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
Susannah TringeEnvironmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
Maria ChuvochinaAustralian Centre for Ecogenomics, The University of QueenslandVerified email at uq.edu.au
Todd DeSantisCo-founder & Vice President, Informatics, Second Genome, Inc.Verified email at secondgenome.com
Gary AndersenLawrence Berkeley LaboratoryVerified email at lbl.gov
David W WaiteSenior Scientist, Ministry for Primary IndustriesVerified email at mpi.govt.nz
Norman PaceProfessor of molecular cellular and developmental biology, University of coloradoVerified email at colorado.edu
Eoin BrodieDeputy Division Director, Climate and Ecosystem Sciences, Lawrence Berkeley National LabVerified email at lbl.gov
Daniel DaleviAweria ABVerified email at aweria.com
Tanja WoykeDOE Joint Genome InstituteVerified email at lbl.gov
Thomas HuberResearch School of Chemistry, Australian National UniversityVerified email at anu.edu.au
Alice Carolyn McHardyHelmholtz Centre for Infection ResearchVerified email at helmholtz-hzi.de
Pierre-Alain ChaumeilBioinformatician, University of QueenslandVerified email at uq.edu.au
Hector Garcia MartinLawrence Berkeley National LaboratoryVerified email at lbl.gov
Michael ImelfortnoneVerified email at uts.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	8887	2006
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	3687	2012
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	3019	2015
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	2971	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	2435	2004
STAMP: statistical analysis of taxonomic and functional profiles DH Parks, GW Tyson, P Hugenholtz, RG Beiko Bioinformatics 30 (21), 3123-3124, 2014	1799	2014
Comparative metagenomics of microbial communities SG Tringe, C Von Mering, A Kobayashi, AA Salamov, K Chen, HW Chang, ... Science 308 (5721), 554-557, 2005	1754	2005
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments T Huber, G Faulkner, P Hugenholtz Bioinformatics 20 (14), 2317-2319, 2004	1750	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	1748	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	1676	2013
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	1332	2010
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	1329	2007
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	1178	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	1103	2006
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	1090	2018
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	1078	1998
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	1033	2013
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	989	2009
CRISPR—a widespread system that provides acquired resistance against phages in bacteria and archaea R Sorek, V Kunin, P Hugenholtz Nature Reviews Microbiology 6 (3), 181-186, 2008	914	2008
Microbial diversity in a hydrocarbon-and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation MA Dojka, P Hugenholtz, SK Haack, NR Pace Applied and Environmental Microbiology 64 (10), 3869-3877, 1998	876	1998

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