Donovan H. Parks

Research interests

Publications

• Greengenes2 unifies microbial data in a single reference tree

  Nature Biotechnology · 2023 · https://doi.org/10.1038/s41587-023-01845-1

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

  Nature Methods · 2023 · https://doi.org/10.1038/s41592-023-01940-w

• GTDB-Tk v2: memory friendly classification with the genome taxonomy database

  Bioinformatics · 2022 · https://doi.org/10.1093/bioinformatics/btac672

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

  Nucleic Acids Research · 2021 · https://doi.org/10.1093/nar/gkab776

• A standardized archaeal taxonomy for the Genome Taxonomy Database

  Nature Microbiology · 2021 · https://doi.org/10.1038/s41564-021-00918-8

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

  Nature Biotechnology · 2020 · https://doi.org/10.1038/s41587-020-0603-3

• Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

  INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · 2020 · https://doi.org/10.1099/ijsem.0.004213

• A complete domain-to-species taxonomy for Bacteria and Archaea

  Nature Biotechnology · 2020 · https://doi.org/10.1038/s41587-020-0501-8

• AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

  Nucleic Acids Research · 2019 · https://doi.org/10.1093/nar/gkz246

• GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

  Bioinformatics · 2019 · https://doi.org/10.1093/bioinformatics/btz848

• An evolving view of methane metabolism in the Archaea

  Nature Reviews Microbiology · 2019 · https://doi.org/10.1038/s41579-018-0136-7

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

  Nature Biotechnology · 2018 · https://doi.org/10.1038/nbt.4229

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

  Nature Microbiology · 2017 · https://doi.org/10.1038/s41564-017-0012-7

• Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

  Frontiers in Microbiology · 2017 · https://doi.org/10.3389/fmicb.2017.00682

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

  Nature Biotechnology · 2017 · 10.1038/nbt.3893

• On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria

  Science · 2017 · https://doi.org/10.1126/science.aal3794

• Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

  Nature Microbiology · 2016 · https://doi.org/10.1038/nmicrobiol.2016.170

• CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

  Genome Research · 2015 · https://doi.org/10.1101/gr.186072.114

• Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

  Science · 2015 · https://doi.org/10.1126/science.aac7745

• STAMP: statistical analysis of taxonomic and functional profiles

  Bioinformatics · 2014 · https://doi.org/10.1093/bioinformatics/btu494

• Identifying biologically relevant differences between metagenomic communities

  Bioinformatics · 2010 · https://doi.org/10.1093/bioinformatics/btq041

• Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

  Applied and Environmental Microbiology · 2009 · https://doi.org/10.1128/aem.01541-09

Current projects

No projects listed.