Reconstructing cellular dynamics from single cell data

Abstract: A grand challenge in single cell studies is to construct a quantitative, predictive, and genome-wide mathematical model describing cellular dynamics. Single-cell (sc)RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. A frontier of research is how to extract dynamical information from the snapshot data. In this talk I will first discuss our recently developed dynamo framework (Qiu et al. Cell, 2022), focusing on the underlying mathematical framework. Then I will discuss our recent efforts of reconstructing full dynamical equations using discrete calculus on graphs (Zhang et al. to be submitted). I will conclude with an example of applying the formalism, together with transition path analyses originally developed in chemical physics, to study how epithelial-to-mesenchymal transition couples with cell cycle (Wang et al. Sci Adv 2020, eLife 2022, Hu et al., in preparation).

algebraic geometrydynamical systemsprobability

Audience: researchers in the topic

( video )

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Seminar on the Mathematics of Reaction Networks

Series comments: Subscription link: list.ku.dk/postorius/lists/morn.list.ku.dk/

This seminar series focuses on progress in mathematical theory for the study of reaction networks, mainly in biology and chemistry. The scope is broad and accommodates works arising from dynamical systems, stochastics, algebra, topology and beyond.

We aim at providing a common forum for sharing knowledge and encouraging discussion across subfields. In particular we aim at facilitating interactions between junior and established researchers. These considerations will be represented in the choice of invited speakers and we will strive to create an excellent, exciting and diverse schedule.

The seminar runs twice a month, typically on the 2nd and 4th Thursday of the month, at 17:00 Brussels time (observe that this webpage shows the schedule in your current time zone). Each session consists of two 25-minute talks followed by 5-minute questions. After the two talks, longer discussions will take place for those interested. To this end, we will use breakout rooms. For this to work well, you need to have the latest version of Zoom installed (version 5.3.0 or higher), and use the desktop client or mobile app (not supported on ChromeOS).

We look forward hearing about new work and meeting many of you over zoom! Many of the talks are recorded; to see the recording, from Past Talks, open details of the listed talk for a video link.

The organizers.

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