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2015 Conference Publication The microbial community of eutherian origin: Effects of maternal microbiota on the placental microbiomeRagonesi, Leanne, Huygens, Flavia, Turner, Ross, Hugenholtz, Philip, Lourie, Rohan, Beagley, Ken and Pelzer, Elise (2015). The microbial community of eutherian origin: Effects of maternal microbiota on the placental microbiome. unknown, unknown, unknown. London, United Kingdom: Elsevier. doi: 10.1016/j.placenta.2015.07.308 |
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2015 Book Chapter AnaerobaculumPatel, Bharat K. C. and Hugenholtz, Philip (2015). Anaerobaculum. Bergey's Manual of Systematics of Archaea and Bacteria. (pp. 1-7) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm01254 |
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2014 Journal Article Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family PlanctomycetaceaeScheuner, Carmen, Tindall, Brian J., Lu, Megan, Nolan, Matt, Lapidus, Alla, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D., Hauser, Loren, Land, Miriam, Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John C., Woyke, Tanja, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goker, Markus, Kyrpides, Nikos C. and Klenk, Hans-Peter (2014). Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Standards in Genomic Sciences, 9 (1) 10, 10. doi: 10.1186/1944-3277-9-10 |
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2014 Journal Article JTD special edition 'Hot Topics in COPD'- the microbiome in COPDChambers, Daniel C., Gellatly, Shaan L., Hugenholtz, Philip and Hansbro, Philip M. (2014). JTD special edition 'Hot Topics in COPD'- the microbiome in COPD. Journal of Thoracic Disease, 6 (11), 1525-1531. doi: 10.3978/j.issn.2072-1439.2014.11.08 |
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2014 Journal Article GroopM: an automated tool for the recovery of population genomes from related metagenomesImelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014). GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 (1) e603, 1-16. doi: 10.7717/peerj.603 |
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2014 Journal Article Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strainsKyrpides, Nikos C., Hugenholtz, Philip, Eisen, Jonathan A., Woyke, Tanja, Goker, Markus, Parker, Charles T., Amann, Rudolf, Beck, Brian J., Chun, Jongsik, Colwell, Rita R., Danchin, Antoine, Dawyndt, Peter, Dedeurwaerdere, Tom, DeLong, Edward F., Detter, John C., De Vos, Paul, Donohue, Timothy J., Dong, Xiu-Zhu, Ehrlich, Dusko S., Fraser, Claire, Gibbs, Richard, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Jansson, Janet K., Keasling, Jay D., Knight, Rob, Labeda, David, Lapidus, Alla ... Klenk, Hans-Peter (2014). Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biology, 12 (8) e1001920, e1001920.1-e1001920.7. doi: 10.1371/journal.pbio.1001920 |
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2014 Journal Article STAMP: Statistical analysis of taxonomic and functional profiles.Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip and Beiko, Robert G. (2014). STAMP: Statistical analysis of taxonomic and functional profiles.. Bioinformatics., 30 (21), 3123-3124. doi: 10.1093/bioinformatics/btu494 |
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2014 Conference Publication Embedding Undergraduate Research throughout Microbiology MajorsWang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy, Tyson, Gene W., Hugenholtz, Philip and Schembri, Mark A. (2014). Embedding Undergraduate Research throughout Microbiology Majors. ASM Conference for Undergraduate Educators, Danvers, MA United States, 15-18 May 2014. |
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2014 Journal Article Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digestersVanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel and Tyson, Gene W. (2014). Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, Advance Online (10), 1-14. doi: 10.1038/ismej.2014.50 |
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2014 Journal Article An expanded genomic representation of the phylum CyanobacteriaSoo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014). An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access (5), 1-42. doi: 10.1093/gbe/evu073 |
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2014 Journal Article CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correctionAngly, Florent E., Dennis, Paul G., Skarshewski, Adam, Vanwonterghem, Inka, Hugenholtz, Philip and Tyson, Gene W. (2014). CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome, 2 (11) 11, 11. doi: 10.1186/2049-2618-2-11 |
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2014 Journal Article A new species of Burkholderia isolated from sugarcane roots promotes plant growthPaungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014). A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 (2), 142-154. doi: 10.1111/1751-7915.12105 |
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2014 Journal Article Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populationsWillner, Dana, Low, Serene, Steen, Jason A., George, Narelle, Nimmo, Graeme R., Schembri, Mark A. and Hugenholtz, Philip (2014). Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations. mBio, 5 (2) e01064-13, e01064-13.1-e01064-13.10. doi: 10.1128/mBio.01064-13 |
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2014 Journal Article Discovery of a novel methanogen prevalent in thawing permafrostMondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014). Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 (1) 3212, 3212.1-3212.7. doi: 10.1038/ncomms4212 |
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2014 Journal Article Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 (T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and MethanolaciniaGoeker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina Del Rio, Tijana, Cheng, Jan-Feng, 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, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2014). Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 (T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Standards in Genomic Sciences, 9 (3), 1076-1088. doi: 10.4056/sigs.5138968 |
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2014 Journal Article Genome sequence of enterotoxigenic Escherichia coli strain B2CVipin Madhavan, T. P., Steen, Jason A., Hugenholtz, Philip and Sakellaris, Harry (2014). Genome sequence of enterotoxigenic Escherichia coli strain B2C. Genome Announcements, 2 (2) e00247-14. doi: 10.1128/genomeA.00247-14 |
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2014 Conference Publication Plant growth promoting rhizobacteria (PGPR) for use in horticulture.Fangrath, S, Mudge, S., Deng, Y, Robinson, N, Schmidt, S, Hugenholtz, P, Ragan, M and Paungfoo-Lonhienne, C (2014). Plant growth promoting rhizobacteria (PGPR) for use in horticulture.. The 29th International Horticultural Congress, Brisbane Convention Centre, Brisbane Qld, Australia, 17 - 22 August 2014. |
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2014 Journal Article Effects of sample treatments on genome recovery via single-cell genomicsClingenpeel, Scott, Schwientek, Patrick, Hugenholtz, Philip and Woyke, Tanja (2014). Effects of sample treatments on genome recovery via single-cell genomics. The ISME Journal, 8 (12), 2546-2549. doi: 10.1038/ismej.2014.92 |
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2014 Journal Article Yeast as a biofertilizer alters plant growth and morphologyLonhienne, Thierry, Mason, Michael G., Ragan, Mark A., Hugenholtz, Philip, Schmidt, Susanne and Paungfoo-Lonhienne, Chanyarat (2014). Yeast as a biofertilizer alters plant growth and morphology. Crop Science, 54 (2), 785-790. doi: 10.2135/cropsci2013.07.0488 |
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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 |
