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 READ AND FOLLOW THE INSTRUCTIONS!!!!!
• 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.
• Final Application deadline: April 5th 2026.
• Final notification: April 7th 2026. Students may receive notifications earlier.

Please read the project description carefully. Deep learning projects:

• No project available.

Other interesting projects:

• CIRCus: Detecting circular patterns in scRNA and CITESeq data (Supervisor: Anne Hartebrodt)
• DUAL-RF: Dual-feature random forests (Supervisor: Dr. Anne Hartebrodt)
• GAMs: Interpretable Generalized Additive Models for Predicting Chemotherapy-Related Complications in Clinical Patients (Supervisor: Dr. Farnaz Rahimi)
• STEM: Signal Temporal Logic Embedding with Missingness Indicators (Supervisor: Dr. Christel Sirocchi)
• DIGGER: DIGGER for intra-protein-complex interactions (Supervisor: Judith Bernett)
• PIB: Investigate inter- vs. intra-protein complex interaction biases in existing PPI databases Supervisor: Judith Bernett)

Projects no longer available:

• VesSkel: Vessel Skeletonization and Graph-Based Phenotype Analysis in Retinal Fundus Images (Supervisor: Anna Möller)
• CATAN: Neuronal network architecture guided by ATAC data. (Supervisor: Dr. Anne Hartebrodt)
• CLACELL: Robust cell type classifier for immune cells (Supervisor: Dr. Anne Hartebrodt)
• THRESH: Knowledge-Guided and Data-Driven Threshold Discovery for Predictive Modelling in Longitudinal Laboratory Data (Supervisor: Dr. Christel Sirocchi)
• SSL: Self-Supervised Learning for Irregular Clinical Time Series Data (Supervisor: Dr. Farnaz Rahimi)

• Time: April 16, 2026, 10:15 – 11:45
• Place: Nürnberger Str. 74, 91052 Erlangen, ground floor, CIP-Pool 1
• Attending the kick-off meeting is mandatory and registration to StudOn will happen on that day.

Application closed.

Winter 2025/2026:

• SUBFOREST: Graph-based sampling of diverse sub-forests (Dr. Christel Sirocchi)
• SRESSTEST: Stress-testing deep learning models on sparse longitudinal health data (Dr. Christel Sirocchi)
• DIAGNOSTIC-CODES: Data-driven and knowledge-guided representations of diagnostic codes  (Dr. Christel Sirocchi)
• APLASIA: Comparative Evaluation of Machine Learning and Deep Learning Approaches for Predicting Aplasia Duration from Multi-Modal EHR Data (Dr. Farnaz Rahimi)
• N-FEVER: Examining Fairness and Interpretability of ML Models in Predicting Neutropenic Fever Post-Chemotherapy (Dr. Farnaz Rahimi)
• FOUNDATION-FLOW: Exploring foundation model approaches for flow cytometry (Supervisor: Paul Martini)
• RNA-LATENT: Latent dimension space in single-cell RNA auto-encoders (Supervisor: Dr. Anne Hartebrodt)
• GENE-CONTEXT: Gene contextualisation (Supervisor: Dr. Anne Hartebrodt)
• DUAL-RF: Dual-feature random forests (Supervisor: Dr. Anne Hartebrodt)
• ALTERNET: Alternative Splicing – aware Gene Regulatory Network Inference (Supervisor: Dr. Anne Hartebrodt)
• STAT: Implementing efficient statistical tests using distributed parallelism in Dask (Supervisor: Fabian Woller)

Summer 2024:

• 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)

Winter 2024/2025:

• 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 feature selection based on SHAP applied to a Graph Convolutional Neural Network (Dr. Hryhorii Chereda)
• Project 13: Properties of feature selection based on Integrated Gradients applied to a Graph Convolutional Neural Network (Dr. Hryhorii Chereda)
• Project 14: 72 hour forecasts for renewable energy percentage (Dr. Anne Hartebrodt)
• Project 15: Rule-based learning for generating semantic descriptions of patient subgroups (Fabian Woller)

• 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.
• This semester, we focus on reproducing the results reported in articles published in the “Systems Biology and Networks” topic area of the proceedings of the 2024, 2025, or 2026 editions of the ISMB – the leading international conference in the field of computational biology.
• The ISMB 2024 proceedings can be found here: https://academic.oup.com/bioinformatics/issue/40/Supplement_1#2183363-7700883
• The ISMB 2025 proceedings can be found here: https://academic.oup.com/bioinformatics/issue/41/Supplement_1#2235509-8199378
• The ISMB 2026 proceedings can be found here: https://academic.oup.com/bioinformatics/issue/42/Supplement_1#2580938-8726292
• Your task in the seminar will be (i) to select a paper from the above-mentioned collections, (ii) to (try to) reproduce the reported results from data download to plotting, and (iii) to present the results of your reproducibility study both in written and oral form.
• To apply for the seminar, please provide the title and DOI of the paper you would like to reproduce in the application form below. In the application text, you should also provide a preliminary assessment of data availability (you should select a paper based on publicly available data) and required computational resources (non-EU students are advised to select papers that can be reproduced on their own hardware, since we’d have to go through export control to give you HPC access which can take quite long).
• 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 8, 2026.
• Final notification: October 9, 2026. Students applying before the application deadline may receive positive notifications earlier, so apply as early as possible.

• Time: October 12,  2026, 12:15 – 13:45
• Place:  Seminar room 2, Nürnberger Str. 74, 91052 Erlangen
• Attending the kick-off meeting is mandatory and registration to StudOn will happen on that day.