Standards in Genomic Sciences

Volume 7, Issue 1

Short Genome Reports

Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov.

Ajay Kumar Mishra, Jean-Christophe Lagier, Catherine Robert, Didier Raoult and Pierre-Edouard Fournier

Stand Genomic Sci 2012; 7(1):1-11

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Short Genome Reports

Complete genome sequence of Treponema pallidum strain DAL-1

Marie Zobaníková, Pavol Mikolka, Darina čejková, Petra Pospíšilová, Lei Chen, Michal Strouhal, Xiang Qin, George M. Weinstock and David Šmajs

Stand Genomic Sci 2012; 7(1):12-21

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Short Genome Reports

Complete genome sequence of the plant-associated Serratia plymuthica strain AS13

Saraswoti Neupane, Roger D. Finlay, Nikos C. Kyrpides, Lynne Goodwin, Sadhna Alström, Susan Lucas, Miriam Land, James Han, Alla Lapidus, Jan-Fang Cheng, David Bruce, Sam Pitluck, Lin Peters, Galina Ovchinnikova, Brittany Held, Cliff Han, John C. Detter, Roxanne Tapia, Loren Hauser, Natalia Ivanova, Ioanna Pagani, Tanja Woyke, Hans-Peter Klenk and Nils Högberg

Stand Genomic Sci 2012; 7(1):22-30

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Short Genome Reports

Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181T)

Patricia Lucas-Elío, Lynne Goodwin, Tanja Woyke, Sam Pitluck, Matt Nolan, Nikos C. Kyrpides, Janine C. Detter, Alex Copeland, Megan Lu, David Bruce, Chris Detter, Roxanne Tapia, Shunsheng Han, Miriam L. Land, Natalia Ivanova, Natalia Mikhailova, Andrew W.B. Johnston and Antonio Sanchez-Amat

Stand Genomic Sci 2012; 7(1):31-43

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Short Genome Reports

Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093T)

Ulrike Kappler, Karen Davenport, Scott Beatson, Susan Lucas, Alla Lapidus, Alex Copeland, Kerrie W. Berry, Tijana Glavina Del Rio, Nancy Hammon, Eileen Dalin, Hope Tice, Sam Pitluck, Paul Richardson, David Bruce, Lynne A. Goodwin, Cliff Han, Roxanne Tapia, John C. Detter, Yun-juan Chang, Cynthia D. Jeffries, Miriam Land, Loren Hauser, Nikos C. Kyrpides, Markus Göker, Natalia Ivanova, Hans-Peter Klenk and Tanja Woyke

Stand Genomic Sci 2012; 7(1):44-58

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Short Genome Reports

Complete genome sequence of Terriglobus saanensis type strain SP1PR4T, an Acidobacteria from tundra soil

Suman R. Rawat, Minna K. Männistö, Valentin Starovoytov, Lynne Goodwin, Matt Nolan, Lauren Hauser, Miriam Land, Karen Walston Davenport, Tanja Woyke and Max M. Häggblom

Stand Genomic Sci 2012; 7(1):59-69

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Short Genome Reports

Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov.

Ajay Kumar Mishra, Jean-Christophe Lagier, Romain Rivet, Didier Raoult and Pierre-Edouard Fournier

Stand Genomic Sci 2012; 7(1):70-81

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Short Genome Reports

Complete genome sequence of Thermovibrio ammonificans HB-1T, a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent

Donato Giovannelli, Jessica Ricci, Ileana Pérez-Rodríguez, Michael Hügler, Charles OʼBrien, Ramaydalis Keddis, Ashley Grosche, Lynne Goodwin, David Bruce, Karen W. Davenport, Chris Detter, James Han, Shunsheng Han, Natalia Ivanova, Miriam L. Land, Natalia Mikhailova, Matt Nolan, Sam Pitluck, Roxanne Tapia, Tanja Woyke and Costantino Vetriani

Stand Genomic Sci 2012; 7(1):82-90

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Short Genome Reports

Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOBT)

Caroline M. Plugge, Anne M. Henstra, Petra Worm, Daan C. Swarts, Astrid H. Paulitsch-Fuchs, Johannes C.M. Scholten, Athanasios Lykidis, Alla L. Lapidus, Eugene Goltsman, Edwin Kim, Erin McDonald, Lars Rohlin, Bryan R. Crable, Robert P. Gunsalus, Alfons J.M. Stams and Michael J. McInerney

Stand Genomic Sci 2012; 7(1):91-106

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Short Genome Reports

Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282T)

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

Stand Genomic Sci 2012; 7(1):107-119

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Short Genome Reports

Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801T)

Thomas Riedel, Brittany Held, Matt Nolan, Susan Lucas, Alla Lapidus, Hope Tice, Tijana Glavina Del Rio, Jan-Fang Cheng, Cliff Han, Roxanne Tapia, Lynne A. Goodwin, Sam Pitluck, Konstantinos Liolios, Konstantinos Mavromatis, Ioanna Pagani, Natalia Ivanova, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Manfred Rohde, Brian J. Tindall, John C. Detter, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk and Nikos C. Kyrpides

Stand Genomic Sci 2012; 7(1):120-130

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Announcements

Community Dialog

Report from the First Snake Genomics and Integrative Biology Meeting

Todd A. Castoe, Edward L. Braun, Anne M. Bronikowski, Christian L. Cox, Alison R. Davis Rabosky, A.P. Jason de Koning, Jason Dobry, Matthew K. Fujita, Matt W Giorgianni, Adam Hargreaves, Christiaan V. Henkel, Stephen P. Mackessy, Denis OʼMeally, Darin R. Rokyta, Stephen M. Secor, Jeffrey W. Streicher, Kenneth P. Wray, Ken D. Yokoyama and David D. Pollock

Stand Genomic Sci 2012; 7(1):150-152

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Community Dialog

RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011

Robert J. Robbins, Guy Cochrane, Neil Davies, Peter Dawyndt, Renzo Kottmann, Leonard (Kris) Krishtalka, Norman Morrison, Éamonn Ó Tuama, Inigo San Gil and John Wooley

Stand Genomic Sci 2012; 7(1):153-158

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Community Dialog

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011

Robert J. Robbins, Linda Amaral-Zettler, Holly Bik, Stan Blum, James Edwards, Dawn Field, George Garrity, Jack A. Gilbert, Renzo Kottmann, Leonard Krishtalka, Hilmar Lapp, Carolyn Lawrence, Norman Morrison, Éamonn Ó Tuama, Cynthia Parr, Inigo San Gil, David Schindel, Lynn Schriml, David Vieglas and John Wooley

Stand Genomic Sci 2012; 7(1):159-165

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Community Dialog

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012)

Éamonn Ó Tuama, John Deck, Gabriel Dröge, Markus Döring, Dawn Field, Renzo Kottmann, Juncai Ma, Hiroshi Mori, Norman Morrison, Peter Sterk, Hideaki Sugawara, John Wieczorek, Linhuan Wu and Pelin Yilmaz

Stand Genomic Sci 2012; 7(1):166-170

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Community Dialog

RCN4GSC Meeting Report: Initiating a Testbed for Managing Data at the Interface of Biodiversity and Genomics/Metagenomics, May 2011

Robert J. Robbins, James Beach, Stan Blum, Peter Dawyndt, John Deck, Renzo Kottmann, Norman Morrison, Éamonn Ó Tuama, Inigo San Gil, David Vieglas, John Wieczorek and John Wooley

Stand Genomic Sci 2012; 7(1):171-174

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White Papers

Cephalopod genomics: A plan of strategies and organization

Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman, Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang and Clifton W. Ragsdale

Stand Genomic Sci 2012; 7(1):175-188

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