Standards in Genomic Sciences

Volume 4, Issue 2

Editorial/Commentary

Short Genome Reports

Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse

Monica Takamiya, Asli Ozen, Morten Rasmussen, Thomas Alter, Tom Gilbert, Dave W. Ussery and Susanne Knøchel

Stand Genomic Sci 2011; 4(2):113-122

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Short Genome Reports

Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3)

Aristeidis Kallimanis, Kurt M. LaButti, Alla Lapidus, Alicia Clum, Athanasios Lykidis, Kostantinos Mavromatis, Ioanna Pagani, Konstantinos Liolios, Natalia Ivanova, Lynne Goodwin, Sam Pitluck, Amy Chen, Krishna Palaniappan, Victor Markowitz, Jim Bristow, Athanasios D. Velentzas, Angelos Perisynakis, Christos C. Ouzounis, Nikos C. Kyrpides, Anna I. Koukkou and Constantin Drainas

Stand Genomic Sci 2011; 4(2):123-130

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Short Genome Reports

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6T)

Ahmet Zeytun, Johannes Sikorski, Matt Nolan, Alla Lapidus, Susan Lucas, James Han, Hope Tice, Jan-Fang Cheng, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Olivier D. Ngatchou-Djao, Miriam Land, Loren Hauser, Cynthia D. Jeffries, Cliff Han, John C. Detter, Susanne Übler, Manfred Rohde, Brian J. Tindall, Markus Göker, Reinhard Wirth, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk and Nikos C. Kyrpides

Stand Genomic Sci 2011; 4(2):131-143

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Short Genome Reports

Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845T)

Konstantinos Mavromatis, Megan Lu, Monica Misra, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxane Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, John C. Detter, Evelyne-Marie Brambilla, Manfred Rohde, Markus Göker, Sabine Gronow, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk and Nikos C. Kyrpides

Stand Genomic Sci 2011; 4(2):144-153

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Short Genome Reports

Complete genome sequence of Marivirga tractuosa type strain (H-43T)

Ioanna Pagani, Olga Chertkov, Alla Lapidus, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Matt Nolan, Elizabeth Saunders, Sam Pitluck, Brittany Held, Lynne Goodwin, Konstantinos Liolios, Galina Ovchinikova, Natalia Ivanova, Konstantinos Mavromatis, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, John C. Detter, Cliff Han, Roxanne Tapia, Olivier D. Ngatchou-Djao, Manfred Rohde, Markus Göker, Stefan Spring, Johannes Sikorski, Tanja Woyke, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk and Nikos C. Kyrpides

Stand Genomic Sci 2011; 4(2):154-162

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Short Genome Reports

Complete genome sequence of Deinococcus maricopensis type strain (LB-34T)

Rüdiger Pukall, Ahmet Zeytun, Susan Lucas, Alla Lapidus, Nancy Hammon, Shweta Deshpande, Matt Nolan, Jan-Fang Cheng, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Mikhailova, Natalia Ivanova, Konstantinos Mavromatis, Amrita Pati, Roxane Tapia, Cliff Han, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Evelyne-Marie Brambilla, Manfred Rohde, Markus Göker, J. Chris Detter, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides and Hans-Peter Klenk

Stand Genomic Sci 2011; 4(2):163-172

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Short Genome Reports

Complete genome sequence of Desulfurococcus mucosus type strain (O7/1T)

Reinhard Wirth, Olga Chertkov, Brittany Held, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxane Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Pagani Ioanna, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Yvonne Bilek, Thomas Hader, Manfred Rohde, Stefan Spring, Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides and Hans-Peter Klenk

Stand Genomic Sci 2011; 4(2):173-182

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Short Genome Reports

Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106)

Ben Temperton, Simon Thomas, Karen Tait, Helen Parry, Matt Emery, Mike Allen, John Quinn, John MacGrath and Jack Gilbert

Stand Genomic Sci 2011; 4(2):183-190

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Short Genome Reports

Complete genome sequence of Bacteroides salanitronis type strain (BL78T)

Sabine Gronow, Brittany Held, Susan Lucas, Alla Lapidus, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Shweta Deshpande, Jan-Fang Cheng, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Amrita Pati, Roxane Tapia, Cliff Han, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Evelyne-Marie Brambilla, Manfred Rohde, Markus Göker, John C. Detter, Tanja Woyke, James Bristow, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk and Jonathan A. Eisen

Stand Genomic Sci 2011; 4(2):191-199

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Short Genome Reports

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6T)

Markus Göker, Sabine Gronow, Ahmet Zeytun, Matt Nolan, Susan Lucas, Alla Lapidus, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinikova, Amrita Pati, Roxane Tapia, Cliff Han, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, Evelyne-Marie Brambilla, Manfred Rohde, John C. Detter, Tanja Woyke, James Bristow, Victor Markowitz, Philip Hugenholtz, Jonathan A. Eisen, Nikos C. Kyrpides and Hans-Peter Klenk

Stand Genomic Sci 2011; 4(2):200-209

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Short Genome Reports

Complete genome sequence ofOceanithermus profundus type strain (506T)

Amrita Pati, Xiaojing Zhang, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxane Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Loren Hauser, Cynthia D. Jeffries, Evelyne-Marie Brambilla, Alina Röhl, Romano Mwirichia, Manfred Rohde, Brian J. Tindall, Johannes Sikorski, Reinhard Wirth, Markus Göker, Tanja Woyke, John C. Detter, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk and Miriam Land

Stand Genomic Sci 2011; 4(2):210-220

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Short Genome Reports

Complete genome sequence of Cellulophaga lytica type strain (LIM-21T)

Amrita Pati, Birte Abt, Hazuki Teshima, Matt Nolan, Alla Lapidus, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxane Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Konstantinos Mavromatis, Galina Ovchinikova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, John C. Detter, Evelyne-Marie Brambilla, K. Palani Kannan, Manfred Rohde, Stefan Spring, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk and Natalia Ivanova

Stand Genomic Sci 2011; 4(2):221-232

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Short Genome Reports

Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139T)

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

Stand Genomic Sci 2011; 4(2):233-243

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Short Genome Reports

The IGS Standard Operating Procedure for Automated Prokaryotic Annotation

Kevin Galens, Joshua Orvis, Sean Daugherty, Heather H. Creasy, Sam Angiuoli, Owen White, Jennifer Wortman, Anup Mahurkar and Michelle Gwinn Giglio

Stand Genomic Sci 2011; 4(2):244-251

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Short Genome Reports

Meeting report of the RNA Ontology Consortium January 8-9, 2011

Amanda Birmingham, Jose C. Clemente, Narayan Desai, Jack Gilbert, Antonio Gonzalez, Nikos Kyrpides, Folker Meyer, Eric Nawrocki, Peter Sterk, Jesse Stombaugh, Zasha Weinberg, Doug Wendel, Neocles B. Leontis, Craig Zirbel, Rob Knight and Alain Laederach

Stand Genomic Sci 2011; 4(2):252-256

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White Papers

A proposal to sequence the genome of a garter snake (Thamnophis sirtalis)

Todd A. Castoe, Anne M. Bronikowski, Edmund D. Brodie, Scott V. Edwards, Michael E. Pfrender, Michael D. Shapiro, David D. Pollock and Wesley C. Warren

Stand Genomic Sci 2011; 4(2):257-270

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Research Articles

Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard

Melissa Beth Duhaime, Renzo Kottmann, Dawn Field and Frank Oliver Glöckner

Stand Genomic Sci 2011; 4(2):271-285

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Short Genome Reports

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets

Norman Morrison, David Hancock, Lynette Hirschman, Peter Dawyndt, Bert Verslyppe, Nikos Kyrpides, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner, Jeff Grethe, Tim Booth, Peter Sterk, Goran Nenadic and Dawn Field

Stand Genomic Sci 2011; 4(2):286-292

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