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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
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Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
TLDR
A meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer identified a core set of 29 species significantly enriched in CRC metagenomes, establishing globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics.
View on Springer
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
TLDR
The combined analysis of heterogeneous CRC cohorts identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.
View on Springer
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
TLDR
With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.
View on PubMed
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
TLDR
PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences, and reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers.
View on Springer
Accessible, curated metagenomic data through ExperimentHub
TLDR
CuratedMetagenomicData provides standardized per-participant metadata linked to bacterial, fungal, archaeal, and viral taxonomic abundances, as well as quantitative metabolic functional profiles, generated by the HUMAnN2 and MetaPhlAn2 pipelines.
View on Nature
Data journals: A survey
TLDR
This study of more than 100 currently existing data journals describes the approaches they promote for data set description, availability, citation, quality, and open access and identifies ways to expand and strengthen the data journals approach as a means to promote data set access and exploitation.
View on Wiley
XPeer: A Self-Organizing XML P2P Database System
TLDR
XPeer is a zero-administration system for sharing and querying XML data that can be used in any application field, being a general purpose XML p2p DBMS, even though its main application is the management of resource descriptions in GRID environments.
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The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
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Static analysis for path correctness of XML queries
TLDR
A precise definition for this class of errors is provided, and a type system that is sound and complete, in its search for such errors, for a core language, under mild restrictions on the use of recursion in type definitions is defined.
View on Cambridge Press
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