P
Philip Hugenholtz
Researcher at University of Queensland
Publications - 478
Citations - 94852
Philip Hugenholtz is an academic researcher from University of Queensland. The author has contributed to research in topics: Genome & Whole genome sequencing. The author has an hindex of 109, co-authored 452 publications receiving 75841 citations. Previous affiliations of Philip Hugenholtz include Lawrence Berkeley National Laboratory & DSM.
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Journal ArticleDOI
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Todd Z. DeSantis,Philip Hugenholtz,Neils Larsen,Mark Rojas,Eoin L. Brodie,Keith Keller,Thomas Huber,Daniel Dalevi,Ping Hu,Gary L. Andersen +9 more
TL;DR: A 16S rRNA gene database (http://greengenes.lbl.gov) was used to provide chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies as mentioned in this paper.
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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.
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An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
Daniel McDonald,Morgan N. Price,Julia K. Goodrich,Julia K. Goodrich,Eric P. Nawrocki,Todd Z. DeSantis,Alexander J. Probst,Alexander J. Probst,Gary L. Andersen,Rob Knight,Rob Knight,Philip Hugenholtz +11 more
TL;DR: A ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology is developed and used to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences.
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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.
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Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
TL;DR: The authors' perspective on microbial diversity has improved enormously over the past few decades in large part due to molecular phylogenetic studies that objectively relate organisms.