| Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities PD Schloss, SL Westcott, T Ryabin, JR Hall, M Hartmann, EB Hollister, ... Applied and environmental microbiology 75 (23), 7537-7541, 2009 | 20989 | 2009 |
| 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 | 8304 | 2015 |
| STAMP: statistical analysis of taxonomic and functional profiles DH Parks, GW Tyson, P Hugenholtz, RG Beiko Bioinformatics 30 (21), 3123-3124, 2014 | 3565 | 2014 |
| GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database PA Chaumeil, AJ Mussig, P Hugenholtz, DH Parks Bioinformatics, 2019 | 3302 | 2019 |
| 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 | 2779 | 2018 |
| 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 | 1618 | 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 | 1595 | 2017 |
| A complete domain-to-species taxonomy for Bacteria and Archaea DH Parks, M Chuvochina, PA Chaumeil, C Rinke, AJ Mussig, ... Nature biotechnology 38 (9), 1079-1086, 2020 | 1076 | 2020 |
| Identifying biologically relevant differences between metagenomic communities DH Parks, RG Beiko Bioinformatics 26 (6), 715-721, 2010 | 964 | 2010 |
| 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 | 921 | 2022 |
| A unified catalog of 204,938 reference genomes from the human gut microbiome A Almeida, S Nayfach, M Boland, F Strozzi, M Beracochea, ZJ Shi, ... Nature biotechnology 39 (1), 105-114, 2021 | 856 | 2021 |
| Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics PN Evans, DH Parks, GL Chadwick, SJ Robbins, VJ Orphan, SD Golding, ... Science 350 (6259), 434-438, 2015 | 750 | 2015 |
| Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota I Vanwonterghem, PN Evans, DH Parks, PD Jensen, BJ Woodcroft, ... Nature microbiology 1 (12), 1-9, 2016 | 530 | 2016 |
| An evolving view of methane metabolism in the Archaea PN Evans, JA Boyd, AO Leu, BJ Woodcroft, DH Parks, P Hugenholtz, ... Nature Reviews Microbiology 17 (4), 219-232, 2019 | 453 | 2019 |
| Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major … DW Waite, M Chuvochina, C Pelikan, DH Parks, P Yilmaz, M Wagner, ... International Journal of Systematic and Evolutionary Microbiology 70 (11 …, 2020 | 445 | 2020 |
| GTDB-Tk v2: memory friendly classification with the genome taxonomy database PA Chaumeil, AJ Mussig, P Hugenholtz, DH Parks Bioinformatics 38 (23), 5315-5316, 2022 | 434 | 2022 |
| Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) DW Waite, I Vanwonterghem, C Rinke, DH Parks, Y Zhang, K Takai, ... Frontiers in microbiology 8, 682, 2017 | 396* | 2017 |
| On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria RM Soo, J Hemp, DH Parks, WW Fischer, P Hugenholtz Science 355 (6332), 1436-1440, 2017 | 358 | 2017 |
| GroopM: an automated tool for the recovery of population genomes from related metagenomes M Imelfort, D Parks, BJ Woodcroft, P Dennis, P Hugenholtz, GW Tyson PeerJ 2, e603, 2014 | 326 | 2014 |
| An expanded genomic representation of the phylum Cyanobacteria RM Soo, CT Skennerton, Y Sekiguchi, M Imelfort, SJ Paech, PG Dennis, ... Genome biology and evolution 6 (5), 1031-1045, 2014 | 301 | 2014 |
Philip HugenholtzAustralian Centre for Ecogenomics, SCMB, The University of QueenslandVerified email at uq.edu.au