Potential PhD Projects

An overview with a few of the advertised 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.

PhD position, Vision circuits lab (Laura Busse), Faculty of Biology, LMU Munich

A PhD position is available in Laura Busse’s group at the Division of Neuroscience at the Faculty of Biology, LMU Munich. We study the neural circuits of visual processing and perception in awake, behaving mice, where we combine electrophysiological recordings using neuropixels probes with genetic tools for circuit manipulation. Our aim is to contribute to the understanding of sensory mechanisms of visual information processing and their dependence on visually guided behavior. The Faculty of Biology at the LMU Munich together with the Graduate School of Systemic Neurosciences (GSN) offer an outstanding environment for a successful PhD in systems neuroscience, with ample opportunities for collaboration with both experimentalists and computational neuroscientists, both within the department as well as with the neighboring Max-Planck-Institute for Biological Intelligence. The LMU Munich ranks among the top 10 universities in Europe. Munich, located in the south of Germany, is regularly ranked among the world’s top cities for quality of living.

The fully funded PhD position is part of an interdisciplinary team-science collaboration within the DFG-funded Collaborative Research Center Robust vision: Inference Principles and neural mechanisms (SFB 1233). In the project, we seek to investigate "Context-adapted representations in the early visual system", combining Neuropixels recordings in thalamus and primary visual cortex, closed-loop virtual reality, eye and face tracking and the generation of naturalistic movies. The project will heavily draw from building “digital twins” of the early visual system with video and internal state input, and will be performed in close collaboration with the labs of Philipp Berens and Katrin Franke at the University of Tübingen and Fabian Sinz at the University of Göttingen. More information about the lab can be found at: https://visioncircuitslab.org.

The project requires strong experimental skills, experience in programming, and the ability to work in a distributed team. Complementary PhD positions based primarily in Tübingen and Göttingen will closely collaborate on the experiments and the development of the digital twins. The position is available now.

Interested candidates are welcome to establish contact via email to busse@bio.lmu.de. Applications should include a CV, a statement of research interests, a cover letter with the expected date of availability, and names and contact information of at least two references. Applications will ideally also go through the LMU Graduate School of Systemic Neuroscience (https://www.gsn.uni-muenchen.de/index.html, deadline 17th February 2025).

Potential PhD projects in the Baier Lab at the Max Planck Institute for Biological Intelligence

1) Neural circuitry for spatial navigation in zebrafish: transpriptomics, connectomics & behavior (https://www.bi.mpg.de/news/2024-11-baier) [Methods: imaging, computation, single-cell RNA sequencing, behavioral assays]

2) Synaptic connectome of the tectum, a sensorimotor hub in the middle of the vertebrate brain [Methods: computation, machine learning, imaging]

3) Multiomic brain atlas of zebrafish: Transcriptional profiling and connectivity of neuronal cell types [Methods: machine learning, imaging, computation, single-cell RNA sequencing]

4) Cichlid neurobiology: Developmental neurobiology of phototaxis behavior in cichlid larvae [Methods: imaging, computation, single-cell RNA sequencing, behavioral assays]

5) Fish psychiatry: Models, molecules, and mechanisms of depression and anxiety in zebrafish [Methods: single-cell RNA sequencing, behavioral assays, imaging]

PhD positions in the Mayer Lab at the Max Planck Institute for Biological Intelligence

The research focuses on gene-regulatory mechanisms shaping inhibitory neuronal diversity and their links to neurodevelopmental disorders.

PhD students will lead projects exploring molecular pathways underlying neural diversity, using advanced techniques such as CRISPR-based perturbations, single-cell sequencing, and chromatin analysis.

This position offers an excellent opportunity to contribute to cutting-edge neuroscience research in an interdisciplinary and collaborative environment.

Multiple PhD positions available on ERC-funded projects, Schroeder Lab at LMU Munich

The newly established group of Prof. Dr. Anna Schroeder at LMU Munich is seeking motivated candidates for multiple PhD positions.

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

Interested candidates are encouraged to reach out via email to anna.schroeder@bio.lmu.de before submitting their applications through the LMU Graduate School of Systemic Neurosciences. The application deadline is February 17th, 2025.

PhD position in Neurovascular biology - vascular brain injury (m/f/d)

Project and task:

The project, which will be carried out in the group of Martin Dichgans, aims to examine the cellular and molecular mechanisms of microvascular brain injury in novel mouse models of cerebral small vessel disease. These models are derived from our gene discovery efforts and show great promise as indicated by a first phenotypic screen. The project involves single-cell and bulk RNA sequencing, spatial transcriptomics, proteomics, and cutting-edge imaging technology (confocal, light-sheet, 2-photon, and electron microscopy), as well as cell culture-related work. All technologies are available in-house (see ISD and SyNergy websites).

Our requirements:

The ideal candidate should hold an MSc degree in biological sciences or related fields and have a solid foundation in basic methods of molecular and cellular biology. Prior experience in vascular research, experimental work in mice, scRNAseq, proteomics, and cutting-edge imaging are considered a plus. The candidate should be creative, self-driven, and a team player - but able to work independently. Essential qualities include fluency in English, rigor in pursuing scientific work, and an interest in disease-oriented research.

Our offers:

The position will be in a highly international, dynamic and “open-door” atmosphere, with access to state-of-the-art laboratory facilities and technology hubs as implemented by the Munich cluster for Systems Neurology (SyNergy, DFG-funded German Excellence Initiative). You will work in a diverse team of experienced staff, PhD students, Postdocs and technicians. There is the possibility to apply for enrollment in the Graduate School for Systemic Neuroscience (GSN), to which our Institute is affiliated. Salary will be according to TV-L and the position is funded for up to 2 years with an option for extension. The Ludwig-Maximilians-University is an equal opportunity employer. Individuals of all nationalities, genders, ages, and those with disabilities are encouraged to apply. We give priority to applicants with a disability and essentially equal qualifications.

Interested candidates should submit their complete application documents (including motivation letter, CV, and transcripts within a single PDF file)

Contact: melanie.roesch@med.uni-muenchen.de (PI to Martin Dichgans)

PhD position on EU funded project at LMU Munich - Wahl Lab

We are looking for motivated candidates (1x fully funded postdoc position and 1x fully funded PhD position) for a EU-funded project unveiling fundamental principles of neuronal repair after stroke to develop novel treatment approaches preventing cognitive decline.

What do we offer?
We are currently building a new team at the Institute of Stroke and Dementia Research (https://neuronal-repair.de) to continue the work we have started at the Brain Research Institute, University of Zurich. You will be integrated in the vital research environment at LMU, the Center of Stroke and Dementia Research (CSD - https://www.isd-research.de/isd-research) as well as of the Excellence Cluster SyNergy (https://www.synergy-munich.de) participating in lectures, seminars and retreats. You will learn state-of-the-art methods in neuroscience such as multiphoton calcium imaging in vivo, optogenetics, chemogenetics, micro-surgeries, histology, and application of deep learning methods.

Aim of the projects?
The projects aim at understanding neuronal rewiring and reorganization as intrinsic repair mechanisms of the brain on a neuronal network level. We would like to understand how neurons form new circuits, reconnect and compensate for lost ones to enable the recovery of impaired sensorimotor and cognitive functions after CNS injury such as stroke. As we would like to understand causal relationships between neuronal rewiring and the behavioral phenotype we also develop deep learning algorithms for further analysis.

What do you bring in?
As a future PhD student: A very good Master or Diploma degree in physics, biomedicine, biology or bioinformatics or related topics; experience in programming (ideally Matlab or Python), ideally some neuroscience background with experience in animal experiments and calcium imaging; scientific creativity and ability to work in a team.
We also require fluency in spoken and written English and ideally some knowledge in German.
The positions are available for the winter semester 2024. Gross salary will be according to the statutes of LMU Munich/ LMU University Hospital.

For informal enquiries please contact
Prof. Dr. Dr. Anna-Sophia Wahl
Institute for Stroke and Dementia Research, LMU Klinikum
Feodor-Lynen Str. 17
D-81377 Munich
Email: AnnaSophia.Wahl@med.uni-muenchen.de
https://neuronal-repair.de/

Seeking Passionate PhD Student for Cutting-Edge Neuro-Inflammation Research - Ertürk Lab

Are you intrigued by the mechanism governing neuroinflammation? Eager to pioneer discoveries leading to innovative therapies for neuroinflammation in acute, chronic or infections disease? Join our groundbreaking neuroinflammation project as a PhD student at the Ertürk lab located at the Institute for Stroke and Dementia Research and the Helmholtz Center Munich (https://www.erturk-lab.com/).

What You Will Do:
• Build on our discoveries on the relationship between the skull bone marrow and neuroinflammation (Cai… Ertürk, Nat. Neuro, 2019; Kolabas…Ertürk, Cell, 2023; Rong … Ertürk, Cell Host&Microbe, 2024)
• Employ advanced tissue clearing methods, such as wildDISCO for whole-body immunolabeling (Mai…Ertürk, Nature Biotechnolgoy 2023), and AI algorithms for in-depth analysis of imaging data (e.g.Todorov..Ertürk, Nat. Methods, 2020; Kaltenecker ..Ertürk, Nat. Methods, 2024; Kaltenecker..Ertürk, bioRxiv, 2024).
• Investigate the molecular mechanisms by which peripheral and central inflammation interact using DISCO-MS (Bhatia, …, Ertürk, Cell, 2022).
• Develop potential therapeutic interventions to modulate pro- and anti-inflammatory pathways (Bhatia…Ertürk, Cell, 2022, and Kobalas…Ertürk, Cell, 2023).
• Publish high-impact research papers and present your findings at international conferences.

What We Offer:
• State-of-the-art facilities for advanced whole-body imaging and computational analysis.
• Collaborative opportunities with leading experts in neuroscience, AI, and oncology.
• A robust international research network, connecting with prominent groups worldwide.
• A dynamic, interactive environment fostering critical thinking and innovative research.

Your Profile:
• A strong background in neuroscience, immunology, or related fields.
• A driven curiosity to explore the uncharted interplay between the nervous system and the brain border regions.
• A commitment to contribute to groundbreaking discoveries that improve patient outcomes.
• Excellent communication skills and a collaborative spirit.

Join Us! Be part of our team to explore this exciting new frontier in nerve-cancer research.
Contact: ali.erturk@helmholtz-munich.de or Stefanie Reitinger for general information stefanie.reitinger@helmholtz-munich.de

PhD position in brain imaging - Kathrin Koch Lab

Are you intrigued by the neural mechanisms underlying obsessive-compulsive disorder (OCD)? Do you want to contribute to groundbreaking research exploring innovative neuromodulation therapies? If so, we invite you to join our pioneering project investigating transcutaneous auricular vagus nerve stimulation (taVNS) as a PhD student.

About the Project:
The planned study will investigate the effects of taVNS on clinical symptoms, vagal tone and brain activation in patients with OCD. This study aims to advance our understanding of the mechanisms of VNS in OCD and provide evidence for its clinical efficacy.

What You Will Do:
• Engage with hospitals and motivate patients to participate in the study
• Collect and analyze imaging data using innovative analysis approaches
• Utilize state-of-the-art neuroimaging and computational methods
• Publish high-impact research articles and present findings at international conferences

What We Offer:
• State-of-the-art facilities for brain imaging (3T MRI at the Klinikum rechts der Isar)
• Collaboration opportunities with leading experts in neuroscience and psychiatry
• A strong international research network, including participation in global initiatives like the ENIGMA collaboration
• An interdisciplinary research environment fostering innovation and scientific excellence

Your Profile:
• Background in neuroscience and neuroimaging
• At least basic programming skills with an interest in acquiring new coding expertise
• Enthusiasm for learning innovative analysis approaches
• Strong analytical and problem-solving skills
• Commitment to contributing to transformative research in OCD treatment

For inquiries please contact:

Prof. Dr. Kathrin Koch
TUM Neuroimaging Center (TUM-NIC)
School of Medicine and Health
Technical University of Munich
https://kathrinkochlab.com/

PhD Project - Michalakis Lab - Engineered adeno-associated virus-based vectors for retinal gene therapy - Mechanistic studies on cellular infection, trafficking and transduction

Scientific background. Vectors based on adeno-associated virus (AAV) have evolved as important technology for somatic gene therapy. Of the 28 gene therapy products that have received market approval, 8 are based on AAV vectors. While the biology of AAV has been thoroughly studied over the last four decades, mechanistic insights into cell infectivity, intracellular transport and vector genome processing prior to transduction are still limited. A crucial first step for successful transduction is the “docking” of AAV vectors to cell surface receptors. Extracellular matrix components, such as heparan sulfate proteoglycans (HSPGs) facilitate the initial attachment of the AAV vector, whereas plasma membrane-bound receptors like the AAV receptor (AAVR) are involved in cell entry and internalization.

Specific aims and methodology. We have previously established engineered AAV variants with modified capsid surface properties and improved tissue-specific
transduction efficiency. The hypothesis is that these improved properties arise from altered affinities for cell-surface receptors and or extracellular matrix components. The
goal of this project is to engineer and develop novel AAV capsids with enhanced transduction efficiencies for different target cell types and to characterize the
mechanisms responsible for the improved properties. The receptor profiles of novel AAV capsid variants will be characterized using state-of-the-art methods and validated with
overexpression (OE) and knockdown (KD) models. The new AAV variants will also be characterized using mouse, pig and human retinal explant cultures as well as human
retinal organoids. The methodology will include gene editing, biochemical, genetic, cell biological and viral gene transfer methods. Potential candidates should have a strong
interest and background in cell biology, molecular biology, gene therapy (virology), mouse physiology and anatomy (focus on the eye), and imaging. Particular interest and
experience in gene editing, bioinformatics, (big) data processing (e.g. RNAseq, proteomics, imaging data) is welcome.

Further information and selected literature.

• https://www.lmu-klinikum.de/augenklinik/forschung/gentherapie/1305646bdc184d5c
• https://www.gsn.uni-muenchen.de/people/faculty/core/michalakis/index.html
• Occelli LM, Zobel L, et al. (2023) Development of a translatable gene augmentation therapy for CNGB1-retinitis pigmentosa. Mol Ther 31(7):2028-2041.
• Riedmayr LM, Hinrichsmeyer KS, et al. (2023) mRNA trans-splicing dual AAV vectors for (epi)genome editing and gene therapy. Nat Comm 14(1):6578.
• Pavlou M, Schön C, et al. (2021) Novel AAV capsids for intravitreal gene therapy of photoreceptor disorders. EMBO Mol Med 13(4):e13392.
• Völkner M, Pavlou M, Büning H, Michalakis S#, Karl MO#. (2021) Optimized Adeno-Associated Virus Vectors for Efficient Transduction of Human Retinal Organoids. Hum Gene Ther. 32, 694-706
• Böhm S*, Splith V*, et al. (2020) A gene therapy for inherited blindness using dCas9-VPRmediated transcriptional activation. Sci Adv 6(34): eaba5614.
• Fischer MD*, Michalakis S*, et al. (2020) Safety and Vision Outcomes of Subretinal Gene Therapy Targeting Cone Photoreceptors in Achromatopsia: A Nonrandomized Controlled Trial. JAMA Ophthalmol 138(6):1-9.

Contact details:
Prof. Dr. Stylianos Michalakis
Department of Ophthalmology
LMU University Hospital
LMU Munich
Mathildenstr. 8, 80336 München
E-mail: michalakis@lmu.de

Open positions - Paquet Lab

PhD position, Neural Dynamics and Behavior Group (Dennis Nestvogel), Max Planck Institute of Psychiatry, Munich

We are seeking a highly motivated candidate to join our team as a PhD student. The overarching goal of our research group is to contribute to a greater understanding of the neural mechanisms that link changes in physiological and bodily states – such as arousal, motor movements and stress – to our ability to process sensory signals from the environment. In addition, we aim to reveal how disruptions in state-dependent processing contribute to the etiology of psychiatric disorders in order to achieve better outcomes for people experiencing deficits in sensory-guided behavior. We utilize cutting-edge neural recording techniques, including in-vivo patch clamp, Neuropixels recordings, optogenetics, mouse behavior, and expansion microscopy.

If you are interested in exploring potential projects and ongoing research in our lab, please reach out via email at nestvogel@psych.mpg.de. We look forward to hearing from you!

https://www.psych.mpg.de/2877720/nestvogel

https://sites.google.com/view/neuraldyamics/home

Doctoral position, ENTRY-DM: MSCA Doctoral network - Interdisciplinary doctoral training on oligonucleotide-based therapies for myotonic dystrophy - PD Dr. Peter Meinke

PhD position in “Molecular Mechanisms of Alzheimer’s Disease” in the Lichtenthaler lab

Background and laboratory:
Alzheimer’s disease is the most common and a deadly neurodegenerative disorder and affects more than 60 million patients worldwide. Drugs targeting the causes of the diseases are largely lacking. The laboratory of Stefan Lichtenthaler studies the molecular mechanisms underlying Alzheimer’s disease. The lab uses biochemical and molecular/cell biological techniques, iPS cells, proteomics, and animal models. More information is found on our webpage: www.dzne.de/lichtenthaler

We offer excellent projects and training in neurodegeneration and protease research. We are an international and interdisciplinary team, are part of several larger research consortia (e.g. DFG-funded excellence cluster SyNergy in Munich and European projects on neurodegeneration), and are located in the German Center for Neurodegenerative Diseases in Munich-Großhadern.

Your project:
Recently, several Alzheimer risk genes (e.g. TREM2) have been discovered which are expressed in microglia, the brain-resident immune cells. As part of an international research consortium, you will elucidate the mechanism and function of a microglia-related Alzheimer risk gene variant using iPSCs differentiated into microglia. Functional studies with CRISPR/Cas9 knock-out and control microglia include phagocytosis and cytokine assays. For mechanistic studies, you will use biochemical assays (e.g. ELISA, Western blots, and proteomics) and microglial cell lines.

Qualifications and experience:
You have a Master's in neurobiology, molecular biology, biochemistry or a related field and experience with cell culture, ideally with stem cells. Experience with molecular biology and biochemical techniques is an advantage. You do not need to have previous knowledge about Alzheimer’s disease or neurodegeneration. You are creative, highly motivated, and you can work independently. Essential qualities include fluency in English and a strong team spirit.

We are looking forward to your application: Stefan.Lichtenthaler@dzne.de

Selected References:
Jocher et al. (2025) Life Sci Alliance 8:e202403080, https://pubmed.ncbi.nlm.nih.gov/40081988/
Schmidt et al. (2024) J Clin Investig 134:e170550, https://pubmed.ncbi.nlm.nih.gov/38888964/
Müller et al. (2023) Mol Neurodegen 18:13; https://pubmed.ncbi.nlm.nih.gov/36810097/
Sebastian Monasor and Müller et al. (2020) Elife,9:e54083; https://pubmed.ncbi.nlm.nih.gov/32510331/
Tüshaus et al. (2020) EMBO J 39, e105693; https://pubmed.ncbi.nlm.nih.gov/32954517/
Parhizkar et al. (2019) Nature Neurosci., 22,191; https://pubmed.ncbi.nlm.nih.gov/30617257/

PhD Position - State-dependent auditory processing in a songbird - Ondracek Lab

PhD position in the Institute of Clinical Neuroimmunology, Meinl Lab

About us: The Institute of Clinical Neuroimmunology is devoted to research into the mechanisms and treatment of multiple sclerosis (MS) and related diseases. Our institute combines research at the biomedical center (BMC) with taking care for patients at the Klinikum Großhadern. This infrastructure is ideally suited for joining basic research with clinically relevant issues.

Background and project: Inflammatory diseases of the CNS comprise a spectrum of disorders, amongst which MS is the most frequent one. These diseases are due to misguided autoreactive immune cells that attack the own nervous system and induce chronic inflammation. We aim to (1) explore the autoimmunity against known target antigens and identify novel targets of autoimmune responses to stratify patients, (2) recognize mechanisms of actions of immunomodulatory drugs applied to patients with MS and related disorders. This specific project aims at understanding the role of B cells and plasma cells in neuroinflammation and will be performed in the BMC in the lab of Prof. Dr. Edgar Meinl.

More details at https://job-portal.lmu.de/jobposting/b7fe9363a94f3dd54b43d7b418ed987bbfaa6c730?ref=homepage