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. Science, 367 (6482)
Related Discipline(s)This course would also be of interest to the following discipline(s):
Biology, Engineering, Pre-Medicine / Health Science