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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
TLDR
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
TLDR
In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations and data-driven social-networking should facilitate identification of spectra and foster collaborations.
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QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
TLDR
QIIME 2 provides new features that will drive the next generation of microbiome research, including interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
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PHF8 Mediates Histone H4 Lysine 20 Demethylation Events Involved in Cell Cycle Progression
TLDR
The identification and characterization of an H4K20me1 demethylase, PHF8, has revealed an intimate link between this enzyme and two distinct events in cell cycle progression.
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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. The…
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Proteomics
TLDR
This paper aims to demonstrate the efforts towards in-situ applicability of EMMARM, as to provide real-time information about the response of the E-modulus of the Higgs particle to Na6(SO4).
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American Gut: an Open Platform for Citizen Science Microbiome Research
TLDR
The utility of the living data resource and cross-cohort comparison is demonstrated to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education.
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SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
TLDR
SIRIUS 4 is a fast and highly accurate tool for molecular structure interpretation from mass-spectrometry-based metabolomics data and integrates CSI:FingerID for searching in molecular structure databases.
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Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
TLDR
This first completed genome for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity, and comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host.
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Best practices for analysing microbiomes
TLDR
This Review focuses on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis.
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