Nanopore long reads, human pluripotent stem cells and cancer

PD Dr. med Franz-Josef Müller

November 02, 2020

We are seeking applicants in a multicenter project funded by the German Federal Ministry of Education and Research (BMBF) for PhD positions. The project will push the boundaries of what is considered technologically possible in the field of third generation sequencing technologies, specifically nanopore sequencing. The work will build upon our recent publication in Nature Biotechnology on targeted nanopore sequencing of disease loci.

Responsibilities:

Successful candidates will work in a high-profile environment and interact with a multidisciplinary team of experts in the fields electrical engineering, molecular biology, epigenetics, human pluripotent stem cell biology, surgical oncology as well as industry partners in the field of applied clinical diagnostics. Alexander Meissner and Franz-Josef Müller will coordinate the project.

The tasks of the successful applicants will include the identification of sequence and structural variants in nanopore datasets from human pluripotent stem cell and tumor samples as well as the analysis of DNA methylation, with an emphasis on prediction of functional outcomes and integration/visualization of multiple datasets.

Qualifications:

The sequencing device has tiny nanopores that can determine both the DNA sequence and the epigenetic signature.

We are looking for highly motivated as well as skilled individuals in the area of next-generation sequencing genome informatics. Eligible candidates should have a Master’s degree or a similar qualification in biological, chemical, physical or computational sciences. The candidates should have a strong background in statistics and computational biology. The position will be offered to individuals with prior experience in machine learning and its application to cancer subtypes or pluripotent stem cells from functional genomics datasets. The early career researcher will have a firm grasp of the programming languages Python or R as well as working knowledge in Linux. The successful applicant will benefit from experience with the analysis and biological interpretation of datasets reflecting epigenetic mechanisms from at least one of the following areas: chromatin conformation capture, ATAC-seq or DNA methylation analysis or similar approaches.

For more information visit the website of the Cellular Phenotyping Group.

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