Related papers: Parameter Identifiability Under Limited Experiment…
Mechanistic growth models play a major role in bioprocess engineering, design, and control. Their reasonable predictive power and their high level of interpretability make them an essential tool for computer aided engineering methods.…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Untargeted metabolomics based on liquid chromatography-mass spectrometry technology is quickly gaining widespread application given its ability to depict the global metabolic pattern in biological samples. However, the data is noisy and…
Mathematical modelling is a widely used approach to understand and interpret clinical trial data. This modelling typically involves fitting mechanistic mathematical models to data from individual trial participants. Despite the widespread…
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…
When mathematical biology models are used to make quantitative predictions for clinical or industrial use, it is important that these predictions come with a reliable estimate of their accuracy (uncertainty quantification). Because models…
Single-cell data provide high-dimensional measurements of the transcriptional states of cells, but extracting insights into the regulatory functions of genes, particularly identifying transcriptional mechanisms affected by biological…
Understanding cell cycle dynamics is crucial for studying biological processes such as growth, development and disease progression. While fluorescent protein reporters like the Fucci system allow live monitoring of cell cycle phases, they…
We develop a general modelling framework for compartmental epidemiological systems structured by continuous variables which are linked to the levels of expression of compartment-specific traits. We start by formulating an individual-based…
Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…
Background. Emerging technologies now allow for mass spectrometry based profiling of up to thousands of small molecule metabolites (metabolomics) in an increasing number of biosamples. While offering great promise for revealing insight into…
We explore the relationship among model fidelity, experimental design, and parameter estimation in sloppy models. We show that the approximate nature of mathematical models poses challenges for experimental design in sloppy models. In many…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Tracking the development of living cells in live-cell time-lapses reveals crucial insights into single-cell behavior and presents tremendous potential for biomedical and biotechnological applications. In microbial live-cell imaging (MLCI),…
Adoptive Cell Transfer therapy of cancer is currently in full development and mathematical modeling is playing a critical role in this area. We study a stochastic model developed by Baar et al. in 2015 for modeling immunotherapy against…
Developments in transcriptomics techniques have caused a large demand in tailored computational methods for modelling gene expression dynamics from experimental data. Recently, so-called single-cell experiments have revolutionised genetic…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
We present a novel mathematical model of heterogeneous cell proliferation where the total population consists of a subpopulation of slow-proliferating cells and a subpopulation of fast-proliferating cells. The model incorporates two…
This paper investigates the identification of observable low-frequency (LF) parameters of battery cell's equivalent circuit models (ECMs) using time-domain voltage and current measurements sampled at low frequency by built-in battery…
Traditional disease transmission models assume that the infectious period is exponentially distributed with a recovery rate fixed in time and across individuals. This assumption provides analytical and computational advantages, however it…