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2013 Journal Article Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial matHarris, J. Kirk, Caporaso, J. Gregory, Walker, Jeffrey J., Spear, John R., Gold, Nicholas J., Robertson, Charles E., Hugenholtz, Philip, Goodrich, Julia, McDonald, Daniel, Knights, Dan, Marshall, Paul, Tufo, Henry, Knight, Rob and Pace, Norman R. (2013). Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME Journal, 7 (1), 50-60. doi: 10.1038/ismej.2012.79 |
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2013 Journal Article Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T))Mavromatis, Konstantinos, Stackebrandt, Erko, Held, Brittany, 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, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Standards in Genomic Sciences, 8 (1), 47-57. doi: 10.4056/sigs.3547050 |
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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 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 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 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 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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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. |
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2012 Journal Article Defining the core Arabidopsis thaliana root microbiomeLundberg, Derek S., Lebeis, Sarah L., Paredes, Sut Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488 (7409), 86-90. doi: 10.1038/nature11237 |
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2012 Journal Article Grinder: a versatile amplicon and shotgun sequence simulatorAngly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip and Tyson, Gene W. (2012). Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40 (12), e94.1-e94.8. doi: 10.1093/nar/gks251 |
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2012 Journal Article Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T))Anderson, Iain, Chertkov, Olga, Chen, Amy, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Mavromatis, Konstantinos (2012). Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Standards in Genomic Sciences, 6 (3), 293-303. doi: 10.4056/sigs.2736042 |
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2012 Journal Article Unlocking the potential of metagenomics through replicated experimental designKnight, Rob, Jansson, Janet, Field, Dawn, Fierer, Noah, Desai, Narayan, Fuhrman, Jed A., Hugenholtz, Phil, van der Lelie, Daniel, Meyer, Folker, Stevens, Rick, Bailey, Mark J., Gordon, Jeffrey I., Kowalchuk, George A. and Gilbert, Jack A. (2012). Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology, 30 (6), 513-520. doi: 10.1038/nbt.2235 |
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2012 Journal Article Fast, accurate error-correction of amplicon pyrosequences using AcaciaBragg, Lauren, Stone, Glenn, Imelfort, Michael, Hugenholtz, Philip and Tyson, Gene W. (2012). Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods, 9 (5), 245-246. doi: 10.1038/nmeth.1990 |
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2012 Journal Article Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samplesWillner, Dana, Daly, Joshua, Whiley, David, Grimwood, Keith, Wainwright, Claire E. and Hugenholtz, Philip (2012). Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS One, 7 (4) e34605, e34605.1-e34605.12. doi: 10.1371/journal.pone.0034605 |
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2012 Journal Article An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaeaMcDonald, Daniel, Price, Morgan N., Goodrich, Julia, Nawrocki, Eric P., DeSantis, Todd Z, Probst, Alexander, Andersen, Gary L, Knight, Rob and Hugenholtz, Philip (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME Journal, 6 (3), 610-618. doi: 10.1038/ismej.2011.139 |
