Biomedical Mathematics Online Colloquium

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 …

Abstract: The study of sleep and circadian rhythms at scale requires novel technologies and approaches that are valid, cost effective and do not pose much of a burden to the participant. Here we will present our recent studies in which we have evaluated several classes of technologies and approaches including wearables, nearables, blood based biomarkers …

Abstract: There has been an increased use of scoring systems in clinical settings for the purpose of assessing risks in a convenient manner that provides important evidence for decision making. Machine learning-based methods may be useful for identifying important predictors and building models; however, their 'black box' nature limits their interpretability as well as clinical …

Abstravt: Latent space dynamics identification (LaSDI) is an interpretable data-driven framework that follows three distinct steps, i.e., compression, dynamics identification, and prediction. Compression allows high-dimensional data to be reduced so that they can be easily fit into an interpretable model. Dynamics identification lets you derive the interpretable model, usually some form of parameterized differential equations …

Abstract:  The effect of malaria on the developing world is devastating. Each year there are more than 200 million cases and over 400,000 deaths, with children under the age of five the most vulnerable. Ambitious malaria elimination targets have been set by the World Health Organization for 2030. These involve the elimination of the disease …