Vol 5, No 3 (2011): Standards in Genomic Sciences
Table of Contents
Editorial/Commentary
The State of Standards in Genomic Sciences |
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| George M. Garrity |
Genome Report
Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria |
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| Jana Grote, Cansu Bayindirli, Kristin Bergauer, Paula Carpintero de Moraes, Huan Chen, Lindsay D’Ambrosio, Bethanie Edwards, Beatriz Fernández-Gómez, Mariam Hamisi, Ramiro Logares, Dan Nguyen, Yoshimi Rii, Emily Saeck, Charles Schutte, Brittany Widner, Matthew Church, Grieg Steward, David Karl, Edward F. DeLong, John Eppley, Stephan C. Schuster, Nikos Kyrpides, Michael Rappe |
Complete genome of the onion pathogen Enterobacter cloacae EcWSU1 |
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| Jodi L. Humann, Mark Wildung, Chun-Huai Cheng, Taein Lee, Jane E. Stewart, Jennifer C. Drew, Eric W. Triplett, Doreen Main, Brenda K. Schroeder |
Complete genome sequence of Hirschia baltica type strain (IFAM 1418T) |
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| Pamela Brown, David T. Kysela, Miguel A. De Pedro, Susan Lucas, Alex Copeland, Alla Lapidus, Tijana Glavina Del Rio, Hope Tice, David Bruce, Lynne Goodwin, Sam Pitluck, John C. Detter, Cliff Han, Frank Larimer, Yun-Juan Chang, Cynthia D. Jeffries, Miriam Land, Loren Hauser, Nikos C. Kyrpides, Natalia Ivanova, Galina Ovchinnikova, Brian J. Tindall, Markus Göker, Hans-Peter Klenk, Yves V. Brun |
Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T) |
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| David Schleheck, Michael Weiss, Sam Pitluck, David Bruce, Miriam L. Land, Shunsheng Han, Roxanne Tapia, Chris C. Detter, Thomas Brettin, James Han, Tanja Woyke, Lynne Goodwin, Len Pennacchio, Matt Nolan, Alasdair M. Cook, Staffan Kjelleberg, Torsten Thomas |
Complete genome sequence of Allochromatium vinosum DSM 180T |
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| Thomas Weissgerber, Renate Zigann, David Bruce, Yun-Juan Chang, John C. Detter, Cliff Han, Loren Hauser, Cynthia D. Jeffries, Miriam Land, A. Christine Munk, Roxanne Tapia, Christine Dahl |
Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1 |
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| Mun Su Rhee, Brélan E. Moritz, Gary Xie, Tijana Glavina Del Rio, Eileen Dalin, Hope Tice, David Bruce, Lynne Goodwin, Olga Chertkov, Thomas Brettin, Cliff Han, Chris C. Detter, Sam Pitluck, Miriam Land, Milind Patel, Mark Ou, Roberta Harbrucker, Lonnie O. Ingram, KT Shanmugam |
Complete genome sequence of Thioalkalivibrio sp. K90mix |
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| Gerard Muyzer, Dimitry Y. Sorokin, Konstantinos Mavromatis, Alla Lapidus, Brian Foster, Hui Sun, Natalia Ivanova, Amrita Pati, Patrik d'Haeseleer, Tanja Woyke, Nikos C. Kyrpides |
Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T) |
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| Hajnalka Kiss, Markus Nett, Nicole Domin, Karin Martin, Julia A. Maresca, Alex Copeland, Alla Lapidus, Susan Lucas, Kerrie Berry, Tijana Glavina Del Rio, Eileen Dalin, Hope Tice, Sam Pitluck, Paul Richardson, David Bruce, Lynne Goodwin, Cliff Han, John C. Detter, Jeremy Schmutz, Thomas Brettin, Miriam Land, Loren Hauser, Nikos C. Kyrpides, Natalia Ivanova, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Donald A. Bryant |
Complete genome sequence of Desulfurispirillum indicum strain S5T |
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| Elisabetta Bini, Ines Rauschenbach, Priya Narasingarao, Valentin Starovoyotov, Lauren Hauser, Cynthia D. Jeffries, Miriam Land, David Bruce, Chris C. Detter, Lynne Goodwin, Shunsheng Han, Brittany Held, Roxanne Tapia, Alex Copeland, Natalia Ivanova, Natalia Mikhailova, Matt Nolan, Amrita Pati, Len Pennacchio, Sam Pitluck, Tanja Woyke, Max Häggblom |
Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T) |
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| Alex Copeland, Kathleen O'Connor, Susan Lucas, Alla Lapidus, Kerrie Berry, John C. Detter, Tijana Glavina Del Rio, Nancy Hammon, Eileen Dalin, Hope Tice, Sam Pitluck, David Bruce, Lynne Goodwin, Cliff Han, Roxanne Tapia, Elizabeth Saunders, Jeremy Schmutz, Thomas Brettin, Frank Larimer, Miriam Land, Loren Hauser, Carmen Vargas, Joaquin J. Nieto, Nikos C. Kyrpides, Natalia Ivanova, Markus Göker, Hans-Peter Klenk, Laszlo N. Csonka, Tanja Woyke |
High quality draft genome sequence of Segniliparus rugosus CDC 945T= (ATCC BAA-974T) |
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| Ashlee M. Earl, Christopher A. Desjardins, Michael G. Fitzgerald, Harindra M. Arachchi, Qiandong Zeng, Teena Mehta, Allison Griggs, Bruce W. Birren, Nadege C. Toney, Janice Carr, James Posey, W. Ray Butler |
Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T) |
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| Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Evelyne Brambilla, Manfred Rohde, Birte Abt, Susanne Verbag, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, Tanja Woyke |
Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent |
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| Markus Göker, Hajnalka Daligault, Romano Mwirichia, Alla Lapidus, Susan Lucas, Shweta Deshpande, Ioanna Pagani, Roxanne Tapia, Jan-Fang Cheng, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Cliff Han, Miriam Land, Loren Hauser, Chongle Pan, Evelyne-Marie Brambilla, Manfred Rohde, Stefan Spring, Johannes Sikorski, Reinhard Wirth, John C. Detter, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk |
Genome sequences published outside of Standards in Genomic Sciences, December 2011 |
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| Oranmiyan W. Nelson, George M. Garrity |
Standard Operating Procedure
SOP for pathway inference in Integrated Microbial Genomes (IMG) |
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| Iain J. Anderson, Amy Chen, Victor Markowitz, Nikos C. Kyrpides, Natalia Ivanova |
The Pathway Tools Pathway Prediction Algorithm |
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| Peter Karp, Mario Latendresse, Ron Caspi |
This work is licensed under a Creative Commons Attribution 3.0 License.
Acknowledgements
We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.
Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.
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