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13th IEEE International Conference on BioInformatics and BioEngineering (2003)
Bethesda, Maryland
Mar. 10, 2003 to Mar. 12, 2003
ISBN: 0-7695-1907-5
TABLE OF CONTENTS
Introduction
Bioinfo-1: Protein Structures and Pathways

A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale (Abstract)

Manesh Shah , Oak Ridge National Laboratory and University of Tennessee
Sergei Passovets , Oak Ridge National Laboratory and University of Tennessee
Li Wang , Oak Ridge National Laboratory and University of Tennessee
Inna Vokler , Oak Ridge National Laboratory and University of Tennessee
Dong Xu , Oak Ridge National Laboratory and University of Tennessee
Kyle Ellrott , University of Tennessee
Ying Xu , Oak Ridge National Laboratory and University of Tennessee
Dongsup Kim , Oak Ridge National Laboratory
Philip LoCascio , Oak Ridge National Laboratory
pp. 3

A Fast Algorithm for RNA Secondary Structure Prediction Including Pseudoknots (Abstract)

Fariza Tahi , Université d' Evry-Val d' Essonne
Mireille Régnier , INRIA Rocquencourt
Stefan Engelen , Université d' Evry-Val d' Essonne
pp. 11

Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data (Abstract)

Yu Chen , Oak Ridge National Laboratory and ORNL-UT Graduate School of Genome Science and Technology
Dong Xu , Oak Ridge National Laboratory and ORNL-UT Graduate School of Genome Science and Technology
Trupti Joshi , Oak Ridge National Laboratory and ORNL-UT Graduate School of Genome Science and Technology
Ying Xu , Oak Ridge National Laboratory and ORNL-UT Graduate School of Genome Science and Technology
pp. 18

Prediction of Contact Maps Using Support Vector Machines (Abstract)

George Karypis , University of Minnesota
Ying Zhao , University of Minnesota
pp. 26
Bioeng-1: Biomedical Data Engineering

Analysis of Atlantic Salmon Skin Mucus: COPS — A Computer-Based System for Protein Pattern Analysis of 1D SDS-PAGE Gels (Abstract)

Bing Wu , Dublin Institute of Technology
Paul Kennedy , Dublin Institute of Technology
Deirdre Cotter , Marine Institute
Ursula MacEvilly , Dublin Institute of Technology
Richard Eibrand , Dublin Institute of Technology
pp. 45

An Open Multiple Instance Learning Framework and Its Application in Drug Activity Prediction Problems (Abstract)

Mei-Ling Shyu , University of Miami
Shu-Ching Chen , Florida International University
Xin Huang , Florida International University
pp. 53

Analysis of Spontaneous Activity in Cultured Brain Tissue Using the Discrete Wavelet Transform (Abstract)

D. Plenz , National Institutes of Health
N. Miltner , University of Toledo
W. Li , University of Toledo
J. Beggs , National Institutes of Health
J. D. Johnson , University of Toledo
K. Owen , University of Toledo
M. Mieier , University of Toledo
pp. 60
Bioinfo-2: Phylogenetic Trees

An Empirical Comparison of Tools for Phylogenetic Footprinting (Abstract)

Mathieu Blanchette , University of Washington
Samson Kwong , University of Washington
Martin Tompa , University of Washington
pp. 69

An Investigation of Phylogenetic Likelihood Methods (Abstract)

Bernard M.E. Moret , University of New Mexico
Tiffani L. Williams , University of New Mexico
pp. 79

Nodal Distance Algorithm: Calculating a Phylogenetic Tree Comparison Metric (Abstract)

Dong-Guk Shin , University of Connecticut
John Bluis , University of Connecticut
pp. 87

A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees (Abstract)

Michael Hu , University of Waterloo
Jonathan Badger , Caprion Pharmaceuticals
Paul Kearney , Caprion Pharmaceuticals
pp. 95
Bioeng-2: Medical Image Processing I

Comparison of Bicubic and Bézier Polynomials for Surface Parameterization in Volumetric Images (Abstract)

Cemil Kirbas , Wright State University
Vishwas Kulkarni , Wright State University
Francis Quek , Wright State University
pp. 107

Evolving Bubbles for Prostate Susrface Detection from TRUS Images (Abstract)

Fan Shao , Nanyang Technological University
Wan Sing NG , Nanyang Technological University
Leck Voon Ling , Nanyang Technological University
pp. 115

Respiratory Gating for MRI and MRS in Rodents (Abstract)

Joel R. Garbow , Washington University at St.Louis
Joseph P. Dugas , Washington University at St.Louis
Mark S. Conradi , Washington University at St.Louis
pp. 126
Bioinfo-3: Bio-Databases I

A Novel Laboratory ersion Management System for Tracking Complex Biological Experiments (Abstract)

Nicole Lam , University of New South Wales
Raymond K. Wong , University of New South Wales
William M. Shui , University of New South Wales
pp. 133

Requirements of Phylogenetic Databases (Abstract)

Francois Barbancon , University of Texas at Austin
William H. Piel , University of Buffalo
Luay Nakhleh , University of Texas at Austin
Michael Donoghue , Yale University
Daniel Miranker , University of Texas at Austin
pp. 141

Filtration of String Proximity Search via Transformation (Abstract)

S. Alireza Aghili , University of California at Santa Barbara
Amr El Abbadi , University of California at Santa Barbara
Divyakant Agrawal , University of California at Santa Barbara
pp. 149
Bioeng-3: Biomedical Imaging, Signaling, and Computation

Vessel Extraction in Medical Images by 3D Wave Propagation and Traceback (Abstract)

Francis K. H. Quek , Wright State University
Cemil Kirbas , Wright State University
pp. 174

A New Approach to Detect Similar Proteins from 2D Gel (Abstract)

Nawaz Khan , Middlesex University
Shahedur Rahman , Middlesex University
pp. 182

A Robotic Device for Minimally Invasive Breast Interventions with Real-Time MRI Guidance (Abstract)

Blake T. Larson , University of Minnesota
Nikolaos V. Tsekos , Washington University at St. Louis
Arthur G. Erdman , University of Minnesota
pp. 190
Bioinfo-4: Sequences and Searching

An Algorithm to Reconstruct a Target DNA Sequence from Its Spectrum Connected at a Given Level (Abstract)

Wen-Jun Zhang , University of Saskatchewan
Fang-Xiang Wu , University of Saskatchewan
Anthony J. Kusalik , University of Saskatchewan
pp. 201

A Model of Random Sequences for <i>de novo</i> Peptide Sequencing (Abstract)

Alejandro Heredia-Langner , Pacific Northwest National Laboratory
Kenneth D. Jarman , Pacific Northwest National Laboratory
Kristin H. Jarman , Pacific Northwest National Laboratory
William R. Cannon , Pacific Northwest National Laboratory
pp. 206
Bioeng-4: Medical Image Processing II

Determining the Asymmetries of Skin Lesions with Fuzzy Borders (Abstract)

Vincent T. Y. Ng , Hong Kong Polytechnic University
Benny Y. M. Fung , Hong Kong Polytechnic University
Tim Lee , British Columbia Cancer Agency
pp. 223

Vessel Extractio Techniques and Algorithms: A Survey (Abstract)

Francis K. H. Quek , Wright State University
Cemil Kirbas , Wright State University
pp. 238

Prostate Gland and Extra-Capsular Tissue 3D Reconstruction and Measurement (Abstract)

Jennifer Seevinck , Old Dominion University
Frederic (Rick) McKenzie , Old Dominion University
Rania Hussein , Old Dominion University
Paul Schellhammer , Eastern Virginia Medical School
Jose Diaz , Eastern Virginia Medical School
pp. 246
Bioinfo-5: Bio-Databases II

Streamlining Biological Data Analysis Using BioFlow (Abstract)

Zhijie Guan , Mississippi State University
Hasan M. Jamil , Mississippi State University
pp. 258

BioSeek: Exploiting Source-Capability Information for Integrated Access to Multiple Bioinformatics Data Sources (Abstract)

Henrique Paques , Georgia Institute of Technology
Dan Rocco , Georgia Institute of Technology
David Buttler , Georgia Institute of Technology
Ling Liu , Georgia Institute of Technology
Calton Pu , Georgia Institute of Technology
Terence Critchlow , Lawrence Livermore National Laboratory
Wei Han , Georgia Institute of Technology
pp. 263
Bioeng-5: Biological Systems and Models

A Biological Mapping of a Learned Avoidance Behavior Model to the Basal Ganglia (Abstract)

Kevin M. Biddell , University of Toledo
Jinghong Li , Countrywide Mortgage Co.
Jeffrey D. Johnson , University of Toledo
pp. 276

Influence of the Thermal Treatment Applied to PAN Gel on Its Length Change and Genrated Force (Abstract)

Toyotaka Watanabe , Gifu University
Suzana Popovic , University of Washington
Fumio Nogata , Gifu University
Akinori Abe , Gifu University
Hiroshia Tamagawa , Gifu University
pp. 281
Panel
Bioinfo-6: Gene Expressions

Analyzing the <i>Escherichia coli</i> Gene Expression Data by a Multilayer Adjusted Tree Organizing Map (Abstract)

Le Gruenwald , University of Oklahoma
Tyrrell Conway , University of Oklahoma
Ning Wei , University of Oklahoma
pp. 289

A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome (Abstract)

Cheng-Yan Kao , National Taiwan University
Huei-Lin Chang , Yuan-Ze University Taiwan
Hsien-Da Huang , National Central University
Jorng-Tzong Horng , National Central University
Baw-Jhiune Liu , Yuan-Ze University
Tsung-Shan Tsou , National Central University
pp. 297

Time Series Analysis of Gene Expression and Location Data (Abstract)

Chen-Hsiang Yeang , Massachusetts Institute of Technology
Tommi Jaakkola , Massachusetts Institute of Technology
pp. 305

Regulating Gene Expression Using Optimal Control Theory (Abstract)

Yunlong Liu , Indiana University-Purdue University Indianapolis and Purdue University
Hui Bin Sun , Indiana University-Purdue University Indianapolis at Indiana University School of Medicine
Hiroki Yokota , Indiana University-Purdue University Indianapolis, Purdue University and Indiana University School of Medicine
pp. 313
Bioinfo-7: Clustering Algorithms and Molecular Structures

Enhanced Biclustering on Expression Data (Abstract)

Haixun Wang , IBM T.J.Watson
Wei Wang , University of North Carolina at Chapel Hill
Philip Yu , IBM T.J.Watson
Jiong Yang , University of Illinois at Urbana-Champaign
pp. 321

Hierarchical Clustering of Gene Expression Data (Abstract)

Feng Luo , University of Texas at Dallas
Kun Tang , University of Texas at Dallas
Latifur Khan , University of Texas at Dallas
pp. 328

Augmenting SSEs with Structural Properties for Rapid Protein Structure Comparison (Abstract)

Zhiyong Huang , National University of Singapore
Chern-Hooi Chionh , National University of Singapore
Kian-Lee Tan , National University of Singapore and Genome Institute of Singapore
Zhen Yao , National University of Singapore
pp. 341
Bioinfo-8: Bio-Databases III

Load Balancing: A Case Study of a Pharmaceutical Drug Candidate Database (Abstract)

S. Li , National Center for Genome Resources
J. Martin , Eli Lilly and Company
Z. Ben Miled , Indiana University-Purdue University Indianapolis
R. J. Oppelt , Eli Lilly and Company
O. Bukhres , Indiana University Purdue University Indianapolis
C. Balagoplakrishna , Eli Lilly and Company
pp. 351

An Assessment of a Metric Space Database Index to Support Sequence Homology (Abstract)

Daniel P. Miranker , University of Texas at Austin
Weijia Xu , University of Texas at Austin
Neha Singh , University of Texas at Austin
Rui Mao , University of Texas at Austin
pp. 375
Bioinfo-9: Clustering Algorithms

DHC:A Density-Based Hierarchical Clustering Method for Time Series Gene Expression Data (Abstract)

Aidong Zhang , State University of New York at Buffalo
Jian Pei , State University of New York at Buffalo
Daxin Jiang , State University of New York at Buffalo
pp. 393

Determination of the Minimum Sample Size in Microarray Experiments to Cluster Genes Using K-means Clustering (Abstract)

Anthony J. Kusalik , University of Saskatchewan
Wen-Jun Zhang , University of Saskatchewan
Fang-Xiang Wu , University of Saskatchewan
pp. 401

A Repulsive Clustering Algorithm for Gene Expression Data (Abstract)

Shiuan-Sz Wang , National Taipei University of Technology
Chyun-Shin Cheng , Tung Nan Institute of Technology
pp. 407
Bioinfo-10: Prediction, Simulation and Mining Models

Uses of Multiagents Systems for Simulation of MAPK Pathway (Abstract)

Vincent Rodin , Laboratoire d'Informatique Indistrielle
Jacques Tisseau , Laboratoire d'Informatique Indistrielle
Gabriel Querrec , Laboratoire d'Informatique Indistrielle
Jean François Abgrall , Laboratoire d'hématologie
Sébastien Kerdelo , Laboratoire d'Informatique Indistrielle
pp. 421

A Framework for Cancer-Related Genes Mining over the Internet (Abstract)

S. N. Chen , Taichung Healthcare & Management University
F. M. Liu , Taichung Healthcare & Management University
W. L. Chan , China Medical College Hospital
R. M. Hu , Taichung Healthcare & Management University
Jeffrey J. P. Tsai , University of Illinois
M. M. Lee , Taichung Healthcare & Management University
S. H. Shih , Taichung Healthcare & Management University
J. G. Chang , China Medical College Hospital
R. M. Chen , Taichung Healthcare & Management University
H. W. Hsiao , Taichung Healthcare & Management University
pp. 426

Predictive Model for Yeast Protein Functions Using Modular Neural Approach (Abstract)

William I. Grosky , University of Michigan-Dearborn
Russell L. Finley Jr. , Wayne State University
Farshad Fotouhi , Wayne State University
Doosung Hwang , Wayne State University
pp. 436
Author Index

Author Index (PDF)

pp. 441
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