Bayesian inference of RNA life-cycle kinetic rates from sequencing data with multiple latent clustering

Enrico Bibbona (Politecnico di Torino)

24-Mar-2022, 16:00-16:30 (2 years ago)

Abstract: We here propose a hierarchical Bayesian model to infer RNA synthesis, processing, and degradation rates from sequencing data, based on an ordinary differential equation system that models the RNA life cycle. We parametrize the latent kinetic rates, that rule the system, with a novel functional form, and estimate their parameters through 6 Dirichlet process mixture models. Owing to the complexity of this approach, we are able to simultaneously perform inference, clustering and model selection. We apply our method to investigate transcriptional and post-transcriptional responses of murine fibroblasts to the activation of proto-oncogene Myc. Our approach uncovers simultaneous regulations of the rates, which had not previously been observed in this biological system.

algebraic geometrydynamical systemsprobability

Audience: researchers in the topic

( video )


Seminar on the Mathematics of Reaction Networks

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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!

The organizers.

Organizers: Daniele Cappelletti*, Stefan Müller*, Tung Nguyen*, Polly Yu*
*contact for this listing

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