UPDATE: CBGI-2001 (Atlantic Symposium on Computational Biology and Genome Information Systems & Technology)

[Cathy Wu]

********* CBGI-2001 ********* 
Atlantic Symposium on Computational Biology and Genome Information
Systems & Technology
March 15-17, 2001, Regal University Center, Durham, N.C., USA
http://www.ee.duke.edu/cbgi/

*** ANNOUNCEMENT OF FINAL PROGRAM ***
http://www.ee.duke.edu/CBGI/program.pdf


Thursday, March 15, 2001

8:30 a.m. - 10:00 a.m. 
REGISTRATION

10:05 a.m. - 10:20 a.m. 
WELCOME:
Dr. Kristina Johnson 
Dean, Pratt School of Engineering, Duke University
Chair: Dr. Howard Clark

10:20 a.m. - 12:00 noon 
Morning Sessions (I and II)

TA-I: DATA MINING IN BIOINFORMATICS
Session Chair: Xiong Wang, California State University at Fullerton,
USA

A Clustering Method Based On Rough Sets And Its Application To
Biochemical Data Analysis
Shoji Hirano, Himeji Institute of Technology, Japan
Tomohiro Okuzaki, Himeji Institute of Technology, Japan
Yutaka Hata, Himeji Institute of Technology, Japan
Shusaku Tsumoto, Shimane Medical University, Japan
Kouhei Tsumoto, Tohoku University, Japan

A Lexical Approach to Text Mining for the Integration of Genomic
Information
Lauren Harrison, Hoffmann-La Roche, Inc., USA
Peter Borgulya, Hoffmann-La Roche, Inc., USA
Olivier Jouve, LexiQuest, USA
Brian Simblist, LexiQuest, USA

Creating Metabolic Network Models using Text Mining and Expert
Knowledge
J. A. Dickerson, Iowa State University, USA
D. Berleant, Iowa State University, USA
Z. Cox, Iowa State University, USA
W. Qi, Iowa State University, USA
E. Wurtele, Iowa State University, USA

Analyzing Protein Surface for Classification: A Geometric Hashing
Approach
Xiong Wang, California State University at Fullerton, USA
Jason T. L. Wang, New Jersey Institute of Technology, USA

TA-II (INVITED SESSION)
Session Chair: Cathy Wu, Director of Bioinformatics, National
Biomedical Research Foundation 

Extracting and Recording Bio-signatures from In vivo Cells using the
L-G Graph
Nikolaos Bourbakis, Director of the Information Technology Research
Institute, Wright State University

Gene Annotation: Some Nasty Facts from the Pre-mRNA Splicing Field
Stephen M. Mount, Associate Professor, Dept. of Cell Biology and
Molecular Genetics, University of Maryland

Prediction of Protein Structure and Function - A Case study of
Envelope Glyco-protein of JE Virus
Ashok Kolaska, Director of Bioinformatics, American Type Culture
Collection

Networks of Small, Dispersed, Interrelated Databases: A Viable
Complement to Large Stand Alone Databases?
Mark Danielsen, Associate Professor, Dept. of Biochemistry and
Molecular Biology, Georgetown University Medical Center

12:00 noon - 1:15 p.m. 
LUNCH ON YOUR OWN

1:15 p.m. - 2:00 p.m.
PLENARY SPEECH:  
Steven L. Salzberg
Senior Director of Bioinformatics, The Institute for Genomic Research 
"Algorithms for Whole Genome Analysis"
Chair: Bruno Sobral, Director, Virginia Bioinformatics Institute, VPI

2:00 p.m. - 3:00 p.m.
KEYNOTE SPEECH:  
Jeffrey M. Trent, Ph.D.
Director, Division of Intramural Research, Chief, Cancer Genetics
Branch, NIH/National Human Genome Research Institute
"Applying Gene Expression Profiling to the Discovery of Cancer Causing
Genes."
Chair: Alexander Shenderov

3:00 p.m. - 3:20 p.m.
COFFEE BREAK

3:20 p.m. - 5:20 p.m. 
Afternoon  Sessions (I, II, and III)

TP-I (INVITED SESSION): PLANT GENOMICS
Session Chair: Dr. Xi Chen, Syngenta (formerly Novartis)

Functional Genomics of Plant Fungal Pathogen.
Stephen Lam, Fungal Targets Group, Syngenta

Application of Model System Genetics and Genomics to Target Based
Pesticide Development
Kim Kamdar, Insect Targets Group, Syngenta

Herbicide Discovery Via Identification of Essential Genes in
Arabidopsis
Joshua Levin, Plant Targets Group, Syngenta

Gene Expression Analysis of a Plant Defense Response; from Profiles to
Promoter Elements.
Bob Dietrich, Natural Resistance Groups, Syngenta

Transcriptional Profiling and Gene Function Discovery with Plant Viral
Vectors
Yijun Ruan,  Sr. Group Leader Of  Genomic Technology, Large Scale
Biology
Corporation

TP-II (INVITED SESSION): ALGORITHMS AND TOOLS FOR MINING BIOLOGICAL
DATA, PART I
Session Chairs: Gautam B. Singh, Oakland Univ., Rochester, MI, USA and
Cliff Cunningham, Duke Univ.

Expressed Sequence Tag Data Mining: The Reality of Virtual Gene
Expression.
Sorin Draghici, Rui P. Martins, Richard E. Leach, and Stephen A.
Krawetz, Wayne State University, School of Medicine, Detroit, MI, USA

Text Mining and Genomic Database Retrieval: Is there a Connection?
Donglin Liu and Gautam Singh, Oakland University, Rochester, MI, USA

Large-Scale Promoter Prediction: Results On The Human Genome And
Consequences For Large-Scale SNP Analysis.
Tom Werner, Genomatix, Germany

Stochastic Modeling of Protein Sequence and Structure
Scott Schmidler, Duke University

TP-III: PROTEIN MOTIF ANALYSIS AND PATTERN DISCOVERY
Chair: Ashok Kolaska, Director of Bioinformatics, American Type
Culture Collection

Data-Driven Generation of Decision Trees for Motif-Based Assignment of
Protein Sequences to Functional Families
Dake Wang, Xiangyun Wang, Vasant Honavar and Drena L. Dobbs

Towards a Comprehensive Collection of Diagnostic Patterns for Protein
Sequence Classification
Bjorn Olsson and Kim Laurio

Association between Statistical and Functional Patterns in
Biomolecules
David K.Y. Chiu, Xin Chen, and Andrew K.C. Wong

Molecular Modeling of Human DNA Repair Protein and Helicase, XPD
(Xeroderma Pigmentosum 
Group D)
Rachelle Bienstock and Bennett Van Houten

Consigned Interdependency for Pattern Discovery from Biomolecular
Sequences
David K.Y. and Thomas W.H. Lui

5:30 p.m. - 6:15 p.m.
PLENARY SPEECH:  
Bruce Shapiro, Ph.D.
Laboratory of Experimental and Computational Biology, National Cancer
Institute, NIH, USA
"Computational Insights into RNA Folding Pathways: Getting from Here
to There"
(Additional Authors: David Bengali, Wojciech Kasprzak, Jin Chu Wu)
Chair: TBA

6:30 p.m. - 7:15 p.m. 
CASH BAR

7:15 p.m. - 9:15 p.m.
DINNER BANQUET
Speaker: 
Kenneth R. Tindall, PhD
Senior Executive Vice President, North Carolina Biotechnology Center
Chair: Howard Clark, Duke University


Friday, March 16, 2001

8:15 a.m. - 9:00 a.m. 
PLENARY SPEECH:
Stephen Altschul
Senior Investigator, National Center for Biotechnology Information,
National Library of Medicine, National Institutes of Health
"Iterated Profile Searches with PSI-BLAST"
Chair: Simon Lin, Duke Univ. Med. Cen.

9:00 a.m. - 10:00 a.m.
KEYNOTE SPEECH:
Joseph Nevins, Ph.D.
James B. Duke Professor, Duke University
Chair: Ron Yager, Iona College

10:00 a.m. - 10:20 a.m.
COFFEE BREAK

10:20 a.m. - 12:00 noon 
Morning Sessions (I and II)

FA-I: FUZZY COMPUTING IN BIOMEDICAL APPLICATIONS
Session Chair: H. D. Cheng, Utah State University, USA

Two-layer Fuzzy Relational Networks: Some Preliminary Results
A. Ciaramella, University of Salerno, Italy)
W. Pedrycz, University of Edmonton, Canada)
R. Tagliaferri, University of Salerno, Italy)

Fuzzy Similarity Measures and Tree Comparison
R. De Sutter, Ghent University, Belgium)
H. De Meyer, Ghent University, Belgium)
B. De Baets, Ghent University, Belgium)
H. Naessens, Hogeschool Gent, Belgium)

Towards the Use of Nearest Neighbor Rules in Bioinformatics
Ronald R. Yager, Iona College, USA

Mammogram Contrast Enhancement Using a Novel Fuzzy Homogeneity Measure
H. D. Cheng, Utah State University, USA)
M. Xue, Utah State University, USA)
R. Freimanis, Bowman Gray School of Medicine, USA)

FA-II (INVITED SESSION): BIOINSPIRED SYSTEMS
Session Chair: Dr. Liam P. Maguire, Intelligent Systems Engineering
Laboratory, Magee College, UK

Neural Networks on "Cultured Probe" Micro-Electrode Arrays: Network
Confinement and Activity Patterns
Wim L.C. Rutten, Institute for Biomedical technology, University of
Twente, Enschede, Netherlands)
J. van Pelt, Netherlands Institute for Brain Research, Amsterdam,
Netherlands)

Selection of Behaviors by Their Consequences in the Human Baby,
Software Agents, and Robots
Philippe Preux, Laboratoire d'Informatique du Littoral Calais, France;
Samuel Delepoulle, URECA & LIL, France;  Jean-Claude Darcheville, Unit
é de Recherche sur l'Évolution du Comportement et des Apprentissages
(URECA), Villeneuve d'Ascq, France

Networks of Real Neurons with an Artificial Body
Massimo Grattarola, Marco Bove, Michele Giugliano, Sergio Martinoia,
Neural and Bioelectronic Technologies Group Department of Biophysical
and Electronic Engineering, University of Genoa, Italy

An Approach for the Realisation of Bio-Inspired Systems on
Programmable Logic Devices
B.P. Glackin, L.P. Maguire, T.M. McGinnity, Intelligent Systems
Engineering Laboratory, University of Ulster, UK

12:00 noon - 1:15 p.m. 
LUNCH ON YOUR OWN

1:15 p.m. - 2:00 p.m. 
PLENARY SPEECH:
Mike West
Duke University
 "Statistical Analysis for Clinical Discriminant Using DNA Micro-array
Data.
Chair: Nik Kasabov, University of Otaga

2:00 p.m. - 3:00 p.m. 
KEYNOTE SPEECH:
Russell F. Doolittle
Center for Molecular Genetics, University of California, San Diego, La
Jolla, CA
"Sequences and Computers: A Personal Reflection on the Digital Age"
Chair: Howard Clark

3:00 p.m. - 3:20 p.m. 
COFFEE BREAK

3:20 p.m. - 5:20 p.m. 
Afternoon Sessions (I, II, III)

FP-I: ADVANCES IN BIOCOMPUTING 
Session Chair: Jason T. L. Wang, New Jersey Institute of Technology,
USA

Complementary Retrieval for Distorted Images
Chun-Jiun Liao, Yuan Ze University, Taiwan
Shu-Yuan Chen, Yuan Ze University, Taiwan

An Algorithm for the Approximate String-Matching Problem
Mourad Elloumi, Faculty of Sciences of Tunis, Tunisia

DNA Word Optimization
Horatio Voicu, Duke University, USA

Influence of Linear Gene Regulatory Model-Reverse Engineering by
Genetic Algorithms 
Shin Ando, University of Tokyo, Japan
Hitoshi Iba, University of Tokyo, Japan

Approximate Searching in Phylogenetic Databases
Katherine G. Herbert, New Jersey Institute of Technology, USA
Huiyuan Shan, New Jersey Institute of Technology, USA
Jason T. L. Wang, New Jersey Institute of Technology, USA

FP-II (INVITED SESSION): UNCERTAINTY ANALYSIS AND FUSION METHODOLOGY: 
THEORY AND APPLICATIONS, PART I
Session Chair: Da Ruan, SCK-CEN, Belgium

Fusing Nonmonotonic Knowledge: Preliminary Results
E. Grégoire, France
 
Evidential Analysis in Bioinformatics
D.A. Bell and J.W. Guan, UK

A New Method for Time Series Prediction Combining Neural Networks,
Fuzzy Logic, and Fractal Theory
Oscar Castillo and Patricia Melin, USA

Controlling Electrochemical Processes Using a New Neuro-Fuzzy-Genetic
Approach
Patricia Melin and Oscar Castillo, USA

FP-III: SEQUENCE SEARCH OPTIMIZATION AND MOLECULAR EVOLUTION
Chair: Nikolaos Bourbakis, Director of the Information Technology
Research Institute, Wright State University

An Optimization Approach to Multiple Sequence Alignment: A Preliminary
Report
Fern Y. Hunt and Anthony J. Kearsley

A Learning Algorithm for the Shortest Superstring Problem
Mark K. Goldberg and Darren T. Lim

Statistical Testing for Protein Functional Divergence after Major
Evolutionary Events
Jianying Gu, Yufeng Wang, Xun Gu

Patterns of Functional Divergence after Gene Duplications in
Vertebrate Gene Families: Altered Functional Constraints
Yufeng Wang, Jianying Gu, and Xun Gu

Information Theory, Evolution and the Origin of Life
Hubert P. Yockey

5:20 p.m. - 6:20 p.m.
DINNER 
Attendees are invited to purchase a buffet dinner at the Regal Hotel
and join us for conversation and socializing followed by an
after-dinner speech in the general meeting room. 

6:30 p.m. - 7:15 p.m.
DINNER SPEAKER:
Thomas LaBean 
Duke University
"Meanderings in Sequence Space: Random Evolution and Rational
Engineering of Bio-polymers"
Chair: Jane Richardson, Duke Univ.

7:15 p.m. - 9:15 p.m.
PANEL DISCUSSION:
"The Future of Genomics Research"
Panelists:
Russell Doolittle, University of California, San Diego, La Jolla
Jim Siedow, Duke University
Bruce Shapiro, NCI
Jacob Maizel, NCI
Panel Chair: Jeff Dangl, University of North Carolina


Saturday, March 17, 2001

8:15 - 9:00 a.m. 
PLENARY SPEECH: 
Cathy Wu, Ph.D.
Director of Bioinformatics, National Biomedical Research Foundation,
Georgetown University Medical Center
"Integrated Protein Family Classification for Functional Genomics"
Chair: Nik Kasabov, University of Otago

9:00 - 10:00 a.m. 
KEYNOTE SPEECH: 
Mark Adams, Ph.D.
Vice President, Genome Programs, Celera Genomics, Maryland
"Sequencing and Analysis of the Human Genome"
Chair: Stanley Burt, Advanced Biomedical Computing Center, SAIC

10:00 a.m. - 10:20 a.m.
COFFEE BREAK

10:20 a.m. - 12:00 noon 
Morning Sessions (I and II)

SA-I (INVITED SESSION): COMPUTATIONAL BIOLOGY AT THE NATIONAL CANCER
INSTITUTE, NATIONAL INSTITUTES OF HEALTH, FREDERICK, MARYLAND
Session Chair: Bruce A. Shapiro, National Cancer Institute, NIH, USA

The Role of High Performance Computing in Exploring Structure-Function
Relationships
Stanley Burt, Advanced Biomedical Computing Center, SAIC, USA

Application of Sequence Analysis Pipelining Tools for High-Throughput
Sample Processing at the Biomedical Computing Center
Robert M. Stephens and Gary W. Smythers, Advanced Biomedical Computing
Center, SAIC, USA

Computational Methods in the Analysis of Ligand-Macromolecule Contacts
Nagarajan Pattiraman, Advanced Biomedical Computing Center, SAIC, USA

Dynamic Models of Virus/Cell Turnover in HIV Infections
D.S. Dimitrov, I.A. Sidorov, Laboratory of Experimental and
Computational Biology; Y. Endo, T. Igarashi, M.A. Martin, Laboratory
of Molecular Microbiology; R.A. Lempicki, J. Lifson,  SAIC; J. Kovacs,
Critical Care Medicine Department; R.T. Davey and H.C. Lane,
Laboratory of Immunoregulation

SA-II (INVITED SESSION): UNCERTAINTY ANALYSIS AND FUSION METHODOLOGY: 
THEORY AND APPLICATIONS, PART II
Session Chair: Da Ruan, SCK-CEN, Belgium

Soft Computing Techniques For Speech Recognition
Mike Nachtegael, Martine De Cock, and Etienne E. Kerre, Belgium
 
On the Fusion of Nuclear Safeguards Relevant Information Based on
Weighted Linguistic Aggregation Operators
Da Ruan, Jun Liu, and Roland Carchon, Belgium

Predicting Regulatory Elements in Repetitive Sequences Using
Transcription Factor Binding Sites
Jorng-Tzong Horng, Wen-Fu Cho, and Cheng-Yan Kao National Central
University, Taiwan, ROC

RSDB-A Database of Repetitive Elements in Complete Genomes
Jorng-Tzong Horng, Jia-Hwang Lin, and Cheng-Yan Kao, National Central
University, Taiwan, ROC

SA-III (INVITED SESSION): ALGORITHMS AND TOOLS FOR MINING BIOLOGICAL
DATA, PART II
Session Chair: Gautam B. Singh, Oakland Univ. Rochester, MI, USA

Native Structure and Structure-based design of Phospholipase A2
inhibitors
Punit Kaur, Vikas Chandra, Jayasankar Jasti and Tej P. Singh, All
India Institute of Medical Sciences, New Delhi, India

Design and Implementation of an Introductory Course for Computer
Applications in Molecular Genetics: A Case Study
Stephen A. Krawetz and David D. Womble, Wayne State University, School
of Medicine, Detroit, MI, USA

The Genomics Drug Discovery Connection: Evolutionary Chemistry
Bruce Eaton, Invenux, Inc., Denver, CO

Statistical Mining of S/MAR Database
Swami Ganapathy and Gautam Singh,  Oakland University, Rochester, MI,
USA

12:00 noon -  1:15 p.m.
LUNCH ON YOUR OWN

1:15 p.m. - 2:15 p.m.
PLENARY SPEECH:  
Jacob V. Maizel, Jr.
Laboratory of Experimental and Computational Biology, National Cancer
Institute, NIH, USA
"Computational Discovery of Important Functional and Structural
Features in mRNA Sequences"
(Additional Author: Shu-Yun Le)
Chair: John C. Brockett, EPA

2:15 p.m. - 3:15 p.m.
PLENARY SPEECH:  
Erich Jarvis
"The Importance of Anatomical Substrates"
Chair: Li Chen, North Dakota State University

3:15 - 3:30 p.m.
COFFEE BREAK

3:30 p.m. - 5:30 p.m. 
Afternoon Sessions (I and II)

SP-I (INVITED SESSION): CLASSIFICATION AND PATTERN RECOGNITION OF GENE
EXPRESSION DATA
Session Chair: Etienne E. Kerre, University Gent

Knowledge Based Neural Networks for On-line and Off-line Modeling and
Rule Extraction
Nikola Kasabov, Melanie Middlemiss, Matthias Futschik
Department of Information Science, University of Otago

Class Prediction and Discovery based on Gene Expression Data
Leping Li, National Institute of Environmental Health Sciences;  Lee
G. Pedersen, National Institute of Environmental Health Sciences,
University of North Carolina; Thomas A. Darden, National Institute of
Environmental Health Sciences; and Clarice R. Weinberg, University of
North Carolina

Data Mining in High Dimensionality
Dr. George Karypis, University Minnesota

Who Needs Genomes?
Barry McMullin, Axel von Kamp, Dublin City University, Ireland
Tim Taylor, University of Abertay Dundee, UK

SP-II: GENE EXPRESSION ANALYSIS
Chair: Mark Danielsen, Associate Professor of Biochemistry and
Molecular Biology, Georgetown University Medical Center

Constructing Bayesian Network Models of Gene Expression Networks from
Microarray Data
Peter Spirtes, Richard Scheines, Department of Philosophy, Carnegie
Mellon University; Clark Glymour, Institute for Human and Machine
Cognition;  Stuart Kauffman, Valerio Aimale, Frank Wimberly,  Bios
Group

Temporal Boolean Network Models of Genetic Networks and Their
Inference from Gene Expression Time Series
Adrian Silvescu and Vasant Honavar, Iowa State University

Expressed Sequenced Tag Data Mining: The Reality of Virtual Gene
Expression
Sorin Draghici, Rui P. Martins, Richard E. Leach, and Stephen A.
Krawetz

Mining Association Rules in Analysis of Transcription Factors
Essential to Gene Expressions
Ruzhu Chen, Qiyou Jiang, Honglin Yuan and Le Gruenwald, University of
Oklahoma

END OF CONFERENCE

-- 
Cathy H. Wu, Ph.D.
CBGI-2001 Co-Organizer
National Biomedical Research Foundation
Georgetown University Medical Center
3900 Reservoir Road, NW, Washington, DC 20007-2195
Phone: (202)687-2121; Fax: (202)687-1662
Email: wuc at nbrf.georgetown.edu


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