Postdoctoral Researcher in Spatial Transcriptional Regulation

Updated: about 1 month ago
Deadline: 31 May 2024

NORPOD is a collaborative postdoctoral program of the Nordic EMBL Partnership for Molecular Medicine . The partnership is a network of four national research centers across the Nordics and the European Molecular Biology Laboratory (EMBL) , with complementary research expertise at the forefront of molecular medicine research. With the NORPOD program, the Nordic EMBL Partnership aims to foster the next generation of researchers in molecular medicine by implementing joint postdoctoral research projects to nurture strong competences and research excellence.

FIMM is currently seeking a Postdoctoral Researcher to join Anniina Färkkilä’s lab, in collaboration with the Kuijjer group at NCMM, through the NORPOD program.

Summary of the project

Spatial tumor-immune interactions are key determinants of therapy responses in ovarian cancer. Our aim is to identify the spatial transcriptional regulation of tumor cell states that drive chemoresistance in ovarian cancer. In this project, we will integrate multiplexed single-cell spatial proteomics, transcriptomics and chromatin states using unique novel spatial technologies and analytical methods. The two EMBL groups have highly synergistic approaches enabling an unprecedented analysis and exploitation of rich spatial multi-omics datasets generated in a unique prospective clinical trial (NCT06117384). The results will pave the way for the development of more effective treatments for ovarian cancer patients.

Tasks

•    Integration of spatial omics data with deep learning-based approaches.
•    Gene regulatory network modeling and analysis in tumor cell subpopulations.

Skills, expertise and/or qualifications

•    PhD degree in computational biology, bioinformatics, biostatistics, computer science, or a related field
•    Strong publication record
•    Proficiency in programming (such as R, Python, MATLAB, Bash)
•    Documented experience with analysis of high-throughput omics data
•    Knowledge in single cell or spatial transcriptomics, gene regulation and/or network biology, and experience with high performance computing is desirable
•    Knowledge in cancer research is a strong advantage
•    Professional proficiency in English with documented communication skillsWillingness to work in a team environment, sharing skills and ideas, and collaborating on projects

Group descriptions

The Färkkila Lab (www.farkkilab.org ) is focused on the discovery and exploitation of spatial vulnerabilities in ovarian cancer using unique integrative systems oncology methods. The Lab has generated a unique spatial multiomics dataset from a clinical trial with 400 patients. The overall goals of the Lab are focused around understanding the dynamics of the tumor microenvironment to develop prognostic and predictive biomarkers and new therapeutic approaches to improve the treatment and survival of patients with ovarian cancer.

The Kuijjer Lab (www.kuijjerlab.org ) develops network-based computational tools to analyze and integrate large-scale omics data. We have a specific research interest in modeling how gene regulatory network rewiring may affect cancer development, progression, and heterogeneity. Our current projects aim at 1) developing fine-tuned models of gene regulation, 2) integration and analysis of patient-specific regulatory networks with multi-modal data, and 3) developing tools for high-resolution mapping of regulatory disruptions in cancer.

Implementation 

The NORPOD Fellow will be employed at the Färkkilä Lab (FIMM, University of Helsinki, Finland). To promote collaboration between the two labs, this position will involve short stays at the Kuijjer Lab (NCMM, University of Oslo, Norway). Successful candidates are expected to travel between the labs to conduct work required for the research project, foster synergies and advance our goals. Expenses related to the research visits will be covered.

Contract & salary

The job is for a fixed term of 2.5 years. 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. The starting salary will be ca. 3,500 – 3,800 euros/month, depending on the appointee’s qualifications and experience and including a salary component based on personal performance. Standard Finnish pension benefits and occupational health care are provided for University employees. We welcome applicants from a variety of gender identities, linguistic and cultural backgrounds. 

Selection process
•    The collaborating PIs of the research project will shortlist and video interview top candidates.
•    Top candidates will be invited for an online interview, conducted by an independent selection panel where they will also be given the opportunity to pitch the project plan.
•    NORPOD Fellowships will be awarded based on the recommendation of the selection panel.

How to apply:

The application should include (i) CV, (II) a one- page statement of motivation for applying for this position, (iii) contact information of at least one reference persons who have agreed to provide a written statement on behalf of the applicant.
To apply, please submit the application through the University of Helsinki electronic recruitment system by clicking on Apply for job. Internal applicants (i.e., current employees of the University of Helsinki) please submit your applications through SAP Fiori https://msap.sap.helsinki.fi.
Please apply no later than 31st of May 2024


The University of Helsinki is an international scientific community of 40,000 students and researchers. It is one of the leading multidisciplinary research universities and ranks among the top 100 international universities in the world.
The Institute for Molecular Medicine Finland (FIMM) is an international research unit focusing on human genomics and personalised medicine at the Helsinki Institute of Life Science (HiLIFE) of the University of Helsinki - a leading Nordic university with a strong commitment to life science research. As part of Academic Medical Center Helsinki in Meilahti campus FIMM collaborates locally with the Faculty of Medicine, Helsinki University Hospital and National Institute for Health and Welfare. FIMM is part of the Nordic EMBL Partnership for Molecular Medicine, composed of the European Molecular Biology Laboratory (EMBL) and the centres for molecular medicine in Norway, Sweden and Denmark, and the EU-LIFE Community.



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