PhD student in precision cancer genomics

PhD student in precision cancer genomics

• Berlin

The Digital Health Center, headed by Prof. Roland Eils, develops and applies state-of-the-art and innovative technologies to healthcare research with a strong focus on machine learning, bioinformatics, imaging and genomics. The department has a strong standing within international consortium (e.g. Human Cell Atlas, ICGC, de.NBI, ELIXIR, EOSC), and have exceptional computational resources (in-house HPC, cloud, Nvidia DGX and FPGA technology).

We have recently established precision genomics medicine platform called PeDiOn, which aims to use whole genome and transcriptome sequencing with the aim to guide the clinical decision making process for cancer patients who do not respond to first line therapy. Building on top of an excellent existing pipeline, we aim to further develop the computational analytics part of the pipeline in the upcoming years.

Tasks:
The Digital Health Center of Roland Eils provides a dynamic, collaborative, challenging, and rewarding research environment. The advertised position will be embedded in the research group of Computational Oncology headed by Dr. Naveed Ishaque.
Your responsibilities are primarily to undertake and publish excellent scientific research, while paying attention to career development and community engagement.
In addition to undertaking your PhD research on precision cancer genomics, you will be responsible for:

• Interacting with other members of the clinical genomics program including management, pathology, genomics and clinical partners

• Analyzing genome sequencing data for prospective patients, working closely with clinicians to identify actionable mutations

• Analyzing genome sequencing data for retrospective studies

• Development of new genomics workflows (e.g. supporting new genome references and genomics lesions such as STRs and enhancer hijacking) and interacting with our Data

• Management Platform team for deployment in a production environment

• Development and implementation of novel computational methods that aid genomics based diagnostics and prognosis

• Interacting with other collaborative sites, in particular the DKFZ and NCT in Heidelberg

Qualifications - Basics:

• A PhD candidate with a recent masters degree in bioinformatics, cancer genomics, computer science, medicine, physics or similar
• Ambitious, self-driven, a thirst for answering scientific questions and aim to build a scientific career in biomedical data science research
• Excellent programming proficiency especially in Python, R, Julia, bash or similar
• Experience in designing and implementing data analysis pipelines
• Experience with next generation sequencing data processing and analysis
• Experience with linux based HPC or cloud environments
• Fluent in English (written and spoken)

Qualifications - Desirable:

• Prior research experience in liquid biopsies, cancer genomics data, single cell 'omics data, or spatial transcriptomics
• Knowledge of transcriptional regulation and epigenomics
• Knowledge of cancer immunology
• Experience with machine learning methods (e.g. RF, NMF, VAE) and frameworks (e.g. PyTorch, TensorFlow, Keras, sklearn)
• Experience with workflow management systems and similar paradigs (e.g. ELIXIR-WES, snakemake, NextFlow)