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References from Method development for cross-study microbiome data mining: Challenges and opportunities. Local targets link to admitted publications; unresolved targets remain external evidence.
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Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken
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NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice
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The National Microbiome Data Collaborative: enabling microbiome science
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Meta-Storms: Efficient Search for Similar Microbial Communities Based on a Novel Indexing Scheme and Similarity Score for Metagenomic Data
2012 · External reference
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Comparison of microbiome samples: methods and computational challenges
2020 · External reference
Gut microbiome, big data and machine learning to promote precision medicine for cancer
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Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
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A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome
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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
10.1128/msystems.00191-16 · 2017 · External reference
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
2016 · External reference
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Unresolved reference
External reference
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Metagenomic species profiling using universal phylogenetic marker genes
10.1038/nmeth.2693 · 2013 · External reference
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10.1038/nmeth.2066 · External reference
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10.1186/s40168-018-0541-1 · External reference
Assessment of quality control approaches for metagenomic data analysis
10.1038/srep06957 · 2014 · External reference
RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data
10.1186/s12864-018-4503-6 · 2018 · External reference
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10.7717/peerj.2584 · External reference
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Evaluating the Information Content of Shallow Shotgun Metagenomics
10.1128/msystems.00069-18 · 2018 · External reference
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
10.1038/s41467-019-13036-1 · 2019 · External reference
RefSeq: an update on prokaryotic genome annotation and curation
10.1093/nar/gkx1068 · 2018 · External reference
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10.1038/s41586-019-1238-8 · External reference
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10.1038/nature24621 · External reference
American Gut: an Open Platform for Citizen Science Microbiome Research
10.1128/msystems.00031-18 · 2018 · External reference
The Sequence Read Archive: explosive growth of sequencing data
10.1093/nar/gkr854 · 2012 · External reference
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
10.1186/1471-2105-9-386 · 2008 · External reference
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10.1093/nar/gky1078 · 2019 · External reference
IMG/M vol 5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
10.1093/nar/gky901 · 2019 · External reference
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10.1093/database/bay055 · External reference
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10.1038/nbt.1823 · External reference
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
10.1186/s13326-016-0097-6 · 2016 · External reference
The metagenomic data life-cycle: standards and best practices
10.1093/gigascience/gix047 · 2017 · External reference
10.1093/nar/gkz764
10.1093/nar/gkz764 · External reference
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data
10.1093/nar/gky1008 · 2019 · External reference
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10.1038/s41592-018-0141-9 · External reference
redbiom: a Rapid Sample Discovery and Feature Characterization System
10.1128/msystems.00215-19 · 2019 · External reference
Identifying and Predicting Novelty in Microbiome Studies
2018 · External reference
Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level
2019 · External reference
GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU
10.1093/bioinformatics/btt736 · 2014 · External reference
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10.1038/nbt.3960 · External reference
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Temporal and technical variability of human gut metagenomes
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A comprehensive evaluation of multicategory classification methods for microbiomic data
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10.1016/j.chom.2015.08.005 · External reference
A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children
2019 · External reference
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10.1038/ismej.2014.32 · External reference
Meta-analysis of gut microbiome studies identifies disease-specific and shared responses
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Multiple-Disease Detection and Classification across Cohorts via Microbiome Search
2020 · External reference
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10.1016/j.inffus.2018.09.012 · External reference
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Development of AI-based pathology biomarkers in gastrointestinal and liver cancer
2020 · External reference
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HCP: A Flexible CNN Framework for Multi-Label Image Classification
10.1109/tpami.2015.2491929 · 2016 · External reference
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Use of Metatranscriptomics in Microbiome Research
10.4137/bbi.s34610 · 2016 · External reference
Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities
10.1128/msystems.00115-19 · 2019 · External reference
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10.1371/journal.pcbi.1002358 · External reference
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10.7717/peerj.6695 · External reference
Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships
10.1186/2049-2618-1-17 · 2013 · External reference
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IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
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From Sample to Multi-Omics Conclusions in under 48 Hours
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