Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Informatics

The GDB Human Genome Data Base Version 6.0
Kenneth H. Fasman, A. Jamie Cuticchia, and David T. Kingsbury

Data Acquisition and Curation Operations for the GDB Human Genome Data Base
A. Jamie Cuticchia, Michael A. Chipperfield, Christopher J. Porter, and C. Conover Talbot Jr.

Architecture of the Genome Data Base Version 6.0
Peter Li, David D. Marquette, Christopher W. Brunn, and Kenneth H. Fasman

The Genome Sequence Data Base (GSDB)
Jillian Burton, Michael J. Cinkosky, David Crowley, Ada Espinosa-Lujan, James W. Fickett, Timothy Gray, Carol Harger, Mohamad Ijadi, Gifford Keen, Michelle March, Mia McLeod, John O'Neill, Alicia Power, Mana Pumilia, David Rider, Jolene Schwertfeger, Nina Thayer, Jennifer Tipton, Charles D. Troup and Shahar Tsadeek

Algorithms in Support of the Human Genome Project
Dan Gusfield, John Kececioglu, R. Ravi, Jim Knight, Gene Lawler, and Archie Cobbs

Software Tools in Support of Physical Mapping efforts at LANL

• GRAM (Genomic Restriction map AsseMbly)
  Soderlund, C., and L. P. MacGavran
• MAP
  Mundt, M.
• SIGMA (System for Integrated Map Assembly)
  Cinkosky, M. J., M. A. Bridgers, W. M. Barber, C. D. Troup, M. Ijadi and J. W. Fickett
• Chromosome 16 Map Browser
  Sutherland, R. D.
• gridHyb
  Beauheim, C., Pecherer, R. M., and Kelly, P.

The Expressed Gene Anatomy Database (EGAD) project
Chris Fields, Owen White, Carol Bult, Mark D. Adams, and Anthony R. Kerlavage

A Prototype 2nd Generation Database schema for large-scale Physical Mapping
Tom Slezak, Mark Wagner, and T. Mimi Yeh

Digiboard - A General Purpose Measurement System Used for FISH Mapping
David J. Ow, Arthur Kobayashi, Mark C. Wagner, and Tom Slezak

Recent Enhancements to the LLNL Genome Browser: Automated Construction & Display of Physical Maps
Mark Wagner, Tom Slezak, and Elbert Branscomb

Integrated Informatics Support for Large-Scale Sequencing at the LBL Human Genome Center
E. Theil, A. Aggarwal, D. Davy, F. Eeckman, T. Fleming, V. Markowitz, J. McCarthy, S. Pitluck, E. Veklerov, M. Zorn

On Generating Accurate Transponson Maps
E. Veklerov, C. Martin, E. Theil

Syndb: A Multi-Species Database For Mapping and Sequence Information
A. Aggarwal, D. Davy, J. McCarthy, and E. Theil

Developing a Graphical SQL Editor for the Genomic Database Federation
Dong-Guk Shin

An Integrated Approach to Genomic Sequence Analysis
Terry Gaasterland, Natalia Alaltsev, and Ross Overbeek

New Techniques for Integration of Biological Data Sources
Peter Buneman, Susan Davidson, and Chris Overton

Object-Protocol Model Tools: Overview and Applications
Victor M. Markowitz, I-Min A. Chen, and Ernest Szeto

SubmitData: Data Submission To Public Genomic Databases
Manfred D. Zorn

Data Management for the Molecular Cytogenetic Resource
Jenny E. Marstaller and Manfred D. Zorn

Automatic Generation of User Interfaces for Genomic Databases
Manfred D. Zorn, Shirdi R. Prem, and Ofer Ben-Shachar

Identification, organization and analysis of mammalian repetitive DNA
Jerzy Jurka

Recursive Relational Representation for DNA and Attribute-Value Lists: Techiques for Reducing Schema Modifications
Robert M. Pecherer, Joe M. Gatewood, and Robert D. Sutherland

Estimation of DNA Substitution Matrices and a Generalized Measure of Evolutionary Distance
W.J. Bruno and L. Arvestad

Combinatorial algorithms for genome sequence analysis
John D. Kececioglu

A Syntactic Pattern Recognition System for DNA Sequences
David Searls

Prediction of Coding Regions in Genomic DNA: Optimal and Suboptimal Parses
Eric E. Snyder and Gary D. Stormo

Gene Recognition, Modeling, and Homology Search in the GRAlL-genQuest System
Manesh Shah, J. Ralph Einstein, Sherri Matis, Ying Xu, Xiaojun Guan, Donna Buley, Sergey Petrov, Loren Hauser, Richard J. Mural, and Edward C. Uberbacher

Biological evaluation of d ^ 2: an algorithm for high performance novel DNA sequence functional assignment.
Winston Hide, John Burke and Daniel Davison

Analysis and Annotation of Nucleic Acid Sequence
David J. States, Ron Cytron, Pankaj Agarwal and Hugh Chou

A Conceptual Model for Genome Mapping Data
Mark Graves and Charles B. Lawrence

Bayes Decoding of Pooling Experiments Using Monte Carlo Methods
W.J. Bruno, E. Knill, A. Schliep, and D.C. Torney

Interactive Algorithms for Rapid Chromosome Copy Number Enumeration of Individual, Whole Cell Nuclei Inside Intact Tissue Specimens
Stephen Lockett, Curtis Thompson, Damir Sudar, James Mullikin, Daniel Pinkel, and Joe Gray

SIGMA: System for Instegrated Genome Map Assembly
Michael J. Cinkosky, Shahar Tsadeek, and James W. Fickett

A Software Tool to Determine Overlaps Between Clones and Existing Restriction Fragment Maps
T. Mimi Yeh and Tom Slezak

Gel Analysis Programs for 'DOG' and STS Content Mapping
S. Pitluck, K. Gong, S. Lewis

Informatics Support for Mapping in Mouse-Human Homology Regions
Sergey Petrov, Manesh Shah, Loren Hauser, Richard Mural, and Edward Uberbacher

A Battery of Programs for STS Content Mapping
Farid Alizadeh, Richard M. Karp, Deborah Weisser, and Geoffrey Zweig

Software Support for High-Throughput DNA Sequencing
Charles Lawrence, Victor Solovyev, Eugene Myers

Software Support for Large Scale Sequencing
Joe Gatewood, Robert M. Pecherer, Elaine Best

BioPOET: Large Scale Sequence Analysis On Workstation Farms
Manfred D. Zorn, Jane F. Macfarlane, Rob Armstrong, Michael H. Cooper, and Nicholas C. Weaver

An Integrated Data Management System for DNA Sequencing
Arthur Kobayashi, David J. Ow, Mark C. Wagner, T. Mimi Yeh, and Tom Slezak

Statistical Methods to Improve DNA Sequencing Accuracy
David O. Nelson and Terence P. Speed

Towards Simplifying Fragment Assembly
Eugene Myers

Bayesian Restoration of a Hidden Markov Chain with Applications to Sequence Alignment
Gary A. Churchill

Estimating Consensus DNA Sequences
Tom Blackwell

GnomeView: User Test Results and Creation of a Client-Server System
Richard J. Douthart and Gregory Thomas

Combinatorial Methods for Gene Recognition
Mikhail Gelfand, Pavel Pevzner, Michael Roytberg

MacAce: ACeDB on the Macintosh
Frank H. Eeckman, Richard Durbin, Cyrus Harmon

ProtWeb and BioWeb--Networking for Biologists
Dan Jacobson

The Estimation, Encoding, and Robust Utilization of Uncertainty Information in DNA Sequences
John R. Hartman, Dianne M. Marsh, and Jeffrey S. Chamberlain