Donovan Parks
Donovan Parks
Bioinformatic Consultant
Verified email at uq.edu.au
Title
Cited by
Cited by
Year
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
161552009
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
36532015
STAMP: statistical analysis of taxonomic and functional profiles
DH Parks, GW Tyson, P Hugenholtz, RG Beiko
Bioinformatics 30 (21), 3123-3124, 2014
20222014
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
13632018
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
8652017
Identifying biologically relevant differences between metagenomic communities
DH Parks, RG Beiko
Bioinformatics 26 (6), 715-721, 2010
8142010
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
PA Chaumeil, AJ Mussig, P Hugenholtz, DH Parks
Bioinformatics, 2019
6962019
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
6482017
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
5112015
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
3102016
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
306*2020
Evaluation of background subtraction algorithms with post-processing
DH Parks, SS Fels
2008 IEEE Fifth International Conference on Advanced Video and Signal Based …, 2008
2782008
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
2542014
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
2212014
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
2192017
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
1982017
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
1862019
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
1492021
GenGIS: A geospatial information system for genomic data
DH Parks, M Porter, S Churcher, S Wang, C Blouin, J Whalley, S Brooks, ...
Genome research 19 (10), 1896-1904, 2009
1372009
GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework
DH Parks, T Mankowski, S Zangooei, MS Porter, DG Armanini, DJ Baird, ...
PloS one 8 (7), e69885, 2013
1112013
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Articles 1–20