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D. Parks · SciRah

Researcher profile · Semantic Scholar

D. Parks

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D. Parks — researcher profile on SciRah

h-index: 52
Works: 125
Citations: 65K

Most-cited papers

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
D. Parks, M. Imelfort, C. Skennerton, P. Hugenholtz +1 more
2015Genome Research12K citations Open access
Semantic Scholar
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
P. Chaumeil, A. Mussig, P. Hugenholtz, D. Parks
2019Bioinform.4,971 citations Open access
Semantic Scholar
STAMP: statistical analysis of taxonomic and functional profiles
D. Parks, G. Tyson, P. Hugenholtz, R. Beiko
2014Bioinform.3,805 citations Open access
Semantic Scholar
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
D. Parks, M. Chuvochina, D. Waite, C. Rinke +3 more
2018Nature Biotechnology3,095 citations Open access
Semantic Scholar
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
R. Bowers, N. Kyrpides, R. Stepanauskas, M. Harmon-Smith +50 more
2017Nature Biotechnology2,286 citations Open access
Semantic Scholar
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
D. Parks, M. Chuvochina, C. Rinke, A. Mussig +2 more
2021Nucleic Acids Res.2,194 citations Open access
Semantic Scholar
GTDB-Tk v2: memory friendly classification with the genome taxonomy database
P. Chaumeil, A. Mussig, P. Hugenholtz, D. Parks
2022bioRxiv1,962 citations Open access
Semantic Scholar
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
D. Parks, C. Rinke, M. Chuvochina, P. Chaumeil +4 more
2017Nature Microbiology1,674 citations Open access
Semantic Scholar
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Alex Chklovski, D. Parks, B. Woodcroft, G. Tyson
2022bioRxiv1,517 citations Open access
Semantic Scholar
A complete domain-to-species taxonomy for Bacteria and Archaea
D. Parks, M. Chuvochina, P. Chaumeil, C. Rinke +2 more
2020Nature Biotechnology1,271 citations Open access
Semantic Scholar
A unified catalog of 204,938 reference genomes from the human gut microbiome
A. Almeida, Stephen Nayfach, M. Boland, F. Strozzi +9 more
2020Nature Biotechnology1,175 citations Open access
Semantic Scholar
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
P. Evans, D. Parks, G. Chadwick, S. Robbins +3 more
2015Science704 citations
Semantic Scholar
Greengenes2 unifies microbial data in a single reference tree
D. McDonald, Yueyu Jiang, M. Balaban, Kalen Cantrell +21 more
2023Nature Biotechnology666 citations Open access
Semantic Scholar
Nonlinear Dimensionality Reduction
D. Parks
2021Computer Vision647 citations
Semantic Scholar
An evolving view of methane metabolism in the Archaea
P. Evans, J. Boyd, Andy O. Leu, B. Woodcroft +3 more
2019Nature Reviews Microbiology525 citations Open access
Semantic Scholar
Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities.
D. Waite, M. Chuvochina, Claus Pelikan, D. Parks +9 more
2020International Journal of Systematic and Evolutionary Microbiology473 citations Open access
Semantic Scholar
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Inka Vanwonterghem, P. Evans, D. Parks, P. Jensen +3 more
2016Nature Microbiology473 citations Open access
Semantic Scholar
A standardized archaeal taxonomy for the Genome Taxonomy Database
C. Rinke, M. Chuvochina, A. Mussig, P. Chaumeil +5 more
2021Nature Microbiology418 citations Open access
Semantic Scholar
On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
R. Soo, J. Hemp, D. Parks, W. Fischer +1 more
2017Science343 citations
Semantic Scholar
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
D. Waite, Inka Vanwonterghem, C. Rinke, D. Parks +9 more
2017Frontiers in Microbiology337 citations Open access
Semantic Scholar
An Expanded Genomic Representation of the Phylum Cyanobacteria
R. Soo, C. Skennerton, Y. Sekiguchi, M. Imelfort +6 more
2014Genome Biology and Evolution265 citations Open access
Semantic Scholar
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life
Kerrin Mendler, Han Chen, D. Parks, B. Lobb +2 more
2018bioRxiv263 citations Open access
Semantic Scholar
SeqCode: a nomenclatural code for prokaryotes described from sequence data
B. Hedlund, M. Chuvochina, P. Hugenholtz, K. Konstantinidis +10 more
2022Nature Microbiology215 citations Open access
Semantic Scholar
Prokaryotic taxonomy and nomenclature in the age of big sequence data
P. Hugenholtz, M. Chuvochina, A. Oren, D. Parks +1 more
2021The ISME Journal169 citations Open access
Semantic Scholar
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)
C. Rinke, Francesco Rubino, Lauren F. Messer, N. Youssef +7 more
2018The ISME Journal161 citations Open access
Semantic Scholar
Roadmap for naming uncultivated Archaea and Bacteria
A. Murray, J. Freudenstein, S. Gribaldo, R. Hatzenpichler +61 more
2020Nature Microbiology131 citations Open access
Semantic Scholar
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
D. Parks, P. Chaumeil, A. Mussig, C. Rinke +2 more
2025Nucleic Acids Research126 citations Open access
Semantic Scholar
Chemotaxis shapes the microscale organization of the ocean’s microbiome
J. Raina, Bennett S. Lambert, D. Parks, C. Rinke +12 more
2022Nature125 citations
Semantic Scholar
Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus
R. Soo, B. Woodcroft, D. Parks, G. Tyson +1 more
2015PeerJ108 citations Open access
Semantic Scholar
A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres
Nurdyana Binte Abdul Rahman, D. Parks, Inka Vanwonterghem, M. Morrison +2 more
2016Frontiers in Microbiology105 citations Open access
Semantic Scholar
A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes
Nurdyana Binte Abdul Rahman, D. Parks, D. Willner, A. Engelbrektson +4 more
2015Microbiome105 citations Open access
Semantic Scholar
Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
Soo Jen Low, M. Džunková, P. Chaumeil, D. Parks +1 more
2019Nature Microbiology100 citations
Semantic Scholar
The importance of designating type material for uncultured taxa.
M. Chuvochina, C. Rinke, D. Parks, M. Rappé +4 more
2019Systematic and Applied Microbiology91 citations Open access
Semantic Scholar
Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
D. Waite, Inka Vanwonterghem, C. Rinke, D. Parks +9 more
2018Frontiers in Microbiology82 citations Open access
Semantic Scholar
Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes
M. Chuvochina, A. Mussig, P. Chaumeil, A. Skarshewski +3 more
2023FEMS Microbiology Letters81 citations Open access
Semantic Scholar
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Y. Sekiguchi, A. Ohashi, D. Parks, Toshihiro Yamauchi +2 more
2015PeerJ80 citations Open access
Semantic Scholar
Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years
Yu-Lin Wang, Jun Ye, Feng Ju, Lei Liu +10 more
2021Microbiome78 citations Open access
Semantic Scholar
Genome-Based Microbial Taxonomy Coming of Age.
P. Hugenholtz, A. Skarshewski, D. Parks
2016Cold Spring Harbor Perspectives in Biology75 citations Open access
Semantic Scholar
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage
Yun Kit Yeoh, Y. Sekiguchi, D. Parks, P. Hugenholtz
2015Molecular biology and evolution73 citations Open access
Semantic Scholar
A proposal for a standardized bacterial taxonomy based on genome phylogeny
D. Parks, M. Chuvochina, D. Waite, C. Rinke +3 more
2018bioRxiv70 citations Open access
Semantic Scholar
Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae
S. McIlroy, Andy O. Leu, Jun Ye, D. Parks +2 more
2020mBio68 citations Open access
Semantic Scholar
Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
R. Bowers, N. Kyrpides, R. Stepanauskas, M. Harmon-Smith +50 more
2018Nature Biotechnology66 citations Open access
Semantic Scholar
Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well
S. Robbins, P. Evans, D. Parks, S. Golding +1 more
2016Frontiers in Microbiology58 citations Open access
Semantic Scholar
Development of the SeqCode: a proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type
W. Whitman, M. Chuvochina, B. Hedlund, P. Hugenholtz +10 more
2022Systematic and Applied Microbiology52 citations Open access
Semantic Scholar
Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
D. Parks, C. Rinke, M. Chuvochina, P. Chaumeil +4 more
2017Nature Microbiology51 citations Open access
Semantic Scholar
A catalogue of 136 microbial draft genomes from Red Sea metagenomes
M. Haroon, L. Thompson, D. Parks, P. Hugenholtz +1 more
2016Scientific Data49 citations Open access
Semantic Scholar
Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy
D. Parks, M. Chuvochina, P. Chaumeil, C. Rinke +2 more
2019bioRxiv48 citations Open access
Semantic Scholar
Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes
J. Emerson, R. Varner, M. Wik, D. Parks +12 more
2021Nature Communications45 citations Open access
Semantic Scholar
Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome
D. Parks, Fabio Rigato, Patricia Vera-Wolf, L. Krause +3 more
2021Frontiers in Microbiology40 citations Open access
Semantic Scholar
Greengenes2 enables a shared data universe for microbiome studies
D. McDonald, Yueyu Jiang, M. Balaban, Kalen Cantrell +21 more
2023bioRxiv37 citations Open access
Semantic Scholar

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B. Hedlund — researcher profile on SciRah

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