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Gene W. Tyson
Researcher at University of Queensland
Publications - 174
Citations - 32226
Gene W. Tyson is an academic researcher from University of Queensland. The author has contributed to research in topics: Metagenomics & Population. The author has an hindex of 64, co-authored 160 publications receiving 22860 citations. Previous affiliations of Gene W. Tyson include University of California, Berkeley & Massachusetts Institute of Technology.
Papers
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Journal ArticleDOI
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
Journal ArticleDOI
STAMP: statistical analysis of taxonomic and functional profiles
TL;DR: UNLABELLED STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles and a user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots.
Journal ArticleDOI
Community structure and metabolism through reconstruction of microbial genomes from the environment
Gene W. Tyson,Jarrod Chapman,Jarrod Chapman,Philip Hugenholtz,Eric E. Allen,Rachna J. Ram,Paul G. Richardson,Victor V. Solovyev,Edward M. Rubin,Daniel S. Rokhsar,Daniel S. Rokhsar,Jillian F. Banfield +11 more
TL;DR: Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
DatasetDOI
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material
TL;DR: Refining a marker set for lineage-specific Gene Loss and Duplication Estimates under Opal Stop Codon Recodings and Mean absolute error of completeness and contamination estimates determined using different universal- and domain-specific marker gene sets.
Journal ArticleDOI
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks,Christian Rinke,Maria Chuvochina,Pierre-Alain Chaumeil,Ben J. Woodcroft,Paul N. Evans,Philip Hugenholtz,Gene W. Tyson +7 more
TL;DR: The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.