Ph.D. student Computational Analysis of Single Cell Multi-omics Data in Breast Cancer at NKI, Netherlands 2022
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.
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. Project 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.
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