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2006
Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, et al. Lineages of acidophilic archaea revealed by community genomic analysis. Science. 2006;314(5807):1933-5. Abstract
Martín HG, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, et al. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol. 2006;24(10):1263-9. Abstract
Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, et al. An experimental metagenome data management and analysis system. Bioinformatics. 2006;22(14):e359-67. Abstract
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069-72. Abstract
DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, et al. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006;34(Web Server issue):W394-9. Abstract
Watt M, Hugenholtz P, White R, Vinall K. Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environ Microbiol. 2006;8(5):871-84. Abstract
Imachi H, Sekiguchi Y, Kamagata Y, Loy A, Qiu Y-, Hugenholtz P, et al. Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl Environ Microbiol. 2006;72(3):2080-91. Abstract
Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, et al. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 2006;34(Database issue):D344-8. Abstract
Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 2006;34(Database issue):D332-4. Abstract
2005
Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol. 2005;71(10):6319-24. Abstract
Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, et al. Comparative metagenomics of microbial communities. Science. 2005;308(5721):554-7. Abstract
Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, et al. SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics. 2005;6:292. Abstract
2004
Hugenholtz P, Stackebrandt E. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol. 2004;54(Pt 6):2049-51. Abstract
Sangwan P, Chen X, Hugenholtz P, Janssen PH. Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl Environ Microbiol. 2004;70(10):5875-81. Abstract
Huber T, Faulkner G, Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics. 2004;20(14):2317-9. Abstract
Schoenborn L, Yates PS, Grinton BE, Hugenholtz P, Janssen PH. Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Appl Environ Microbiol. 2004;70(7):4363-6. Abstract
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37-43. Abstract
Ginige MP, Hugenholtz P, Daims H, Wagner M, Keller J, Blackall LL. Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl Environ Microbiol. 2004;70(1):588-96. Abstract
2003
Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol. 2003;69(12):7210-5. Abstract
Baker BJ, Hugenholtz P, Dawson SC, Banfield JF. Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl Environ Microbiol. 2003;69(9):5512-8. Abstract
Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, et al. Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol. 2003;53(Pt 4):1155-63. Abstract
Janssen PH, Hugenholtz P. Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae. Arch Microbiol. 2003;179(5):321-8. Abstract
Uzal FA, Hugenholtz P, Blackall LL, Petray S, Moss S, Assis RA, et al. PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues. Vet Microbiol. 2003;91(2-3):239-48. Abstract
Rossetti S, Blackall LL, Majone M, Hugenholtz P, Plumb JJ, Tandoi V. Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community. Microbiology (Reading, Engl). 2003;149(Pt 2):459-69. Abstract
2002
Sait M, Hugenholtz P, Janssen PH. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol. 2002;4(11):654-66. Abstract