Postdoctoral Researcher in deep learning modeling of the tumor microenvironment

Karolinska Institutet

Application deadline

May 2, 2024

Postdoctoral Researcher in deep learning modeling of the tumor microenvironment

Do you want to contribute to improving human health?

Decscription of the researchgroup

Our lab is advancing precision cancer medicine through deep learning models of the molecular networks within cells. The models encompass metabolism, signaling, and gene regulation and are constrained to align with physical interactions between biomolecules. We train the models on high-throughput datasets, including metabolomics, proteomics, and transcriptomics and use them to identify systems-level mechanisms in cancer to enhance treatment efficacy by uncovering new drug targets, biomarkers, and resistance mechanisms. We are specifically interested in cancer-stroma interactions in pancreatic cancer.

The long-term goal of our lab is to enable computer-aided design of precision cancer medicine. The lab is situated at the Science for Life Laboratory (SciLifeLab) and the position is funded by its Data Driven Life Science program (DDLS).

Your mission

You will develop a deep learning model of the tumor microenvironment (TME) in pancreatic cancer with the goal of identifying novel therapeutic targets and biomarkers for modifying the TME to enhance treatment outcomes.

In this postdoc position you will:

  • Design a high-throughput stimulus-response experiment in cancer and stroma cells, that will be conducted by our core facilities.
  • Train a model to infer ligand patterns in the TME from patient data, aiding classification of disease states and identification of potential biomarkers.
  • Expand the model to simulate dynamic interactions between pancreatic cancer and stroma cells to uncover self-sustaining ligand secretion patterns.
  • Predict molecular targets within pancreatic cancer and stroma networks that can modify the TME to improve patient outcomes.

If you are ready to make an impact in the fight against cancer and contribute to groundbreaking research at the intersection of deep learning and cell biology, we encourage you to apply!

Your profile

To be eligible for employment as a postdoctor a doctoral degree or a foreign degree deemed to be equivalent to a doctoral degree is required. This eligibility requirement must be fulfilled at the latest at the time of the employment decision. It is considered as an advantage if you have completed your doctoral degree within the last three years, if there are special reasons, your degree may have been completed earlier.

Required qualifications:

  • Strong programming skills in languages such as Python.
  • Experience analyzing high-throughput biological data.
  • Proven ability to conduct independent research and communicate findings effectively.
  • Highly motivated with the ability to work both independently and collaboratively within a team.
  • Proficiency in written and spoken English.

Other desirable qualifications:

  • Familiarity with cancer biology, particularly in context of the tumor microenvironment.
  • Experience with deep learning models and automatic differentiation.
  • Experience with GitHub or other version control systems.
  • Experience designing high throughput experiments.

Our lab values diversity and inclusion, and we are committed to fostering an environment where all individuals feel empowered to contribute their unique perspectives and skills towards our shared goal of advancing precision cancer medicine.

What do we offer?

A creative and inspiring environment with wide-ranging expertise and interests. Karolinska Institutet is one of the world’s leading medical universities. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. At KI, you get to meet researchers working with a wide range of specialisms and methods, giving you ample opportunity to exchange knowledge and experience with the various scientific fields within medicine and health. It is the crossover collaborations, which have pushed KI to where it is today, at the forefront of global research. Several of the people you meet in healthcare are educated at KI. A close relationship with the health care providers is important for creating groundbreaking top quality education and research. Karolinska Institutet is also a state university, which entitles you to several benefits through our collective agreement.

Location: Stockholm

Deep learning models of cancer mechanisms – Avlant Nilsson’s Group | Karolinska Institutet (


An employment application must contain the following documents in English or Swedish:

  • A complete resumé, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
  • A complete list of publications
  • A summary of current work (no more than one page)

The application is to be submitted through the Varbi recruitment system.

Last updated: 2024-04-12

Content Responsible: Hampus Persson(