Research Assistant: Visualizing Protein Distribution in the BrainSemester Course

Major Discipline(s)
Biomedicine / Biotechnology, Computer Science
Elective Course
Fall/Spring semester

The Human Protein Atlas aims to visualize protein expression and protein distribution in all major organs and tissues of the human body. The laboratory of Jan Mulder at the Karolinska Institute is responsible for the brain section of the Human Protein Atlas, providing data on protein expression in various regions of the brain of different mammalian species. By using transcriptomics and antibody-based approaches to visualize protein location and transcriptomics approaches to detect protein expression, this research group aims to solve some of the biological mysteries related to (human) brain functions and brain diseases.

In our lab, we have generated very complex data with many layers and dimensions that cannot be captured in a single image. These include 3D volumed data on protein distribution in a tissue block that we currently share using Youtube. In collaboration with the startup Atomontage, we explored possibilities to share 3D data and to make this free, explorable, and interactive. As a research student on this project, you will get a raw 3D image set (stack of >1000 16-bit images) and use image processing tools (ImageJ, Matlab, or your favorite) and Atomontage webtools to generate a 3D model presenting the biological truth. You will then create tools and features to help/guide the users when exploring the data. Your principle mentor will be Jan Mulder, but you are also partnered with other bioinformatic researchers in the lab, the human protein atlas IT group, and developers at Atomontage.


Research Assistantship Hours: You will spend 180 hours directly engaged in research, together with an additional 5 hours in professional workshops and co-curricular activities, during your RAship.   


Select Mentor Publications:

Gilvesy A; Husen E; Magloczky Z; Mihaly O; Hortobágyi T; Kanatani S; Heinsen H; Renier N; Hökfelt T; Mulder J; Uhlen M; Kovacs GG; Adori C. (2022) Spatiotemporal characterization of cellular tau pathology in the human locus coeruleus-pericoerulear complex by three-dimensional imaging. Acta neuropathologica. 2022 Oct 144(4):651-676.

Sjöstedt, E., Zhong, W., Fagerberg, L., Karlsson, M., Mitsios, N., Adori, C., Oksvold, P.,Edfors, F., Limiszewska, A., Hikmet, F., Huang, J., Du, Y., Lin, L., Dong, Z., Yang, L., Liu, X., Jiang, H., Xu, X., Wang, J., … Mulder, J. (2020). An atlas of the protein-coding genes in the human, pig, and Mouse Brain. Science367 (6482)

Related Discipline(s)

This course would also be of interest to the following discipline(s):
Biology, Engineering, Pre-Medicine / Health Science


Nicholas Mitsios

DIS Stockholm Semester Faculty

BSc in Molecular Biology (Liverpool, 1998) and PhD in Molecular Biology of Ischemic Stroke (Manchester, 2005). Currently a researcher at the Department of Neuroscience, Karolinska Institute and the Brain Profiling sub-unit of the Human Protein Atlas (HPA) project since 2011. Research focuses on the central nervous systems of mammals, with an emphasis on the identification of proteins involved in brain normal development and pathophysiology. With DIS since 2020.

Jan Mulder

DIS Stockholm Semester Faculty

PhD in molecular neurobiology (Rijksuniversiteit Groningen, 2005), MSc in biology (Rijksuniversiteit Groningen, 2000).  Senior researcher and group leader at Science for Life laboratory, department of Neuroscience, Karolinska Institute since 2010. Group leader of the brain profiling efforts within the Human Protein Atlas project since 2010. Research in identifying the cellular location of proteins linked to brain function and disease. With DIS since 2017.  

Emma Gerrits

DIS Stockholm Semester Faculty

Bachelor of Science, Life Science and Technology, University of Groningen, 2016 Master of Science, Biology, University of Groningen, 2018 Ph.D., Molecular Neurobiology and Bioinformatics, University of Groningen, 2022 Ph.D. student, University Medical Center Groningen, 2018-2022 Postdoctoral researcher, Karolinska Institutet, 2022-present. With DIS since 2023