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Genome Bioinformatics Abstract Index 

DOE Human Genome Program    
Contractor-Grantee Workshop VII   
January 12-16, 1999  Oakland, CA
 
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78. The Genome Annotation Collaboration: An Overview 

Jay R. Snoddy, Morey Parang, Sergey Petrov, Richard Mural, Manesh Shah, Ying Xu, Sheryl Martin, Phil LoCascio, Kim Worley1, Manfred Zorn2, Sylvia Spengler2, Donn Davy2, Chris Overton3, Edward C. Uberbacher, and the Genome Annotation Consortium 
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee;  
1Baylor College of Medicine, Houston, Texas; 2Lawrence Berkeley National Laboratory, Berkeley, California; and 3University of Pennsylvania, Philadelphia, Pennsylvania 
ube@ornl.gov 
http://compbio.ornl.gov/gac 


78a. Our Vision for a New Macromolecular Structure Database --The New Protein Databank  

Helen M. Berman1, Gary Gilliland2, Peter Arzberger3, Phil Bourne4, John Westbrook5, Phoebe Fagan6 

1Rutgers University 
2National Institute of Standards and Technology (NIST) 
3UC San Diego Supercomputer Center 
4San Diego State College 
5Rutgers University 
6NIST 

79. Visualization, Navigation, and Query of Genomes: The Genome Channel and Beyond 

Morey Parang, Richard Mural, Manesh Shah, Doug Hyatt, Miriam Land, Jay Snoddy, Edward C. Uberbacher, and the Genome Annotation Consortium 
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 
ube@ornl.gov 
http://compbio.ornl.gov/gac 

80. Genome Annotation Data Management and Data Administration: Developing Summary Results for User Navigation, Genome Research, Improved Data Processing, and Quality Metrics 

Jay R. Snoddy, Miriam Land, Sheryl Martin, Morey Parang, Inna Volker, Denise Schmoyer, Manesh Shah, Sergey Petrov, Edward C. Uberbacher, and the Genome Annotation Consortium 
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 
v8v@ornl.gov 
http://compbio.ornl.gov/gac 

81. Data Management for Genome Analysis and Annotation: Engineering a Fundamental Infrastructure for Data that Supports Collaboration in Genome Annotation 

Sergey Petrov, Jay R. Snoddy, Michael D. Galloway, Sheryl Martin, Miriam Land, Morey Parang, Tom Rowan, Denise D. Schmoyer, Manesh Shah, Inna E. Vokler, Edward C. Uberbacher, and the Genome Annotation Consortium 
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 
ptv@ornl.gov 
http://compbio.ornl.gov/gac 

82. Genome Channel Analysis Engine: A System for Automated Analysis of Genome Channel Data 

Manesh Shah, Morey Parang, Doug Hyatt, Michael Galloway, Richard Mural, Kim Worley1, Edward C. Uberbacher, and the Genome Annotation Consortium 
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee and 1Baylor College of Medicine, Houston, Texas 
x9m@ornl.gov 
http://compbio.ornl.gov/gac 

83. GRAIL-EXP: Multiple Gene Modeling Using Pattern Recognition and Homology 

Ying Xu, Manesh Shah, Doug Hyatt, Richard Mural, Edward C. Uberbacher, and the Genome Annotation Consortium 
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 
ube@ornl.gov 
http://compbio.ornl.gov/gac 

84. High-Performance Computing Servers 

Phil LoCascio, Doug Hyatt, Manesh Shah, Al Geist, Bill Shelton, Ray Flannery, Jay Snoddy, Edward Uberbacher, and the Genome Annotation Consortium 
Life Sciences Division and Computer Sciences and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 
locasciop@ornl.gov 
http://compbio.ornl.gov/gac 

85. DOE Joint Genome Institute Public WWW Site 

Robert D. Sutherland and Linda Ashworth 
Los Alamos National Laboratory, Los Alamos, New Mexico, and Lawrence Livermore National Laboratory, Livermore, California 
rds@lanl.gov 

86. JGI Informatics and the PSF Network 

Tom Slezak, Mark Wagner, Lisa Corsetti, Sam Pitluck, Arthur Kobayashi, Mimi Yeh, Brian Yumae, and Peg Folta 
Joint Genome Institute; Lawrence Livermore National Laboratory, Livermore, California and Lawrence Berkeley National Laboratory, Berkeley, California 
slezak@llnl.gov 

87. Verification of Finished Sequence at JGI-LLNL 

Karolyn J. Burkhart-Schultz, Amy M. Brower, Arthur Kobayashi, Matt Nolan, Melissa Ramirez, and Jane E. Lamerdin 
Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 
burkhartschultz1@llnl.gov 

88. Informatics for Production Sequencing at LLNL 

Arthur Kobayashi, David J. Ow, Matt P. Nolan, Stephan Trong, Tory Bobo, Tom Slezak, Mark C. Wagner, T. Mimi Yeh, Lisa Corsetti, Jane Lamerdin, Paula McCready, Evan W. Skowronski, and Anthony V. Carrano 
Lawrence Livermore National Laboratory, Livermore, California 
kobayashi1@llnl.gov 

89. A Workflow-Based LIMS for High-Throughput Sequencing, Genotyping, and Genetic Diagnostic Environments 

Peter Cartwright 
Cimarron Software, Salt Lake City, Utah 
pc@cimsoft.com 

90. A Simulation Extension of a Workflow-Based LIMS 

Peter Cartwright 
Cimarron Software, Salt Lake City, Utah 
pc@cimsoft.com 

91. A Graphical Work-Flow Environment Seamlessly Integrating Database Querying and Data Analysis 

Dong-Guk Shin1, Lung-Yung Chu1, Lei Liu1, Nori Ravi1, Joseph Leone2, Rich Landers2, and Wally Grajewski2 
1Computer Science & Engineering, University of Connecticut, Storrs, CT 06269-3155 and 2CyberConnect EZ, LLC, Storrs, CT 06268 
shin@engr.uconn.edu 

92. Data Visualization for Distributed Bioinformatics 

Gregg Helt, Suzanna Lewis, Nomi Harris, and Gerald M. Rubin 
Berkeley Drosophila Genome Project, University of California, Berkeley, California 
gregg@fruitfly.berkeley.edu 

93. A Figure of Merit for DNA Sequence Data 

Mark O. Mundt, Allon G. Percus, and David C. Torney 
Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 
dct@lanl.gov 

94. Probabilistic Basecalling 

Terry Speed, Lei Li, Dave Nelson, and Simon Cawley 
University of California, Berkeley 
scawley@stat.berkeley.edu 

95. The FAKtory Sequence Assembly System 

Susan J. Miller, Eugene W. Myers, Kedarnath A. Dubhashi, and Daniel E. Garrison 
University of Arizona, Tucson, Arizona 
susanjo@cs.arizona.edu 

96. Hidden Markov Models in Biosequence Analysis: Recent Results and New Methods 

Christian Barrett, Mark Diekhans, Richard Hughey, Tommi Jaakkola, Kevin Karplus, David Kulp, Stephen Winters-Hilt, and David Haussler 
Computer Science Department, University of California, Santa Cruz, CA 95064 haussler@cse.ucsc.edu 

97. Java Based Restriction Map Display 

Mark C. Wagner, Jan-Fang Cheng, Steve Lowry, Robert Sutherland, Norman Doggett, Laurie A. Gordon, and Anne S. Olsen 
Joint Genome Institute, Lawrence Livermore National Laboratory, 7000 East Avenue, L-452, Livermore, CA 94550 
wagner5@llnl.gov 

98. Mapping Data 

Lixin Tang, Jeremy Boulton1, Benjamin Liau1, Hui Zhang2, Wei Qin3, Sung Ha Huh1, Yicheng Cao, Robert Xuequn Xu, Glen George1, and Ung-Jin Kim 
Division of Biology, 1Computer Science, 2Atmospheric Chemistry, and 3Electrical Engineering, California Institute of Technology, Pasadena, CA 91125 
xux@cco.caltech.edu 

99. A Relational Database and Web/CGI Approach in the Analysis and Data Presentation of Large-Scale BAC-EST Hybridization Screens 

Robert Xuequn Xu, Chang-Su Lim, Bum-Chan Park, Mei Wang, Jonghyeob Lee, Aaron Rosin, Eunpyo Moon, Melvin Simon, and Ung-Jin Kim 
Division of Biology, Caltech, Pasadena, CA 91125 
xux@cco.caltech.edu 

100. A Distributed Object System for Automated Processing and Tracking of Fluorescence Based DNA Sequence Data 

Michael C. Giddings, Jessica M. Severin, Michael Westphall, and Lloyd M. Smith 
University of Wisconsin, Madison, Wisconsin 
jseverin@chem.wisc.edu 


100a. Recent advances in high-throughput genomic sequencing: Magnetic Capture of Plasmids  

Kevin McKernan, Paul McEwan, Will Morris, Nicole Stange-Thomann, Imani Torruella-Miller, Andrew Sheridan, Alan Wagner, Dudley Wyman, Boris Pavlin, James Benn, Eric S. Lander, Lauren Linton 
Whitehead Institute/MIT Center for Genome Research 
kevinmc@genome.wi.mit.edu 


101. Arraydb: CGH-Array Tracking Database 

Donn Davy, Daniel Pinkel, Donna Albertson, Steve Clark, Joel Palmer, Don Uber, Arthur Jones, Joe Gray, and Manfred Zorn  
Lawrence Berkeley National Laboratory, Berkeley, Calfornia 
dfdavy@lbl.gov 

102. BCM Search Launcher -- Analysis of the Genome Sequence 

Kim C. Worley and Pamela A. Culpepper 
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 
kworley@bcm.tmc.edu 

103. Profile Search 
Manfred D. Zorn and David Demirjian 
Lawrence Berkeley National Laboratory, Berkeley, Calfornia 

  • DGDemirjian@lbl.gov 

    • 104. Computer Analysis of DNA Sequence Data to Locate SECIS Elements 

    Michael Giddings, Olga Gurvich, Marla Berry, John Atkins, and Raymond Gesteland 
    University of Utah, Department of Human Genetics, 15 N. 2030 E. rm. 6160, Salt Lake City, UT 84112-5330 
    giddings@genetics.utah.edu 

    105. Sequence Landscapes 

    Gary D. Stormo, Samuel Levy, and Fugen Li 
    MCD Biology, University of Colorado, Boulder, CO 80309-0347 
    stormo@colorado.edu 

    106. Protein Fold Prediction in the Context of Fine-Grained Classifications 

    Inna Dubchak, Chris Mayor, Sylvia Spengler, and Manfred Zorn  
    E. O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720  
    ildubchak@lbl.gov 

    107. Comparative Analyses of Syntenic Blocks 

    Jonathan E. Moore and James A. Lake 
    Molecular Biology Institute, University of California, Los Angeles, CA 90095 
    Lake@mbi.ucla.edu 

    108. Sensitive Detection of Distant Protein Relationships Using Hidden Markov Model Alignment 

    Xiaobing Shi and David J. States 
    Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 

    109. Multiple Sequence Alignment with Confidence Estimates 

    David J. States 
    Institute for Biomedical Computing, Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 

     
    110. Improved Specificity and Sensitivity in Sequence Similarity Search Through the Use of Suboptimal Alignment Based Score Filtering 

    Lisa Gu and David States 
    Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 


    110a. Expert System for Long-Read Base-Calling in DNA Sequencing by Capillary Electrophoresis  

    Arthur W. Miller and Barry L. Karger 
    Barnett Institute, Northeastern University, 360 Huntington Ave., Boston, MA 02115 

    111. Screening for Large-Scale Variations in Human Genome Structure 

    S. MacMillan1, C. Hott1, D. Anderson1, E. C. Rouchka2, B. D. Dunford-Shore, B. Brownstein1, R. Mazzarella2, V. Nowotny2, and D. J. States2 
    Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 

    112. Probabilistic Physical Map Assembly 

    David J. States, Thomas W. Blackwell, John McCrow, and Volker Nowotny 
    Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 

    113. Multi-Resolution Molecular Sequence Classification 

    David J. States, Zhengyan Kan, and Brian Dunford-Shore 
    Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 

    114. PQ Edit--A Web-Based Database Table Editor and the Relational Database Abstraction Layer 

    Brian H. Dunford-Shore and David J. States 
    Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 

    115. Allele Frequency Estimation from Sequence Trace Data 

    David G. Politte, David R. Maffitt, and David J. States 
    Washington University in St. Louis, St. Louis, Missouri 
    states@ibc.wustl.edu 

    116. Improved Detection of Single Nucleotide Polymorphisms (SNPs)  

    Scott L. Taylor, Natali Kolker, and Deborah A. Nickerson  
    Department of Molecular Biotechnology, University of Washington, Box 357730, Seattle, WA 98195  
    stay@u.washington.edu 

    117. The Genome Sequence DataBase (GSDB): Advances in Data Access, Analysis, and Quality 

    C.A. Harger, M. Booker, A. Farmer, W. Huang, J. Inman, D. Kipart, C Kodira, S. Root, F. Schilkey, J. Schwertfeger, A. Siepel, M.P. Skupski, D. Stamper, N. Thayer, R. Thompson, J. Wortman, J.J. Zhuang, and M.M. Harpold 
    National Center for Genome Resources, 1800 Old Pecos Trail, Suite A, Santa Fe, NM 87505 
    cah@ncgr.org 

    118. Analysis of Ribosomal RNA Sequences by Combinatorial Clustering 

    Poe Xing, Casimir Kulikowski, Ilya Muchnik, Inna Dubchak, Sylvia Spengler, Manfred Zorn, and Denise Wolf 
    DIMACS and CS Department, Rutgers University, New Jersey; Lawrence Berkeley National Laboratory, Berkeley, Calfornia 
    xingpoe@cs.rutgers.edu 

    119. Ribosomal RNA Alignment Using Stochastic Context Free Grammars 

    Michael P.S. Brown 
    University of California at Santa Cruz, Santa Cruz, California 
    mpbrown@cse.ucsc.edu 

    120. Ribosomal Database Project II 

    James R. Cole, B. Maidak, T.G. Lilburn, B. Li, C.T. Parker, S. Pramanik, G.M. Garrity, T.M. Schmidt, and Jim Tiedje 
    Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 
    colej@pilot.msu.edu