DOE Genome Contractor-Grantee Workshop IX
January 27-31, 2002 Oakland, CA
Human Genome Project Information
Genomes to Life Program Overview
Sequencing
Table
of Contents
Abstracts
Sequencing
Resources
Table
of Contents
Abstracts
Instrumentation
Table
of Contents
Abstracts
Functional
Analysis and Resources
Table
of Contents
Abstracts
Bioinformatics
Table
of Contents
Abstracts
Microbial
Cell Project
Table
of Contents
Abstracts
Microbial
Genome Program
Table
of Contents
Abstracts
Ethical,
Legal, and Social Issues
Table
of Contents
Abstracts
Low
Dose Ionizing Radiation
Table
of Contents
Abstracts
Infrastructure
Table
of Contents
Abstracts
Abstracts from Previous Meetings
Bioinformatics Abstract Index
74. Understanding Protein Interactions
Xiaoqun Joyce Duan, Ioannis Xenarios, and David Eisenberg
Eric Poe Xing, Denise M. Wolf, Inna Dubchak, Sylvia Spengler, Manfred Zorn, Ilya Muchnik, and Casimir Kulikowski
76. THE RDP-II (Ribosomal Database Project)
James R. Cole, Timothy G. Lilburn, Paul R. Saxman, Bonnie L. Maidak, Charles T. Parker, Sunandana Chandra, Ryan J. Farris, George M. Garrity, Thomas M. Schmidt, and James M. Tiedje
77. A Random Walk Down the Genomes: a Case Study of DNA Evolution in VALIS
Yi Zhou, Archisman Rudra, Salvatore Paxia, and Bud Mishra
78. A Graph Data Model to Unify Biological Data
Frank Olken
79. Protein Data Bank: Unifying the Archive
Gary Gilliland and The PDB Team
80. Protein Structure Predictions by PROSPECT
Dong Xu, Dongsup Kim, Christal Secrest, Victor Olman, and Ying Xu
81. Protein Fold-Recognition Using HMMs and Secondary Structure Prediction
Kevin Karplus
82. Protein Engineering in Structural Genomics
Patrice Koehl and Michael Levitt
83. Classifying G-Protein Coupled Receptors with Support Vector Machines
Rachel Karchin, Kevin Karplus, and David Haussler
84. Protein Structure Determination Through Combining Protein Threading and Sparse NMR Data
Ying Xu, Dong Xu, Dongsup Kim, and Oakley Crawford
85. GAP: Genomics Annotation Platform
Konstantin M. Skorodumov, Evgeny Raush, Maxim Totrov, Ruben Abagyan, and Matthieu Schapira
86. Genome to Proteome and Back Again: ProteomeWeb
Carol S. Giometti, Sandra L. Tollaksen, Gyorgy Babnigg, Tripti Khare, Claudia I. Reich, Gary J. Olsen, John R. Yates III, Jizhong Zhou, Ken Nealson, and Derek Lovley
87. Computational Experiments on RNA Phylogeny
Frank Olken, James R. Cole, Gary J. Olsen, Craig A. Stewart, David Hart, Donald K. Berry, and Sylvia J. Spengler
88. Identifying Transcription Factor Binding Sites by Cross-Species Comparison
Lee Ann McCue, William Thompson, C. Steven Carmack, and Charles E. Lawrence
89. VISTA: Integrated Tool for Comparative Genomics
I. Dubchak, Lior Pachter, A. Poliakov, I. Ovcharenko, and E. Rubin
90. Beyond Terascale Biological Computing: GIST and Genomes To Life
Philip LoCascio, Doug Hyatt, Frank Larimer, Manesh Shah, Inna Vokler, and Ed Uberbacher
91. A Computational Pipeline for Genome-Scale Analysis of Protein Structures and Functions
Serguei Passovets, Manesh Shah, Li Wang, Dong Xu, and Ying Xu
N. Maltsev, G. X. Yu, E. Marland, S. Bhatnagar, R. Lusk, and E. Selkov
Erich Baker, Doug Hyatt, Barbara Jackson, Gwo-Liang Chen, Denise Schmoyer, Yesim Aydin-Son, David McWilliams, Fred Baes, Stefan Kirov, Michael Galloway, Michael Leuze, Line Pouchard, Brynn Jones, Ed Michaud, Bem Culiat, Gene Rinchik, Dabney Johnson, Ed Uberbacher, Darla Miller, Frank Larimer, Jay Snoddy, ORNL Life Sciences Division, and the Tennessee Mouse Genome Consortium
94. The ORNL Genome Analysis Toolkit, Pipeline and DAS Server
Manesh Shah, Doug Hyatt, Frank Larimer, Philip LoCascio, Inna Vokler, and Edward C. Uberbacher
95. GrailEXP: Gene Recognition Using Neural Networks and Similarity Search
Doug Hyatt, Frank Larimer, Philip LoCascio, Victor Olman, Manesh Shah, Ying Xu, and Edward C. Uberbacher
96. The Genome Channel: a Foundation for Genomes to Life and Comparative Genomics
Miriam Land, Frank Larimer, Jay Snoddy, Denise Schmoyer, Doug Hyatt, Manesh Shah, Inna Vokler, Philip LoCascio, Gwo-Liang Chen, Loren Hauser, and Ed Uberbacher
97. Automated Visualization of Large Scale Bacterial Transcriptional Regulatory Pathways
Carla Pinon, Amit Puniyani, Peter Karp, and Harley McAdams
98. Integrating Computational and Human-Curated Annotations for the Mouse Genome
Carol J. Bult and the Mouse Genome Informatics Group
Gabriela G. Loots, Ivan Ovcharenko, Inna Dubchak, and Edward M. Rubin
100. Managing Targets and Reactions in a Finishing Database
Mark Mundt, Judith Cohn, Mira Dimitrijevic-Bussod, Marie-Claude Krawczyk, Roxanne Tapia, Al Williams, Larry Deaven, and Norman Doggett
101. Encoding Sequence Quality in BLAST Output by Color Coding
Sam Pitluck, Paul F. Predki, and Trevor L. Hawkins
102. Whole Genome Assembly with JAZZ
Jarrod Chapman, Nicholas Putnam, and Dan Rokhsar
103. Assembly and Exploration of the Public Human Genome Working Draft
Terrence S. Furey, Jim Kent, and David Haussler
104. Shotgun Sequence Assembly Algorithms for Distributed Memory Machines
Frank Olken
105. Benefits of J2EE Architecture for Informatics Support of Genomic Sequencing
Roxanne Tapia, Judith Cohn, and Mark Mundt
106. Production Workflow Tracking and QC Analysis at the Joint Genome Institute
Heather Kimball, Stephan Trong, Art Kobayashi, Sam Pitluck, Yunian Lou, and Matt Nolan
107. Goals, Design, and Implementation of a Versatile MicroArray Data Base
Marc Rejali, Marco Antoniotti, Vera Cherpinsky, Caroline Leventhal, Salvatore Paxia, Archisman Rudra, Joe West, and Bud Mishra
L.E. Peterson
L. E. Peterson, M. A. Coleman, E. Yin, B. J. Marsh, K. Sorensen, J. Tucker, and A. J. Wyrobek
110. EXCAVATOR: Gene Expression Data Analysis Using Minimum Spanning Trees
Ying Xu, Dong Xu, Victor Olman, and Li Wang
111. Flexible Customization of Micro-Array Data Analysis Pipeline
Dong-Guk Shin, Ravi Nori, Jae-Guon Nam, and Jeffrey Maddox
112. Correspondence Mapping Algorithms
Lidia Cassier, Robert Lucito, Vivek Mittal, Joseph West, Michael Wigler, William Casey, and Bud Mishra
113. Haplotyping with Phased RFLPs: Algorithms and Mathematical Models
Will Casey, Thomas Anantharaman, and Bud Mishra
114. Information Management Infrastructure for the Systematic Annotation of Vertebrate Genomes
V. Babenko, B. Brunk, J. Crabtree, S. Diskin, Y. Kondrahkin, J. Mazzarelli, S. McWeeney, D. Pinney, A. Pizzaro, J. Schug, V. Bogdanova, A. Katohkin, V. Nadezhda, E. Semjonova, V. Trifonoff, N. Kolchanov, M. Bucan, and C. Stoeckert
115. Manual Annotation of the Human and Mouse Gene Index: www.allgenes.org
Brian Brunk, Jonathan Crabtree, Sharon Diskin, Joan Mazzarelli, Chris Stoeckert, Nico Zigouras, Vera Bogdanova, Alexey Katohkin, Nikolay Kolchanov, Vorbjeva Nadezhda, Elena Semjonova, and Vladimir Trifonoff
116. The Comprehensive Microbial Resource
Owen White, Lowell Umayam, Tanja Dickinson, and Jeremy Peterson
208. In Silico Discovery: Challenges in Integration and Knowledge Extraction
Su Chung
210. Bioinformatics for Genome Analysis
Claudia I. Reich and Gary J. Olsen
220. Understanding Protein Interactions
Xiaoqun Joyce Duan, Ioannis Xenarios, Lukasz Salwinski, Charlotte Dean, and David Eisenberg