A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions
Background Differential abundance analysis (DAA) is one central statistical task in
microbiome data analysis. A robust and powerful DAA tool can help identify highly confident …
microbiome data analysis. A robust and powerful DAA tool can help identify highly confident …
[HTML][HTML] A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies
Background In microbiome disease association studies, it is a fundamental task to test which
microbes differ in their abundance between groups. Yet, consensus on suitable or optimal …
microbes differ in their abundance between groups. Yet, consensus on suitable or optimal …
Performance of gut Microbiome as an independent diagnostic tool for 20 diseases: cross-cohort validation of machine-learning classifiers
Cross-cohort validation is essential for gut-microbiome-based disease stratification but was
only performed for limited diseases. Here, we systematically evaluated the cross-cohort …
only performed for limited diseases. Here, we systematically evaluated the cross-cohort …
MIDASim: a fast and simple simulator for realistic microbiome data
Background Advances in sequencing technology has led to the discovery of associations
between the human microbiota and many diseases, conditions, and traits. With the …
between the human microbiota and many diseases, conditions, and traits. With the …
Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa
R Giliberti, S Cavaliere, IE Mauriello… - PLoS computational …, 2022 - journals.plos.org
Machine learning-based classification approaches are widely used to predict host
phenotypes from microbiome data. Classifiers are typically employed by considering …
phenotypes from microbiome data. Classifiers are typically employed by considering …
Zero is not absence: censoring-based differential abundance analysis for microbiome data
Motivation Microbiome data analysis faces the challenge of sparsity, with many entries
recorded as zeros. In differential abundance analysis, the presence of excessive zeros in …
recorded as zeros. In differential abundance analysis, the presence of excessive zeros in …
Accommodating multiple potential normalizations in microbiome associations studies
Background Microbial communities are known to be closely related to many diseases, such
as obesity and HIV, and it is of interest to identify differentially abundant microbial species …
as obesity and HIV, and it is of interest to identify differentially abundant microbial species …
Viral genomic variation and the severity of genital HSV-2 infection as quantified by shedding rate: a viral genome-wide association study
Background The clinical severity of genital HSV-2 infection varies widely among infected
persons with some experiencing frequent genital lesions while others are asymptomatic …
persons with some experiencing frequent genital lesions while others are asymptomatic …
Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies
L Kodalci, O Thas - Plos one, 2023 - journals.plos.org
Microbiome data obtained with amplicon sequencing are considered as compositional data.
It has been argued that these data can be analysed after appropriate transformation to log …
It has been argued that these data can be analysed after appropriate transformation to log …
Gut microbiome and symptoms in females with irritable bowel syndrome: a cross-sectional analysis
Irritable bowel syndrome (IBS), a disorder of gut-brain interaction, is associated with
abdominal pain and stool frequency/character alterations that are linked to changes in …
abdominal pain and stool frequency/character alterations that are linked to changes in …