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

PhD Position : Sleep, vocal learning, and the basal ganglia-thalamocortical network

We are seeking a highly-motivated PhD student for a DFG-funded, 3-year PhD position to join our research group Sleep-dependent memory consolidation in birds.

www.mls.ls.tum.de/zoologie/arbeitsgruppe-ondracek/ 
https://www.ondraceklab.com/ 

This project integrates electrophysiological, behavioral, and computational approaches to investigate how neural population activity changes as a function of behavioral state in the songbird.

The project will be carried out at the Chair of Zoology at the Technical University of Munich, located at the TUM Life Sciences Campus in Weihenstephan-Freising. https://www.mls.ls.tum.de/zoologie/startseite/

Project Background

During vocal learning, a juvenile bird transitions from acoustically simple, highly variable “subsongs” to complex and stereotypical adult songs through a process of motor learning. Critically involved in this learning process is a set of interconnected brain areas that make up a basal ganglia-thalamocortical circuit known as the Anterior Forebrain Pathway (AFP). Although these brain areas have been extensively characterized individually during singing, little is known about spontaneous neural dynamics across the intact circuit and during different behavioral states.

In this project, we will build from our preliminary work (Lorenz et al., 2025) to chronically implant multishank Neuropixels 2.0 probes in the brains of adult and juvenile male zebra finches to simultaneously record from multiple brain areas across behavioral states.

1. Lorenz C, Das A, Centeno EGZ, Yeganegi H, Duvoisin R, Ursu R, Retailleau A, Giret N, Leblois A, Hahnloser RHR, Ondracek JM. Sharp Waves, Bursts, and Coherence: Activity in a Songbird Vocal Circuit Is Influenced by Behavioral State. J Neurosci. 2025 Nov 19;45(47):e1903242025.

2. Yeganegi H, Ondracek JM. Local sleep in songbirds: different simultaneous sleep states across the avian pallium. J Sleep Res. 2025 Jun;34(3):e14344.

3. Yeganegi H, Ondracek JM. Multi-channel recordings reveal age-related differences in the sleep of juvenile and adult zebra finches. Sci Rep. 2023 May 27;13(1):8607.

4. Shein-Idelson M, Ondracek JM, Liaw HP, Reiter S, Laurent G. Slow waves, sharp waves, ripples, and REM in sleeping dragons. Science. 2016 Apr 29;352(6285):590-5.

Required skills

• MSc or equivalent degree in neuroscience, electrical engineering, or biology with emphasis on systems or computational neuroscience
• Experience using electrophysiological and computational approaches
• Proficiency in at least one programming language (e.g. Python, MATLAB)
• Strong analytical and signal processing skills
• Highly motivated and able to work independently
• English language speaking and writing skills

Our Offer

The doctoral candidate will be employed by TUM (65 % TV-L E13) for a total duration of three years. Successful applicants will be enrolled in the Graduate School of Systemic Neurosciences (GSN) program at the Ludwig Maximilian University of Munich and receive a structured doctoral training.

The student will benefit from international research exchanges and collaborations with France and Switzerland, in addition to the networking opportunities available within the vibrant neuroscience community in Munich.

Contact: Dr. Janie Ondracek, janie.ondracek@tum.de

PhD Position - Vascular Zonation-specific Mechanisms in Cerebral Small Vessel Disease (Munich), Institute for Stroke and Dementia Research (ISD), LMU Munich, Dichgans Lab

Are you excited about neurovascular biology, omics technologies, and cutting-edge microscopy? Do you want to pursue a PhD that combines fundamental mechanistic discovery with strong translational relevance?

If yes, consider joining the group in an ambitious new project funded within a newly established DFG Collaborative Research Center (CRC) on neurovascular diseases, starting in 2026.

Project overview: Our goal is to uncover how vascular zonation-specific mechanisms in brain endothelial cells contribute to cerebral small vessel disease (SVD) and stroke. Building on recent discoveries identifying FOXF2 as a major genetic risk factor for SVD, the project will investigate how endothelial dysfunction unfolds across distinct vascular segments (arterioles, capillaries, venules) and how this affects vascular–glial crosstalk, astrocyte biology, and neurovascular function.

Your work will combine: • Multi-omics approaches (single-cell RNA-seq, spatial transcriptomics such as MERFISH, cell-type–specific proteomics) • Advanced microscopy (confocal, light-sheet imaging, electron microscopy) • In vivo experimentation in mouse models (including inducible endothelial/pericyte-specific Foxf2 models, BBB assays, MCAO stroke models) • Bioinformatics and data integration in collaboration with experienced computational researchers. You will be part of a highly interdisciplinary team and receive day-to-day supervision from experienced postdoctoral researchers.

Your training environment: As a PhD student , you will join one of Munich’s renowned graduate programs: • Graduate School of Neuroscience (GSN); • International Max Planck Research School for Biological Intelligence (IMPRS-BI); or the • Integrated Research Training Group of CRC 1744. You will be integrated into both the new CRC and the Munich Cluster for Systems Neurology (SyNergy). Both provide exceptional training opportunities including structured mentoring, advanced technical workshops, diversity support, retreats, and travel funding.

Your profile: We are looking for a highly motivated student who: • Holds (or will soon complete) a Master’s degree in Biomedical Science, Neuroscience, Molecular Biology, Human Biology, Neuroengineering, or a related field • Has experience or strong interest in bioinformatics, transcriptomics/proteomics, imaging, and/or in vivo mouse work • Is passionate about neurovascular biology, cell biology, and disease mechanisms • Enjoys working in a collaborative, multidisciplinary research environment • Communicates well in written and spoken English. Experience with mouse models, omics data analysis, or advanced imaging is an advantage but not required.

We offer: • A stimulating scientific environment within the ISD, SyNergy, and the new CRC 1744 • Integration into multidisciplinary teams with state-of-the-art infrastructure for omics and imaging • Close supervision by the PI and postdoctoral researchers • Opportunities to present at national and international conferences • A strong, supportive community of PhD students and early-career researchers.

Contact: Prof. Martin Dichgans (Institute for Stroke and Dementia Research, LMU Munich); isd.applications@med.uni-muenchen.de