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(c) The Open Journal, 2008-2023

Dr. Philip Hugenholtz

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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.

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
78. 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