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2007 Journal Article CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeatsBland, Charles, Ramsey, Teresa L., Sabree, Fareedah, Lowe, Michael, Brown, Kyndall, Kyrpides, Nikos C. and Hugenholtz, Philip (2007). CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8 (1) 209, 209-1-209-8. doi: 10.1186/1471-2105-8-209 |
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2007 Journal Article Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsMavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerry, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., Rigoutsos, Isidore, Salamov, Asaf, Korzeniewski, Frank, Land, Miriam, Lapidus, Alla, Grigoriev, Igor, Richardson, Paul, Hugenholtz, Philip and Kyrpides, Nikos C. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4 (6), 495-500. doi: 10.1038/nmeth1043 |
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2007 Other Outputs Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyondOehmen, Christopher S., Sofia, Heidi J., Baxter, Douglas, Szeto, Ernest, Hugenholtz, Philip, Kyrpides, Nikos, Markowitz, Victor and Straatsma, Tjerk P. (2007). Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond. Oak Ridge, TN, United States: Office of Scientific and Technical Information (OSTI). doi: 10.2172/960403 |
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2007 Journal Article Quantitative phylogenetic assessment of microbial communities in diverse environmentsvon Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, L. J., Ward, N. and Bork, P. (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315 (5815), 1126-1130. doi: 10.1126/science.1133420 |
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2007 Journal Article Accurate phylogenetic classification of variable-length DNA fragmentsMcHardy, Alice Carolyn, Martin, Hector Garcia, Tsirigos, Aristotelis, Hugenholtz, Philip and Rigoutsos, Isidore (2007). Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods, 4 (1), 63-72. doi: 10.1038/NMETH976 |
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2007 Journal Article Evolutionary conservation of sequence and secondary structures in CRISPR repeatsKunin, Victor, Sorek, Rotem and Hugenholtz, Philip (2007). Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology, 8 (4 Article # R61) R61, R61-1-R61-3. doi: 10.1186/gb-2007-8-4-r61 |
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2007 Journal Article Building on basic metagenomics with complementary technologiesWarnecke, F and Hugenholtz, P (2007). Building on basic metagenomics with complementary technologies. Genome Biology, 8 (12) 231, 231.1-231.5. doi: 10.1186/gb-2007-8-12-231 |
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2007 Journal Article Riding giantsHugenholtz, Philip (2007). Riding giants. Environmental Microbiology, 9 (1), 5-5. doi: 10.1111/j.1462-2920.2006.01222_4.x |
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2006 Journal Article Lineages of acidophilic archaea revealed by community genomic analysisBaker, Brett J., Tyson, Gene W., Webb, Richard I., Flanagan, Judith, Hugenholtz, Philip, Allen, Eric E. and Banfield, Jillian F. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314 (5807), 1933-1935. doi: 10.1126/science.1132690 |
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2006 Journal Article An experimental metagenome data management and analysis system (vol 22, pg 359, 2006)Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system (vol 22, pg 359, 2006). Bioinformatics, 22 (20), 2580-2580. doi: 10.1093/bioinformatics/btl436 |
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2006 Journal Article NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genesDeSantis, T. Z., Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y. M., Phan, R. and Andersen, G. L. (2006). NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research, 34 (suppl 2), W394-W399. doi: 10.1093/nar/gkl244 |
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2006 Journal Article Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)Watt, Michelle, Hugenholtz, Philip, White, Rosemary and Vinall, Kerry (2006). Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environmental Microbiology, 8 (5), 871-884. doi: 10.1111/j.1462-2920.2005.00973.x |
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2006 Journal Article Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environmentsImachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, Kimura, Nobutada, Wagner, Michael, Ohashi, Akiyoshi and Harada, Hideki (2006). Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology, 72 (3), 2080-2091. doi: 10.1128/AEM.72.3.2080-2091.2006 |
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2006 Conference Publication An experimental metagenome data management and analysis systemMarkowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system. 14th Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, 6-10 August 2006. Oxford, U.K.: Oxford University Press. doi: 10.1093/bioinformatics/btl217 |
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2006 Journal Article Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARBDeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., KELLER, K., Huber, T. L., Dalevi, D., Hu, P. and Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72 (7), 5069-5072. doi: 10.1128/AEM.03006-05 |
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2006 Conference Publication Metagenomic analysis of phosphorus removing sludge communitiesMartín, Héctor García, Kunin, Victor, Ivanova, Natalia, Warnecke, Falk, Peterson, S. B., Barry, Kerrie, McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf, Szeto, Ernest, Dalin, Eileen, Putnam, Nik, Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of phosphorus removing sludge communities. ISME Vienna 2006: 11th International Symposium on Microbial Ecology. The hidden powers: Microbial communities in action, Vienna, Austria, 20-25 August 2006. Kenes International. |
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2006 Journal Article The integrated microbial genomes (IMG) systemMarkowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, Zhao, Xueling, Dubchak, Inna, Hugenholtz, Philip, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Ivanova, Natalia and Kyrpides, Nikos C. (2006). The integrated microbial genomes (IMG) system. Nucleic Acids Research, 34 (Supp. 1), D344-D348. doi: 10.1093/nar/gkj024 |
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2006 Journal Article The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwideLiolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip and Kyrpides, Nikos C. (2006). The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Research, 34 (Supp. 1), D332-D334. doi: 10.1093/nar/gkj145 |
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2006 Journal Article Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communitiesMartín, Hector Garcia, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W., McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf A., Szeto, Ernest, Dalin, Eileen, Putnam, Nik H., Shapiro, Harris J., Pangilinan, Jasmyn L., Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology, 24 (10), 1263-1269. doi: 10.1038/nbt1247 |
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2005 Journal Article SNP-VISTA: An interactive SNP visualization toolShah, Nameeta, Teplitsky, Michael V., Minovitsky, Simon, Pennacchio, Len A., Hugenholtz, Philip, Hamann, Bernd and Dubchak, Inna L. (2005). SNP-VISTA: An interactive SNP visualization tool. BMC Bioinformatics, 6 (1) 292. doi: 10.1186/1471-2105-6-292 |
