Related papers: Statistical Methods for Microbiome Analysis: A bri…
In the modern world, technology is at its peak. Different avenues in programming and technology have been explored for data analysis, automation, and robotics. Machine learning is key to optimize data analysis, make accurate predictions,…
This issue includes six articles that develop and apply statistical methods for the analysis of gene sequencing data of different types. The methods are tailored to the different data types and, in each case, lead to biological insights not…
Genetic data are now routinely used to study the history of population size, subdivision, and gene flow. A variety of formal statistical methods is available for testing hypotheses and fitting models to data. Yet it is often unclear which…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the…
Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic…
Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical…
What is a complex network? How do we characterize complex networks? Which systems can be studied from a network approach? In this text, we motivate the use of complex networks to study and understand a broad panoply of systems, ranging from…
The microbiome-gut-brain-axis field is multidisciplinary, benefiting from the expertise of microbiology, ecology, psychiatry, computational biology, and epidemiology amongst other disciplines. As the field matures and moves beyond a basic…
A key aspect of the design of evolutionary and swarm intelligence algorithms is studying their performance. Statistical comparisons are also a crucial part which allows for reliable conclusions to be drawn. In the present paper we gather…
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…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
Microarray is one of the essential technologies used by the biologist to measure genome-wide expression levels of genes in a particular organism under some particular conditions or stimuli. As microarrays technologies have become more…
Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…
Microorganisms are widely distributed in the human daily living environment. They play an essential role in environmental pollution control, disease prevention and treatment, and food and drug production. The analysis of microorganisms is…
The intricate interplay between host organisms and their gut microbiota has catalyzed research into the microbiome's role in disease, shedding light on novel aspects of disease pathogenesis. However, the mechanisms through which the…
Data analysis impacts virtually every aspect of our society today. Often, this analysis is performed on an existing dataset, possibly collected through a process that the data scientists had limited control over. The existing data analyzed…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
This manuscript introduces a new analytical approach for studying the time evolution of disease spread on a finite size network. Our methodology can accommodate any disease with a general infectivity profile. This new approach is able to…