Theses, Projects, and Seminar

• We always have open topics for BSc and MSc theses or projects. If you are interested in doing your thesis with us, please apply using the form below. Please write an application text where you formulate a research question and provide an outline of your chosen approach. This will include a couple of relevant references for your task as well as a rough timeline for your project.
• We are aware that not all applicants have relevant expertise in bioinformatics and will evaluate the application accordingly. You are welcome to submit your own topic, related to network science and bioinformatics in the broader sense. To help you understand what work we are involved in, please have a look at the example topics below or at our publications.
• Applications which are formulated in a generic fashion, do not adhere to the instructions above, contain very vague statements, or were written by LLMs will be disregarded.

• Topic single cell analysis
• Topic gene regulatory networks
• Topic carbon-aware computing

• The application for the Project Biomedical Network Science uniquely happens via the submission form below. Please fill the form completely, incomplete submissions will simply be disregarded without any further notice.
• Please choose one of the project proposals below as your preferred option. For this project, please find three relevant and recent papers which address the problem and which suggest a solution to the question/problem statement formulated in the project proposal. Summarize the three papers in 2-3 sentences each. Pick any of the three articles and state the three references from its reference list which you deem the most influential for the method or content proposed in the article (e.g., an LLM model for some specific task could rely on the transformer architecture proposed in “Attention is all you need” by Vaswani et al.). To summarize, your application text will contain the full citations of your three chosen papers, a 2-3 sentence summary of those papers, and the top 3 references of one of the three articles. Please also choose a second project as a fallback option. You don’t need to submit anything further for your second choice.
• Applications which are formulated in a generic fashion, do not adhere to the instructions above, contain very vague statements, or were written by LLMs will be disregarded.
• No need to sign-up for the course on StudOn. We will manually admit the selected applicants provided they show up at the kick-off meeting.
• Application will be open starting 14th of Feburary, please check this website again for updated project proposals.
  
• Application deadline: April 14th 2025.
  

• Project 1:  Gene regulatory network inference using nf-core and nextflow for community driven pipelines (Supervisor: Nicolai Meyerhoefer)
• Project 2: Deep Learning-based Imputation Techniques for Handling Missing Values in Healthcare Data (Supervisor: Dr. Farnaz Rahimi)
• Project 3: Examining Fairness and Interpretability of ML Models in Predicting Neutropenic Fever Post-Chemotherapy (Supervisor: Dr. Farnaz Rahimi)
• Project 4: Developing a Graphical User Interface for a Python-based Flow cytometry Data Analysis and Classification tool (Supervisor: Paul Martini)
• Project 5: Towards a foundation model for flow cytometry (Supervisor: Paul Martini)
• Project 6: Latent dimension space in single-cell RNA auto-encoders (Supervisor: Dr. Anne Hartebrodt)
• Project 7: Online federated cell type classification (Supervisor: Dr. Anne Hartebrodt)
• Project 8: Web resource for gene contextualisation (Supervisor: Dr. Anne Hartebrodt)
• Project 9: Efficient implementations of statistical test accounting for confounders on large-scale datasets (Supervisor: Fabian Woller)
• Project 10: Investigating informative missingness in time series laboratory data (Dr. Christel Sirocchi)
• Project 11: Clustering patient trajectories in electronic health records (Dr. Christel Sirocchi)
• Project 12:  Properties of SHAP values derived from GCNNs (Dr. Hryhorii Chereda)
• Project 13: Properties of Integrated Gradient Values derived from GCNNS (Dr. Hryhorii Chereda)
• Project 14: 72 hour forecasts for renewable energy percentage (Dr. Anne Hartebrodt)

• Time: 29.04.2025 12:15 (12ct)
• Place: Seminar room Werner-von-Siemensstr. 61, 3.17 (Subject to change, due to AIBE moving to a new building)
• Attendance of the Kick-off meeting is mandatory.

Please only submit the form once!

Application will close on 14th of April.

• The application for the Seminar Network Medicine uniquely happens via the submission form below. Please fill the form completely, incomplete submissions will simply be disregarded without any further notice.
• In the seminar, you will present a paper of your choice from the Network Medicine field and will write a 4-page perspective or mini-review essay where you critically engage with the research landscape surrounding the paper of your choice. To apply for the seminar, please identify two potential papers. To individuate them, you can use literature databases such as PubMed or Scopus or you can do a snowball search starting with our publications (however, please do not suggest papers authored by us). For each of the two papers, describe two strengths and two weaknesses in 2-3 sentences. To summarize, your application text will contain the full citations of your two chosen papers and 2-3 sentence descriptions of two strong and two weak points for both of them.
• Applications which are formulated in a generic fashion, do not adhere to the instructions above, contain very vague statements, or were written by LLMs will be disregarded.
• No need to sign-up for the course on StudOn. We will manually admit the selected applicants provided they show up at the kick-off meeting.
• Application deadline: October 6, 2024.

• Time: October 17,  2024, 12:15 – 13:45
• Place:  Room 10.150, 10th floor, Martensstraße 3 (Wolfgang-Händler-Hochhaus Informatik), 91058 Erlangen

• Project 1:  Federated carbon-aware machine learning (supervised by Anne Hartebrodt)
• Project 2: Pseudotime informed GRN inference (supervised by Anne Hartebrodt)
• Project 3: Alphafold3: really as good as they claim? (supervised by Nicolai Meyerhöfer)
• Project 4: Gene-regulatory Kolmogorov-Arnold networks (supervised by Nicolai Meyerhöfer)
• Project 5: Fourier transforms as activation functions in CNNs (supervised by Suryadipto Sarkar)
• Project 6: Cancer grading from histological images (supervised by Suryadipto Sarkar)
• Project 7: Automated cell type calling for high-resolution spatial omics (supervised by David B. Blumenthal)
• Project 8: Boundary-aware node centralities for spatial graphs (supervised by David B. Blumenthal)
• Project 9: Differential analysis of multi-modal omics data from IBD mouse models (supervised by David B. Blumenthal)