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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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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 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 |
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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 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 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 Integrating ecology into biotechnologyMcMahon, KD, Martin, HG and Hugenholtz, P (2007). Integrating ecology into biotechnology. Current Opinion in Biotechnology, 18 (3), 287-292. doi: 10.1016/j.copbio.2007.04.007 |
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2007 Journal Article Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosaFlanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P. and Bristow, J. (2007). Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology, 45 (6), 1954-1962. doi: 10.1128/JCM.02187-06 |
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2007 Journal Article Increasing focus on environmental biotechnology in the face of pressing environmental challengesHugenholtz, Philip and Ron, Eliora Z. (2007). Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology, 18 (3), 235-236. doi: 10.1016/j.copbio.2007.05.004 |
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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 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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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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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 |
