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Sequencing
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Informatics
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Ethical,
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Infrastructure
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Abstracts
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Ordering Information
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- Informatics at the Center for Applied Genomics
Donn Davy, Tom Cloutier, Colin Collins, Manfred Zorn, Joe Gray
University of California at San Francisco/Lawrence Berkeley National Laboratory
- The Genome Channel and Genome Annotation
Consortium
Ed Uberbacher, Richard Mural, Manesh Shah, Ying Xu, Sheryl Martin, Sergey
Petrov, Jay Snoddy, Morey Parang - Oak Ridge National Laboratory
Manfred Zorn, Sylvia Spengler, Donn Davy - Lawrence Berkeley National Laboratory
Terry Gaasterland - Argonne National Laboratory
Peter Schad - The National Center for Genome
Resources
Stan Letovsky, Bob Cottingham - The Genome Database
David Haussler - University of California Santa Cruz
Pavel Pevzner - University of Southern California
Chris Overton - University of Pennsylvania
- GRAIL and GenQuest Sequence Annotation
Tools
Ying Xu, Manesh B. Shah, J. Ralph Einstein, Morey Parang, Jay Snoddy, Sergey Petrov,
Victor Olman, Ge Zhang, Richard J. Mural and Edward C. Uberbacher
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory,
Oak Ridge, TN 37831-1060
- The Stationary Statistical Properties of Human Coding
Sequences
David C. Torney, Clive C. Whittaker, and Gouchun Xie
Los Alamos National Laboratory, Theoretical Division, Los Alamos, New Mexico 87545,
and Merck and Company, Inc., West Point, Pennsylvania
- WIT/WIT2: A System for Supporting
Metabolic Reconstruction and Comparative Analysis of Sequenced
Genomes
Ross Overbeek,* Natalia Maltsev,* Gordon Pusch,* and Evgeni Selkov * **
* Mathematics and Computer Science Division, Argonne National Laboratory, and **
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142292
Pushchino, Moscow region, Russia
- Internet Release of the Metabolic Pathways Database,
MPW
Evgeni Selkov, Jr.,* Yuri Grechkin,* and Evgeni Selkov * **
* Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences,
142292
Pushchino, Moscow region, Russia, and **
Mathematics and Computer Science Division,
Argonne National Laboratory, Argonne, 9700 S.
Cass Ave., MCS-221, IL 60439-4844, USA
- Metabolic Reconstruction from Sequenced
Genomes
Evgeni Selkov,*+ Natalia Maltsev,* and Ross Overbeek*
* Mathematics and Computer Science Division, Argonne National Laboratory, Argonne,
9700 S. Cass Ave., MCS-221, IL 60439-4844, USA,
+ Institute of Theoretical and Experimental
Biophysics, Russian Academy of Sciences, 142292
Pushchino, Moscow region, Russia
- From Genomic Sequence to Protein
Expression: A Model for Functional Genomics
Tracy J. Wright, Simone Abmayr, Min S. Park, Darrell O. Ricke, Cleo Naranjo, Becky
Welsh-Breitinger, Karen Denison and Michael R. Altherr
Genomics Group, Mail Stop M888, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545
- FAKtory: A Customizable Fragment Assembly
System
Eugene W. Myers, Susan J. Larson, Brad W. Traweek, Kedarnath A. Dubhashi
University of Arizona, Tucson, AZ
- Divide-and-Conquer Multiple Sequence
Alignment
Dan Gusfield, Jens Stoye
Department of Computer Science, University of California, Davis, CA 95616, USA
- Sequence Assembly Validation by
Restriction Digest Analysis
Eric C. Rouchka and David J. States
Washington University
- Segmentation Based Analysis of
Genomic Sequence
Eric C. Rouchka and David J. States
Washington University
- Swedish and Finnish Quality Based
Finishing Tools for a Production Sequencing Facility
Matt P. Nolan, Jane E. Lamerdin, Stephanie A. Stilwagen, Glenda G. Quan, Ami
L.
Kyle, Anthony V. Carrano
Joint Genome Institute, Lawrence Livermore National Laboratory
- Informatics to Support Increased Throughput and
Quality Assurance in a Production Sequencing Facility
Arthur Kobayashi, David J. Ow, Tom Slezak,
Mark C. Wagner, Matt P. Nolan, T. Mimi Yeh,
Stephan Trong, Anthony V. Carrano
LLNL HGC; Joint Genome Institute
- Software Tools for Data Analysis in
Automated DNA Sequencing
Michael C. Giddings, Jessica Severin, Michael
Westphall, and Lloyd M. Smith
University of Wisconsin-Madison Chemistry
Dept., 1101 University Ave., Madison, WI 53703
- Treasures and Artifacts from Human
Genome Sequence Analysis
Darrell O. Ricke and Larry L. Deaven
Los Alamos National Laboratory, Center for
Human Genome Studies, Los Alamos, New Mexico 87545
- Annotating and Masking Repetitive
Sequences with RepeatMasker
Arian F.A. Smit and Phil Green
Human Genome Center, Department of Medicine,
University of Washington, Seattle, WA 98195
- Why Is Basecalling Hard to Do Well?
Sources of Variability in DNA Sequencing Traces and Their
Consequences
David O. Nelson
Human Genome Center
Lawrence Livermore National Laboratory
Terence P. Speed
Statistics Department
University of California, Berkeley
- A Statistical Model for Basecalling
Lei Li, David O. Nelson, and Terence P. Speed
Department of Statistics, University of California, Berkeley
- An Expert System for Base Calling in
Four-Color DNA Sequencing by Capillary and Slab Gel Electrophoresis
Arthur W. Miller and Barry L. Karger
Barnett Institute, Northeastern University, Boston, MA 02115
- Web-Based Tools for the Analysis and
Display of DNA Trace Data
Judith D. Cohn, Mark O. Mundt, A. Christine
Munk, Larry L. Deaven and Darrell O. Ricke
Los Alamos National Laboratory, Los Alamos, New Mexico 87545
- Joint Genome Institute's (JGI) Informatics Plans and
Needs
Darrell O. Ricke, Tom Slezak, Sam Pitluck, and Elbert Branscomb
Joint Genome Institute
- Restriction Map Display on the World
Wide Web
Mark C. Wagner, Thomas R. Slezak, Arthur Kobayashi, David J. Ow, Linda K.
Ashworth, Laurie A. Gordon, Anne S. Olsen, Anthony V. Carrano
Joint Genome Institute, Lawrence Livermore
National Laboratory, Livermore, CA 94550
- The BCM Search Launcher -- Providing Enhanced
Sequence Analysis Search Services
Kim C. Worley, Pamela A. Culpepper, Daniel B. Davison
Department of Molecular and Human Genetics and Department of Cell Biology, Baylor
College of Medicine, Houston, TX
- SubmitData Data Submission Framework
David Demirjian, Sushil Nachnani, Manfred Zorn
Lawrence Berkeley National Laboratory
- Graphical Ad hoc Query Interface for
Federated Genome Databases
Dong-Guk Shin,1 Lung-Yung Chu,1 Wally
Grajewski,1 Joseph Leone,2 Thomas Barnes,2 and
Rich Landers2
1 Computer Science & Eng., University of
Connecticut, Storrs, CT 06269-3155
2 CyberConnect EZ, LLC, Storrs, CT 06268
- Towards a Comprehensive Conceptual
Consensus of the Expressed Human Genome: A Novel Error Analytical
Approach to EST Consensus Databases
Robert Miller, John Burke, Alan Christoffels and Winston Hide
South African National Bioinformatics Institute
The University of the Western Cape, Private Bag X17, Cape Town, South Africa
- Query and Display of Comprehensive
Maps in GDB
Stanley Letovsky, Robert Cottingham and GDB Staff
Genome Database, Johns Hopkins University, Baltimore MD
- GSDB - New Capabilities and Unique Data
Sets
A. Farmer, C. Harger, S. Hoisie, P. Hraber, D. Kiphart, L. Krakowski, M. McLeod, J.
Schwertfeger, A. Siepel, G. Singh, M. Skupski, D. Stamper, P. Steadman, N. Thayer, R.
Thompson, P. Wargo, M. Waugh, J.J. Zhuang, and P.A. Schad
- Database Transformations for
Biological Applications*
G. Christian Overton, Susan B. Davidson, Peter Buneman
Dept. of Computer and Information Science,
University of Pennsylvania, Philadelphia, PA 19104
- Exploring Heterogeneous Biological
Databases with the OPM Multidatabase Tools
Victor M. Markowitz, I-Min A. Chen, Anthony Kosky, Ernest Szeto
Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- The OPM Data Management Toolkits
Anno 1997
Victor M. Markowitz, I-Min A. Chen, Anthony
Kosky, Ernest Szeto, William Barber, Thodoros Topaloglou
Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Quality Control in Sequence Assembly
Analysis
Mark O. Mundt, Judith D. Cohn, Tracy L. Ricke,
P. Scott White, Larry L. Deaven and Darrell O. Ricke
Los Alamos National Laboratory, Life Sciences
Division and Center for Human Genome Studies,
Los Alamos, New Mexico 87545
- Automating the Detection of Human
DNA Variations
Scott L. Taylor, Mark J. Rieder, and Deborah A. Nickerson
Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195
- Fast and More Accurate
Distance-Based Phylogenetic Construction
William J. Bruno, Aaron L. Halpern, Nicholas D. Socci
Los Alamos National Laboratory
- Determining the Important Physical-Chemical
Parameters Within Various Local Environments of Proteins
Jeffrey M. Koshi and William J. Bruno
Los Alamos National Laboratory, Theoretical Biology and Biophysics
- Improving Software Usability and
Accessibility
Ryan Carroll and Ruth Ann Manning
ApoCom Inc., 1020 Commerce Park Drive, Suite
F, Oak Ridge TN 37830-8026
- bioWidgets: Visualization
Componentry for Genomics
Steve Fischer, Jonathan Crabtree, Mark Gibson and G. Christian Overton (PI)
Department of Genetics, University of Pennsylvania; Philadelphia, PA 19104
- Research on Data and Workflow
Management for Laboratory Informatics
Nathan Goodman
The Jackson Laboratory
- Method of Differentiation Between
Similar Protein Folds
I. Dubchak, I. Muchnik, S. Spengler, M. Zorn
Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Embedding HMMs: A Method for Recognizing
Protein Homologs in DNA
David Kulp, David Haussler
Baskin Center for Computer Engineering and Information Sciences, University of
California, Santa Cruz, CA 95064
- Data Visualization for Distributed
Bioinformatics
Gregg Helt, Suzannah Lewis, Nomi Harris, and Gerald M. Rubin
Berkeley Drosophila Genome Project
- Gene Hunting Without Sequencing Genomic
Clones: The "Twenty Questions" Game with Genes
Guorong Xu, Sing-Hoi Sze, Cheng-Pin Liu, Pavel A. Pevzner and Norman Arnheim
Molecular Biology Program, Department of Computer Science,
Department of Mathematics, University of Southern California, Los Angeles, CA 90089-1340
- The Metabolic Pathway Database and Metabolic
Reconstruction from Sequenced Genomes
Evgeni Selkov,1, 2 Milyausha Galimova,2 Igor
Goryanin,2 Yuri Grechkin,2 Natalia Ivanova,2 Yuri
Komarov,2 Niels Larsen,3 Natalia Maltsev,2 Natalia
Mikhailova,2 Valery Nenashev,2 Ross Overbeek,1
Lyudmila Pronevich,2 Gordon Pusch,1 and Evgeni Selkov,
Jr.,2
1 Mathematics and Computer Science Division, Argonne National Laboratory,
Argonne, IL
2 Institute of Theoretical and Experimental Biophysics, Russian Academy of
Sciences, 142292 Pushchino, Moscow region, Russia
3 Center of Microbial Ecology, Michigan State University
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