Standards in Genomic Sciences

Volume 5, Issue 3

Editorial/Commentary

The State of Standards in Genomic Sciences

George M. Garrity

Stand Genomic Sci 2011; 5(3):262-268

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Short Genome Reports

Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria

Jana Grote, Cansu Bayindirli, Kristin Bergauer, Paula Carpintero de Moraes, Huan Chen, Lindsay DʼAmbrosio, Bethanie Edwards, Beatriz Fernández-Gómez, Mariam Hamisi, Ramiro Logares, Dan Nguyen, Yoshimi M. Rii, Emily Saeck, Charles Schutte, Brittany Widner, Matthew J. Church, Grieg F. Steward, David M. Karl, Edward F. DeLong, John M. Eppley, Stephan C. Schuster, Nikos C. Kyrpides and Michael S. Rappé

Stand Genomic Sci 2011; 5(3):269-278

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Short Genome Reports

Complete genome of the onion pathogen Enterobacter cloacae EcWSU1

Jodi L. Humann, Mark Wildung, Chun-Huai Cheng, Taein Lee, Jane E. Stewart, Jennifer C. Drew, Eric W. Triplett, Doreen Main and Brenda K. Schroeder

Stand Genomic Sci 2011; 5(3):279-286

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Short Genome Reports

Complete genome sequence of Hirschia baltica type strain (IFAM 1418T)

Olga Chertkov, Pamela J.B. 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 and Yves V. Brun

Stand Genomic Sci 2011; 5(3):287-297

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Short Genome Reports

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T)

David Schleheck, Michael Weiss, Sam Pitluck, David Bruce, Miriam L. Land, Shunsheng Han, Elizabeth Saunders, Roxanne Tapia, Chris Detter, Thomas Brettin, James Han, Tanja Woyke, Lynne Goodwin, Len Pennacchio, Matt Nolan, Alasdair M. Cook, Staffan Kjelleberg and Torsten Thomas

Stand Genomic Sci 2011; 5(3):298-310

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Short Genome Reports

Complete genome sequence of Allochromatium vinosum DSM 180T

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 and Christiane Dahl

Stand Genomic Sci 2011; 5(3):311-330

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Short Genome Reports

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Mun Su Rhee, Brélan E. Moritz, Gary Xie, T. Glavina del Rio, E. Dalin, H. Tice, D. Bruce, L. Goodwin, O. Chertkov, T. Brettin, C. Han, C. Detter, S. Pitluck, Miriam L. Land, Milind Patel, Mark Ou, Roberta Harbrucker, Lonnie O. Ingram and K. T. Shanmugam

Stand Genomic Sci 2011; 5(3):331-340

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Short Genome Reports

Complete genome sequence of Thioalkalivibrio sp. K90mix

Gerard Muyzer, Dimitry Y. Sorokin, Konstantinos Mavromatis, Alla Lapidus, Brian Foster, Hui Sun, Natalia Ivanova, Amrita Pati, Patrik Dʼhaeseleer, Tanja Woyke and Nikos C. Kyrpides

Stand Genomic Sci 2011; 5(3):341-355

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Short Genome Reports

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)

Hajnalka Kiss, Markus Nett, Nicole Domin, Karin Martin, Julia A. Maresca, Alex Copeland, Alla Lapidus, Susan Lucas, Kerrie W. 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 and Donald A. Bryant

Stand Genomic Sci 2011; 5(3):356-370

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Short Genome Reports

Complete genome sequence of Desulfurispirillum indicum strain S5T

Elisabetta Bini, Ines Rauschenbach, Priya Narasingarao, Valentin Starovoytov, Lauren Hauser, Cynthia D. Jeffries, Miriam Land, David Bruce, Chris 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 and Max Häggblom

Stand Genomic Sci 2011; 5(3):371-378

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Short Genome Reports

Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T)

Alex Copeland, Kathleen OʼConnor, Susan Lucas, Alla Lapidus, Kerrie W. 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 and Tanja Woyke

Stand Genomic Sci 2011; 5(3):379-388

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Short Genome Reports

High quality draft genome sequence of Segniliparus rugosus CDC 945T= (ATCC BAA-974T)

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 and W. Ray Butler

Stand Genomic Sci 2011; 5(3):389-397

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Short Genome Reports

Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T)

Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Marcel Huntemann, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Evelyne-Marie Brambilla, Manfred Rohde, Birte Abt, Susanne Verbarg, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk and Tanja Woyke

Stand Genomic Sci 2011; 5(3):398-406

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Short Genome Reports

Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent

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 and Hans-Peter Klenk

Stand Genomic Sci 2011; 5(3):407-415

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Standard Operating Procedures

SOP for pathway inference in Integrated Microbial Genomes (IMG)

Iain Anderson, Amy Chen, Victor Markowitz, Nikos Kyrpides and Natalia Ivanova

Stand Genomic Sci 2011; 5(3):420-423

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Short Genome Reports

The Pathway Tools Pathway Prediction Algorithm

Peter D. Karp, Mario Latendresse and Ron Caspi

Stand Genomic Sci 2011; 5(3):424-429

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