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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 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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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 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 |
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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 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 |
