Dr. Philip Hugenholtz |
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Publications |
| Download | 106. |
Dr Victor Kunin,
Dr Philip Hugenholtz,
PyroTagger: A fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data The Open Journal, Article 1, February 21, 2010.
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| 105. |
Pagani I, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Chertkov O, Davenport K, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Kannan KP, Djao OD, Rohde M, Pukall R, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP
Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Stand Genomic Sci 4:1p.100-10. February 20, 2011. PMID:21475592 | |
| 104. |
Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Beck B, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP
Complete genome sequence of Isosphaera pallida type strain (IS1B). Stand Genomic Sci 4:1p.63-71. February 20, 2011. PMID:21475588 | |
| 103. |
Abt B, Lu M, Misra M, Han C, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A
Complete genome sequence of Cellulophaga algicola type strain (IC166). Stand Genomic Sci 4:1p.72-80. February 22, 2011. PMID:21475589 | |
| 102. |
Lang E, Teshima H, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Kopitz M, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC
Complete genome sequence of Weeksella virosa type strain (9751). Stand Genomic Sci 4:1p.81-90. February 22, 2011. PMID:21475590 | |
| 101. |
Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Del Rio TG, Tice H, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A
Complete genome sequence of Truepera radiovictrix type strain (RQ-24). Stand Genomic Sci 4:1p.91-9. February 22, 2011. PMID:21475591 | |
| 100. |
Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC
Complete genome sequence of Leadbetterella byssophila type strain (4M15). Stand Genomic Sci 4:1p.2-12. March 4, 2011. PMID:21475582 | |
| 99. |
Pitluck S, Sikorski J, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Djao OD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M
Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). Stand Genomic Sci 4:1p.54-62. February 20, 2011. PMID:21475587 | |
| 98. |
Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S
Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Stand Genomic Sci 4:1p.45-53. February 22, 2011. PMID:21475586 | |
| 97. |
Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP
Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Stand Genomic Sci 4:1p.36-44. February 20, 2011. PMID:21475585 | |
| 96. |
Chertkov O, Sikorski J, Nolan M, Lapidus A, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Djao OD, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Han C, Detter JC, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC
Complete genome sequence of Thermomonospora curvata type strain (B9). Stand Genomic Sci 4:1p.13-22. February 20, 2011. PMID:21475583 | |
| 95. |
Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S
Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci 2:1p.87-95. February 28, 2010. PMID:21304681 | |
| 94. |
Pati A, Labutti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A
Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci 2:1p.49-56. January 28, 2010. PMID:21304677 | |
| 93. |
Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP
The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010p.690737. December 23, 2010. PMID:21234345 | |
| 92. |
Lykidis A, Chen CL, Tringe SG, McHardy AC, Copeland A, Kyrpides NC, Hugenholtz P, Macarie H, Olmos A, Monroy O, Liu WT
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J 5:1p.122-30. August 5, 2010. PMID:20686509 | |
| 91. |
Yilmaz S, Allgaier M, Hugenholtz P
Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat. Methods 7:12p.943-4. December 2010. PMID:21116242 | |
| 90. |
Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, Hugenholtz P
Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol. 8:11p.e1000546. November 16, 2010. PMID:21103409 | |
| 89. |
He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat. Methods 7:10p.807-12. September 19, 2010. PMID:20852648 | |
| 88. |
Yilmaz S, Haroon MF, Rabkin BA, Tyson GW, Hugenholtz P
Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. ISME J 4:10p.1352-6. May 27, 2010. PMID:20505753 | |
| 87. |
Ivanova N, Tringe SG, Liolios K, Liu WT, Morrison N, Hugenholtz P, Kyrpides NC
A call for standardized classification of metagenome projects. Environ. Microbiol. 12:7p.1803-5. July 2010. PMID:20653767 | |
| 86. |
Burnum KE, Callister SJ, Nicora CD, Purvine SO, Hugenholtz P, Warnecke F, Scheffrahn RH, Smith RD, Lipton MS
Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J p. . July 8, 2010. PMID:20613792 | |
| 85. |
He S, Dr Victor Kunin, Haynes M, Martin HG, Ivanova N, Rohwer F, Hugenholtz P, McMahon KD
Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environ. Microbiol. 10:3p. . February 9, 2010. PMID:20148930 | |
| 84. |
Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P
Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS ONE 5:1p.e8812. January 21, 2010. PMID:20098679 | |
| 83. |
Engelbrektson A, Dr Victor Kunin, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J p. . January 21, 2010. PMID:20090784 | |
| 82. |
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Dr Victor Kunin, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Dr Jonathan A Eisen
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:7276p.1056-60. December 2009. PMID:20033048 | |
| 81. |
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 38:Database issuep.D346-54. November 13, 2009. PMID:19914934 | |
| Download | 80. |
Dr Victor Kunin, Engelbrektson A, Ochman H, Hugenholtz P
Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ. Microbiol. 10:3p. . August 27, 2009. PMID:19725865 |
| 79. |
Kristiansson E, Hugenholtz P, Dalevi D
ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes. Bioinformatics 23:6p. . August 20, 2009. PMID:19696045 | |
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Hugenholtz P, Hooper SD, Kyrpides NC
Focus: Synergistetes. Environ. Microbiol. 11:6p.1327-9. June 2009. PMID:19635113 | |
| 77. |
Tschöp MH, Hugenholtz P, Karp CL
Getting to the core of the gut microbiome. Nat. Biotechnol. 27:4p.344-6. April 2009. PMID:19352371 | |
| 76. |
Hugenholtz P, Kyrpides NC
A changing of the guard. Environ. Microbiol. 11:3p.551-3. March 2009. PMID:19278443 | |
| 75. |
Mavromatis K, Dr Natalia Ivanova, Anderson I, Dr Athanasios Lykidis, Hooper SD, Sun H, Dr Victor Kunin, Lapidus A, Hugenholtz P, Patel B, Kyrpides NC
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS ONE 4:1p.e4192. January 15, 2009. PMID:19145256 | |
| Download | 74. |
Dr Victor Kunin, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P
A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 72:4p.557-78, Table of Contents. December 2008. PMID:19052320 |
| 73. |
Tringe SG, Hugenholtz P
A renaissance for the pioneering 16S rRNA gene. Curr. Opin. Microbiol. 11:5p.442-6. October 8, 2008. PMID:18817891 | |
| 72. |
Wrighton KC, Agbo P, Warnecke F, Weber KA, Brodie EL, Desantis TZ, Hugenholtz P, Andersen GL, Coates JD
A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. ISME J 2:11p.1146-56. September 4, 2008. PMID:18769460 | |
| 71. |
Peterson SB, Warnecke F, Madejska J, McMahon KD, Hugenholtz P
Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environ. Microbiol. 10:10p.2692-703. July 17, 2008. PMID:18643843 | |
| 70. |
Hugenholtz P, Tyson GW
Microbiology: metagenomics. Nature 455:7212p.481-3. September 2008. PMID:18818648 | |
| 69. |
Dalevi D, Dr Natalia Ivanova, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM
Annotation of metagenome short reads using proxygenes. Bioinformatics 24:16p.i7-13. August 2008. PMID:18689842 | |
| 68. |
Blank LM, Hugenholtz P, Nielsen LK
Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci. J. Mol. Evol. 67:1p.13-22. June 13, 2008. PMID:18551332 | |
| 67. |
Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Dr Victor Kunin, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl. Acad. Sci. U.S.A. 105:23p.8102-7. June 5, 2008. PMID:18535141 | |
| Download | 66. |
Dr Victor Kunin, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol. Syst. Biol. 4p.198. June 3, 2008. PMID:18523433 |
| 65. |
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol. 26:5p.541-7. May 2008. PMID:18464787 | |
| 64. |
Warnecke F, Hugenholtz P
Building on basic metagenomics with complementary technologies. Genome Biol. 8:12p.231. January 2007. PMID:18177506 | |
| 63. |
Sorek R, Dr Victor Kunin, Hugenholtz P
CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6:3p.181-6. March 2008. PMID:18157154 | |
| 62. |
Dalevi D, Desantis TZ, Fredslund J, Andersen GL, Markowitz VM, Hugenholtz P
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. BMC Bioinformatics 6p.402. October 18, 2007. PMID:17949484 | |
| Download | 61. |
Dr Victor Kunin, He S, Warnecke F, Peterson SB, Garcia Martin H, Haynes M, Ivanova N, Blackall LL, Breitbart M, Rohwer F, McMahon KD, Hugenholtz P
A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res. 18:2p.293-7. December 12, 2007. PMID:18077539 |
| 60. |
Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Dr Athanasios Lykidis, Mavromatis K, Hugenholtz P, Kyrpides NC
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 36:Database issuep.D534-8. October 11, 2007. PMID:17932063 | |
| 59. |
Yamada T, Yamauchi T, Shiraishi K, Hugenholtz P, Ohashi A, Harada H, Kamagata Y, Nakamura K, Sekiguchi Y
Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. ISME J 1:3p.246-55. May 31, 2007. PMID:18043635 | |
| 58. |
Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Dr Victor Kunin, Dalevi D, Madejska J, Mr Edward Kirton, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:7169p.560-5. November 2007. PMID:18033299 | |
| 57. |
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 6p.209. June 18, 2007. PMID:17577412 | |
| 56. |
Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl. Acad. Sci. U.S.A. 104:29p.11889-94. July 9, 2007. PMID:17620602 | |
| Download | 55. |
Dr Victor Kunin, Sorek R, Hugenholtz P
Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8:4p.R61. January 2007. PMID:17442114 |
| 54. |
McMahon KD, Martin HG, Hugenholtz P
Integrating ecology into biotechnology. Curr. Opin. Biotechnol. 18:3p.287-92. May 16, 2007. PMID:17509863 | |
| 53. |
Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J
Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J. Clin. Microbiol. 45:6p.1954-62. April 4, 2007. PMID:17409203 | |
| 52. |
Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods 4:6p.495-500. April 29, 2007. PMID:17468765 | |
| 51. |
von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P
Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315:5815p.1126-30. February 1, 2007. PMID:17272687 | |
| 50. |
Hugenholtz P
Riding giants. Environ. Microbiol. 9:1p.5. January 2007. PMID:17227401 | |
| 49. |
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I, Martín HG
Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods 4:1p.63-72. December 10, 2006. PMID:17179938 | |
| 48. |
Baker BJ, Tyson GW, Dr Richard Ian Webb, Flanagan J, Hugenholtz P, Allen EE, Banfield JF
Lineages of acidophilic archaea revealed by community genomic analysis. Science 314:5807p.1933-5. December 2006. PMID:17185602 | |
| 47. |
Garcia Martin H, Ivanova N, Dr Victor Kunin, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P, García Martín H
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 24:10p.1263-9. September 24, 2006. PMID:16998472 | |
| 46. |
Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Dr Athanasios Lykidis, Anderson I, Mavromatis K, Dr Konstantinos Mavrommatis, Dr Victor Kunin, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC
An experimental metagenome data management and analysis system. Bioinformatics 22:14p.e359-67. July 2006. PMID:16873494 | |
| 45. |
DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:Web Server issuep.W394-9. July 2006. PMID:16845035 | |
| 44. |
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:7p.5069-72. July 2006. PMID:16820507 | |
| 43. |
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. 8:5p.871-84. May 2006. PMID:16623744 | |
| 42. |
Imachi H, Sekiguchi Y, Kamagata Y, Loy A, Qiu YL, Hugenholtz P, Kimura N, Wagner M, Ohashi A, Harada H
Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl. Environ. Microbiol. 72:3p.2080-91. March 2006. PMID:16517657 | |
| 41. |
Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak IL
SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics 6p.292. December 8, 2005. PMID:16336665 | |
| 40. |
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. 34:Database issuep.D332-4. January 2006. PMID:16381880 | |
| 39. |
Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Dr Athanasios Lykidis, Mavromatis K, Ivanova N, Kyrpides NC
The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34:Database issuep.D344-8. January 2006. PMID:16381883 | |
| 38. |
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. 71:10p.6319-24. October 2005. PMID:16204553 | |
| 37. |
Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM
Comparative metagenomics of microbial communities. Science 308:5721p.554-7. April 2005. PMID:15845853 | |
| 36. |
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. 54:Pt 6p.2049-51. November 2004. PMID:15545432 | |
| 35. |
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. 70:10p.5875-81. October 2004. PMID:15466527 | |
| 34. |
Huber T, Faulkner G, Hugenholtz P
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:14p.2317-9. April 8, 2004. PMID:15073015 | |
| 33. |
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. 70:7p.4363-6. July 2004. PMID:15240320 | |
| 32. |
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:6978p.37-43. February 1, 2004. PMID:14961025 | |
| 31. |
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. 70:1p.588-96. January 2004. PMID:14711691 | |
| 30. |
Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH
Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 69:12p.7210-5. December 2003. PMID:14660368 | |
| 29. |
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. 69:9p.5512-8. September 2003. PMID:12957940 | |
| 28. |
Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K
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. 53:Pt 4p.1155-63. July 2003. PMID:12892144 | |
| 27. |
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. 179:5p.321-8. March 26, 2003. PMID:12658332 | |
| 26. |
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.) 149:Pt 2p.459-69. February 2003. PMID:12624208 | |
| 25. |
Sait M, Hugenholtz P, Janssen PH
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4:11p.654-66. November 2002. PMID:12460273 | |
| 24. |
Uzal FA, Hugenholtz P, Blackall LL, Petray S, Moss S, Assis RA, Fernandez Miyakawa M, Carloni G
PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues. Vet. Microbiol. 91:2-3p.239-48. February 2003. PMID:12458172 | |
| 23. |
Hall SJ, Hugenholtz P, Siyambalapitiya N, Keller J, Blackall LL
The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Sci. Technol. 46:1-2p.267-72. January 2002. PMID:12216635 | |
| 22. |
Björnsson L, Hugenholtz P, Tyson GW, Blackall LL
Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology (Reading, Engl.) 148:Pt 8p.2309-18. August 2002. PMID:12177325 | |
| 21. |
Thomsen TR, Kjellerup BV, Nielsen JL, Hugenholtz P, Nielsen PH
In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. Environ. Microbiol. 4:7p.383-91. July 2002. PMID:12123474 | |
| 20. |
McDevitt CA, Hugenholtz P, Hanson GR, McEwan AG
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Mol. Microbiol. 44:6p.1575-87. June 2002. PMID:12067345 | |
| 19. |
Hugenholtz P
Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:2p.REVIEWS0003. January 29, 2002. PMID:11864374 | |
| 18. |
Hugenholtz P, Tyson GW, Blackall LL
Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods Mol. Biol. 179p.29-42. January 2002. PMID:11692872 | |
| 17. |
Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA, Wagner M
Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bacteriol. 183:20p.6028-35. October 2001. PMID:11567003 | |
| 16. |
Dalevi D, Hugenholtz P, Blackall LL
A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. Int. J. Syst. Evol. Microbiol. 51:Pt 2p.385-91. March 2001. PMID:11321083 | |
| 15. |
Hugenholtz P, Tyson GW, Dr Richard Ian Webb, Wagner AM, Blackall LL
Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67:1p.411-9. January 2001. PMID:11133473 | |
| 14. |
Fuerst JA, Hugenholtz P
Microorganisms should be high on DNA preservation list. Science 290:5496p.1503. November 2000. PMID:11185503 | |
| 13. |
Crocetti GR, Hugenholtz P, Bond PL, Schuler A, Keller J, Jenkins D, Blackall LL
Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation. Appl. Environ. Microbiol. 66:3p.1175-82. March 2000. PMID:10698788 | |
| 12. |
Sandler SJ, Hugenholtz P, Schleper C, DeLong EF, Pace NR, Clark AJ
Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker. J. Bacteriol. 181:3p.907-15. February 1999. PMID:9922255 | |
| 11. |
Dojka MA, Hugenholtz P, Haack SK, Pace NR
Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:10p.3869-77. October 1998. PMID:9758812 | |
| 10. |
Hugenholtz P, Goebel BM, Pace NR
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:18p.4765-74. September 1998. PMID:9733676 | |
| 9. |
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR
Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:2p.366-76. January 1998. PMID:9440526 | |
| 8. |
Blackall LL, Rossetti S, Christensson C, Cunningham M, Hartman P, Hugenholtz P, Tandoi V
The characterization and description of representatives of 'G' bacteria from activated sludge plants. Lett. Appl. Microbiol. 25:1p.63-9. July 1997. PMID:9248083 | |
| 7. |
Seviour EM, Blackall LL, Christensson C, Hugenholtz P, Cunningham MA, Bradford D, Stratton HM, Seviour RJ
The filamentous morphotype Eikelboom type 1863 is not a single genetic entity. J. Appl. Microbiol. 82:4p.411-21. April 1997. PMID:9134715 | |
| 6. |
Fuerst JA, Gwilliam HG, Lindsay M, Lichanska A, Belcher C, Vickers JE, Hugenholtz P
Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon. Appl. Environ. Microbiol. 63:1p.254-62. January 1997. PMID:8979353 | |
| 5. |
Hugenholtz P, Pace NR
Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 14:6p.190-7. June 1996. PMID:8663938 | |
| 4. |
Bond PL, Hugenholtz P, Keller J, Blackall LL
Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl. Environ. Microbiol. 61:5p.1910-6. May 1995. PMID:7544094 | |
| 3. |
Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P, Golecki J, Gad'on N, Gorlenko VM, Kompantseva EI, Drews G
Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int. J. Syst. Bacteriol. 44:3p.427-34. July 1994. PMID:7520734 | |
| 2. |
Hugenholtz P, Fuerst JA
Heterotrophic bacteria in an air-handling system. Appl. Environ. Microbiol. 58:12p.3914-20. December 1992. PMID:1476435 | |
| 1. |
Hugenholtz P, MacRae IC
Stimulation of aldrin and dieldrin loss from soils treated with carbon amendments and saturated-ring analogues. 45:2p.223-7. August 1990. PMID:2400837 |