[HTML][HTML] Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment
LJ Marcos-Zambrano… - Frontiers in …, 2021 - frontiersin.org
The number of microbiome-related studies has notably increased the availability of data on
human microbiome composition and function. These studies provide the essential material …
human microbiome composition and function. These studies provide the essential material …
[HTML][HTML] Microbiome datasets are compositional: and this is not optional
Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers,
metagenomes or metatranscriptomes are commonplace and being used to study human …
metagenomes or metatranscriptomes are commonplace and being used to study human …
[HTML][HTML] Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia
Although microbial populations in the gut microbiome are associated with COVID-19
severity, a causal impact on patient health has not been established. Here we provide …
severity, a causal impact on patient health has not been established. Here we provide …
[HTML][HTML] Establishing microbial composition measurement standards with reference frames
Differential abundance analysis is controversial throughout microbiome research. Gold
standard approaches require laborious measurements of total microbial load, or absolute …
standard approaches require laborious measurements of total microbial load, or absolute …
QIIME 2 enables comprehensive end‐to‐end analysis of diverse microbiome data and comparative studies with publicly available data
QIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the
popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully …
popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully …
[HTML][HTML] Consistent and correctable bias in metagenomic sequencing experiments
Marker-gene and metagenomic sequencing have profoundly expanded our ability to
measure biological communities. But the measurements they provide differ from the truth …
measure biological communities. But the measurements they provide differ from the truth …
[HTML][HTML] Endometrial microbiota composition is associated with reproductive outcome in infertile patients
I Moreno, I Garcia-Grau, D Perez-Villaroya… - Microbiome, 2022 - Springer
Background Previous evidence indicates associations between the female reproductive tract
microbiome composition and reproductive outcome in infertile patients undergoing assisted …
microbiome composition and reproductive outcome in infertile patients undergoing assisted …
[HTML][HTML] scCODA is a Bayesian model for compositional single-cell data analysis
Compositional changes of cell types are main drivers of biological processes. Their
detection through single-cell experiments is difficult due to the compositionality of the data …
detection through single-cell experiments is difficult due to the compositionality of the data …
A novel sparse compositional technique reveals microbial perturbations
The central aims of many host or environmental microbiome studies are to elucidate factors
associated with microbial community compositions and to relate microbial features to …
associated with microbial community compositions and to relate microbial features to …
Deep learning and its application in geochemical mapping
Abstract Machine learning algorithms have been applied widely in the fields of natural
science, social science and engineering. It can be expected that machine learning …
science, social science and engineering. It can be expected that machine learning …