Related papers: Prediction of source nutrients for microorganisms …
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
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…
Detecting and quantifying products of cellular metabolism using Mass Spectrometry (MS) has already shown great promise in many biological and biomedical applications. The biggest challenge in metabolomics is annotation, where measured…
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions-including those that have yet to be…
Our view of the microbial world and its impact on human health is changing radically with the ability to sequence uncultured or unculturable microbes sampled directly from their habitats, ability made possible by fast and cheap next…
Genetic and environmental perturbation experiments have been used to study microbes in a bid to gain insight into transcriptional regulation, adaptive evolution, and other cellular dynamics. These studies have potential in enabling rational…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…
Many foraging microorganisms rely upon cellular transport networks to deliver nutrients, fluid and organelles between different parts of the organism. Networked organisms ranging from filamentous fungi to slime molds demonstrate a…
Metabolomic data can potentially enable accurate, non-invasive and low-cost prediction of coronary artery disease. Regression-based analytical approaches however might fail to fully account for interactions between metabolites, rely on a…
The classification of diabetes and prediabetes by static glucose thresholds obscures the pathophysiological dysglycemia heterogeneity, primarily driven by insulin resistance (IR), beta-cell dysfunction, and incretin deficiency. This review…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter ``probiotic" treatments intended to alter the…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective…
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…