DOE Genome Contractor-Grantee Workshop IX January 27-31, 2002 Oakland, CA |
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Human Genome Project Information Genomes to Life Program Overview Sequencing Sequencing
Resources Instrumentation Functional
Analysis and Resources Bioinformatics Microbial
Cell Project Microbial
Genome Program Ethical,
Legal, and Social Issues Low
Dose Ionizing Radiation Infrastructure Abstracts from Previous Meetings
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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 |
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