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  1. Anaerococcus senegalensis strain JC48T sp. nov. is the type strain of A. senegalensis sp. nov. a new species within the genus Anaerococcus. This strain whose genome is described here was isolated from the fecal f...

    Authors: Jean-Christophe Lagier, Khalid El Karkouri, Thi-Tien Nguyen, Fabrice Armougom, Didier Raoult and Pierre-Edouard Fournier
    Citation: Standards in Genomic Sciences 2012 6:6010116
  2. Clostridium clariflavum is a Cluster III Clostridium within the family Clostridiaceae isolated from thermophilic anaerobic sludge (Shiratori et al, 2009). This species is of interest because of its similarity to ...

    Authors: Javier A. Izquierdo, Lynne Goodwin, Karen W. Davenport, Hazuki Teshima, David Bruce, Chris Detter, Roxanne Tapia, Shunsheng Han, Miriam Land, Loren Hauser, Cynthia D. Jeffries, James Han, Sam Pitluck, Matt Nolan, Amy Chen, Marcel Huntemann…
    Citation: Standards in Genomic Sciences 2012 6:6010104
  3. Sulfuricurvum kujiense Kodama and Watanabe 2004 is the type species of the monotypic genus Sulfuricurvum, which belongs to the family Helicobacteraceae in the class Epsilonproteobacteria. The species is of intere...

    Authors: Cliff Han, Oleg Kotsyurbenko, Olga Chertkov, Brittany Held, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Lynne A. Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova…
    Citation: Standards in Genomic Sciences 2012 6:6010094
  4. Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1T is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest becaus...

    Authors: Linda Meincke, Alex Copeland, Alla Lapidus, Susan Lucas, Kerrie W. Berry, Tijana Glavina Del Rio, Nancy Hammon, Eileen Dalin, Hope Tice, Sam Pitluck, Paul Richardson, David Bruce, Lynne Goodwin, Cliff Han, Roxanne Tapia, John C. Detter…
    Citation: Standards in Genomic Sciences 2012 6:6010074
  5. Serratia plymuthica are plant-associated, plant beneficial species belonging to the family Enterobacteriaceae. The members of the genus Serratia are ubiquitous in nature and their life style varies from endophyti...

    Authors: Saraswoti Neupane, Nils Högberg, Sadhna Alström, Susan Lucas, James Han, Alla Lapidus, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Lin Peters, Galina Ovchinnikova, Megan Lu, Cliff Han, John C. Detter, Roxanne Tapia…
    Citation: Standards in Genomic Sciences 2012 6:6010054
  6. Arthrospira platensis is a cyanobacterium that is extensively cultivated outdoors on a large commercial scale for consumption as a food for humans and animals. It can be grown in monoculture under highly alkaline...

    Authors: Supapon Cheevadhanarak, Kalyanee Paithoonrangsarid, Peerada Prommeenate, Warunee Kaewngam, Apiluck Musigkain, Somvong Tragoonrung, Satoshi Tabata, Takakazu Kaneko, Jeerayut Chaijaruwanich, Duangjai Sangsrakru, Sithichoke Tangphatsornruang, Juntima Chanprasert, Sissades Tongsima, Kanthida Kusonmano, Wattana Jeamton, Sudarat Dulsawat…
    Citation: Standards in Genomic Sciences 2012 6:6010043
  7. Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the ...

    Authors: Iain Anderson, Brian J. Tindall, Manfred Rohde, Susan Lucas, James Han, Alla Lapidus, Jan-Fang Cheng, Lynne Goodwin, Sam Pitluck, Lin Peters, Amrita Pati, Natalia Mikhailova, Ioanna Pagani, Hazuki Teshima, Cliff Han, Roxanne Tapia…
    Citation: Standards in Genomic Sciences 2012 6:6010031
  8. Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1T was the first isolate within the phylum “Thermus-Deinococcus” to exhibit optimal growt...

    Authors: Alex Copeland, Wei Gu, Montri Yasawong, Alla Lapidus, Susan Lucas, Shweta Deshpande, Ioanna Pagani, Roxanne Tapia, Jan-Fang Cheng, Lynne A. Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati…
    Citation: Standards in Genomic Sciences 2012 6:6010021
  9. Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii. This strain is of interest because it is one of f...

    Authors: Megan J. Huggett, Darin H. Hayakawa and Michael S. Rappé
    Citation: Standards in Genomic Sciences 2012 6:6010011
  10. Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan...

    Authors: Virginia Chow, Guang Nong, Franz J. St. John, John D. Rice, Ellen Dickstein, Olga Chertkov, David Bruce, Chris Detter, Thomas Brettin, James Han, Tanja Woyke, Sam Pitluck, Matt Nolan, Amrita Pati, Joel Martin, Alex Copeland…
    Citation: Standards in Genomic Sciences 2012 6:6010001
  11. The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes. This article provides a detailed presentation of the PathoLogic algorithm. T...

    Authors: Peter D. Karpe, Mario Latendresse and Ron Caspi
    Citation: Standards in Genomic Sciences 2011 5:5030424
  12. One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG ter...

    Authors: Iain Anderson, Amy Chen, Victor Markowitz, Nikos Kyrpides and Natalia Ivanova
    Citation: Standards in Genomic Sciences 2011 5:5030420
  13. Desulfurobacterium thermolithotrophum L’Haridon et al. 1998 is the type species of the genus Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of interest because it represents ...

    Authors: 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…
    Citation: Standards in Genomic Sciences 2011 5:5030407
  14. Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not ...

    Authors: 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…
    Citation: Standards in Genomic Sciences 2011 5:5030398
  15. Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus in the family Segniliparaceae. A unique and interesting feature of this family is the presence of extremely long carbon...

    Authors: 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
    Citation: Standards in Genomic Sciences 2011 5:5030389
  16. Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called ‘moderately halophilic bacteria’ current...

    Authors: Alex Copeland, Kathleen O’Connor, 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…
    Citation: Standards in Genomic Sciences 2011 5:5030379
  17. Desulfurispirillum indicum strain S5T is a strictly anaerobic bacterium isolated from river sediment in Chennai, India. D. indicum belongs to the deep branching phylum of Chrysiogenetes, which currently only incl...

    Authors: 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…
    Citation: Standards in Genomic Sciences 2011 5:5030371
  18. Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the ph...

    Authors: 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…
    Citation: Standards in Genomic Sciences 2011 5:5030356
  19. Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was is...

    Authors: Gerard Muyzer, Dimitry Y. Sorokin, Konstantinos Mavromatis, Alla Lapidus, Brian Foster, Hui Sun, Natalia Ivanova, Amrita Pati, Patrik D’haeseleer, Tanja Woyke and Nikos C. Kyrpides
    Citation: Standards in Genomic Sciences 2011 5:5030341
  20. Bacillus coagulans is a ubiquitous soil bacterium that grows at 50–55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacte...

    Authors: 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…
    Citation: Standards in Genomic Sciences 2011 5:5030331
  21. Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacterium belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus Allochromatium contains curre...

    Authors: 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
    Citation: Standards in Genomic Sciences 2011 5:5030311
  22. Parvibaculum lavamentivorans DS-1T is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1T ...

    Authors: 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…
    Citation: Standards in Genomic Sciences 2011 5:5030298
  23. The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the comp...

    Authors: 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…
    Citation: Standards in Genomic Sciences 2011 5:5030287
  24. Previous studies have shown that the members of the Enterobacter cloacae complex are difficult to differentiate with biochemical tests and in phylogenetic studies using multilocus sequence analysis, strains of th...

    Authors: 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
    Citation: Standards in Genomic Sciences 2011 5:5030279
  25. Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain is of interest because it is one of the first known isolates from a globally ubiquitous clade of marine bacteria known...

    Authors: 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 M. Rii, Emily Saeck, Charles Schutte, Brittany Widner, Matthew J. Church…
    Citation: Standards in Genomic Sciences 2011 5:5030269
  26. ClaMS — “Classifier for Metagenomic Sequences” — is a Java application for binning assembled contigs in metagenomes using user-specified training sets and initial parameters. Since ClaMS trains on sequence com...

    Authors: Amrita Pati, Lenwood S. Heath, Nikos C. Kyrpides and Natalia Ivanova
    Citation: Standards in Genomic Sciences 2011 5:5020248
  27. This report details the outcome of the 1st International Earth Microbiome Project Conference. The 2-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on the 14th–15th June 2011, and was hos...

    Authors: Jack A. Gilbert, Mark Bailey, Dawn Field, Noah Fierer, Jed A. Fuhrman, Bin Hu, Janet Jansson, Rob Knight, George A. Kowalchuk, Nikos C. Kyrpides, Folker Meyer and Rick Stevens
    Citation: Standards in Genomic Sciences 2011 5:5020243
  28. The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This rep...

    Authors: Nicolas Le Novère, Michael Hucka, Nadia Anwar, Gary D. Bader, Emek Demir, Stuart Moodie and Anatoly Sorokin
    Citation: Standards in Genomic Sciences 2011 5:5020230
  29. Genotyping experiments are widely used in clinical and basic research laboratories to identify associations between genetic variations and normal/abnormal phenotypes. Genotyping assay techniques vary from sing...

    Authors: Jie Huang, Daniel Mirel, Elizabeth Pugh, Chao Xing, Peter N. Robinson, Alexander Pertsemlidis, LiangHao Ding, Julia Kozlitina, Joseph Maher, Jonathan Rios, Michael Story, Nishanth Marthandan and Richard H. Scheuermann
    Citation: Standards in Genomic Sciences 2011 5:5020224
  30. We present MINEMO (Minimal Information for Neural ElectroMagnetic Ontologies), a checklist for the description of event-related potentials (ERP) studies. MINEMO extends MINI (Minimal Information for Neuroscience ...

    Authors: Gwen Frishkoff, Jason Sydes, Kurt Mueller, Robert Frank, Tim Curran, John Connolly, Kerry Kilborn, Dennis Molfese, Charles Perfetti and Allen Malony
    Citation: Standards in Genomic Sciences 2011 5:5020211
  31. Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit mi...

    Authors: J. D. Neufeld, K. Engel, J. Cheng, G. Moreno-Hagelsieb, D. R. Rose and T. C. Charles
    Citation: Standards in Genomic Sciences 2011 5:5020203
  32. This report summarizes the proceedings of the 2nd Annual Argonne Soils Workshop held at Argonne National Laboratory October 6–8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, m...

    Authors: Sarah L. O’Brien, Elizabeth M. Glass, Jennifer M. Brulc, Jack A. Gilbert, Dionysios A. Antonopoulos and Folker Meyer
    Citation: Standards in Genomic Sciences 2011 5:5020198
  33. The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is ...

    Authors: Oranmiyan W. Nelson and George M. Garrity
    Citation: Standards in Genomic Sciences 2011 5:5010154
  34. Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of deg...

    Authors: Aristeidis Kallimanis, Eugenia Karabika, Kostantinos Mavromatis, Alla Lapidus, Kurt M. LaButti, Konstantinos Liolios, Natalia Ivanova, Lynne Goodwin, Tanja Woyke, Athanasios D. Velentzas, Angelos Perisynakis, Christos C. Ouzounis, Nikos C. Kyrpides, Anna I. Koukkou and Constantin Drainas
    Citation: Standards in Genomic Sciences 2011 5:5010144
  35. Caminibacter mediatlanticus strain TB-2T [1], is a thermophilic, anaerobic, chemolithoautotrophic bacterium, isolated from the walls of an active deep-sea hydrothermal vent chimney on the Mid-Atlantic Ridge and t...

    Authors: Donato Giovannelli, Steven Ferriera, Justin Johnson, Saul Kravitz, Ileana Pérez-Rodríguez, Jessica Ricci, Charles O’Brien, James W. Voordeckers, Elisabetta Bini and Costantino Vetriani
    Citation: Standards in Genomic Sciences 2011 5:5010135
  36. Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene fr...

    Authors: Olga Chertkov, Alex Copeland, Susan Lucas, Alla Lapidus, Kerrie W. Berry, John C. Detter, Tijana Glavina Del Rio, Nancy Hammon, Eileen Dalin, Hope Tice, Sam Pitluck, Paul Richardson, David Bruce, Lynne Goodwin, Cliff Han, Roxanne Tapia…
    Citation: Standards in Genomic Sciences 2011 5:5010112
  37. Flexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the family Deferribacteraceae. The species is of interest because of its isolated phylogenetic location in a genomically ...

    Authors: Alla Lapidus, Olga Chertkov, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Marcel Huntemann, Konstantinos Mavromatis…
    Citation: Standards in Genomic Sciences 2011 5:5010086
  38. Haemophilus parasuis is a member of the family Pasteurellaceae and is the etiologic agent of Glässer’s disease in pigs, a systemic syndrome associated with only a subset of isolates. The genetic basis for virulen...

    Authors: Michael A. Mullins, Karen B. Register, Darrell O. Bayles, David W. Dyer, Joanna S. Kuehn and Gregory J. Phillips
    Citation: Standards in Genomic Sciences 2011 5:5010061
  39. Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at...

    Authors: Iain Anderson, Carla Risso, Dawn Holmes, Susan Lucas, Alex Copeland, Alla Lapidus, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Samuel Pitluck, Elizabeth Saunders, Thomas Brettin, John C. Detter, Cliff Han, Roxanne Tapia, Frank Larimer…
    Citation: Standards in Genomic Sciences 2011 5:5010050
  40. Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause ...

    Authors: Amrita Pati, Sabine Gronow, Megan Lu, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Konstantinos Mavromatis…
    Citation: Standards in Genomic Sciences 2011 5:5010041
  41. Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like ot...

    Authors: Konstantinos Liolios, Johannes Sikorski, Meagan Lu, Matt Nolan, Alla Lapidus, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Marcel Huntemann, Natalia Ivanova, Ioanna Pagani…
    Citation: Standards in Genomic Sciences 2011 5:5010030
  42. Fluviicola taffensis O’Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-seque...

    Authors: Tanja Woyke, Olga Chertkov, 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…
    Citation: Standards in Genomic Sciences 2011 5:5010021
  43. Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shallow hydrothermal vent system at...

    Authors: Iain Anderson, Reinhard Wirth, Susan Lucas, Alex Copeland, Alla Lapidus, Jan-Fang Cheng, Lynne Goodwin, Samuel Pitluck, Karen Davenport, John C. Detter, Cliff Han, Roxanne Tapia, Miriam Land, Loren Hauser, Amrita Pati, Natalia Mikhailova…
    Citation: Standards in Genomic Sciences 2011 5:5010012
  44. The Coccolithoviridae is a recently discovered group of viruses that infect the marine coccolithophorid Emiliania huxleyi. Emiliania huxleyi virus 84 (EhV-84) has a 160–180 nm diameter icosahedral structure and a...

    Authors: Jozef I. Nissimov, Charlotte A. Worthy, Paul Rooks, Johnathan A. Napier, Susan A. Kimmance, Matthew R. Henn, Hiroyuki Ogata and Michael J. Allen
    Citation: Standards in Genomic Sciences 2011 5:5010001