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2009 Journal Article Complete genome sequence of Cryptobacterium curtum type strain (12-3(T))Mavrommatis, Konstantinos, Pukall, Ruediger, Rohde, Christine, Chen, Feng, Sims, David, Brettin, Thomas, Kuske, Cheryl, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, D'haeseleer, Patrik, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2009). Complete genome sequence of Cryptobacterium curtum type strain (12-3(T)). Standards in Genomic Sciences, 1 (2), 93-100. doi: 10.4056/sigs.12260 |
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2009 Journal Article Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122(T))Land, Miriam, Pukall, Ruediger, Abt, Birte, Goeker, Markus, Rohde, Manfred, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jefferies, Cynthia C., Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Chain, Patrick ... Lapidus, Alla (2009). Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122(T)). Standards in Genomic Sciences, 1 (1), 21-28. doi: 10.4056/sigs.1162 |
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2009 Book Chapter Single cell whole genome amplification of uncultivated organismsPodar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplification of uncultivated organisms. Uncultivated microorganisms. (pp. 241-256) edited by Slava S. Epstein. Heidelberg, Germany: Springer . doi: 10.1007/978-3-540-85465-4_10 |
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2008 Journal Article A bioinformatician's guide to metagenomicsKunin, V., Copeland, A., Lapidus, A., Mavromatis, K. and Hugenholtz, P. (2008). A bioinformatician's guide to metagenomics. Microbiology and Molecular Biology Reviews, 72 (4), 557-578. doi: 10.1128/MMBR.00009-08 |
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2008 Journal Article A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cellsWrighton, Kelly C., Agbo, Peter, Warnecke, Falk, Weber, Karrie A., Brodie, Eoin L., DeSantis, Todd Z., Hugenholtz, Philip, Andersen, Gary L. and Coates, John D. (2008). A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. The ISME Journal, 2 (11), 1146-1156. doi: 10.1038/ismej.2008.48 |
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2008 Journal Article A renaissance for the pioneering 16S rRNA geneTringe, SG and Hugenholtz, P (2008). A renaissance for the pioneering 16S rRNA gene. Current Opinions in Microbiology, 11 (5), 442-446. doi: 10.1016/j.mib.2008.09.011 |
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2008 Journal Article Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removalPeterson, S. Brook, Warnecke, Falk, Madejska, Julita, McMahon, Katherine D. and Hugenholtz, Philip (2008). Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environmental Microbiology, 10 (10), 2692-2703. doi: 10.1111/j.1462-2920.2008.01690.x |
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2008 Journal Article Microbiology: MetagenomicsHugenhotz, Philip and Tyson, Gene W. (2008). Microbiology: Metagenomics. Nature, 455 (7212), 481-483. doi: 10.1038/455481a |
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2008 Journal Article Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic StreptococciLars M. Blank, Philip Hugenholtz and Nielsen, Lars K. (2008). Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic Streptococci. Journal of Molecular Evolution, 67 (1), 13-22. doi: 10.1007/s00239-008-9117-1 |
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2008 Journal Article Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial matKunin, Victor, Raes, Jeroen, Harris, J. Kirk, Spear, John R., Walker, Jeffrey J., Ivanova, Natalia, Von Mering, Christian, Bebout, Brad M., Pace, Norman R., Bork, Peer and Hugenholtz, Philip (2008). Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Molecular Systems Biology, 4 (1) 198, 198. doi: 10.1038/msb.2008.35 |
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2008 Journal Article A korarchaeal genome reveals insights into the evolution of the ArchaeaElkins, James G., Podar, Mircea, Graham, David E., Makarova, Kira S., Wolf, Yuri, Randau, Lennart, Hedlund, Brian P., Brochier-Armanet, Celine, Kunin, Victor, Anderson, Iain, Lapidus, Alla, Goltsman, Eugene, Barry, Kerrie, Koonin, Eugene V., Hugenholtz, Philip, Kyrpides, Nikos, Wanner, Gerhard, Richardson, Paul, Keller, Martin and Stetter, Karl O. (2008). A korarchaeal genome reveals insights into the evolution of the Archaea. Proceedings of the National Academy of Sciences of the United States of America, 105 (23), 8102-8107. doi: 10.1073/pnas.0801980105 |
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2008 Journal Article The minimum information about a genome sequence (MIGS) specificationField, Dawn, Garrity, George, Gray, Tanya, Morrison, Norman, Selengut, Jeremy, Sterk, Peter, Tatusova, Tatiana, Thomson, Nicholas, Allen, Michael J., Angiuoli, Samuel V., Ashburner, Michael, Axelrod, Nelson, Baldauf, Sandra, Ballard, Stuart, Boore, Jeffrey, Cochrane, Guy, Cole, James, Dawyndt, Peter, De Vos, Paul, dePamphilis, Claude, Edwards, Robert, Faruque, Nadeem, Feldman, Robert, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Goldstein, Philip, Guralnick, Robert, Haft, Dan ... Wipat, Anil (2008). The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26 (5), 541-547. doi: 10.1038/nbt1360 |
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2008 Journal Article CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaeaSorek, R, Kunin, V and Hugenholtz, P (2008). CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology, 6 (3), 181-186. doi: 10.1038/nrmicro1793 |
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2008 Journal Article A bacterial metapopulation adapts locally to phage predation despite global dispersalKunin, V., He, S., Warnecke, F., Peterson, S. B., Martin, H. G., Haynes, M., Ivanova, N., Blackall, L. L., Breitbart, M., Rohwer, F., McMahon, K. D. and Hugenholtz, P. (2008). A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research, 18 (2), 293-297. doi: 10.1101/gr.6835308 |
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2008 Journal Article IMG/M: A data management and analysis system for metagenomesMarkowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, Chen, I-Min A., Grechkin, Yuri, Dubchak, Inna, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Hugenholtz, Philip and Kyrpides, Nikos C. (2008). IMG/M: A data management and analysis system for metagenomes. Nucleic Acids Research, 36 (Supp. 1), D534-D538. doi: 10.1093/nar/gkm869 |
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2008 Conference Publication Annotation of metagenome short reads using proxygenesDalevi, Daneil, Ivanova, Natalia N., Mavromatis, Konstantinos, Hooper, Sean D., Szeto, Ernest, Hugenholtz, Philip, Kyrpides, Nikos C. and Markowitz, Victor M. (2008). Annotation of metagenome short reads using proxygenes. Joint Meeting of the 7th European Conference on Computational Biology and the 5th Meeting of the Bioinformatics Italian Society (ECCB 2008), Cagliari, Italy, 22-26 September 2008. Oxford, U.K.: Oxford University Press. doi: 10.1093/bioinformatics/btn276 |
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2007 Journal Article Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termiteWarnecke, Falk, Luginbuehl, Peter, Ivanova, Natalia, Ghassemian, Majid, Richardson, Toby H., Stege, Justin T., Cayouette, Michelle, McHardy, Alice C., Djordjevic, Gordana, Aboushadi, Nahla, Sorek, Rotem, Tringe, Susannah G., Podar, Mircea, Martin, Hector Garcia, Kunin, Victor, Dalevi, Daniel, Madejska, Julita, Kirton, Edward, Platt, Darren, Szeto, Ernest, Salamov, Asaf, Barry, Kerrie, Mikhailova, Natalia, Kyrpides, Nikos C., Matson, Eric G., Ottesen, Elizabeth A., Zhang, Xinning, Hernandez, Myriam, Murillo, Catalina ... Leadbetter, Jared R. (2007). Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 450 (7169), 560-565. doi: 10.1038/nature06269 |
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2007 Journal Article Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming toolDalevi, Daniel, DeSantis, Todd Z., Fredslund, Jakob, Andersen, Gary L., Markowitz, Victor M. and Hugenholtz, Philip (2007). Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. BMC Bioinformatics, 8 (1) 402. doi: 10.1186/1471-2105-8-402 |
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2007 Journal Article Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludgesYamada, Takeshi, Yamauchi, Toshihiro, Shiraishi, Koji, Hugenholtz, Philip, Ohashi, Akiyoshi, Harada, Hideki, Kamagata, Yoichi, Nakamura, Kazunori and Sekiguchi, Yuji (2007). Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. The ISME Journal, 1 (3), 246-255. doi: 10.1038/ismej.2007.28 |
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2007 Journal Article Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouthMarcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Losekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, Szeto, Ernest, Platt, Darren, Hugenholtz, Philip, Relman, David A. and Quake, Stephen R. (2007). Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America, 104 (29), 11889-11894. doi: 10.1073/pnas.0704662104 |
