Quantitative Developmental Biology labOpen OpportunitiesBrain organoids recapitulate important features of human neurodevelopment and allow us to study this key developmental process at unprecedented scale and resolution. In the past, single-cell genomics technologies, including single-cell RNA-sequencing (scRNA-seq), have been used to study the molecular heterogeneity of brain development in organoid models. However, these assays dissociate the tissue and thus have limited capacity to learn about emerging spatial properties like regionalization or patterning. To overcome this limitation, the Treutlein lab applies highly-multiplexed spatial transcriptomic and proteomics technologies (e.g. MERSCOPE, 4i) to jointly measure spatial organization and molecular properties of organoids. Such datasets provide a unique opportunity to study the interplay between cellular communication, gene regulation, and spatial organization. However, a key challenge remains the integration of imaging and sequencing data across replicates, conditions, and time points to learn faithful cellular representations that can be mined for regulatory interactions. Thus, the aim of this thesis will be to develop new computational methods to infer meaningful cellular representations from rich and diverse spatial datasets. - Cell Development (incl. Cell Division and Apoptosis), Knowledge Representation and Machine Learning, Modeling and Simulation, Neurosciences
- Master Thesis
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