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2013 Journal Article Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndromeWillner, Dana L., Hugenholtz, Philip, Yerkovich, Stephanie T., Tan, Maxine E., Daly, Joshua N., Lachner, Nancy, Hopkins, Peter M. and Chambers, Daniel C. (2013). Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome. American Journal of Respiratory and Critical Care Medicine, 187 (6), 640-647. doi: 10.1164/rccm.201209-1680OC |
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2013 Journal Article In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recoveryHaroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip and Tyson, Gene W. (2013). In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology, 531, 3-19. doi: 10.1016/B978-0-12-407863-5.00001-0 |
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2013 Journal Article Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus ThermanaerovibrioPalaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. ... Woyke, Tanja (2013). Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences, 9 (1), 57-70. doi: 10.4056/sigs.4237901 |
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2013 Journal Article Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H-T), and emendation of the species Turneriella parvaStackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Klenk, Hans-Peter (2013). Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H-T), and emendation of the species Turneriella parva. Standards in Genomic Sciences, 8 (2), 228-238. doi: 10.4056/sigs.3617113 |
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2013 Journal Article Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineageHaroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500 (7464), 567-570. doi: 10.1038/nature12375 |
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2013 Conference Publication Granule shearing enables the high resolution microbial identityLu, Y., Slater, F., Bello Mendoza, R., Jensen, P., Hugenholtz, P. and Batstone, D. J. (2013). Granule shearing enables the high resolution microbial identity. 13th World Congress on Anaerobic Digestion (AD 13), Santiago de Compostela, Spain, 25-28 June, 2013. London, United Kingdom: International Water Association (IWA). |
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2013 Journal Article Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T))Huntemann, Marcel, Stackebrandt, Erko, Held, Brittany, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Woyke, Tanja, Hugenholtz, Philip ... Lapidus, Alla (2013). Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Standards in Genomic Sciences, 8 (2), 177-187. doi: 10.4056/sigs.3637201 |
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2013 Journal Article Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removalFlowers, Jason J., He, Shaomei, Malfatti, Stephanie, Glavina del Rio, Tijana, Tringe, Susannah G., Hugenholtz, Philip and McMahon, Katherine D. (2013). Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME Journal, 7 (12), 2301-2314. doi: 10.1038/ismej.2013.117 |
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2013 Journal Article Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T))Mavromatis, Konstantinos, Stackebrandt, Erko, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Woyke, Tanja (2013). Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Standards in Genomic Sciences, 8 (1), 26-36. doi: 10.4056/sigs.3527032 |
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2013 Conference Publication Longitudinal holistic profiling of the lung transplant microbiomeWillner, D., Ab-Ghani, N. A., Yerkovich, S., Tan, M. E., Hopkins, P. M., Chambers, D. C. and Hugenholtz, P. (2013). Longitudinal holistic profiling of the lung transplant microbiome. 33rd Annual Meeting and Scientific Sessions of the International Society for Heart and Lung Transplantation, Montreal, Canada, 24-27 April 2013. Philadelphia, PA, United States: Elsevier. doi: 10.1016/j.healun.2013.01.004 |
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2013 Journal Article Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013Garrity, George M., Banfield, Jill, Eisen, Jonathan, van der Lelie, Niels, McMahon, Trina, Rusch, Doug, Delong, Edward, Moran, Mary Ann, Currie, Cameron, Furhman, Jed, Hallam, Steve, Hugenholtz, Phil, Moran, Nancy, Nelson, Karen, Roberts, Richard and Stepanauskas, Ramunas (2013). Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013. Standards in Genomic Sciences, 8 (3), 561-570. doi: 10.4056/sigs.4638348 |
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2013 Journal Article Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) projectKyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil and Klenk, Hans-Peter (2013). Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9 (3), 628-634. doi: 10.4056/sigs.5068949 |
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2013 Journal Article Metagenomics and community profiling: culture-independent techniques in the clinical laboratoryWillner, Dana and Hugenholtz, Phil (2013). Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clinical Microbiology Newsletter, 35 (1), 1-9. doi: 10.1016/j.clinmicnews.2012.12.001 |
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2013 Journal Article High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T))Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Han, Cliff, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Bruce, David, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Kyrpides, Nikos C. (2013). High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Standards in Genomic Sciences, 8 (1), 37-46. doi: 10.4056/sigs.3537045 |
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2013 Journal Article Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug)Stackebrandt, Erko, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2013). Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Standards in Genomic Sciences, 8 (1), 15-25. doi: 10.4056/sigs.3507020 |
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2013 Journal Article Respiratory syncytial virus infection is associated with increased bacterial load in the upper respiratory tract in young childrenChappell, K.J., Brealey, J.C., Mackay, I.M., Bletchly, C., Hugenholtz, P., Sloots, T.P., Sly, P.D. and Young, P.R. (2013). Respiratory syncytial virus infection is associated with increased bacterial load in the upper respiratory tract in young children. Journal of Medical Microbiology & Diagnosis, S (1), 1-9. doi: 10.4172/2161-0703.S1-005 |
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2013 Journal Article Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African RiftLiolos, Konstantinos, Abt, Birte, Scheuner, Carmen, Teshima, Hazuki, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Standards in Genomic Sciences, 8 (2), 165-176. doi: 10.4056/sigs.3607108 |
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2012 Journal Article Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T))Anderson, Iain, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Ivanova, Natalia (2012). Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Standards in Genomic Sciences, 7 (2), 210-220. doi: 10.4056/sigs.3117229 |
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2012 Journal Article Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral TaggingDeng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2012). Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging. Mbio, 3 (6) e00373-12. doi: 10.1128/mBio.00373-12 |
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2012 Journal Article Guest commentary: the human microbiome and the promise of clinical ecologyHugenholtz, Phil (2012). Guest commentary: the human microbiome and the promise of clinical ecology. Microbiology Australia, 33 (3), 90-90. |
