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Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/bies.201600188openalex-snapshot
Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons
inferredcites →https://doi.org/10.1007/978-1-4939-2239-0_3openalex-snapshot
Predicting Bacterial Community Assemblages Using an Artificial Neural Network Approach
inferredcites →https://doi.org/10.1007/s11222-016-9696-4openalex-snapshot
Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC
inferredcites →https://doi.org/10.1016/j.chom.2014.08.014openalex-snapshot
The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
inferredcites →https://doi.org/10.1016/j.mib.2015.04.004openalex-snapshot
Metagenomics meets time series analysis: unraveling microbial community dynamics
inferredcites →https://doi.org/10.1016/j.syapm.2017.11.008openalex-snapshot
Comparison of DNA extraction methods for human gut microbial community profiling
inferredcites →https://doi.org/10.1016/s0020-0255(69)80013-7openalex-snapshot
On the choice of sampling rates in parametric identification of time series
inferredcites →https://doi.org/10.1021/es026000bopenalex-snapshot
Microbial Source Tracking: State of the Science
inferredcites →https://doi.org/10.1038/4441022aopenalex-snapshot
Human gut microbes associated with obesity
inferredcites →https://doi.org/10.1038/ismej.2011.11openalex-snapshot
Reproducibility and quantitation of amplicon sequencing-based detection
inferredcites →https://doi.org/10.1038/ismej.2017.107openalex-snapshot
Modeling time-series data from microbial communities
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nature12820openalex-snapshot
Diet rapidly and reproducibly alters the human gut microbiome
inferredcites →https://doi.org/10.1038/nature24460openalex-snapshot
Quantitative microbiome profiling links gut community variation to microbial load
inferredcites →https://doi.org/10.1038/nbt.3981openalex-snapshot
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
inferredcites →https://doi.org/10.1038/nmeth.1650openalex-snapshot
Bayesian community-wide culture-independent microbial source tracking
inferredcites →https://doi.org/10.1038/nmeth.1975openalex-snapshot
Predicting bacterial community assemblages using an artificial neural network approach
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nrg2825openalex-snapshot
Tackling the widespread and critical impact of batch effects in high-throughput data
inferredcites →https://doi.org/10.1038/s41564-018-0202-yopenalex-snapshot
Recognizing the reagent microbiome
inferredcites →https://doi.org/10.1038/s41598-017-05260-wopenalex-snapshot
Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa
inferredcites →https://doi.org/10.1073/pnas.1501305112openalex-snapshot
Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock
inferredcites →https://doi.org/10.1093/bioinformatics/btx549openalex-snapshot
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing
inferredcites →https://doi.org/10.1093/cid/cis580openalex-snapshot
Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation
inferredcites →https://doi.org/10.1093/oso/9780198524847.001.0001openalex-snapshot
Analysis of Longitudinal Data
inferredcites →https://doi.org/10.1111/j.1472-765x.2007.02198.xopenalex-snapshot
Detection of Actinobacteria cultivated from environmental samples reveals bias in universal primers
inferredcites →https://doi.org/10.1111/j.2517-6161.1956.tb00216.xopenalex-snapshot
On the Estimation of Small Frequencies in Contingency Tables
inferredcites →https://doi.org/10.1126/scitranslmed.aad0917openalex-snapshot
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
inferredcites →https://doi.org/10.1128/aem.01451-14openalex-snapshot
Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles
inferredcites →https://doi.org/10.1128/aem.64.8.3110-3113.1998openalex-snapshot
Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants
inferredcites →https://doi.org/10.1186/gb-2011-12-5-r50openalex-snapshot
Moving pictures of the human microbiome
inferredcites →https://doi.org/10.1186/gb-2014-15-7-r89openalex-snapshot
Host lifestyle affects human microbiota on daily timescales
inferredcites →https://doi.org/10.1186/s12866-015-0351-6openalex-snapshot
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
inferredcites →https://doi.org/10.1186/s40168-016-0175-0openalex-snapshot
Adjusting microbiome profiles for differences in microbial load by spike-in bacteria
inferredcites →https://doi.org/10.1186/s40168-017-0237-yopenalex-snapshot
Normalization and microbial differential abundance strategies depend upon data characteristics
inferredcites →https://doi.org/10.1186/s40168-018-0584-3openalex-snapshot
Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
inferredcites →https://doi.org/10.1186/s40168-018-0605-2openalex-snapshot
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
inferredcites →https://doi.org/10.1186/s40168-019-0660-3openalex-snapshot
Dynamic interaction network inference from longitudinal microbiome data
inferredcites →https://doi.org/10.1214/ss/1177009939openalex-snapshot
Bayesian Experimental Design: A Review
inferredcites →https://doi.org/10.1371/journal.pcbi.1002624openalex-snapshot
Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems
inferredcites →https://doi.org/10.1371/journal.pcbi.1005706openalex-snapshot
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
inferredcites →https://doi.org/10.1371/journal.pcbi.1006960openalex-snapshot
Modeling the temporal dynamics of the gut microbial community in adults and infants
inferredcites →https://doi.org/10.1371/journal.pone.0020447openalex-snapshot
Towards the Human Colorectal Cancer Microbiome
inferredcites →https://doi.org/10.1371/journal.pone.0088999openalex-snapshot
Impact of Technical Sources of Variation on the Hand Microbiome Dynamics of Healthcare Workers
inferredcites →https://doi.org/10.1534/genetics.108.094201openalex-snapshot
Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots
inferredcites →https://doi.org/10.17713/ajs.v45i4.122openalex-snapshot
Compositional uncertainty should not be ignored in high-throughput sequencing data analysis
inferredcites →https://doi.org/10.3389/fmicb.2015.00130openalex-snapshot
Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences
inferredcites →https://doi.org/10.48550/arxiv.1712.00067openalex-snapshot
Inference of Dynamic Regimes in the Microbiome
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/ajp.22970openalex-snapshot
Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research
inferred← citeshttps://doi.org/10.1007/s00248-022-02060-2openalex-snapshot
A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses
inferred← citeshttps://doi.org/10.1007/s13199-025-01078-7openalex-snapshot
Exploring the influence of seed bacteria and fungi on seed germination and seedling traits in Brachypodium congeners
inferred← citeshttps://doi.org/10.1016/j.aca.2021.338620openalex-snapshot
Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review
inferred← citeshttps://doi.org/10.1016/j.soilbio.2020.108042openalex-snapshot
You must choose, but choose wisely: Model-based approaches for microbial community analysis
inferred← citeshttps://doi.org/10.1038/s41591-019-0464-9openalex-snapshot
Community ecology as a framework for human microbiome research
inferred← citeshttps://doi.org/10.1038/s41592-019-0431-xopenalex-snapshot
FEAST: fast expectation-maximization for microbial source tracking
inferred← citeshttps://doi.org/10.1038/s41598-024-53506-1openalex-snapshot
Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing
inferred← citeshttps://doi.org/10.1101/2020.04.11.20061911openalex-snapshot
Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection
inferred← citeshttps://doi.org/10.1101/2020.08.03.233692openalex-snapshot
Data-driven causal analysis of observational time series in ecology
inferred← citeshttps://doi.org/10.1101/2025.02.27.639550openalex-snapshot
Ecological relationships between human gut bacteria predicted from analysis of dense microbiome time series data from US travelers in Bangladesh
inferred← citeshttps://doi.org/10.1111/jbi.14560openalex-snapshot
Environmental and geographical factors structure cauliflower coral's algal symbioses across the Indo‐Pacific
inferred← citeshttps://doi.org/10.1128/mbio.01150-24openalex-snapshot
Interpolation of microbiome composition in longitudinal data sets
inferred← citeshttps://doi.org/10.1128/spectrum.02251-22openalex-snapshot
Effects of Lumacaftor-Ivacaftor on Airway Microbiota-Mycobiota and Inflammation in Patients with Cystic Fibrosis Appear To Be Linked to Pseudomonas aeruginosa Chronic Colonization
inferred← citeshttps://doi.org/10.1136/bmjopen-2026-120775openalex-snapshot
Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort
inferred← citeshttps://doi.org/10.33540/820openalex-snapshot
Lessons from the Amazon biome: impact of management practices on aboveground-belowground interactions Márcio Fernandes
inferred← citeshttps://doi.org/10.3389/fcimb.2026.1837109openalex-snapshot
Design, processing, and modeling for longitudinal multiomics microbiome data
inferred← citeshttps://doi.org/10.3389/fmicb.2022.909313openalex-snapshot
Temporal Alignment of Longitudinal Microbiome Data
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1559521openalex-snapshot
Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges
inferred← citeshttps://doi.org/10.70675/5167078fzc81dz457az88b6zce4defb6df49openalex-snapshot
Effet des thérapies protéiques sur l’axe intestin-poumon dans la mucoviscidose
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