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Microorganisms such as bacteria and fungi play essential roles in many application fields, like biotechnique, medical technique and industrial domain. Microorganism counting techniques are crucial in microorganism analysis, helping…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
High-throughput metabolomics investigations, when conducted in large human cohorts, represent a potentially powerful tool for elucidating the biochemical diversity and mechanisms underlying human health and disease. Large-scale metabolomics…
What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…
Data mining environment produces a large amount of data, that need to be analyzed, patterns have to be extracted from that to gain knowledge. In this new era with boom of data both structured and unstructured, in the field of genomics,…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…
Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…
Accurate estimates of microbial species abundances are needed to advance our understanding of the role that microbiomes play in human and environmental health. However, artificially constructed microbiomes demonstrate that intuitive…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
Many studies have been performed to characterize the dynamics and stability of the microbiome across a range of environmental contexts [Costello et al., 2012, Faust et al., 2015]. For example, it is often of interest to identify time…
A taxonomy is a standardized framework to classify and organize items into categories. Hierarchical taxonomies are ubiquitous, ranging from the classification of organisms to the file system on a computer. Characterizing the typical…
Many scientific datasets are compositional in nature. Important biological examples include species abundances in ecology, cell-type compositions derived from single-cell sequencing data, and amplicon abundance data in microbiome research.…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a…
Clustering is a common technique for statistical data analysis, which is used in many fields, including machine learning, data mining, pattern recognition, image analysis and bioinformatics. Clustering is the process of grouping similar…