Parks, Donovan H.

CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 12,496

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 3,603

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology

Genomics and Phylogenetic StudiesResearch Data Management Practices

Cited by 2,624

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 2,402

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 1,882

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023) · Nature Methods

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 1,705

A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 1,367