Biomedical Mathematics Online Colloquium

Abstract: Almost all biological systems possess the ability to gather environmental information and modulate their behaviors to adaptively respond to changing environments. While animals excel at sensing odors, even simple bacteria can detect faint chemicals using stochastic receptors. They then navigate towards or away from the chemical source by processing this sensed information through intracellular …

Abstract: The Hypothalamic-Pituitary-Adrenal (HPA) axis is the key regulatory pathway responsible for maintaining homeostasis under conditions of real or perceived stress. Endocrine responses to stressors are mediated by adrenocorticotrophic hormone (ACTH) and corticosteroid (CORT) hormones. In healthy, non-stressed conditions, ACTH and CORT exhibit highly correlated ultradian pulsatility with an amplitude modulated by circadian processes. Disruption …

Abstract: Interpreting data using mechanistic mathematical models provides a foundation for discovery and decision-making in all areas of science and engineering. Key steps in using mechanistic mathematical models to interpret data include: (i) identifiability analysis; (ii) parameter estimation; and (iii) model prediction. Here we present a systematic, computationally efficient likelihood-based workflow that addresses all three …

Abstract: Surface Plasmon Resonance (SPR) assays are a standard approach for quantifying kinetic parameters in antibody-antigen binding reactions. Classical SPR approaches ignore the bivalent structure of antibodies, and use simplified ODE models to estimate effective reaction rates for such interactions. In this work we develop a new SPR protocol, coupling a model that explicitly accounts …

Abstract: I will report on some recent results on modelling the heart, the external circulation, and their application to problems of clinical relevance. I will show that a proper integration between PDE-based and machine-learning algorithms can improve the computational efficiency and enhance the generality of our iHEART simulator.

Abstract: TBD

Abstract: The regulation and maintenance of an organ’s shape and structure is a major outstanding question in developmental biology. The Drosophila wing imaginal disc serves as a powerful system for elucidating design principles of the shape formation in epithelial morphogenesis.

Abstract: Circadian rhythms in physiology and behavior are regulated by circadian clocks, ubiquitous molecular transcriptional-translational feedback loops that cycle with a periodicity of ~24 hours. Circadian clocks serve as cellular timekeepers regulating important cell-type specific functions. The phase of circadian rhythms and circadian clocks throughout the body are entrained to the light cycle by signals …

Abstract: Wearable health trackers have shifted from gadgets for sports enthusiasts to valuable health sentinels over the last few years and that transformation is gathering pace. What do these devices really measure about sleep? What types of devices are there, and which can we trust? Which of the many sleep measures reported, contribute to a …

Abstract: Biological phenomena are notorious for crossing several temporal and spatial scales. While often it may be sufficient to focus on a single scale, it is not rare that we have to consider several scales simultaneously. Computational modeling and simulation of biological systems thus frequently requires to include diverse temporal and spatial scales. A popular …

Abstract: In typical single-cell RNA-seq (scRNA-seq) data analysis, a clustering algorithm is applied to find discrete cell clusters as putative cell types, and then a statistical test is employed to identify the differentially expressed (DE) genes between the cell clusters. However, this common procedure suffers the ``double dipping'' issue: the same data are used twice …

Abstract: The realization that microbiomes, associated with virtually all multicellular organisms, have tremendous impact on their host health is considered as one of the most important scientific discoveries in the last decade. The host associated microbiomes, composed of tens to hundreds of co-existing microbial species, are highly heterogenous at multiple scales (e.g. between different hosts …