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
Christian RinkeProf in Environmental Microbiology, University of Innsbruck, AUT & Honorary Associate Prof, UQ, AUSVerified email at uibk.ac.at
Nikos C KyrpidesJoint Genome Institute, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
Maria ChuvochinaAustralian Centre for Ecogenomics, The University of QueenslandVerified email at uq.edu.au
Natalia IvanovaDOE Joint Genome InstituteVerified email at lbl.gov
Linda Louise BlackallProfessor of Environmental MicrobiologyVerified email at unimelb.edu.au
Pierre-Alain ChaumeilBioinformatician, University of QueenslandVerified email at uq.edu.au
David W WaiteSenior Scientist, Ministry for Primary IndustriesVerified email at mpi.govt.nz
Todd DeSantisCo-founder & Vice President, Informatics, Second Genome, Inc.Verified email at secondgenome.com
Susannah TringeEnvironmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
Gary AndersenLawrence Berkeley LaboratoryVerified email at lbl.gov
Aaron J MussigThe University of QueenslandVerified email at uq.edu.au
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
Eoin BrodieDeputy Division Director, Climate and Ecosystem Sciences, Lawrence Berkeley National LabVerified email at lbl.gov
Daniel DaleviCentiro Solutions ABVerified email at centiro.com
Rob KnightWolfe Family Chair at Rady Children's; Director, Center for Microbiome Innovation; Professor, UCSDVerified email at ucsd.edu

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	11853	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	8644	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	5347	2012
STAMP: statistical analysis of taxonomic and functional profiles DH Parks, GW Tyson, P Hugenholtz, RG Beiko Bioinformatics 30 (21), 3123-3124, 2014	3634	2014
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	3498	2020
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	3334	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	2901	2018
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	2865	2004
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	2812	2012
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	2421	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	2044	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	1839	2020
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments T Huber, G Faulkner, P Hugenholtz Bioinformatics 20 (14), 2317-2319, 2004	1816	2004
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	1683	2017
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	1630	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	1546	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	1495	2010
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	1368	2013
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	1365	2008
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	1317	2017

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