2 PhD positions in bioinformatics and experimental biology

We are looking for two highly motivated PhD candidates (one in bioinformatics and one in experimental biology) interested in investigating how cancer cells change the 3D genome to hijack gene regulation for aberrant expression of oncogenes from high-level genomic amplifications. The bioinformatics part of the project will involve whole genome sequencing and epigenetic analysis of several hundred tumor samples from breast and lung cancer patients to identify significantly recurrent changes to their 3D genome. In the experimental biology part, we will model recurrent oncogenic changes to the 3D genome observed in these cancers using CRISPR-based approaches to understand the mechanism of oncogenic transcription and resulting novel cancer vulnerabilities..

Your responsibilities may include, but are not limited to, the following activities:

• Bioinformatics PhD student: Analysis of sequencing data from short-read and long-read WGS, methylation, HiC, ATAC, ChIP, and RNAseq data starting from the raw data/ fastq files.
• Bioinformatics PhD student: Identify significantly recurrent genomic changes in cohorts of tumor samples, developing generalizable tools and pipelines in the process.
• Experimental biology PhD student: Isolation and processing of primary patient tumor tissue and cell lines for multi-omic sequencing
• Experimental biology PhD student: Analysis and interpretation of variant calls from WGS and epigenetic analysis of cell lines
• Experimental biology PhD student: CRISPR perturbations of cell lines and validation experiments of cell growth and oncogene expression
• Work with the other group members and collaborators in Berlin and other institutions across the world.
• Contribute to all levels of the research you are engaged including experimental design, data analysis, visualization, and writing.

Your profile

• Bioinformatics PhD student: MSc in Bioinformatics, Data Science, Computer Science, Biostatistics or similar.
• Bioinformatics PhD student: Experience in computational biology (sequencing and data analysis, classification tools, pipeline development in HPC environments)
• Experimental biology PhD student: MSc in Biology, Biochemistry, Bioengineering, or similar.
• Experimental biology PhD student: Experience in experimental biology (tissue culture, molecular biology, biochemistry). Experience in functional genomics (CRISPR-perturbation) is beneficial.
• Strong intrinsic motivation, scientific curiosity, organizational skills, and a strong interest in learning about novel technologies.
• Strong communication skills in written and spoken English.
• Being collaborative and proactive.

We offer a friendly, collaborative, and fast-paced environment that strives for scientific excellence, investigating clinically impactful questions, and developing each team member. The successful applicant will work closely with an international and interdisciplinary group, including clinicians, bioinformaticians, and biologists. The environment provides many opportunities to learn new skills, and we are deeply committed to excellent mentorship. The pay scale will be the standard 65% E13 PhD contract. We also offer a chance to affiliate with the CompCancer grad school for the bioinformatics PhD student and the BSIO for the experimental biology PhD student.

Please send your application as a single pdf file, including a cover letter indicating your research interests, potential starting date, a curriculum vitae, publication list, and contact information of up to three references to frank.dubois@charite.de.