ohio State University
Xuan Zhang , Ohio State University
Gagan Agrawal , Ohio State University
pp. 177-184

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
Louiqa Raschid , University of Maryland at College Park
Woei-Jyh Lee , University of Maryland at College Park
pp. 185-192

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

Guoliang Xue , Arizona State University
Edward B. Suh , Translational Genomics Research Institute
Jeffrey W. Touchman , Arizona State University and Translational Genomics Research Institute
Weiyi Zhang , Arizona State University
Tie Wang , Arizona State University
pp. 193-200

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

Aidong Zhang , State University of New York at Buffalo
Pengjun Pei , State University of New York at Buffalo
pp. 201-209

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

Shin Ishii , Nara Institute of Science and Technology
Kikuya Kato , Osaka Medical Center for Cancer and Cardiovascular Diseases
Shigeyuki Oba , Nara Institute of Science and Technology
pp. 210-217

GroupAdaBoost for Selecting Important Genes (Abstract)

Shinto Eguchi , The Institute of Statistical Mathematics
Takashi Takenouchi , Nara Institute of Science and Technology
Masaru Ushijima , Japanese Foundation for Cancer Research
pp. 218-221

Tracking Human Breath in Infrared Imaging (Abstract)

Ioannis Pavlidis , University of Houston
Zhen Zhu , University of Houston
Jin Fei , University of Houston
pp. 227-231

Detecting Abnormal Patterns in WCE Images (Abstract)

N. Bourbakis , Wayne State University and AIIS Inc.
pp. 232-238
Short Papers

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

Huiqing Liu , Institute for Infocomm Research
Ling Li , Institute for Infocomm Research
Jinyan Li , Institute for Infocomm Research
pp. 246-249

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

Karuturi R. Krishna Murthy , Genome Institute of Singapore
Wing-Kin Sung , Genome Institute of Singapore and National University of Singapore
Yingren Liu , National University of Singapore
pp. 250-257

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

Abdullah N. Arslan , University of Vermont
Dan He , University of Vermont
pp. 258-262

Structural Data Mining on Secondary Genomic Structure (Abstract)

Keith C. C. Chan , Hong Kong Polytechnic University
Winnie W. M. Lam , Hong Kong Polytechnic University
pp. 263-266

Normalization of Microarray Data by Iterative Nonlinear Regression (Abstract)

Jianhua Xuan , The Catholic University of America
Eric Hoffman , Children's National Medical Center
Yue Wang , Virginia Polytechnic Institute and State University
Robert Clarke , Georgetown University
pp. 267-270

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

Amutha Ramaswamy , Ohio State University
Ilya Ioshikhes , Ohio State University
Li Wang , Ohio State University
pp. 271-275

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

Wing-Kin Sung , Genome Institute of Singapore
Lance D. Miller , Genome Institute of Singapore
Yi Li , Genome Institute of Singapore
pp. 276-280

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

Qingquan Wu , Northeastern University and Shanghai Baosight Ltd.
Guoren Wang , Northeastern University
Baichen Chen , Northeastern University
Di Wang , Northeastern University
pp. 281-284

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

Anguraj Sadanandam , University of Nebraska Medical Center
Hesham Ali , University of Nebraska at Omaha
Rakesh Singh , University of Nebraska Medical Center
Xiaolu Huang , University of Nebraska at Omaha
pp. 285-289

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

Xiaohua Hu , Drexel University
Yuchun Tang , Georgia State University
Zhen Huang , Georgia State University
Yan-Qing Zhang , Georgia State University
pp. 290-293

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

Dhundy Bastola , University of Nebraska Medical Center
Xutao Deng , University of Nebraska at Omaha
Huimin Geng , University of Nebraska Medical Center
Hesham Ali , University of Nebraska at Omaha
pp. 294-298

Constructing Phylogenetic Networks from Trees (Abstract)

Sergey Bereg , University of Texas at Dallas
Kathryn Bean , University of Texas at Dallas
pp. 299-305

Stochastic Model of Protease-Ligand Reactions (Abstract)

Douglas Raiford , Wright State University
Travis Doom , Wright State University
Paul Anderson , Wright State University
Deacon Sweeney , Wright State University
Michael Raymer , Wright State University
pp. 306-310

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

Chuan Yi Tang , National Tsing Hua University
Chun Yuan Lin , National Tsing Hua University
Chiao Yun Yang , National Tsing Hua University
Chuen-Der Huang , Hsiuping Institute of Technology
Ken-Li Lin , National Chiao Tung University and Chung Hua University
Hsiu-Ming Chang , National Tsing Hua University
Chin-Teng Lin , National Chiao Tung University
D. Frank Hsu , Fordham University
pp. 311-315

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

Guang-Lin Hsieh , TamKang University
Zong-Ting Hsieh , TamKang University
Eugene Lai , TamKang University
Chin-Tang Hsieh , TamKang University
Guo-Ming Hong , TamKang University
pp. 316-319

Phylogenetic Networks Based on the Molecular Clock Hypothesis (Abstract)

Y. Zhang , University of Texas at Dallas
S. Bereg , University of Texas at Dallas
pp. 320-323

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

D. Kavraki , AIIS Inc.
S. Makrogiannis , Wright State University
N. Bourbakis , AIIS Inc. and Wright State University
pp. 324-327
Author Index

Author Index (PDF)

pp. 328-329
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