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2010 Journal Article Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207(T))LaButti, Kurt, Mayilraj, Shanmugam, Clum, Alicia, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2010). Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207(T)). Standards in Genomic Sciences, 3 (1), 85-92. doi: 10.4056/sigs.1092865 |
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2010 Journal Article Complete genome sequence of Meiothermus silvanus type strain (VI-R2(T))Sikorski, Johannes, Tindall, Brian J., Lowry, Stephen, Lucas, Susan, Nolan, Matt, Copeland, Alex, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Lapidus, Alla (2010). Complete genome sequence of Meiothermus silvanus type strain (VI-R2(T)). Standards in Genomic Sciences, 3 (1), 37-46. doi: 10.4056/sigs.1042812 |
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2010 Journal Article Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228(T))Mavromatis, Konstantinos, Yasawong, Montri, Chertkov, Olga, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Tapia, Roxanne, Han, Cliff, Bruce, David, Goodwin, Lynne, Pati, Amrita, Chen, Ami, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Brambilla, Evelyne, Spring, Stefan, Goeker, Markus, Sikorski, Johannes ... Kyrpides, Nikos C. (2010). Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228(T)). Standards in Genomic Sciences, 3 (2), 136-144. doi: 10.4056/sigs.1143106 |
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2010 Journal Article Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288(T))Sikorski, Johannes, Lapidus, Alla, Chertkov, Olga, Lucas, Susan, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Brambilla, Evelyne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Bruce, David, Detter, Chris, Tapia, Roxanne, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288(T)). Standards in Genomic Sciences, 3 (1), 57-65. doi: 10.4056/sigs.1062906 |
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2009 Journal Article A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaWu, Dongying, Hugenholtz, Philip, Mavromatis, Konstantinos, Pukall, Ru¨diger, Dalin, Eileen, Ivanova, Natalia N., Kunin, Victor, Goodwin, Lynne, Wu, Martin, Tindall, Brian J., Hooper, Sean D., Pati, Amrita, Lykidis, Athanasios, Spring, Stefan, Anderson, Iain J., D'haeseleer, Patrik, Zemla, Adam, Singer, Mitchell, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Han, Cliff, Chen, Feng, Cheng, Jan-Fang, Lucas, Susan, Kerfeld, Cheryl, Lang, Elke, Gronow, Sabine, Chain, Patrick ... Elsen, Jonathan A. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462 (7276), 1056-1060. doi: 10.1038/nature08656 |
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2009 Journal Article Complete genome sequence of anaerococcus prevotii type strain (PC1 T)Labutti, Kurt, Pukall, Rüdiger, Steenblock, Katja, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Göker, Markus ... Lapidus, Alla (2009). Complete genome sequence of anaerococcus prevotii type strain (PC1 T). Standards in Genomic Sciences, 1 (2), 159-165. doi: 10.4056/sigs.24194 |
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2009 Journal Article Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T)Han, Cliff, Spring, Stefan, Lapidus, Alla, del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Saunders, Elizabeth, Chertkov, Olga, Brettin, Thomas, Göker, Markus, Rohde, Manfred, Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T). Standards in Genomic Sciences, 1 (1), 54-62. doi: 10.4056/sigs.22138 |
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2009 Journal Article Complete genome sequence of Rhodothermus marinus type strain (R-10 T)Nolan, Matt, Tindall, Brian J., Pomrenke, Helga, Lapidus, Alla, Copeland, Alex, del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Han, Cliff, Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Ovchinikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Göker, Markus, Bristow, James ... Detter, John C. (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10 T). Standards in Genomic Sciences, 1 (3), 283-291. doi: 10.4056/sigs.46736 |
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2009 Journal Article Complete genome sequence of Atopobium parvulum type strain (IPP 1246 T)Copeland, Alex, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Pukall, Rüdiger, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Detter, John C. (2009). Complete genome sequence of Atopobium parvulum type strain (IPP 1246 T). Standards in Genomic Sciences, 1 (2), 166-173. doi: 10.4056/sigs.29547 |
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2009 Journal Article The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadataLiolios, Konstantinos, Chen, I-Min A., Mavromatis, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Markowitz, Victor M. and Kyrpides, Nikos C. (2009). The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research, 38 (Supp. 1) gkp848, D346-D354. doi: 10.1093/nar/gkp848 |
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2009 Journal Article ShotgunFunctionalizeR: An R-package for functional comparison of metagenomesKristiansson, Erik, Hugenholtz, Philip and Dalevi, Daniel (2009). ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes. Bioinformatics, 25 (20), 2737-2738. doi: 10.1093/bioinformatics/btp508 |
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2009 Journal Article Genome project standards in a new era of sequencingChain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V. ... Detter, J. C. (2009). Genome project standards in a new era of sequencing. Science, 326 (5950), 236-237. doi: 10.1126/science.1180614 |
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2009 Journal Article Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimatesKunin, Victor, Engelbrekston, Anna, Ochman, Howard and Hugenholtz, Philip (2009). Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12 (1), 118-123. doi: 10.1111/j.1462-2920.2009.02051.x |
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2009 Journal Article Focus: SynergistetesHugenholtz, P, Hooper, SD and Kyrpides, NC (2009). Focus: Synergistetes. Environmental Microbiology, 11 (6), 1327-1329. doi: 10.1111/j.1462-2920.2009.01949.x |
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2009 Journal Article Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1)Herlemann, D. P. R., Geissinger, O., Ikeda-Ohtsubo, W., Kunin, V., Sun, H., Lapidus, A., Hugenholtz, P. and Brune, A. (2009). Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Applied and Environmental Microbiology, 75 (9), 2841-2849. doi: 10.1128/AEM.02698-08 |
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2009 Journal Article Getting to the core of the gut microbiomeTschop, MH, Hugenholtz, P and Karp, CL (2009). Getting to the core of the gut microbiome. Nature Biotechnology, 27 (4), 344-346. doi: 10.1038/nbt0409-344 |
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2009 Journal Article A changing of the guard: Genomics updateHugenholtz, P and Kyrpides, NC (2009). A changing of the guard: Genomics update. Environmental Microbiology, 11 (3), 551-553. doi: 10.1111/j.1462-2920.2009.01888.x |
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2009 Journal Article Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix oreniiMavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Hooper, Sean D., Sun, Hui, Kunin, Victor, Lapidus, Alla, Hugenholtz, Philip, Patel, Bharat and Kyrpides, Nikos C. (2009). Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One, 4 (1) e4192, e4192.1-e4192.8. doi: 10.1371/journal.pone.0004192 |
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2009 Conference Publication Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumenYannarell, A. C., Hess, M., Hugenholtz, P. and Mackie, R. I. (2009). Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumen. Conference on Gastrointestinal Function, Chicago, USA, 20–22 April 2009. New York, NY United States: Springer. doi: 10.1007/s00248-009-9496-x |
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2009 Journal Article Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T))Saunders, Elizabeth, Pukall, Ruediger, Abt, Birte, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C. ... Han, Cliff (2009). Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T)). Standards in Genomic Sciences, 1 (2), 174-182. doi: 10.4056/sigs.33592 |
