Prof. Ozgun Gokce PhD

Spatial Dynamics of Neurodegeneration

Medical Faculty, UKB, University of Bonn & DZNE

Long before symptoms emerge, neurodegeneration begins with subtle shifts in the state and behavior of individual brain cells. The Gokce Lab traces these changes across molecular, spatial, and structural scales, revealing which genes each cell activates, where it resides in the tissue, and how its ultrastructure changes.

See our publications Join the lab

Spatial transcriptomics of the mouse hippocampus: individual RNA molecules in colour across the tissue

What we do

We map how brain cells change with age and disease. One cell at a time, in place.

An interdisciplinary group at the University of Bonn and DZNE, where biologists, engineers, physicians, and computational scientists work on the same data.

Single-cell genomics, spatial transcriptomics, electron microscopy, machine learning, and new methods when a question demands them.

What the data look like

Where this work is published

Rotating three-dimensional UMAP of single-cell transcriptomes, each colour a cell state — Every cell has an address.

MERFISH map of the hippocampus with individual transcripts resolved in situ — Spatial patterns reveal where neurodegeneration begins and how it spreads.

Cover of Neuron, the issue carrying the lab's white matter aging study — White matter aging drives microglial diversity. *Neuron*, 2021.

News

Full news archive

December 2024paper

Three community papers on single-cell and spatial genomics in neuroscience
Ozgun Gokce co-led three companion papers in Nature Neuroscience setting out how single-cell and spatially resolved genomics experiments should be designed, validated and interpreted in the nervous system.
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August 2024paper

T cells trigger myelin damage in a mouse model of amyloidosis
Shreeya Kedia, Hao Ji, Peter Androvič, Cem Buğra Kaboğlu and colleagues found that CD8+ T cells drive microglia into a damaging interferon-activated state, and that removing those T cells or blocking the pathway reduces myelin damage in amyloid-depositing mice.
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August 2023paper

Skull bone marrow has its own molecular identity
Work with the Ertürk lab found that the marrow inside the skull differs from marrow elsewhere in the body and changes distinctly in neurological disease.
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Selected papers

All publications

CD8+ T cells induce interferon-responsive oligodendrocytes and microglia in white matter agingKaya T, Mattugini N, Liu L, Ji H, … Gokce O, Simons MNature Neuroscience · 2022doi.org/10.1038/s41593-022-01183-6
White matter aging drives microglial diversitySafaiyan S, Besson-Girard S, … Gokce O, Simons MNeuron · 2021doi.org/10.1016/j.neuron.2021.01.027
Spatial transcriptomics-correlated electron microscopy maps transcriptional and ultrastructural responses to brain injuryAndrovic P, Schifferer M, Perez Anderson K, … Gokce ONature Communications · 2023doi.org/10.1038/s41467-023-39447-9
T cell-mediated microglial activation triggers myelin pathology in a mouse model of amyloidosisKedia S, Ji H, … Gokce O, Simons MNature Neuroscience · 2024doi.org/10.1038/s41593-024-01682-8

The people behind it

Meet the team

The lab group together in the corridor of the institute

Three lab members at the sequencing bench

Two lab members going through single-cell data together at a screen

The lab sitting along a jetty by a lake on a lab outing

Working here

We take PhD students, postdocs and master's students who want to work at the boundary between experiment and computation. You do not need to arrive fluent in both. You do need to want to be.

Open positions and how to apply