Potential PhD Projects

An overview of a few potential projects that PhD candidates could start in the upcoming winter semester. Please note that this list is not comprehensive and that many projects are arranged individually during the Interview Phase with our 160+ GSN Faculty Members.

Seeking Passionate PhD Student for Cutting Edge Neuro–Metabolism Research, Ertürk Lab

Are you fascinated by how the nervous system controls the entire body? Do you want to uncover how neural circuits contribute to metabolic disorders and other systemic diseases? Join our team at the Ertürk Lab as a PhD student and work at the interface of neuroscience, whole body imaging and AI.

What You Will Do
• Perform advanced tissue clearing and light sheet microscopy to map the nervous system across the whole mouse body at single cell resolution.
• Use wildDISCO and related whole body immunolabeling approaches to visualize autonomic, sensory and central circuits that regulate metabolic organs such as liver, pancreas, adipose tissue and gut.
• Apply and further develop AI based analysis tools for 3D image registration, cell detection and circuit quantification to extract meaningful biological insights from large scale datasets.
• Investigate how changes in peripheral and central nervous system connectivity and activity contribute to metabolic disorders and systemic disease states.
• Collaborate with biologists, clinicians and AI scientists to integrate imaging, molecular and functional data into a coherent picture of whole body neuro control.
• Publish your work in high impact journals and present at international conferences.

What We Offer
• State of the art platforms for tissue clearing, light sheet microscopy and large scale computational analysis.
• A highly interdisciplinary and international environment that combines neuroscience, metabolism, AI and systems biology.
• Close collaborations with leading groups worldwide and access to unique whole body imaging pipelines established in the Ertürk Lab.
• Mentoring and career development toward both academic and industry paths.

Your Profile
• Master’s degree in neuroscience, biomedical sciences, systems biology, biomedical engineering or a related field.
• Strong interest in how the nervous system controls whole body physiology and metabolic disease.
• Practical experience in at least one of the following is a plus: microscopy or imaging, tissue processing, programming (for example Python, Matlab), machine learning or data analysis.
• Curious, proactive mindset and willingness to learn new experimental and computational methods.
• Good communication skills and a collaborative working style in an interdisciplinary team.

Join Us
Be part of our team to explore how the whole body nervous system drives metabolic disorders and other systemic diseases. 

https://www.erturk-lab.com 

PhD Position in Chronic Neuroinflammation and Microglial Innate Immune Memory, Liesz Lab

We are seeking a highly motivated PhD student to join our research group at the Institute for Stroke and Dementia Research (ISD), LMU Munich. The project focuses on mechanisms of chronic neuroinflammation after brain injury, with a particular emphasis on microglia biology, long-term epigenetic reprogramming and innate immune memory in microglial cells. Using state-of-the-art approaches including single-cell and spatial transcriptomics, functional imaging, epigenetic profiling, mouse models of stroke and neuroinflammation, as well as established collaborations with computational and clinical partners, the project aims to define how microglia retain pathological memory and drive long-term brain dysfunction.

The ideal candidate holds a Master’s degree in neuroscience, immunology, molecular biology or a related field, and brings enthusiasm for mechanistic in vivo and ex vivo research. Experience with neuroimmunology, mouse work, imaging, or omics technologies is an advantage but not required. We are looking for a curious, ambitious, and collaborative scientist who enjoys working in an interdisciplinary and international team.

We offer a stimulating research environment within the ISD, the SyNergy Cluster and a newly established Collaborative Research Center on Stroke Research, with access to advanced imaging platforms, single-cell and spatial multiomics pipelines, high-performance computing, and close interaction with international experts. The PhD student will be embedded in structured graduate training programs and benefit from excellent supervision, career development support, and opportunities for conference participation and international exchange.

Contact: Liesz Lab: https://www.isd-research.de/liesz-lab

Arthur.Liesz@med.uni-muenchen.de

PhD scholarships in Neurophilosophy, Research Center for Neurophilosophy and Ethics of Neurosciences, Prof. Dr. Stephan Sellmaier

Projects in the research center fall in the following areas:

• philosophy of cognitive neuroscience (explanation, reduction)
• philosophy and cognitive science of agency (mental causation, free will, moral psychology, abilities)
• philosophy and cognitive science of reasoning (e.g. deductive and non-deductive reasoning, logic and neural networks, decision making)
• ethics of neuroscience (research ethics, enhancement)
• philosophy of perception
• philosophy and social cognition
• social and animal cognition

In the new application round we encourage applications in smaller focus areas in order to build research groups. In the 2024/25 round the focus areas are:

• human agency (esp. mental causation, complex action, multi-tasking, attention, reductive and non-reductive explanation of agency)
• animal cognition

However, single exceptional and independent projects in one of the other areas are also encouraged.

Applicants should have advanced training in philosophy (typically a Master’s degree in philosophy) and a genuine interest in the neurosciences. This includes the willingness to acquire substantial knowledge of empirical work relevant to their philosophical project. Cooperative projects with empirical scientists in the network of the MCN are strongly encouraged.

PhD position available, Schroeder Lab at LMU Munich

The recently established group of Prof. Dr. Anna Schroeder at LMU Munich is seeking a motivated candidate for a PhD position.

Our lab investigates the neural circuits underlying emotions, motivations, and physiological needs, focusing on how these internal states shape behavior in dynamic environments. Specifically, we study the subthalamic circuits of the zona incerta, an enigmatic brain region that integrates internal states, external sensory cues, and past experiences to adapt behavior flexibly.

To address these questions, we employ cutting-edge molecular, cellular, and circuit-level approaches including in vivo calcium imaging with 2-photon microscopy or Miniscopes, whole-cell patch-clamp electrophysiology, single-cell RNA sequencing, optogenetics, chemogenetics and viral circuit tracing. We also leverage state-driven behavioral paradigms, advanced machine learning techniques and transgenic mouse models to dissect the neural circuit mechanisms driving behavior.

Our ultimate goal is to advance understanding of brain function and develop novel therapeutic strategies for psychiatric disorders through neuromodulation. Prof. Schroeder is deeply committed to training, mentorship and career development for lab members. The lab offers state-of-the-art neuroscience in a very supportive environment.

For more information, visit https://www.annaschroederlab.com 

Open PhD Position (65% TV-L E13) - Local Regulation of Axonal Stability by the Cytoskeleton and Organelle Interactions, Institute for Neuronal Cell Biology, TUM – Munich, Leischner-Brill Lab

Are you interested in axonal biology, cytoskeletal dynamics, and organelle interactions? Do you want to apply cutting-edge imaging and molecular approaches to uncover mechanisms of neuronal remodeling?

If yes, join our newly funded DFG project led by PD Dr. Monika Leischner-Brill. The project investigates how microtubule post-translational modifications (PTMs) and their interactions with organelles, such as the endoplasmic reticulum, regulate axonal stability during developmental synapse elimination—a process relevant to neurodegeneration.

Project overview (what you will do):
You will contribute to one integrated research program with three main objectives:
• Analyze retrograde signaling and its impact on microtubules and their posttranslational modifications during the synapse elimination phase.
• Explore activity-dependent transcriptional control of microtubule stability using translatome profiling.
• Gene editing of cytoskeletal candidates derived from the screen above.

Key techniques include:
• Confocal microscopy, Airyscan imaging
• Quantitative immunostaining and image analysis
• Viral-mediated genetic manipulations (AAV-based Cre/CRISPR)
• RiboTag-based translatome sequencing and bioinformatics

Training environment: Employee-status PhD position (65% TV-L E13) • Embedded in the Institute for Neuronal Cell Biology (TUM) and the SyNergy Excellence Cluster • Access to state-of-the-art imaging platforms, transcriptomics hubs, and structured PhD programs • International, collaborative environment with mentoring, retreats, and conference travel support.

Your profile: • Master’s degree in biomedical neuroscience, neuroscience, molecular biology, or related field • Strong interest in • Strong interest in axonal biology and willingness to work with mouse models • Experience in one or more of the following: microscopy, image analysis, molecular biology, bioinformatics • Team spirit, curiosity, high motivation, and commitment to rigorous and reproducible science • Very good written and spoken English

We offer: Close supervision and integration into a dynamic research team • Cutting-edge infrastructure for imaging, omics, and genetic manipulation • Access to established models, imaging technologies, and omics platforms and a large and vibrant collaborative network • An international, supportive research environment with career development support, regular retreats, and conference travel opportunities to present your results.

Contact: Monika.Leischner-Brill(a)tum.de

Open position for GSN PhD candidate - "Reprogramming, CRISPR, Epigenetics, Stem Cell Research, Neurobiology", Department of Physiological Genomics, Stricker Lab

Project title: Advancing Therapeutic Reprogramming through CRISPRa RNP Technology

Project description: Recent advances in genome engineering technologies have fundamentally transformed our capacity to manipulate genetic material with precision, opening up unprecedented avenues in basic research, biotechnology, and medicine. Among these tools, the CRISPR-Cas system has emerged as a particularly powerful and versatile platform for targeted genome editing and transcriptional regulation. Owing to its simplicity, programmability, and adaptability, CRISPR has seen widespread adoption across diverse genomic applications. Beyond genome editing, CRISPR has been successfully adapted for transcriptional activation (CRISPRa), enabling the upregulation of endogenous genes without altering the DNA sequence1. This strategy offers tremendous potential for the precise modulation of gene expression, functional genomic studies, and the engineering of desired cellular phenotypes in both therapeutic and biotechnological contexts2.

One particularly promising application of CRISPRa is in cell identity reprogramming — a strategy with transformative potential for regenerative medicine. By reactivating developmentally important genes, cell types lost to disease (e.g., neurons in neurodegenerative conditions) can potentially be replaced through in situ reprogramming of neighboring cells3,4. However, the clinical and in vivo application of CRISPR-based reprogramming has been significantly hindered by the limitations of viral delivery systems, which pose challenges in terms of delivery efficiency, immunogenicity, and potential genotoxicity.

To address this, we have developed a non-viral, RNP-based CRISPRa platform utilizing a potent transcriptional activator — dCas9-VPR5. We have successfully purified highly active dCas9-VPR protein from insect cells at high yield and demonstrated its efficient assembly with chemically synthesized guide RNAs into functional dCas9-VPR ribonucleoprotein complexes (dRNPs). These complexes can be delivered with high efficiency into human stem cells, their differentiated progeny, and primary cells. Our data show that targeted gene activation via dRNPs is both rapid and transient, with induction levels reaching up to 100000-fold, including for developmentally silenced genes. Optimization of dosing parameters enables the simultaneous activation of as many as 35 genes, underscoring the scalability of the system for complex reprogramming applications.

Most recently, we demonstrated that dRNPs can drive cell fate specification and conversion in vitro, for instance, inducing neuronal reprogramming from human glia cells⁵.

As next steps, we aim to extend this technology to:

- … Neuronal Subtype Reprogramming. Neuronal subtypes exhibit a high degree of molecular, functional, and connectivity-specific specialization, which underlies the complexity of brain circuits and their selective vulnerability in disease. A major challenge for direct neuronal reprogramming is therefore not only the generation of generic neurons, but the faithful conversion into highly specialized and mature neuronal subtypes. Successfully addressing this challenge will be essential to model disease mechanisms accurately and to unlock the full therapeutic potential of reprogrammed neurons.

- … the in vivo settings. To facilitate this, we have generated novel mouse reporter lines capable of visualizing CRISPRa-induced gene activation and cell reprogramming (unpublished). By combining these models with optimized strategies for RNP delivery, our goals are to verify, characterize, and quantify CRISPRa RNP delivery and gene activation in vivo; And to establish functional reprogramming protocols in vivo, particularly within neurodegenerative and metabolically compromised environments.

- … the Organoid system. Brain organoids offer a powerful and versatile model to study human brain development and disease in a physiologically relevant context that cannot be fully captured by animal models. They enable the investigation of genetic, cellular, and circuit-level mechanisms underlying neurodevelopmental and neurodegenerative disorders, as well as patient-specific disease phenotypes. As such, brain organoids hold strong potential for advancing translational research, drug discovery, and personalized medicine.

Any of these available projects have the potential to establish a safe, efficient, and scalable framework for non-viral, CRISPRa-mediated cell therapy, paving the way for in situ regeneration strategies in a range of neural disease contexts.

1 Stricker, S. H., Koferle, A. & Beck, S. From profiles to function in epigenomics. Nat Rev Genet 18, 51-66, doi:10.1038/nrg.2016.138 (2017).
2 Breunig, C. et al. CRISPR-tools for physiology & cell state changes - potential of transcriptional engineering and epigenome editing. Physiol Rev, doi:10.1152/physrev.00034.2019 (2020).
3 Baumann, V. et al. Targeted removal of epigenetic barriers during transcriptional reprogramming. Nature communications 10, 2119, doi:10.1038/s41467-019-10146-8 (2019).
4 Stricker, S. H. & Gotz, M. Epigenetic regulation of neural lineage elaboration: Implications for therapeutic reprogramming. Neurobiol Dis 148, 105174, doi:10.1016/j.nbd.2020.105174 (2021).
5 Schmidt, T. et al. Efficient DNA- and virus-free engineering of cellular transcriptomic states using dCas9 ribonucleoprotein (dRNP) complexes. Nucleic Acids Res 53, doi:10.1093/nar/gkaf235 (2025).

Contact: Prof. Dr. Stefan H. Stricker stefan.stricker@med.uni-muenchen.de