From owner-bionews@hgmp.mrc.ac.uk Thu Jan 25 17:18:31 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3361D17B28; Thu, 25 Jan 2001 17:18:25 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6022) id 6250517B48; Thu, 25 Jan 2001 17:18:20 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 3E3C517C15; Wed, 24 Jan 2001 21:51:08 +0000 (GMT) To: bionet-announce@net.bio.net From: wuc@NBRF.Georgetown.Edu (Cathy Wu) Newsgroups: bionet.announce Subject: UPDATE: CBGI-2001 (Atlantic Symposium on Computational Biology and Genome Information Systems & Technology) Organization: National Biomedical Research Foundation Message-ID: <3A6F4D33.2566BC33@nbrf.georgetown.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1569A17C14; Wed, 24 Jan 2001 21:51:00 +0000 (GMT) X-Received: from nbrf.georgetown.edu (nbrf.georgetown.edu [141.161.237.70]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C92F241682 for ; Wed, 24 Jan 2001 21:50:04 +0000 (GMT) X-Received: from nbrf1.nbrfnet.georgetown.edu by NBRF.Georgetown.Edu (PMDF V5.2-31 #34596) with ESMTP id <01JZAJCFBKGW9FM94N@NBRF.Georgetown.Edu> for bionews@net.bio.net; Wed, 24 Jan 2001 16:45:05 -0400 (EDT) X-Received: from NBRF1/SpoolDir by nbrf1.nbrfnet.georgetown.edu (Mercury 1.48) ; Wed, 24 Jan 2001 16:46:38 -0500 X-Received: from SpoolDir by NBRF1 (Mercury 1.48); Wed, 24 Jan 2001 16:46:31 -0500 X-Received: from nbrf.georgetown.edu (141.161.236.227) by nbrf1.nbrfnet.georgetown.edu (Mercury 1.48) with ESMTP; Wed, 24 Jan 2001 16:46:29 -0500 X-To: bionews@net.bio.net X-Reply-To: wuc@NBRF.Georgetown.Edu X-Mailer: Mozilla 4.76 [en] (WinNT; U) X-Accept-Language: en,pdf Date: Thu, 25 Jan 2001 17:18:20 +0000 (GMT) Sender: owner-bionews@hgmp.mrc.ac.uk Precedence: bulk ********* 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@nbrf.georgetown.edu --- .