Philip Hugenholtz

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Donovan ParksUniversity of QueenslandVerified email at uq.edu.au
Gene W. TysonProfessor, Centre for Microbiome Research, Queensland University of TechnologyVerified email at qut.edu.au
Maria ChuvochinaAustralian Centre for Ecogenomics, The University of QueenslandVerified email at uq.edu.au
Christian RinkeProfessor, University of Innsbruck, Austria & Honorary Associate Professor, UQ, AustraliaVerified email at uibk.ac.at
Nikos C KyrpidesJoint Genome Institute, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
Natalia IvanovaDOE Joint Genome InstituteVerified email at lbl.gov
Pierre-Alain ChaumeilBioinformatician, University of QueenslandVerified email at uq.edu.au
Todd DeSantisCo-founder & Vice President, Informatics, Second Genome, Inc.Verified email at secondgenome.com
Linda Louise BlackallProfessor of Environmental MicrobiologyVerified email at unimelb.edu.au
David W WaiteSenior Scientist, Ministry for Primary IndustriesVerified email at mpi.govt.nz
Susannah TringeEnvironmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
Aaron J MussigThe University of QueenslandVerified email at uq.edu.au
Gary AndersenLawrence Berkeley LaboratoryVerified email at lbl.gov
Ben J WoodcroftMicrobial informatics group leader, Centre for Microbiome Research, QUTVerified email at qut.edu.au
Tanja WoykeDOE Joint Genome InstituteVerified email at lbl.gov
Mark MorrisonUniversity of QueenslandVerified email at uq.edu.au
Michael ImelfortnoneVerified email at uts.edu.au
Rob KnightWolfe Family Chair at Rady Children's; Director, Center for Microbiome Innovation; Professor, UCSDVerified email at ucsd.edu
Eoin BrodieDeputy Division Director, Climate and Ecosystem Sciences, Lawrence Berkeley National LabVerified email at lbl.gov
Rochelle M. SooUniversity of QueenslandVerified email at uq.edu.au

Philip Hugenholtz

Australian Centre for Ecogenomics, SCMB, The University of Queensland

Verified email at uq.edu.au - Homepage

microbial ecology and evolution


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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	12115	2006
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	9699	2015
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	5503	2012
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	4050	2020
STAMP: statistical analysis of taxonomic and functional profiles DH Parks, GW Tyson, P Hugenholtz, RG Beiko Bioinformatics 30 (21), 3123-3124, 2014	3844	2014
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	3368	1998
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	3141	2018
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	2944	2012
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	2906	2004
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	2513	2013
Comparative metagenomics of microbial communities SG Tringe, C Von Mering, A Kobayashi, AA Salamov, K Chen, HW Chang, ... Science 308 (5721), 554-557, 2005	2064	2005
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	1947	2020
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea RM Bowers, NC Kyrpides, R Stepanauskas, M Harmon-Smith, D Doud, ... Nature Biotechnology 35 (8), 725-731, 2017	1877	2017
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments T Huber, G Faulkner, P Hugenholtz Bioinformatics 20 (14), 2317-2319, 2004	1812	2004
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life DH Parks, C Rinke, M Chuvochina, PA Chaumeil, BJ Woodcroft, ... Nature Microbiology 2 (11), 1533-1542, 2017	1731	2017
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	1561	2007
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	1502	2010
Emerging pathogenic links between microbiota and the gut–lung axis KF Budden, SL Gellatly, DLA Wood, MA Cooper, M Morrison, ... Nature Reviews Microbiology 15 (1), 55-63, 2017	1436	2017
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy DH Parks, M Chuvochina, C Rinke, AJ Mussig, PA Chaumeil, ... Nucleic Acids Research 50 (D1), D785-D794, 2022	1394	2022
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	1394	2008

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