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2014 Journal Article Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.Deng, Li, Ignacio-Espinoza, J. Cesar, Gregory, Ann C., Poulos, Bonnie T., Weitz, Joshua S., Hugenholtz, Philip and Sullivan, Matthe B. (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.. Nature, 513 (7517), 242-245 + 13. doi: 10.1038/nature13459 |
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2013 Journal Article Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface propertiesBraff, William A., Willner, Dana, Hugenholtz, Philip, Rabaey, Korneel and Buie, Cullen R. (2013). Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties. PLoS ONE, 8 (1) e76751, e76751.1-e76751.7. doi: 10.1371/journal.pone.0076751 |
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2013 Journal Article Erratum: 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). Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 501 (7468), 578-578. doi: 10.1038/nature12619 |
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2013 Journal Article Defining the core Arabidopsis thaliana root microbiomeLundberg, Derek S., Lebeis, Sarah L., Paredes, Sur 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. (2013). Defining the core Arabidopsis thaliana root microbiome. Nature, 501 (7468 SUPPL.). |
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2013 Journal Article Insights into the phylogeny and coding potential of microbial dark matterRinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip and Woyke, Tanja (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499 (7459), 431-437. doi: 10.1038/nature12352 |
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2013 Journal Article Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct SwitchgrassD'haeseleer, Patrik, Gladden, John M., Allgaier, Martin, Chain, Patrik S. G., Tringe, Susannah G., Malfatti, Stephanie A., Aldrich, Joshua T., Nicora, Carrie D., Robinson, Errol W., Pasa-Tolic, Ljiljana, Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2013). Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Plos One, 8 (7) e68465, e68465.1-e68465.11. doi: 10.1371/journal.pone.0068465 |
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2013 Journal Article Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomesAlbertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 (6), 533-538+. doi: 10.1038/nbt.2579 |
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2013 Journal Article From deep sequencing to viral tagging: recent advances in viral metagenomicsWillner, Dana and Hugenholtz, Philip (2013). From deep sequencing to viral tagging: recent advances in viral metagenomics. Bioessays, 35 (5), 436-442. doi: 10.1002/bies.201200174 |
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2013 Journal Article Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termitesHe, Shaomei, Ivanova, Natalia, Kirton, Edward, Allgaier, Martin, Bergin, Claudia, Scheffrahn, Rudolf H., Kyrpides, Nikos C., Warnecke, Falk, Tringe, Susannah G. and Hugenholtz, Philip (2013). Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One, 8 (4) e61126, e61126. doi: 10.1371/journal.pone.0061126 |
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2013 Journal Article Shining a light on dark sequencing: characterising errors in Ion Torrent PGM dataBragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip and Tyson, Gene W. (2013). Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. Plos Computational Biology, 9 (4) e1003031, e1003031.1-e1003031.18. doi: 10.1371/journal.pcbi.1003031 |
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2013 Journal Article Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging (vol 3, e00373, 2012)Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2013). Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging (vol 3, e00373, 2012). Mbio, 4 (1). doi: 10.1128/mBio.00516-12 |
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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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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 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 |
