The Community for Technology Leaders
13th IEEE International Conference on BioInformatics and BioEngineering (2006)
Arlington, Virginia
Oct. 16, 2006 to Oct. 18, 2006
ISBN: 0-7695-2727-2
TABLE OF CONTENTS
Introduction
Session 1 : Protein Structure, Function, and Classification

IUP: Intrinsically Unstructured Protein predictor - A software tool for analyzing polypeptide sequences (Abstract)

Mary Qu Yang , National Institutes of Health, Bethesda, MD 20852 USA
Jack Y. Yang , Harvard Medical School and Massachusetts General
pp. 3-11

A Language Modeling Text Mining Approach to the Annotation of Protein Community (Abstract)

Daniel D. Wu , Drexel University, Chestnut, Philadelphia, PA
Xiaodan Zhang , Drexel University, Chestnut, Philadelphia, PA
Xiaohua Zhou , Drexel University, Chestnut, Philadelphia, PA
Xiaohua Hu , Drexel University, Chestnut, Philadelphia, PA
pp. 12-19

FIK Model: Novel Efficient Granular Computing Model for Protein Sequence Motifs and Structure Information Discovery (Abstract)

Phang C. Tai , Georgia State University, Atlanta, GA
Bernard Chen , Georgia State University, Atlanta, GA
Robert Harrison , Georgia State University, Atlanta, GA
Yi Pan , Georgia State University, Atlanta, GA
pp. 20-26

On Integrating Peptide Sequence Analysis and Relational Distance-Based Indexing (Abstract)

Rui Mao , University of Texas at Austin
Weijia Xu , University of Texas at Austin
Daniel P. Miranker , University of Texas at Austin
Shu Wang , University of Texas at Austin
pp. 27-34

Assessing protein function using a combination of supervised and unsupervised learning (Abstract)

Jack Y. Yang , Harvard University
Mary Qu Yang , National Institutes of Health, Bethesda, Maryland 20852 U.S.A.
pp. 35-44
Session 2 : Pattern Discovery and Data Mining

Partition Frequency Distance based Filter Method for Finding Approximate Repetitions in DNA Sequences (Abstract)

Changyong Yu , Northeastern University, Shenyang 110004, China
Yi Zhao , Northeastern University, Shenyang 110004, China
Baichen Chen , Northeastern University, Shenyang 110004, China
Qingquan Wu , Northeastern University, Shenyang 110004, China
Guoren Wang , Northeastern University, Shenyang 110004, China
Ge Yu , Northeastern University, Shenyang 110004, China
Di Wang , Northeastern University, Shenyang 110004, China
pp. 45-52
Session 2 : Pattern Discovery and Data Mining

Mining the Database of Transcription Binding Sites (Abstract)

Wei Peng , Florida International Universi
Tao Li , Florida International University
Giri Narasimhan , Florida International University
pp. 61-64

Discovering DNA Motifs with Nucleotide Dependency (Abstract)

Francis Y.L. Chin , University of Hong Kong
Henry C.M. Leung , University of Hong Kong
pp. 70-80
Session 3: Microarrays

Exploratory Tools for Follow?Up Studies to Microarray Experiments (Abstract)

Ruoming Jin , Kent State University, Kent OH
Gagan Agrawal , Ohio State University, Columbus OH
Kaushik Sinha , Ohio State University, Columbus OH
Helen Piontkivska , Kent State University, Kent OH
pp. 81-85

Mining Positive and Negative Co-regulation Patterns from Microarray Data (Abstract)

Guoren Wang , Northeastern University, China
Ge Yu , Northeastern University, China
Yuhai Zhao , Northeastern University, China
Ying Yin , Northeastern University, China
pp. 86-93

Building a Classifier for Integrated Microarray Datasets through Two-Stage Approach (Abstract)

Youngmi Yoon , Yonsei University, Korea
Sanghyun Park , Yonsei University, Korea
Jongchan Lee , Yonsei University, Korea
pp. 94-102

IntClust: A Software Package for Clustering Replicated Microarray Data (Abstract)

Tao Li , Florida International University
Wei Peng , Florida International University
pp. 103-109

Quick Hierarchical Biclustering on Microarray Gene Expression Data (Abstract)

Kenneth Wei-Liang Mock , National University of Singapore
Liping Ji , National University of Singapore
Kian-Lee Tan , National University of Singapore
pp. 110-120
Session 4: Sequence Alignment and Database Search

Large Grain Size Stochastic Optimization Alignment (Abstract)

Quinn Snell , Brigham Young University
Hyrum Carroll , Brigham Young University
Mark Clement , Brigham Young University
Perry Ridge , Brigham Young University
Dan Sneddon , Brigham Young University
pp. 127-134

Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model (Abstract)

James Cole , Michigan State University, East Lansing, Michigan
Sakti Pramanik , Michigan State University, East Lansing, Michigan
Qiang Xue , Michigan State University, East Lansing, Michigan
pp. 135-140

A Tool for Supporting Integration Across Multiple Flat?File Datasets (Abstract)

Gagan Agrawal , Ohio State University
Xuan Zhang , Ohio State University
pp. 141-148

Simplicity in RNA Secondary Structure Alignment: Towards biologically plausible alignments (Abstract)

Guohui Lin , University of Alberta, Canada
Eleni Stroulia , University of Alberta, Canada
Rimon Mikhaiel , University of Alberta, Canada
pp. 149-158
Session 5: Phylogenies, Trees, and Visualization

Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees (Abstract)

Usman Roshan , New Jersey Institute of Technology
Satish Chikkagoudar , New Jersey Institute of Technology
Dennis R. Livesay , California State Polytechnic University, Pomona
pp. 159-164

Learning the Tree of Phenotypes Using Genomic Data and VISDA (Abstract)

David J. Miller , Pennsylvania State University
Yuanjian Feng , Virginia Polytechnic Institute and State University
Yitan Zhu , Virginia Polytechnic Institute and State University
Jianhua Xuan , Virginia Polytechnic Institute and State University
Zuyi Wang , The Catholic University of America
pp. 165-170

Visualization of DNA/RNA Structure using Temporal CGRs (Abstract)

Donya Quick , Southern Methodist University Dallas, Texas
Jim Waddle , Southern Methodist University Dallas, Texas
Margaret H. Dunham , Southern Methodist University Dallas, Texas
Monnie McGee , Southern Methodist University Dallas, Texas
Yuhang Wang , Southern Methodist University Dallas, Texas
pp. 171-178

Isolation and Visualization of Codon Usage Biases (Abstract)

Michael L. Raymer , Wright State University
Dan E. Krane , Wright State University
Douglas W. Raiford , Wright State University
Travis E. Doom , Wright State University
pp. 179-183

Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data Exploration (Abstract)

Daniel A. Keim , University of Konstanz
Royal Truman , Mannheim
Klaus Neuhaus , Technical University of Munich
Daniela Oelke , University of Konstanz
pp. 183-192

Evidence of Multiple Maximum Likelihood Points for a Phylogenetic Tree (Abstract)

D. Chu , University of Sydney, Australia
R. P. Brent , Australian National University
B. B. , University of Sydney, Australia
P. Wang , University of Sydney, Australia
C. Wang , University of Sydney, Australia
A. Y. Zomaya , University of Sydney, Australia
M. Tarawneh , University of Sydney, Australia
pp. 193-200
Session 6: DNA & RNA Sequence and Structure

A New Kernel Method for RNA Classification (Abstract)

Xiaoming Wu , Shepherd University, Shepherdstown, WV
Katherine G. Herbert , Montclair State University, Montclair, NJ
Jason T. L. Wang , New Jersey Institute of Technology, University Heights, Newark
pp. 201-208

RADAR: An InteractiveWeb-Based Toolkit for RNA Data Analysis and Research (Abstract)

Bin Tian , UMDNJ-NJMS,NJ
Mugdha Khaladkar , New Jersey Institute of Technology,Newark
Vivian Bellofatto , New Jersey Medical School
Jason T. L. Wang , NJIT, NJ
Kaizhong Zhang , University of Western Ontario, London,Canada
pp. 209-212

Parsimony approach to test the Evolving Master Gene hypothesis for human Alu repeats (Abstract)

Michael Raymer , Wright State University
Travis Doom , Wright State University
Sridhar Ramachandran , Wright State University
Dan Krane , Wright State University
pp. 213-219

Unsupervised Gene Selection For High Dimensional Data (Abstract)

Jean Gao , University of Texas Arlington
Young Bun Kim , University of Texas Arlington
pp. 227-234
Session 7: Clustering, Similarity Metrics, and Near Neighbor Methods

Using Gene Clustering to Identify Discriminatory Genes with Higher Classification Accuracy (Abstract)

Randy Goebel , University of Alberta Edmonton, Alberta, Canada
Mohammad R. Salavatipour , University of Alberta Edmonton, Alberta, Canada
Guohui Lin , University of Alberta Edmonton, Alberta, Canada
Lizhe Xu , The Research Institute for Children-University of New Orleans
Zhipeng Cai , University of Alberta Edmonton, Alberta
Yi Shi , University of Alberta Edmonton, Alberta, Canada
pp. 235-242

Semi-Supervised Clustering Models for Clinical Risk Assessment (Abstract)

Roy Harper , Ulster Community & Hospitals Trust, Northern Ireland, UK
Yongyang Huo , University of Ulster, Jordanstown, UK
Paul McCullagh , University of Ulster, Jordanstown, UK
Francisco Azuaje , University of Ulster, Jordanstown, UK
pp. 243-250

Prediction of Protein Function Using Common-Neighbors in Protein-Protein Interaction Networks (Abstract)

Chuan Lin , State University of New York at Buffalo
Daxin Jiang , Nanyang Technological University, Singapore
Aidong Zhang , State University of New York at Buffalo
pp. 251-260

Determining Molecular Similarity for Drug Discovery using the Wavelet Riemannian Metric (Abstract)

Emmanuel R. Yera , San Francisco State University, San Francisco, CA
Elinor Velasquez , San Francisco State University, San Francisco, CA
Rahul Singh , San Francisco State University, San Francisco, CA
pp. 261-268

Assigning Schema Labels Using Ontology And Hueristics (Abstract)

Gagan Agrawal , Ohio State University, Columbus OH
Xuan Zhang , Ohio State University, Columbus OH
Ruoming Jin , Kent State University, Kent OH
pp. 269-280
Session 8: Regulatory and Metabolic Networks and Bioengineering I

Optimal Multi-Objective Control Method for Discrete Genetic Regulatory Networks (Abstract)

Osman Abul , Norwegian University of Science and Technology, Trondheim, Norway
Reda Alhajj , Global University, Beirut, Lebanon
Faruk Polat , Middle East Technical University, Ankara, Turkey
pp. 281-284

Methods for Random Modularization of Biological Networks (Abstract)

Vladimir Filkov , University of California, Davis
Zachary M. Saul , University of California, Davis
pp. 285-288

Efficient Modularization of Weighted Protein Interaction Networks using k-Hop Graph Reduction (Abstract)

Woochang Hwang , State University of New York at Buffalo
Aidong Zhang , State University of New York at Buffalo
Young-Rae Cho , State University of New York at Buffalo
pp. 289-298

A Computational Inference Framework for analyzing Gene Regulation Pathway using Microarray Data (Abstract)

Winfried Krueger , University of Connecticut Health Center
John Bluis , University of Connecticut
Jeffrey Maddox , University of Connecticut
Yoo-Ah Kim , University of Connecticut
Nathan Viniconis , University of Connecticut
Dong-Guk Shin , University of Connecticut
David Rowe , University of Connecticut Health Center
Alan Wong , University of Connecticut
Ravi Nori , University of Connecticut
Hsin-Wei Wang , University of Connecticut Health Center
pp. 299-306
Session 9: Bioengineering II

Leveraging Chemical Background Knowledge for the Prediction of Growth Inhibition (Abstract)

Stefan Hechtl , Institut fur Informatik I12, Technische Universitat Munchen, Germany
Stefan Kramer , Institut fur Informatik I12, Technische Universitat Munchen, Germany
Lothar Richter , Institut fur Informatik I12, Technische Universitat Munchen, Germany
pp. 319-324

A Supervised Learning Approach to Predicting Coronary Heart Disease Complications in Type 2 Diabetes Mellitus Patients (Abstract)

Francisco Azuaje , University of Ulster, Jordanstown, UK
Marisol Giardina , University of Ulster, Jordanstown, UK
Roy Harper , Ulster Community & Hospitals Trust, Northern Ireland, UK
Paul McCullagh , University of Ulster, Jordanstown, UK
pp. 325-331

Prediction of labor for pregnant women using high-resolution mass spectrometry data (Abstract)

Kevin P. Rosenblatt , University of Hawaii, Manoa, Honolulu, HI
Jung Hun Oh , University of Texas, Arlington, TX
Prem Gurnani , University of Texas at Southwestern Medical Center, Dallas, TX
Jean Gao , University of Texas, Arlington, TX
Animesh Nandi , University of Texas at Southwestern Medical Center, Dallas, TX
Peter Bryant-Greenwood , University of Hawaii, Manoa, Honolulu, HI
pp. 332-339

Noninvasive Study of the Human Heart using Independent Component Analysis (Abstract)

Chung-Kuan Cheng , University of California, San Diego
Tong Lee Chen , Intuit, 2525 Garcia Ave, Mountain View, CA
Jeng-Ren Duann , SoftMax, Inc., 4350 Executive Dr., Suite 201, San Diego, CA
Scott Makeig , University of California, San Diego
Yi Zhu , University of California, San Diego
Wanping Zhang , University of California, San Diego
Tzyy-Ping Jung , SoftMax, Inc., 4350 Executive Dr., Suite 201, San Diego, CA
pp. 340-347

The Role of Timing in Speech Perception and Speech Production Processes and its Effects on Language Impaired Individuals (Abstract)

Nikolaos Bourbakis , Wright State University, OH, 2AIIS Inc., OH, USA
Anna Esposito , Second University of Napoli, Italy
pp. 348-356
Author Index

Author Index (PDF)

pp. 370
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