Peer-reviewed paper Oct 9, 2018 MBio Microbiome studies Prof Philip Hugenholtz A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes Wood DLA, Lachner N, Tan JM, ..., Soyer HP, Hugenholtz P. doi: 10.1128/mBio.01432-18
Peer-reviewed paper Aug 27, 2018 Nature Biotechnology Genome-based taxonomy Prof Philip Hugenholtz A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Parks DH, Chuvochina M, Waite, DW, ..., Chaumeil PA, Hugenholtz P. doi: 10.1038/nbt.4229
Peer-reviewed paper Jun 1, 2018 Nucleic Acids Research Metagenomic analysis Prof Gene Tyson GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes Boyd JA, Woodcroft BJ, ..., Tyson GW. doi: 10.1093/nar/gky174
Peer-reviewed paper Sep 11, 2017 Nature Microbiology Genome discovery Prof Gene Tyson Prof Philip Hugenholtz Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks DH, Rinke C, Chuvochina M, ..., Hugenholtz P, Tyson GW. doi: 10.1038/s41564-017-0012-7
Peer-reviewed paper Aug 1, 2017 Nature Biotechnology Genome discovery Prof Philip Hugenholtz Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers RM, Kyrpides NC, Stepanauskas R, ..., Hugenholtz P, Woyke T. doi: 10.1038/nbt.3893
Peer-reviewed paper May 14, 2015 Genome Research Metagenomic analysis Prof Gene Tyson Prof Philip Hugenholtz CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks DH, Imelfort M, Skennerton CT, ..., Hugenholtz P, Tyson GW. doi: 10.1101/gr.186072.114
Peer-reviewed paper Nov 1, 2014 Bioinformatics Metagenomic analysis Prof Gene Tyson Prof Philip Hugenholtz STAMP: statistical analysis of taxonomic and functional profiles Parks DH, Tyson GW, Hugenholtz P, ..., Beiko RG. doi: 10.1093/bioinformatics/btu494
Peer-reviewed paper Sep 30, 2014 PeerJ Metagenomic analysis Prof Gene Tyson Prof Philip Hugenholtz GroopM: an automated tool for the recovery of population genomes from related metagenomes. Imelfort M, Parks DH, Woodcroft BJ, ..., Hugenholtz P, Tyson GW. doi: 10.7717/peerj.603. eCollection 2014
Peer-reviewed paper May 26, 2013 Nature Biotechnology Genome discovery Prof Gene Tyson Prof Philip Hugenholtz Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Albertsen M, Hugenholtz P, Skarshewski A, ..., Tyson GW, Nielsen P. doi: 10.1038/nbt.2579
