Careers And Study

Ph.D. student Computational Analysis of Single Cell Multi-omics Data in Breast Cancer

Function description

The lab of Elzo de Wit is interested in genome function and dynamics. We aim to strongly integrate wet-lab and computational biology. We use a multitude of genomics methods such as ChIPseq, (single-cell) ATAC-seq and Hi-C to study the interplay between nuclear organization, chromatin states and gene expression.

The lab of Wilbert Zwart studies epigenetics in cancer, with a strong focus on hormone-driven tumors, including breast cancer. We have established strong connections with the clinic, and are engaged with numerous clinical groups, embedding our fundamental and translational research on epigenetic gene regulation in the most-clinically relevant context.

Breast cancer is classically recognized as a heterogenous disease. We aim to chart the regulatory landscape in primary human breast cancers as well as the paired metastatic lesions from the same patients with single cell ATACseq and 10X Multiome to study the evolution of tumors in patients. In addition, we will study tumor evolution in patient-derived xenografts using single cell methods. For the project we will gather single cell data for a large cohort of patients and models. Your task will be to analyze these data with state-of-the-art analysis software and to develop novel tools to integrate complex multi-omic datasets. Your analyses will provide a basic understanding of how well-known transcriptional programs in breast cancer are regulated, reveal acquired dependencies on the transcription factors driving these programs, and how these transcriptional programs have changed in treatment resistant metastases.

Job requirements

We seek an ambitious PhD student with a strong affinity for computational biology and biological problem solving. Strong commitment, proven programming experience, and high motivation and enthusiasm to work together with experimentalists is required. Wet-lab experience is a pre.


You will be employed for a period of at least four years, with a possibility for extension. For a PhD student the gross salary per month is € 2.882,- to a maximum of € 3.322,- according to the standard PhD scales. The salary depends on previous experience. The terms of employment will be in accordance with the CAO Hospitals (Collective Labour Agreement for Hospitals).

For further information about the position please contact Dr. Elzo de Wit ( +31 20 512 7889; or prof. dr. Wilbert Zwart (+31 20 512 2101;

Acquisition for this vacancy is not appreciated.

The NKI values diversity and is committed to creating an inclusive work environment that stimulates the best in each individual. Applications of all individuals are welcomed regardless of age, ancestry, religion, disability, distance from the labor market, sexual orientation or gender identity.


  • Hours per week: 36
  • Salary level: Dutch Collective Labour Agreement for Hospitals
Nastassja  Drenthe

Nastassja Drenthe

Elzo  de Wit

Elzo de Wit

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