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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 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 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, e94.1-e94.8. doi: 10.1093/nar/gks251 |
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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 Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cowsGodoy-Vitorino, Filipa, Goldfarb, Katherine C., Karaoz, Ulas, Leal, Sara, Garcia-Amado, Maria A., Hugenholtz, Philip, Tringe, Susannah G., Brodie, Eoin L. and Dominguez-Bello, Maria Gloria (2012). Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME Journal, 6 (3), 531-541. doi: 10.1038/ismej.2011.131 |
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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 |
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2012 Journal Article Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T))Han, Cliff, Kotsyurbenko, Oleg, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes ... Detter, John C. (2012). Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Standards in Genomic Sciences, 6 (1), 94-103. doi: 10.4056/sigs.2456004 |
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2012 Journal Article Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T))Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, 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, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Woyke, Tanja (2012). Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Standards in Genomic Sciences, 7 (1), 107-119. doi: 10.4056/sigs.3216895 |
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2012 Journal Article Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)Copeland, Alex, Zeytun, Ahmet, Yassawong, Montri, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Mavromatis, Konstantinos, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Goeker, Markus, Detter, John C. ... Lapidus, Alla (2012). Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT). Standards in Genomic Sciences, 6 (2), 240-250. doi: 10.4056/sigs.2756060 |
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2012 Journal Article Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (=HR1)Mavromatis, Konstantinos, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Bruce, David, Goodwin, Lynne A., Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2012). Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (=HR1). Standards in Genomic Sciences, 6 (2), 210-219. doi: 10.4056/sigs.2816096 |
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2012 Journal Article Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))Anderson, Iain, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, 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, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Chang, Yun-juan, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C. ... Klenk, Hans-Peter (2012). Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Standards in Genomic Sciences, 6 (2), 155-164. doi: 10.4056/sigs.2665915 |
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2012 Journal Article Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T))Goeker, Markus, Saunders, Elisabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, 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, Palaniappan, Krishna, Land, Miriam, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2012). Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences, 6 (2), 230-239. doi: 10.4056/sigs.2726028 |
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2012 Journal Article Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T))Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, 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, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Kyrpides, Nikos C. (2012). Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Standards in Genomic Sciences, 7 (1), 120-130. doi: 10.4056/sigs.3296896 |
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2012 Journal Article Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T))Copeland, Alex, Zhang, Xiaojing, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Djao, Olivier D. Ngatchou, Goeker, Markus, Sikorski, Johannes, Tindall, Brian J. ... Mavromatis, Konstantinos (2012). Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences, 6 (2), 145-154. doi: 10.4056/sigs.2475579 |
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2012 Journal Article Genome sequence of the homoacetogenic bacterium holophaga foetida type strain (TMBS4(T))Anderson, Iain, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, 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, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2012). Genome sequence of the homoacetogenic bacterium holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences, 6 (2), 174-184. doi: 10.4056/sigs.2746047 |
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2012 Journal Article Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T))Huntemann, Marcel, Teshima, Hazuki, 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, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2012). Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Standards in Genomic Sciences, 6 (2), 185-193. doi: 10.4056/sigs.2786069 |
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2012 Journal Article Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveysWerner, Jeffrey J., Koren, Omry, Hugenholtz, Philip, DeSantis, Todd Z., Walters, William A., Caporaso, J. Gregory, Angenent, Largus T., Knight, Rob and Ley, Ruth E (2012). Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME Journal, 6 (1), 94-103. doi: 10.1038/ismej.2011.82 |
