PhD in Complex Systems for Quantitative Biomedicine

Contacts

Supervisor

Curriculum vitae

Phd thesis

Topic Modelling to analyze spatial transcriptomic datasets

My PhD project is focused on the application of Topic Modelling techniques to get insights from large datasets of high complexity in the context of spatial transcriptomics.

First step concerns adaptation of topic modeling tools to the specific challenges
that spatial transcriptomics entails, including data normalization and high levels of noise.
Second, the application of the developed methods to datasets collected from several
tissues and organs (such as brain or bones) and with different techniques
(e.g., TOMO-seq and 10x Visium). Specifically, the goal is to identify patterns of gene
expression that will give insights into the spatial organization of tissues.

The project is supervised in collaboration with the lab
Dr A. Scialdone (Helmholtz Zentrum Muenchen), which will ensure access to published and
unpublished datasets, and whose expertise in -omic data analysis will complement our
expertise in modelling of complex systems.

Research activities

Interest:

• Physics of Complex Systems;
• Computational Systems Biology;
• Application of machine learning to analyze the behaviour of complex systems.