Related papers: Statistical Methods for Microbiome Analysis: A bri…
We analyze several florae (collections of plant species populating specific areas) in different geographic and climatic regions. For every list of species we produce a taxonomic classification tree and we consider its statistical…
Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depend on the context and…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…
Meta-analysis is routinely performed in many scientific disciplines. This analysis is attractive since discoveries are possible even when all the individual studies are underpowered. However, the meta-analytic discoveries may be entirely…
In microbial studies, samples are often treated under different experimental conditions and then tested for microbial survival. A technique, dating back to the 1880's, consists of diluting the samples several times and incubating each…
With rapidly increasing data, clustering algorithms are important tools for data analytics in modern research. They have been successfully applied to a wide range of domains; for instance, bioinformatics, speech recognition, and financial…
In recent years, ideas from statistics and scientific computing have begun to interact in increasingly sophisticated and fruitful ways with ideas from computer science and the theory of algorithms to aid in the development of improved…
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…
The development of modern information technologies permits to collect and to analyze huge amounts of statistical data in different spheres of life. The main problem is not to only to collect but to process all relevant information. The…
The study of immune cellular composition has been of great scientific interest in immunology because of the generation of multiple large-scale data. From the statistical point of view, such immune cellular data should be treated as…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…
Data analysis is a powerful tool in all experimental sciences. Statistical methods, such as sampling theory, computer technologies necessary for handling large amounts of data, skill in analysing information contained in different types of…
Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational…
In this paper, I present a summary on some works that utilized static analysis techniques for understanding biological systems. Control flow analysis, context dependent analysis, and other techniques were employed to investigate the…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
One of the major research questions regarding human microbiome studies is the feasibility of designing interventions that modulate the composition of the microbiome to promote health and cure disease. This requires extensive understanding…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative…
One of the major and serious threats that the Internet faces today is the vast amounts of data and files which need to be evaluated for potential malicious intent. Malicious software, often referred to as a malware that are designed by…