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Philip Hugenholtz
Philip Hugenholtz
Australian Centre for Ecogenomics, SCMB, The University of Queensland
Verified email at uq.edu.au - Homepage
Title
Cited by
Cited by
Year
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
TZ DeSantis, P Hugenholtz, N Larsen, M Rojas, EL Brodie, K Keller, ...
Applied and environmental microbiology 72 (7), 5069-5072, 2006
99442006
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
DH Parks, M Imelfort, CT Skennerton, P Hugenholtz, GW Tyson
Genome research 25 (7), 1043-1055, 2015
42942015
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
D McDonald, MN Price, J Goodrich, EP Nawrocki, TZ DeSantis, A Probst, ...
The ISME journal 6 (3), 610-618, 2012
42432012
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
P Hugenholtz, BM Goebel, NR Pace
Journal of bacteriology 180 (18), 4765-4774, 1998
31101998
Community structure and metabolism through reconstruction of microbial genomes from the environment
GW Tyson, J Chapman, P Hugenholtz, EE Allen, RJ Ram, PM Richardson, ...
Nature 428 (6978), 37-43, 2004
25672004
STAMP: statistical analysis of taxonomic and functional profiles
DH Parks, GW Tyson, P Hugenholtz, RG Beiko
Bioinformatics 30 (21), 3123-3124, 2014
23532014
Defining the core Arabidopsis thaliana root microbiome
DS Lundberg, SL Lebeis, SH Paredes, S Yourstone, J Gehring, S Malfatti, ...
Nature 488 (7409), 86-90, 2012
20402012
Insights into the phylogeny and coding potential of microbial dark matter
C Rinke, P Schwientek, A Sczyrba, NN Ivanova, IJ Anderson, JF Cheng, ...
Nature 499 (7459), 431-437, 2013
18722013
Comparative metagenomics of microbial communities
SG Tringe, C Von Mering, A Kobayashi, AA Salamov, K Chen, HW Chang, ...
Science 308 (5721), 554-557, 2005
18632005
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
T Huber, G Faulkner, P Hugenholtz
Bioinformatics 20 (14), 2317-2319, 2004
17882004
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
DH Parks, M Chuvochina, DW Waite, C Rinke, A Skarshewski, ...
Nature biotechnology 36 (10), 996-1004, 2018
16492018
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
F Warnecke, P Luginbühl, N Ivanova, M Ghassemian, TH Richardson, ...
Nature 450 (7169), 560-565, 2007
13962007
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
V Kunin, A Engelbrektson, H Ochman, P Hugenholtz
Environmental microbiology 12 (1), 118-123, 2010
13922010
The minimum information about a genome sequence (MIGS) specification
D Field, G Garrity, T Gray, N Morrison, J Selengut, P Sterk, T Tatusova, ...
Nature biotechnology 26 (5), 541-547, 2008
12492008
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
TZ DeSantis, P Hugenholtz, K Keller, EL Brodie, N Larsen, YM Piceno, ...
Nucleic acids research 34 (suppl_2), W394-W399, 2006
11482006
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
M Albertsen, P Hugenholtz, A Skarshewski, KL Nielsen, GW Tyson, ...
Nature biotechnology 31 (6), 533-538, 2013
11422013
Novel division level bacterial diversity in a Yellowstone hot spring
P Hugenholtz, C Pitulle, KL Hershberger, NR Pace
Journal of bacteriology 180 (2), 366-376, 1998
11161998
First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community
W Ahmed, N Angel, J Edson, K Bibby, A Bivins, JW O'Brien, PM Choi, ...
Science of the Total Environment 728, 138764, 2020
10642020
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
PA Chaumeil, AJ Mussig, P Hugenholtz, DH Parks
Bioinformatics 36 (6), 1925-1927, 2020
10532020
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
D Wu, P Hugenholtz, K Mavromatis, R Pukall, E Dalin, NN Ivanova, ...
Nature 462 (7276), 1056-1060, 2009
10322009
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