Publications

Below is a selected list of my publications.

1. Hediyeh-zadeh*, S., Toh*, T. S., Dufva, O., Serra, G., Jakhmola, R., Fourneaux, C., ... Garnett, M. J. Perturbation-guided mapping of colorectal cancer cell states to causal mechanisms. bioRxiv, 2026-03.
2. Zheng*, Z., Hediyeh-Zadeh*, S., Liu, J., Theis, F. J. Beyond single-axis designs: multi-objective optimization for complex perturbation atlases. ICLR 2026 MLGenX.
3. Pinto, G. R., Cho, S. H., Ozleyen, S. Y., Von Schack, D., Apruzzese, W., Hediyeh-Zadeh*, S., Theis*, F. J. Structured and interpretable patient embeddings from Single-Cell Foundation Models. ICLR 2026 Gen2. Co-last author.
4. Schunke, L., Hediyeh-Zadeh, S., Salas, S. M., Can, A. O., Munich, H., Theis, F. J. Generative Modeling of Spatial Transcriptomics via Gaussian Mixture Flow Matching. ICLR 2026 Gen2.
5. Litinetskaya, A., Shulman, M., Hediyeh-zadeh, S., Moinfar, A. A., Curion, F., Szalata, A., ... Theis, F. J. Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases. bioRxiv, 2024-07.
6. Xu*, Q., Halle*, L., Hediyeh-Zadeh, S., Kuijs, M., Riedweg, R., Kilik, U., ... Camp, J. G. An integrated transcriptomic cell atlas of human endoderm-derived organoids. Nature Genetics, 2025, 1-12.
7. Kuemmerle, L. B., Luecken, M. D., Firsova, A. B., Barros de Andrade e Sousa, L., Strasser, L., Mekki, I. I., ... Hediyeh-zadeh, S. (11/21), ... Theis, F. J. Probe set selection for targeted spatial transcriptomics. Nature Methods, 2024, 1-11.
8. Ali*, M., Kuijs*, M., Hediyeh-Zadeh, S., Treis, T., Hrovatin, K., Palla, G., ... Theis, F. J. GraphCompass: spatial metrics for differential analyses of cell organization across conditions. Bioinformatics, 40(Supplement_1), July 2024, i548-i557. DOI
9. Baldoni, P. L.*, Chen, Y.*, Hediyeh-Zadeh, S., Liao, Y., Dong, X., Ritchie, M. E., ... Smyth, G. K. Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR. Nucleic Acids Research, 52(3), 2024, e13-e13.
10. De Donno, C., Hediyeh-Zadeh, S., Moinfar, A. A., Wagenstetter, M., Zappia, L., Lotfollahi, M., Theis, F. J. Population-level integration of single-cell datasets enables multi-scale analysis across samples. Nature Methods, 2023. Helmholtz Munich Best Paper Award.
11. Hediyeh-Zadeh, S., Webb, A. I., Davis, M. J. MsImpute: Estimation of missing peptide intensity data in label-free quantitative mass spectrometry. Molecular and Cellular Proteomics, 2023. Outstanding Technological Innovation article by MCP journal.
12. Heumos*, L., Schaar*, A. C., Lance, C., Litinetskaya, A., ... Hediyeh-Zadeh, S., ... Schiller, H., and Theis, F. J. Best practices for single-cell analysis across modalities. Nat Rev Gen, 2023.
13. Lotfollahi, M., Rybakov, S., Hrovatin, K., Hediyeh-Zadeh, S., Talavera-Lopez, C., Misharin, A. V., Theis, F. J. Biologically informed deep learning to query gene programs in single-cell atlases. Nature Cell Biology, 2023, 1-14.
14. Hediyeh-zadeh, S., Lotfollahi, M., Theis, F. J. Continual single-cell architecture surgery for reference mapping. ICML 2022 Workshop on Computational Biology.
15. Hediyeh-Zadeh, S., Fischer, T., Theis, F. Disentanglement via mechanism sparsity by replaying realizations of the past. ICLR 2024 Workshop on Machine Learning for Genomics Explorations.
16. Hediyeh-zadeh*, S., Whitfield*, H. J., Kharbanda, M., Curion, F., Bhuva, D. D., Theis, F. J., Davis, M. J. Identification of cell types, states and programs by learning gene set representations. bioRxiv, 2023-09.
17. Aliee, H., Kapl, F., Hediyeh-Zadeh, S., Theis, F. J. Conditionally Invariant Representation Learning for Disentangling Cellular Heterogeneity. arXiv preprint arXiv:2307.00558, 2023.

Students

PhD students, MSc / BSc students.

Mentoring/Co-supervision

• Zihe Zheng, PhD, TUM/Helmholtz Munich, 2025.
• Suhan Cho, PhD, TUM/Helmholtz Munich, 2025.
• Goncalo Pinto, PhD, TUM/Helmholtz Munich, 2025.

Supervision

• Lisa Schunke, MSc CS Informatics, TUM, 2025. Now PhD applicant Vienna.
• Layla Zadina, BSc Robotics, TUM, 2025.
• Lars Pechowski, BSc Mathematics, TUM, 2025.
• Zhiyuhan Song, MSc CS Informatics, TUM, 2025.
• Johannes Weindl, MSc CS Informatics, TUM, 2024.
• Mikkel Rassmusen, MSc CS, DTU, 2024. Now PhD graduate student DTU.
• Ismail Benayed, BSc Robotics, TUM, 2024.
• Georgiana Barbut, MSc Robotics, TUM, 2024. Now PhD applicant Vienna.
• Rashika Jakhmola, MSc Mathematics, TUM. Now PhD graduate student DKFZ.
• Lucas Ronchetti, BSc CS, TUM, 2023.
• Tom Fischer, MSc Mathematics, TUM, 2023.
• Rasmus Moller Larsen, MSc CS, DTU, 2023. Now PhD graduate student Helmholtz Munich.
• Jack Finlay, Visiting HIDA scholar, Duke University, 2023.
• Yi Xie, Visiting student, WEHI, 2019. Now PhD student China.

Contact

Email

soroor.hediyehzadeh@helmholtz-munich.com

Address

Helmholtz Zentrum München
Ingolstädter Landstraße 1
85768 Neuherberg, Germany