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Donovan Parks
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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
202342009
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
73252015
STAMP: statistical analysis of taxonomic and functional profiles
DH Parks, GW Tyson, P Hugenholtz, RG Beiko
Bioinformatics 30 (21), 3123-3124, 2014
33432014
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
PA Chaumeil, AJ Mussig, P Hugenholtz, DH Parks
Bioinformatics, 2019
27962019
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
25372018
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
1470*2017
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
14162017
Identifying biologically relevant differences between metagenomic communities
DH Parks, RG Beiko
Bioinformatics 26 (6), 715-721, 2010
9602010
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
9542020
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
7142021
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
7092015
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
6672022
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
4892016
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
4012019
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
3882020
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
374*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
3392017
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
3132014
Evaluation of background subtraction algorithms with post-processing
DH Parks, SS Fels
2008 IEEE fifth international conference on advanced video and signal based …, 2008
2992008
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
2842014
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