Postdoctoral fellowship in computational single-cell spatial multi-omics for cancer immunotherapy

Are you passionate about the tumor microenvironment, immune evasion and integrative multi-omics in cancer? Join us and experience Finland, the happiest country in the world! In Helsinki, you will find an international dynamic culture combined with an excellent quality of life close to nature and with the cleanest air in the world.
Our research
A postdoctoral position based on the EU funded project SPACE is provided in Anniina Farkkila’s lab (http://farkkilab.org), located at Biomedicum, University of Helsinki, Finland. The lab is part of Research Program for Systems Oncology, Faculty of Medicine, and Helsinki Institute for Life Sciences. We are an interdisciplinary team of clinicians, biologists, bioinformaticians, and data scientists working together to improve the treatment and lives of cancer patients.
The overall goal is to discover how the tumor cells evade the immune system in ovarian cancer, with prospects of leading to major scientific breakthroughs and successful translation of the findings into clinical trials. We aim to integrate genomic profiles (WES, ctDNA, RNAseq), with single-cell and spatial information from spatial genomics, proteomic and transcriptomic data and associate the findings to clinical data using machine learning.
We have collected a unique set of multi-omics, multi-site spatial data from more than 300 patients in the prospective Oncosys-OVA study, including sequencing, imaging and curated clinical data. Our multidisciplinary team has also developed experimental and functional models to validate findings emerging from the data, generating a unique environment to drive scientific discoveries with clinical relevance.
Our lab received a prestigious ERC grant in 2022 and has received steady funding from e.g. the Research Council of Finland, Sigrid Jusélius Foundation, and Cancer Foundation. We also actively collaborate with esteemed research institutes globally, including Harvard Medical School and Netherlands Cancer Institute.
Your mission
You will be expected to bring expertise in computational techniques on single-cell spatial multi-omics and co-mentor doctoral and master’s students.
You will have the opportunity to participate in e.g.:
- Single-cell spatial atlas of high-grade serous ovarian cancer. Discovering associations of tumor mutations with single-cell tumor microenvironment using data science and machine learning.
- Pixel-based spatial molecular profiling based on imaging datasets. Developing deep learning approaches for automated extraction of features from the tumor micro-environment associated with clinical-molecular profiles.
- 3D reconstruction of the spatial structures and functional features for diagnostic and prognostic stratification of ovarian cancer patients.
- Multimodal data integration from our large genomic, single-cell proteomic and transcriptomic datasets to find clinically meaningful features for precision oncology.
Requirements
•    Solid background in bioinformatics or computational biology. Knowledge in machine/deep learning.
•    Experience working with high-performance computing, containers and packages. Previous experience working with clusters, cloud computing, and virtual machines.
•    Proficiency in Linux, and proficiency in programming languages such as R, Python, and Matlab (for 3D reconstruction project).
•    Previous working experiences relevant with image analysis/computer vision or single-cell omics data.
•    Basic knowledge and interest in cancer biology or immunology are expected.
What we offer
-   You will be immersed in the rich interdisciplinary culture of the research program. We offer excellent training and coaching towards an ambitious career.
-   Our mentality is to maintain a highly collaborative and enthusiastic atmosphere in the Lab and exploit our rich international scientific networks. You will have a chance to expand your research connections.
-   The research will be highly clinically relevant within the precision oncoloty and immuno-oncological area. Our multidisciplinary approaches have unique prospects of changing your scientific discovery into clinical biomarkers to be tested in prospective trials with direct patient benefit. This postdoc experience will be a solid basis for your next-level career.
-   A monthly salary and benefits according to the Helsinki University standards will be applied (around 3400-4000€/month). The salary will guarantee a high quality of life in Helsinki.
The position is available as soon as the selected candidate is available. The project initially allows a 2-3 year fixed-term position. A trial period of 6 months will be applied. Salary will depend upon the applicant's level of skills, knowledge, and abilities and is based on the university salary system.

How to apply

Applications should be submitted through the University of Helsinki Recruitment System via the Apply now button.

Applicants who are currently employed by the University of Helsinki are requested to submit their application via the SAP Fiori portal at https://msap.sap.helsinki.fi.

To apply send in a single PDF
1. Cover letter including three referees (max 1 page)
2. CV (max 2 pages)
3. Publication list

For further information contact anniina.farkkila(at)helsinki.fi