• Publications
  • Influence
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) andExpand
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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP communityExpand
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QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers.Expand
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Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. TheExpand
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PHF8 Mediates Histone H4 Lysine 20 Demethylation Events Involved in Cell Cycle Progression
While reversible histone modifications are linked to an ever-expanding range of biological functions, the demethylases for histone H4 lysine 20 and their potential regulatory roles remain unknown.Expand
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Proteomics
1 Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA 2 School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK 3 Departments ofExpand
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Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
  • X. He, J. McLean, +10 authors W. Shi
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences
  • 22 December 2014
Significance TM7 is one of the most enigmatic bacterial phyla among the uncultivated candidate phyla referred to as “microbial dark matter,” and it has potential pathogenic associations. We revealedExpand
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American Gut: an Open Platform for Citizen Science Microbiome Research
We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals newExpand
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Mass spectral molecular networking of living microbial colonies
Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, andExpand
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Minimum Information about a Biosynthetic Gene cluster.
A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters,Expand
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