Philip Hugenholtz

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Gene W. TysonProfessor, Centre for Microbiome Research, Queensland University of TechnologyVerified email at qut.edu.au
Donovan ParksBioinformatic ConsultantVerified email at uq.edu.au
Nikos C KyrpidesJoint Genome Institute, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
Christian RinkeARC Future Fellow, University of QueenslandVerified email at uq.edu.au
Linda Louise BlackallProfessor of Environmental MicrobiologyVerified email at unimelb.edu.au
Natalia IvanovaDOE Joint Genome InstituteVerified email at lbl.gov
Maria ChuvochinaAustralian Centre for Ecogenomics, The University of QueenslandVerified email at uq.edu.au
Susannah TringeEnvironmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
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
Gary AndersenLawrence Berkeley LaboratoryVerified email at lbl.gov
Pierre-Alain ChaumeilBioinformatician, University of QueenslandVerified email at uq.edu.au
Tanja WoykeDOE Joint Genome InstituteVerified email at lbl.gov
Eoin BrodieDeputy Division Director, Climate and Ecosystem Sciences, Lawrence Berkeley National LabVerified email at lbl.gov
Ben J WoodcroftMicrobial informatics group leader, Centre for Microbiome Research, QUTVerified email at qut.edu.au
Norman PaceProfessor of molecular cellular and developmental biology, University of coloradoVerified email at colorado.edu
Daniel DaleviAweria ABVerified email at aweria.com
Michael ImelfortnoneVerified email at uts.edu.au
Hector Garcia MartinLawrence Berkeley National LaboratoryVerified email at lbl.gov
Mark MorrisonUniversity 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	9944	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	4294	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	4243	2012
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	3110	1998
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	2567	2004
STAMP: statistical analysis of taxonomic and functional profiles DH Parks, GW Tyson, P Hugenholtz, RG Beiko Bioinformatics 30 (21), 3123-3124, 2014	2353	2014
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	2040	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	1872	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	1863	2005
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments T Huber, G Faulkner, P Hugenholtz Bioinformatics 20 (14), 2317-2319, 2004	1788	2004
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	1649	2018
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	1396	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	1392	2010
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	1249	2008
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	1148	2006
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	1142	2013
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	1116	1998
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	1064	2020
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	1053	2020
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	1032	2009

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