Reference health
EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research
1 of 61 checkable references need attention · checked 2026-08-25
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
References needing attention
does not resolve to a known work10.16288/j.yczz.19-222
The 60 checked references that resolve
resolves10.1016/j.cell.2021.03.024
The long-term genetic stability and individual specificity of the human gut microbiome
resolves10.1038/nature08821
A human gut microbial gene catalogue established by metagenomic sequencing
resolves10.1038/s41587-019-0202-3
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
resolves10.1186/s40168-018-0590-5
The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids
resolves10.1016/j.mib.2019.10.010
Reductionist synthetic community approaches in root microbiome research
resolves10.1038/s41587-019-0104-4
NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice
resolves10.3390/agronomy12123129
Maize Rotation Combined with Streptomyces rochei D74 to Eliminate Orobanche cumana Seed Bank in the Farmland
resolves10.1016/j.gpb.2022.08.006
Sequence-Based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes
resolves10.1038/s41587-019-0209-9
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
resolves10.1038/s41596-020-00444-7
High-throughput cultivation and identification of bacteria from the plant root microbiota
resolves10.1128/aem.01541-09
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
resolves10.1093/nar/gky1008
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data
resolves10.1007/s13238-020-00724-8
A practical guide to amplicon and metagenomic analysis of microbiome data
resolves10.1097/cm9.0000000000000871
A guide to human microbiome research: study design, sample collection, and bioinformatics analysis
resolves10.1093/bioinformatics/btu494
STAMP: statistical analysis of taxonomic and functional profiles
resolves10.1038/nbt.2676
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
resolves10.1002/imt2.5
ImageGP: An easy‐to‐use data visualization web server for scientific researchers
resolves10.1093/nar/gkab301
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
resolves10.1371/journal.pone.0163962
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
resolves10.1002/imt2.32
ggClusterNet: An R package for microbiome network analysis and modularity‐based multiple network layouts
resolves10.1093/bioinformatics/btu393
<i>circlize</i>
implements and enhances circular visualization in R
resolves10.1016/j.jgg.2021.06.005
The rice histone methylation regulates hub species of the root microbiota
resolves10.1136/gutjnl-2018-315988
Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus
resolves10.1038/s41396-020-0720-5
Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt
resolves10.1016/j.jgg.2020.11.006
The oral microbiome of pregnant women facilitates gestational diabetes discrimination
resolves10.1038/s43705-022-00182-9
Machine learning and deep learning applications in microbiome research
resolves10.1136/gutjnl-2022-328216
Overcoming regional limitations: transfer learning for cross-regional microbial-based diagnosis of diseases
resolves10.1136/gutjnl-2019-318977
Tracing the accumulation of in vivo human oral microbiota elucidates microbial community dynamics at the gateway to the GI tract
resolves10.1093/nar/gkx295
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
resolves10.1038/s41596-019-0264-1
Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data
resolves10.1126/science.aau6389
A specialized metabolic network selectively modulates
<i>Arabidopsis</i>
root microbiota
resolves10.1038/ismej.2011.139
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
resolves10.1016/j.jclepro.2018.12.182
N2O and NO emission from a biological aerated filter treating coking wastewater: Main source and microbial community
resolves10.1016/j.jgg.2021.07.007
EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online
resolves10.3389/fgene.2021.706907
ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram
resolves10.1007/s11427-019-9521-2
Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota
resolves10.1007/s11427-018-9284-4
Root microbiota shift in rice correlates with resident time in the field and developmental stage
resolves10.1016/j.jgg.2021.08.015
The role of genotype and diet in shaping gut microbiome in a genetic vitamin A deficient mouse model
resolves10.1126/science.aaw9285
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
resolves10.1073/pnas.1616564113
Root nodule symbiosis in
<i>Lotus japonicus</i>
drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities
resolves10.1016/j.gpb.2021.08.001
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types
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