相关论文: Robust estimation of microbial diversity in theory…

We wish to formally test for changes in the taxonomic diversity of a community, especially in the presence of high latent diversity. Drawing on the meta-analysis literature, we construct a model for diversity that accounts for covariate…

Quantification of measurement uncertainty is crucial for robust scientific inference, yet accurate estimates of this uncertainty remain elusive for ecological measures of diversity. Here, we address this longstanding challenge by deriving a…

Several factors affect the structure of communities, including biological, physical and chemical phenomena, impacting the quantification of biodiversity, measured by diversity indexes such as Shannon's entropy. Then, once a point estimate…

Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…

Several theoretical frameworks have been proposed to explain observed biodiversity patterns, ranging from the classical niche-based theories, mainly employing a continuous formalism, to neutral theories, based on statistical mechanics of…

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 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…

The Shannon entropy is a fundamental measure for quantifying diversity and model complexity in fields such as information theory, ecology, and genetics. However, many existing studies assume that the number of species is known, an…

In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply count-only measures such as Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use classical…

Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…

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…

High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a…

Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy-based diversity indices, or diversity indices…

We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of…

We introduce a new dominance concept consisting of three new dominance metrics based on Lloyd's (1967) mean crowding index. The new metrics link communities and species, whereas existing ones are applicable only to communities. Our…

Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…

The paper presents the investigation and implementation of the relationship between diversity and the performance of multiple classifiers on classification accuracy. The study is critical as to build classifiers that are strong and can…

Recently, the Shannon entropy, which was introduced originally as a measure of information amount, has been widely used as a useful index of various diversities such as biodiversity and geodiversity. In this work we have evaluated the…

Using a sample from a population to estimate the proportion of the population with a certain category label is a broadly important problem. In the context of microbiome studies, this problem arises when researchers wish to use a sample from…

Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…