Related papers: Microbial correlation: a semi-parametric model for…
Inflammatory bowel diseases (IBD) are complex diseases in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when they are exposed to yet unclear environmental factors. The complexity of this class…
In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…
Complex biological processes are usually experimented along time among a collection of individuals. Longitudinal data are then available and the statistical challenge is to better understand the underlying biological mechanisms. The…
Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers…
Compositional data arise in many areas of research in the natural and biomedical sciences. One prominent example is in the study of the human gut microbiome, where one can measure the relative abundance of many distinct microorganisms in a…
The success of metabolomics studies depends upon the "fitness" of each biological sample used for analysis: it is critical that metabolite levels reported for a biological sample represent an accurate snapshot of the studied organism's…
This study develops a Bayesian semi-parametric model to examine the longitudinal growth and appetite phenotypes in children from the GUSTO cohort, with a focus on understanding the relationship between eating behaviours and growth outcomes…
In microbiome analysis, researchers often seek to identify taxonomic features associated with an outcome of interest. However, microbiome features are intercorrelated and linked by phylogenetic relationships, making it challenging to assess…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
In biomedical applications it is often necessary to estimate a physiological response to a treatment consisting of multiple components, and learn the separate effects of the components in addition to the joint effect. Here, we extend…
The human microbiome plays an important role in human health and disease status. Next generating sequencing technologies allow for quantifying the composition of the human microbiome. Clustering these microbiome data can provide valuable…
We investigate some chemostat models incorporating wall growth, competition, random fluctuations on the dilution rate, and different consumption functions (Monod and Haldane). We analyze the asymptotic behavior of the solutions of the…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…