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
Microbial Genome Program Abstract Index
132. Optical Map Based Sequence Validation of Microbes
Marco Antoniotti, Thomas Anantharaman, Violet Chang, David Schwartz, and Bud Mishra
133. Interaction of Cytochrome c3 with Uranium
Judy D. Wall and Barbara Rapp-Giles
Alexander Beliaev, Dorothea K. Thompson, Carol S. Giometti, Kenneth H. Nealson, Alison E. Murray, James M. Tiedje, and Jizhong Zhou
135. Microarray Analysis of Sugar Metabolism Gene Networks in Thermotoga maritima
Arvin D. Ejaz, Amy M. Mikula, Tu Nguyen, Ken Noll, Karen E. Nelson, and Steven R. Gill
136. Gene Expression Profiles in Nitrosomonas europaea, An Obligate Chemolithoautotroph
Daniel Arp, Martin Klotz, and Jizhong Zhou
Derek R. Lovley, Madellina Coppi, Stacy Cuifo, Susan Childers, Ching Lean Franz Kaufmann, Daneil Bond, Teena Mehta, and Mary Rothermich
138. Genome Sequencing of Gemmata obscuriglobus
Naomi Ward, Margaret K. Butler, Rebecca L. Smith, and John A. Fuerst
139. Genome Sequence of Methanococcus maripaludis, a Genetically Tractable Methanogen
Erik L. Hendrickson, Maynard Olson, Gary Olsen, and John A. Leigh
140. The Genome of Ferroplasma acidarmanus: Clues to Life in Acid
Larry Croft, Amanda Barry, Paul Predki, Stephanie Stilwagen, Genevieve Johnson, Thomas M. Gihring, Brett J. Baker, Jennifer Macalady, George F. Mayhew, Valerie Burland, Teresa Janecki, Charles W. Kaspar, Brian Fox, and Jillian F. Banfield
141. Genome Sequence of the Metal-Reducing Bacterium, Shewanella oneidensis
John F. Heidelberg, Ian T. Paulsen, Karen E. Nelson, William C. Nelson, Jonathan A. Eisen, Barbara Methe, Eric J. Gaidos, Owen White, Kenneth H. Nealson, and Claire M. Fraser
142. The Colwellia Strain 34H Genome Sequencing Project
Barbara Methe, Matthew Lewis, Bruce Weaver, Jan Weidman, William Nelson, Adrienne Huston, Jody Deming, and Claire Fraser
143. Complete Genome Sequence of Acidithiobacillus ferrooxidans Strain ATCC23270
Herve Tettelin, Keita Geer, Jessica Vamathevan, Florenta Riggs, Joel Malek, Maureen Levins, Mobolanle Ayodeji, Sofiya Shatsman, Getahun Tsegaye, Stephanie McGann, Robert J. Dodson, Robert Blake, and Claire Fraser
144. The Complete Genome Sequence of the Green Sulfur Bacterium Chlorobium tepidum
Jonathan A. Eisen, Karen E. Nelson, Ian T. Paulsen, John F. Heidelberg, Martin Wu, Robert J. Dodson, Robert Deboy, Michelle L. Gwinn, William C. Nelson, Daniel H. Haft, Erin K. Hickey, Jeremy D. Peterson, A. Scott Durkin, James L. Kolonay, Fan Yang, Ingeborg Holt, Lowell A. Umayam, Tanya Mason, Michael Brenner, Terrance P. Shea, Debbie Parksey, Tamara V. Feldblyum, Cheryl L. Hansen, M. Brook Craven, Diana Radune, Jessica Vamathevan, Hoda Khouri, Owen White, J. Craig Venter, Tanja M. Gruber, Karen A. Ketchum, Hervé Tettelin, Donald A. Bryant, and Claire M. Fraser
145. The Genome Sequences of Bacillus anthracis Strain Ames
T. D. Read, E. Holtzapple, and S. Peterson
146. The Complete Genome Sequence of Pseudomonas putida KT 2440
Karen E. Nelson, Burkhard Tuemmler, and Claire M. Fraser
147. Genome Sequence of Methylococcus capsulatus
Naomi Ward, Jonathan Eisen, Claire Fraser, George Dimitrov, Scott Durkin, Lingxia Jiang, Hoda Khouri, Katherine Lee, David Scanlan, Nils Kåre Birkeland, Live Bruseth, Ingvar Eidhammer, Svenn H. Grindhaug, Ingeborg Holt, Harald B. Jensen, Inge Jonasen, Øivind Larsen, and Johan Lillehaug
S. Stilwagen, P. F. Predki, A. Bhattacharyya, H. Feil, W. S. Feil, F. Larimer, K. Frankel, S. Lucas, D. Rokhsar, E. Branscomb, and T. Hawkins
P. Chain, W. Regala, L. Vergez, S. Stilwagen, F. Larimer, D. Arp, N. Hommes, A. Hooper, S. Chisholm, G. Rocap, B. Brahamsha, B. Palenik, and J. Lamerdin
Yuri Y. Londer, P. Raj Pokkuluri, William C. Long, and Marianne Schiffer
151. Microbial Metal and Metalloid Metabolism and Beyond
Lynda B. M. Ellis, Larry P. Wackett, Wenjun Kang, Bo Hou, and Tony Dodge
152. A Potential Thermobifida fusca Xyloglucan Degrading Operon
Diana Irwin, Mark Cheng, Bosong Xiang, and David B. Wilson
153. Proteome Flux in Photosynthesis and Respiration Mutants of Synechocystis sp. PCC 6803
Julian P. Whitelegge, Kym F. Faull, Robby Roberson, and Wim Vermaas
Ashlee M. Earl and John R. Battista
155. The Genome of a White Rot Fungus: How to Eat Dead Wood
Nicholas Putnam, Jarrod Chapman, Susan Lucas, Luis Larrondo, Maarten Gelpke, Kevin Helfenbein, Jeff Boore, Randy Berka, Doug Hyatt, Frank Larimer, Dan Cullen, Paul Predki, Trevor Hawkins, and Dan Rokhsar
156. Metabolic Pathway Elucidation for Microbial Genomes
Imran Shah, Ronald Taylor, and Shilpa Rao
157. Annotation of Shewanella oneidensis MR-1 from a Metabolic and Protein-Family View
Monica Riley and Margrethe H. Serres
158. Modeling DNA repair in Deinococcus radiodurans
Shwetal S. Patel and Jeremy S. Edwards
159. A Novel Combinatorial Biology Method to Functionally Characterize Microbial ORFs
Diane J. Rodi and Lee Makowski
160. Annotation of Draft Microbial Genomes
Frank W. Larimer, Loren Hauser, Miriam Land, Doug Hyatt, Manesh Shah, Philip LoCascio, Edward C. Uberbacher, and Inna Vokler
161. Annotation of Microbial Genomes Relevant to DOE’s Carbon Management and Sequestration Program
F. Larimer, L. Hauser, M. Land, D. Hyatt, M. Shah, S. Stilwagen, P. Predki, D. Arp, A. Hooper, S. Chisholm, G. Rocap, B. Palenik, J. Waterbury, R. Atlas, J. Meeks, C. Harwood, R. Tabita, P. Chain, and J. Lamerdin
162. A Genome-Wide Search for Archaeal Promoter Elements
Enhu Li, Aaron A. Best, Gretchen M. Colon, Claudia I. Reich, and Gary J. Olsen
163. New Markov Model Approaches to Deciphering Microbial Genome Function
John M. Logsdon, Jr., Mark. A. Ragan, and Mark Borodovsky
T. L. Marsh, S-H Kim, N. M. Isaacs, S. Eichorst, and K. Konstantinidis
165. Lateral Gene Transfer and the History of Bacterial Genomes
Howard Ochman
Michel Marharbiz, William Holtz, Roger Howe, and Jay D. Keasling
167. Optical Mapping: New Technologies and Applications
David C. Schwartz, Shiguo Zhou, Ana Garic-Stankovic, Alex
Lim, Eileen Dimalanta, Arvind Ramanathan, Tian Wu, Ossmat Azzam, Casey Lamers,
Brian Lepore, Aaron Anderson, Michael Bechner, Erika Kvikstad, Natalie Kaech,
Andrew Kile,
Jessica Severin, Rodney Runnheim, Danile Forrest, Christopher Churas, Galex
Yen, Jonathan Day, Bud Mishra, and Thomas Anantharaman
168. Spectroscopic Studies of Desulfovibrio desulfuricans Cytochrome c3
William H. Woodruff, Judy D. Wall, Robert J. Donohoe, and Geoffrey B. West
169. Identification and Isolation of Active, Non-Cultured Bacteria for Genome Analysis
Cheryl R. Kuske, Susan M. Barns, Ellie Redfield, and Leslie E. Sommerville
170. Assembly of Microbial Sub-Genomes from Beneath a Leaking High-Level Radioactive Waste Tank
Fred Brockman, Margie Romine, Greg Newton, Amber Alford, Shu-mei Li, Jim Fredrickson, Kristen Kadner, Paul Richardson, and Paul Predki
171. The Marine Environment from a Cyanobacterial Perspective
Brian Palenik, Ian Paulsen, Bianca Brahamsha, Rebecca Langlois, and John Waterbury
172. Metagenomic Analysis of Uncultured Cytophaga and Beta-1,4 Glycanases in Marine Consortia
David L. Kirchman and Matthew T. Cottrell
173. Rational Design and Application of DNA Signatures
P. Scott White, John Nolan, Rich Okinaka, Paul Jackson, and Paul Keim
174. Pathogen Detection: Successes and Limitations of TaqMan® PCR and Limitations of TaqMan® PCR
Shea N. Gardner, Thomas A. Kuczmarski, Elizabeth A. Vitalis, and Tom Slezak
J. A. Eisen, F. T. Robb, J. Gonzalez, T. Sokolova, L. J. Tallon, K. Jones, A. S. Durkin, and C. M. Fraser
Carloine S. Harwood
207. Environmental Genomics and Microbial Ecology
Edward F. DeLong
209. Microbial Defense Systems: Ecology, Evolution and Application
Margaret (Peg) Riley
211. Gene Transfer: Past and Present
Claudia I. Reich, Carl R. Woese, and Gary J. Olsen
212. Genomic Analysis of Geobacter Species Living in Pure Culture and in Subsurface Environments
Derek R. Lovley
George M. Garrity and Timothy G. Lilburn
P. Chain, W. Regala, L. Vergez, S. Stilwagen, F. Larimer, D. Arp, N. Hommes, A Hooper, S. Chisholm, G. Rocap, B. Brahamsha, B. Palenik, and J. Lamerdin
219. Analyzing the Metagenome: Accessing the Uncultured Microbial World
Jo Handelsman