PhD in Systems Biology

11.07.2024, Wissenschaftliches Personal

Deng’s lab takes an integrated approach to study the interactions between virome, microbiome, and the human host. In contrast to the classical approaches commonly used in phage research, we are using single-cell technologies, multi-omics methods, culture-independent techniques, and machine learning to study phages and their interaction with the bacterial and human host for developing novel therapeutics. Ultimately, we are aiming to develop personalized phage-based treatments against infections by multi-resistant bacteria and for manipulating the human microbiome in dysbiosis associated diseases.

The successful candidate will explore the intricate interplay between viral and microbial communities and their impact on human health using advanced computational techniques. You will closely collaborate with wet lab scientists who will provide you with first-hand data. This role offers a unique opportunity to contribute to cutting-edge research in microbiome science, which has potential implications for therapy.

Required Qualifications:
• MSc in Computer Science, Systems Biology, or a related field.
• Proficiency in programming (R or Python, and Bash).
• Strong written and verbal communication skills in English.

Our Offer:
• Working in an innovative, well-stablished and scientifically stimulating surrounding.
• Working as part of a young and motivated team.
• Further training opportunities.
• The possibility to work with first-hand datasets.
Term: The position starts as soon as possible with a standard public service salary (TVöD EG 13). Duration: 3 years; option of further extension.

How to Apply:
Please send your electronic application (in English) in a single PDF file – including cover letter, and CV. For any question, please contact Dr. Mohammadali Khan Mirzaei, email: m.khanmirzaei@helmholtz-munich.de.

Deadline for applications:
until the position is filled

Lab Webpage:
https://www.mls.ls.tum.de/pmd/startseite/
https://www.helmholtz-munich.de/en/viro/research-groups/emmy-noether-research-group-virus-in-nature-and-health

Related publication:
1. Ru, J., Khan Mirzaei, M., Xue, J., Peng, X., & Deng, L. (2023). ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis. Gut Microbes, 15(1). https://doi.org/10.1080/19490976.2023.2192522
2. Ramaboli, M. C., Ocvirk, S., Khan Mirzaei, M., Eberhart, B. L., Valdivia-Garcia, M., Metwaly, A., Neuhaus, K., Barker, G., Ru, J., Nesengani, L. T., Mahdi-Joest, D., Wilson, A. S., Joni, S. K., Layman, D. C., Zheng, J., Mandal, R., Chen, Q., Perez, M. R., Fortuin, S., ... O’Keefe, S. J. D. (2024). Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer. Nature Communications, 15(3379). https://doi.org/10.1038/s41467-024-46265-0
3. Orberg, E. T., Meedt, E., Hiergeist, A., Xue, J., Heinrich, P., Ru, J., Ghimire, S., Miltiadous, O., Lindner, S., Tiefgraber, M., Göldel, S., Eismann, T., Schwarz, A., Göttert, S., Jarosch, S., Steiger, K., Schulz, C., Gigl, M., Fischer, J. C., ... Poeck, H. (2024). Bacteria and bacteriophage consortia are associated with protective intestinal metabolites in patients receiving stem cell transplantation. Nature Cancer, 5, 187–208. https://doi.org/10.1038/s43018-023-00669-x
4. Luo S, Ru J, Khan Mirzaei M, Xue J, Peng X, Ralser A, Hadi JL, Mejías-Luque R, Gerhard M, Deng L. Helicobacter pylori infection alters gut virome by expanding temperate phages linked to increased risk of colorectal cancer. Gut. 2023 Nov 2: gutjnl-2023-330362. doi: 10.1136/gutjnl-2023-330362. Epub ahead of print. PMID: 37918887.
5. Džunková, M., Low, S. J., Daly, J. N., Deng, L., Rinke, C., & Hugenholtz, P. (2019). Defining the human gut host–phage network through single-cell viral tagging. Nature Microbiology, 4, 2192–2203. https://doi.org/10.1038/s41564-019-0526-2

Kontakt: m.khanmirzaei@helmholtz-munich.de