Created: 28th February 1999, last updated: 7th April 1999, © 1999 ABRF

SATURDAY, MARCH 20

Plenary Session 1: Genomes and Function

Chair: Kenneth A. Walsh (University of Washington, Seattle, WA)

Russell F. Doolittle (University of California, San Diego, CA)--"A Decade of Genomics"

Michael Y. Galperin (National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD)--"Hits and Misses in Functional Genomics: First Lessons From a Comparison of Bacterial and Archaeal Protein Sequences"

Scientific Session 1: Bioinformatics: Macromolecular Structure Databases

Chair: Helen M. Berman (Rutgers University, Piscataway, NJ)

Helen M. Berman (Rutgers University, Piscataway, NJ)--"Our Vision and Implementation for the New PDB"

Phil Bourne (University of California, San Diego, CA)--"PDB Live!"

Scientific Session 2: Technological Advances: DNA Sequence Analysis

Chair: Paul Matsudaira (MIT, Cambridge, MA)

Paul Matsudaira (MIT, Cambridge, MA)--"Ultrafast DNA Genotyping and Sequencing on Microfabricated Devices"

Barry L. Karger (Northeastern University, Boston, MA)--"DNA Analysis by Capillary Array Electrophoresis: Long-Range Sequencing and Automated Fraction Collection"

Richard A. Mathies (University of California, Berkeley, CA)--"Microfabricated DNA Analysis Systems"

Research Group Presentations

Group Session 1:  Nucleic Acids

Group Session 2:  DNA Sequence

Group Session 3:  Protein Sequence

Group Session 4:  Internal Protein Sequence

Group Session 5:  Peptide Synthesis

Scientific Session 3: Functional Analysis: Gene Array Expression Analysis

Chair: John Quackenbush (The Institute for Genome Research, Rockville, MD)

John Quackenbush (The Institute for Genome Research, Rockville, MD)--"Evaluation of Differential Expression Patterns in Highly Metastatic Human Colon Tumor Cells Using a cDNA Microarray System"

Michael Bittner (NHGRI, National Institutes of Health, Bethesda, MD)--"Expression Profiling: A First Look at the Cell as a System"

Janet A. Warrington (Affymetrix Inc., Santa Clara, CA)--"Mars and Venus on Chips: Measuring Variation in Expression in Normal Human Tissues"

Scientific Session 4: Technological Advances: Mass Spectrometry of Proteins

Chair: Karl Clauser (Millenium Pharmaceuticals, Inc., Cambridge, MA)

Karl Clauser (Millennium Pharmaceuticals, Inc., Cambridge, MA)--"Using Automated LC/MS/MS on Digests of Complex Protein Mixtures: Can One Get Identities and Differences?"

Rachel R. Ogorzalek Loo (Parke-Davis Pharmaceutical, Ann Arbor, MI)--"Virtual 2-D Gel Electrophoresis: Visualization and Analysis of the E. coli Proteome by Mass Spectrometry"

Tutorial Session 1: Bioinformatics and Education

Chair: Chuck Staben (University of Kentucky, Lexington, KY)

Chuck Staben (University of Kentucky, Lexington)--"Genomics and Bioinformatics Instruction: Challenges and Initiatives"

Donald O. Natvig (University of New Mexico, NM)--"The Neurospora Genome Project at the University of New Mexico"

Bettie J. Graham (National Human Genome Research Institute, Bethesda, MD)--"Genome Research Training and Career Development"

Tutorial Session 2: Practical Uses of Internet Tools

Chair: Ken Mitchelhill (The John Holt Protein Structure Laboratory, Victoria, Australia)

Johanna R. McEntyre (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD)--"Development of New Text-Search Methods and Their Use for the Integration of Bioinformatics Information Resources"

Ken I. Mitchelhill (The John Holt Protein Structure Laboratory, Victoria, Australia)--"Sequence Database Searching Using Short Query Sequences

Richard S. Johnson (Immunex Corporation, Seattle, WA)--"Internet Tools for the Analysis of Mass Spectrometry Data"

Tutorial Session 3: Genotyping in a Shared Facility

Chair: Duane Bartley (Johns Hopkins University, Baltimore, MD)

Duane A. Bartley (Johns Hopkins University, Baltimore, MD)--"Fragment Analysis: It's Not Just for Genotyping Anymore!"

Linda W. Ballard (University of Utah, Salt Lake City, UT)--"Genotyping: Real Projects, Real Problems"

SUNDAY, MARCH 21

Plenary Session 2: Chromatin Structure and Gene Regulation

Chair: David Landsman, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD)

C. David Allis (University of Virginia, Charlottesville, VA)--"Linking Histone Modifications to Gene Activation"

Alan P. Wolffe (National Institutes of Health, Bethesda, MD)--"Chromatin Control of Transcription"

ABRF Award Presentation

Awardee: Marvin H. Caruthers (University of Colorado, Boulder, CO)--"Synthesis of Oligonucleotides and Oligonucleotide Analogs"

Scientific Session 5: Gene Identification: Identifying Gene Products and Protein Motifs

Chair: Andreas Baxevanis (National Institutes of Health, Bethesda, MD)

Andreas D. Baxevanis (National Institutes of Health, Bethesda, MD)--"Protein Sequence Analysis: BLAST and Beyond"

Christopher W. V. Hogue (University of Toronto, Toronto, Canada)--"Protein Structure Analysis: Databases, Visualization, and Prediction"

Scientific Session 6: Bioinformatics: Large Scale DNA Sequencing: The Pyrococcus furiosus Genome Project

Chair: Robert Weiss (University of Utah, Salt Lake City, UT)

Robert Weiss (University Of Utah, Salt Lake City, UT)--"The Genome Sequence of a Hyperthermophilic Archaeon: Pyroccoccus furiosus"

Dennis L. Maeder (UMBI, Baltimore, MD)--"Genome Comparison Using CROSS"

Research Group Presentations

Group Session 6:  Fragment Analysis

Group Session 7:  Survey Committee

Group Session 8:  Mass Spectrometry

Group Session 9:  Quality and Compliance

Group Session 10:  Education

Scientific Session 7: Gene Identification: Software Methods for Finding Genes in Large DNA Sequences

Chair: Warren Gish (Washington University School of Medicine, St. Louis, MO)

Warren Gish (Washington University School of Medicine, St. Louis, MO)--"Analysis and Annotation of the Human Genome"

Christopher Burge (MIT, Cambridge, MA)--"Combining Intrinsic and Extrinsic Information to Identify Genes"

Scientific Session 8: Functional Analysis: Posttranslational Modifications

Chair: Ken Walsh (University of Washington, Seattle, WA)

Kenneth A. Walsh (University of Washington, Seattle, WA)--"The Need for Analysis of Posttranslational Modifications"

Matthew C. Posewitz (Memorial Sloan-Kettering Cancer Center, New York, NY)--"Selective Purification of Phosophopeptides for Mass Spectrometric Analysis"

Hsieng Lu (Amgen Inc., Thousand Oaks, CA)--"Analysis of Complex Disulfide Bridges by Mass Spectrometry in Conjunction With Chemical Methods"

Tutorial Session 4: DNA Sequence Analysis in a Core Laboratory

Chair: Theodore Thannhauser (Cornell University, Ithaca, NY)

Theodore W. Thannhauser (Cornell University, Ithaca, NY)--"DNA Sequencing in a University-Based Core Facility: Automating the Process"

George S. Grills (Albert Einstein College of Medicine, Bronx, NY)--"Optimizing DNA Sequencing Quality and Throughput"

Tutorial Session 5: Characterization of Biotechnology Pharmaceuticals

Chair: Elizabeth Fowler (AutoImmune Inc., Lexington, KY)

Elizabeth Fowler (AutoImmune, Inc., Lexington, KY)--"Aspects to Consider in Characterizing Biopharmaceutical Proteins"

Eric W. Kuhn (AutoImmune, Inc., Lexington, KY)--"Characterization of Collagen, a Natural Product Biopharmaceutical"

Kalyan Rao Anumula (SmithKline Beecham, King of Prussia, PA)--"Approaches to Characterization of the Carbohydrate Moieties of Glycoproteins"

Tutorial Session 6: Practical Aspects of Mass Spectrometry

Chair: Roland Annan (SmithKline Beecham, King of Prussia, PA)

Roland S. Annan (Smith Kline Beecham, King of Prussia, PA) and Paul Tempst (Memorial Sloan-Kettering Cancer Center, New York, NY)--"Practical Considerations for Obtaining Usable Mass Spectral Data"

MONDAY, MARCH 22

Plenary Session 3: New and Emerging Techniques in Structural Biology

Chair: Paul Matsudaira (MIT, Cambridge, MA)

David C. Schwartz (New York University, New York, NY)--"Optical Mapping: A Complete System for Whole-Genome Shotgun Mapping"

Joachim Frank (Wadsworth Center, Albany, NY)--"Structure and Function of the Ribosome as Explored by Three-Dimensional Cryo-electron Microscopy"

Scientific Session 9: Technological Advances: Recent Advances in Synthetic Protein Construction and Utility

Chair: Gregg Fields (Florida Atlantic University, Boca Raton, FL)

Gregg Fields (Florida Atlantic University, Boca Raton, FL)--"Are There Simple Methods for Creating Protein-Like Architectures?"

Kevin H. Mayo (University of Minnesota, Minneapolis, MN)--"Design and Structural Analysis of alpha-Sheet-Forming Peptides"

Scientific Session 10: Gene Identification: Comprehensive Gene Mapping and Single Nucleotide Polymorphisms

Chair: Tara Matise (Rockefeller University, New York, NY)

Tara Matise (Rockefeller University, New York, NY)--"Construction of Dynamic Chromosome Maps"

Eric Lai (GlaxoWellcome Inc., Research Triangle Park, NC)--"Large-Scale SNP Discovery and Their Use in Complex Disease Gene Identification"

Scientific Session 11: Bioinformatics: Database Design and Sequence Annotation

Chair: B. F. Francis Ouellette (University of British Columbia, Vancouver, Canada)

B. F. Francis Ouellette (University of British Columbia, Vancouver, Canada)--"GenBank"

Ilene Mizrachi (NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD)--"Data Flow at NCBI"

Scientific Session 12: Functional Analysis: Protein Identification Using Mass Spectrometry

Chair: John T. Stults (Genentech, Inc., San Francisco, CA)

Leigh Anderson (Large Scale Biology Corp., Rockville, MD)--"Pharmaceutical Proteomics: Targets, Functions, and Mechanisms"

Hanno Langen (F. Hoffmann-La Roche AG, Basel, Switzerland)--"Combination of Mass Spectrometry and 2D Electrophoresis: Powerful Tools for Biological Experiments"

Ruedi Aebersold (University of Washington, Seattle, WA)--"The Proteome: Analysis and Utility"

Tutorial Session 7: Implementing Genechip Microarrays in Facility Laboratories

Chair: George Grills (Albert Einstein College of Medicine, Bronx, NY)

George S. Grills (Albert Einstein College of Medicine, Bronx, NY)--"Problems and Pleasures of Implementing Microarray Technologies"

Aldo B. Massimi (Albert Einstein College of Medicine, Bronx, NY)--"Implementation of a Custom cDNA Microarray Facility at AECOM"

Hans Albertsen (Huntsman Cancer Institute, Salt Lake City, UT)--"Macroarrays in a Shared Facilty: Practical and Scientific Experiences From the Huntsman Cancer Institute"

Suzanne Sandmeyer (University of California College of Medicine, Irvine, CA)--"A User's-Eye View of the Affymetrix Gene Expression System: The Early Days"

Tutorial Session 8: Protein Identification in Gels and Database Handling

Chair: Len Packman (University of Cambridge, Cambridge, UK)

Scott D. Patterson (Amgen Inc., Thousand Oaks, CA)--"Experiences With the Use of the LCQ Ion Trap Mass Spectrometer for Protein Identification"

Len C. Packman (University of Cambridge, Cambridge, MA)--"Browsing MS Data: Compiling Results and Sharing Information Through a Web-Based Electronic Notebook"

Tutorial Session 9: Integration of Bioinformatics and the Chemistry Shared Resource

Chair: Clayton Naeve (St. Jude Children's Research Hospital, Memphis, TN)

Clayton Naeve (St. Jude Children's Research Hospital, Memphis, TN)--"Integrating Bioinformatics and the Chemistry Shared Resource"

Elizabeth A. Greene and Mary Kay Dolejsi (Fred Hutchinson Cancer Research Center, Seattle, WA)--"It Flows Both Ways: How the Chemistry Core Informs Bioinformatics"

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