Increasingly, researchers are discovering associations between microbiome and a wide
range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on …

Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …

Identifying differentially abundant microbes is a common goal of microbiome studies.
Multiple methods are used interchangeably for this purpose in the literature. Yet, there are …

Broad-spectrum antibiotics for suspected early-onset neonatal sepsis (sEONS) may have
pronounced effects on gut microbiome development and selection of antimicrobial …

Characterizing biomarkers based on microbiome profiles has great potential for translational
medicine and precision medicine. Here, we present microbiomeMarker, an R/Bioconductor …

ABSTRACT A large amount of sequencing data is produced in microbial community ecology
studies using the high-throughput sequencing technique, especially amplicon-sequencing …

Differential abundance (DA) analysis of microbiome data continues to be a challenging
problem due to the complexity of the data. In this article we define the notion of “sampling …

The microbiota comprises the microorganisms that live in close contact with the host, with
mutual benefit for both counterparts. The contribution of the gut microbiota to the emergence …

The data output from microbiome research is growing at an accelerating rate, yet mining the
data quickly and efficiently remains difficult. There is still a lack of an effective data structure …

It is challenging to associate features such as human health outcomes, diet, environmental
conditions, or other metadata to microbial community measurements, due in part to their …