Positions in our lab
PhD position in tumor epigenome evolution
Are you passionate about uncovering the hidden drivers of cancer evolution? Join the computational cancer biology lab of Martin Schaefer as a PhD student, where you’ll develop models of tumor epigenome evolution to identify epigenetic drivers of late stage carcinogenesis.
Project overview:
Cancer is driven by alterations on all molecular levels. While our knowledge about the contribution of point mutations to the phenotypic hallmarks of cancer has advanced substantially over the last decade, we still need to solve the puzzle of how the numerous quantitative changes (eg epigenetic or transcriptional) are related to cancer initiation and progression. We are looking for a computational postdoc to develop models of selection to identify epigenetic drivers of carcinogenesis.
Your work will contribute to solving one of the most critical puzzles in cancer biology - linking quantitative molecular changes to cancer initiation and progression - by analyzing cutting-edge data types such as WGBS, EM-seq, and ONT sequencing generated from our in-house cohort of gastrointestinal cancer patients. On the methodological site, this project will combine methods from machine learning and population genomics.
Your role will involve investigating key questions such as:
- Identifying alterations under selection in late-stage tumors.
- Understanding how epigenetic changes facilitate adaptation to metastatic niches.
- Exploring how selection pressures reveal tumor vulnerabilities.
The successful candidate will work together in close collaboration with other members of the lab as well as with wet lab and clinical collaborators.
Learn more:
This is a continuation of our previous work, in particular: Heery and Schaefer. NAR. 2021 and Alfieri, Caravagna and Schaefer. Nat Comm. 2023. Watch also a video describing our quest for identifying epigenetic drivers of tumor evolution.
About us and the application procedure
What we offer:
- World-class research environment: The IEO, located on the IFOM-IEO campus in central Milan, is renowned for its excellence in cancer research, with a strong emphasis on genomics, clinical applications, and the mechanistic understanding of cancer biology.
- Collaborative and diverse team: You’ll be part of a dynamic, interdisciplinary and international community that fosters collaboration between computational and experimental scientists.
- State-of-the-art infrastructure: Access to excellent HPC infrastructure and core facilities, ensuring you have the resources to excel in your research.
- Learning opportunities: You will receive close supervision and mentorship, with significant opportunities to expand your expertise in network biology, machine learning, and programming.
More information on our institute can be found here: www.research.ieo.it.
Requirements:
- For postdoc candidates: PhD in Bioinformatics, Computer Science, Biophysics or a related field.
- For PhD candidates: Master in a computational discipline.
- Background in population genomics, machine learning or network biology.
- Proficiency in programming languages (e.g., Python, R).
- Experience with large-scale data analysis and high-performance computing.
- Enthusiasm for learning and applying new computational methods to biological questions.
How to apply:
For informal inquiries or to send an application (which should include a CV, cover letter, a list of publications and contact details of 2 - 3 referees) please contact: martin.schaefer@ieo.it. Please note that candidates interested in pursuing a PhD will additionally need to apply to and enroll in our graduate school upon initial acceptance.
Bachelor and master theses
We are always looking for bachelor and master students interested in doing their thesis or internships with us. Please directly contact: martin.schaefer@ieo.it.
The workplace
The European Institute of Oncology (IEO) is one of Europe’s leading cancer research institutes. The lab is in the Department of Experimental Oncology (DEO), which is located on the IFOM-IEO campus in a central location of Milan. The IEO hosts an international and vibrant research community (with a growing computational component). It is strong in genomics analyses, clinical aspects and mechanistic understanding of cancer. The IEO has an excellent HPC infrastructure and core facilities. The institute and the lab provide a collaborative and diverse work environment. The working language is English.