Computational master internship on single cell biology

Basak lab is recruiting offering a computational biology project on single cell biology for a master internship (9 months)

General scope of the research group

We are interested in understanding the molecular mechanisms behind neural stem cell fate choices during brain development, and how this is dysregulated in autism.

Internship project

Analysis of autism-linked cell type specific gene regulatory networks using single cell RNA sequencing datasets

Aim of the project: We will determine the how autism-linked genes are connected in different cells types of the developing and adult brain through reconstruction of the gene regulatory landscape using published singe cell sequencing datasets

Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder marked primarily by impaired social interaction. Even though this disorder affects ~1% of the western world, there is no cure yet. Research in the last decade suggests that defects in ASD patients start as early as prenatal stages where the function of neural stem cells and the process of neurogenesis are affected. A major question in the field is how dysfunction of over 100 autism-linked genes, which are functionally and structurally diverse, can cause the similar symptoms. Thus, there is urgent need to discover common fundamental mechanisms that drive ASD pathology.

Computational work: We have recently established a pipeline to reconstruct gene regulatory networks of the developing mouse brain in a cell type specific manner. This allowed us to quantify cell-type specific transcriptional units and ‘hubs’ that connect ASD-linked genes. 

The student will further improve this pipeline and extend the analysis to other brain regions and neurodevelopmental disorders.

Requirements: The students have to be enrolled at a master program. She/he must have basic knowledge in python/R/Bash and a motivation for 100% computational work. Basic knowledge in cell and developmental biology will be useful. For this reason, the student should be willing to learn more on brain development and neuroscience.

Deliverables: At the end of the project, the student will be up-to-date with the latest methods of single cell analysis. She/he will be able to retrieve, process, analyze and visualize next generation sequencing data

More information

Duration of the internship: 9 Months

Starting Date: Flexible, up to February 2022

Location: The work will be carried out at the Translational Neuroscience Dept. UMC Brain Center

Contact: Please e-mail your CV and a motivation to Onur Basak (o.basak@umcutrecht.nl)

Lab website

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