Computational Postdoc

Computational Postdoc Wesseling/Thommen Lab — Investigating immune surveillance in premalignant breast lesions through spatial and functional profiling

We are recruiting a postdoctoral fellow to spearhead a cutting-edge project at the interface of tumor immunology, pathology, and translational cancer research, connecting experimental immune profiling, advanced data analysis, and clinical interpretation in Ductal carcinoma in Situ (DCIS), a breast cancer precursor lesion. The results from this project are expected to inform future strategies to enhance immune control in early cancer and may lay the groundwork for integrating immune profiling into the clinical management of premalignant breast disease in the future. The postdoc will serve as the scientific lead of this project within the Wesseling and Thommen groups in close collaboration with the Schumacher group at the Netherlands Cancer Institute. The project is a follow up of the work that has been done in the international Cancer Grand Challenge PRECISION project (PRECISION | Cancer Grand Challenges)

The successful candidate will be expected to develop analysis pipelines for high-dimensional immune datasets including single cell/spatial transcriptomics and multiplex imaging, to lead the design of functional experiments in ex vivo models (optionally also execution of wet lab experiments), to integrate the results with clinical, pathological, and genomic data from large retrospective cohorts, and to drive AI-assisted analyses in collaboration with computational experts. The role requires an innovative and critical mind to define key biological questions and design the computational strategies to address them.

Why this postdoc?

• New frontier in cancer research: contribute to an emerging key challenge in cancer research by unraveling the natural defense mechanisms that prevent or promote the development of malignant disease.

• Pioneering expertise: work among leading experts in early detection, ex vivo modeling, and tumor immunology.

• Translational impact: collaborate with experimentalists, computational scientists and clinicians to transform future risk stratification and reduce overtreatment in premalignant breast disease.

• World class ecosystem and mentorship: the NKI offers highly visible research groups and inspiring scientific mentors, strong core facilities and a vibrant international community in the heart of Amsterdam.

You will:

• Coordinate, analyze, and interpret high-dimensional immune datasets to identify key immune features associated with cancer progression or containment

• Lead the design and execution of functional immune profiling in HER2-positive premalignant disease, including ex vivo patient-derived tumor fragment assays and functional TCR repertoire analyses.

• Integrate the identified immune features with clinical, pathological, and genomic data from large retrospective cohorts with long-term follow-up.

• Drive AI-assisted analysis of H&E-stained slides in collaboration with pathologists and computational experts to develop scalable immune readouts.

• PhD or MD/PhD in computational biology/immunology or in tumor immunology/ molecular pathology with computational expertise.

• Strong experience with human tissue-based research and immunological assays.

• Hands on experience in one or more of the following:

  • Single cell and/or spatial transcriptomics, ideally in the context of cancer immunolog

  • Multiplex imaging or digital pathology

  • Integrative analysis of multi-omics data

• Solid computational literacy (e.g., R, Python, or equivalent) and ability to work with high-dimensional datasets.

• Strong drive and inherent excitement to discover novel biology with complex computational analyses and translate them into clinical strategies.

• Proven track record of scientific productivity and ability to work independently in a collaborative, multidisciplinary environment.

• Fluent in English.

Your development opportunities and employment conditions

The basis for your employment conditions is in accordance with the CLA Hospitals. You will receive from us:

• A contract for 4 years, for 36 hours per week. Preferred start date: flexible (ideally soon);

• A gross monthly salary between € 4.539,- and € 5.395,-, based on a 36-hour working week, in line with FWG55 and depending on your experience;

• 144 holiday hours and 57 hours of Personal Life Budget, with full-time employment;

• Annual holiday pay of 8.33% and a fixed end-of-year bonus of 8.33%;

• A travel allowance of €0.23 per km;

• Free parking at the Netherlands Cancer Institute. And with our bicycle plan and discount on public transport we also make it attractive for you to leave the car at home;

• Personal mentorship from established PIs and senior scientists; clear milestones and career development plans for a strong and visible scientific profile;

• A great opportunity in a specialised hospital where you can also continue to learn and grow yourself if you wish: the AVL Academy offers innovative and inspiring education in the field of oncology professional knowledge, skills and personal development;

• Opportunity to exercise during working hours at our Fit Boutiqs;

• An active staff association.

Interested?

If you are passionate about joining us to push the boundaries of immune profiling in premalignant breast cancer through computation, please submit your application by using the apply button. Please provide a cover letter, CV with publications and contact details of two references. Make sure to include all the information in one or two files, as there is no option to submit everything separately.

This vacancy is open for applications until March 20.

For further information about the position, please contact Esther Lips (Wesseling lab) e.lips@nki.nl or Daniela Thommen (Thommen lab) d.thommen@nki.nl.

For questions about the application procedure, please contact Daphne Heemskerk (Recruitment), d.heemskerk@nki.nl.