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Bacteria pose unique challenges for genome-wide association studies (GWAS) because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome. While methods developed for human studies can correct…

A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…

The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial…

Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…

Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg.…

Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…

More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to…

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments…

The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine learning based biomarker development for multiple diseases and conditions. The microbiome is often analyzed…

Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…

Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…

High dimensional and heterogeneous count data are collected in various applied fields. In this paper, we look closely at high-resolution sequencing data on the microbiome, which have enabled researchers to study the genomes of entire…

Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through…

Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…

Bacteriophages (phages) are key regulators of bacterial populations and hold great promise for applications such as phage therapy, biocontrol, and industrial fermentation. The success of these applications depends on accurately determining…

The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…

Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…

In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the…

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…