Postdoctoral Researcher in Single-Cell Epigenetics – Karolinska Institutet, Solna

Job Description

The Lambo research team at the department of Oncology-Pathology (OnkPat) is an exciting new research group that studies the epigenetic mechanisms by which tumors adapt to treatment. We use cutting edge experimental and computational methods to study epigenetics, in particular methods that utilize single cell sequencing technologies, which includes new technologies to generate single cell DNA methylation at scale. We are an interdisciplinary group that combines experimental perturbations, computational analysis and AI modelling with the goal to bridge the gap between basic tumor biology and clinical implementation. As a postdoctoral researcher at our team, you have the exciting opportunity to explore a largely uncharted field of research, to pursue your own ideas and to make the next step in your career.

A creative and inspiring environment with wide-ranging expertise and interests
The Department of Oncology-Pathology is a department where preclinical and clinical cancer research are tightly interconnected. More than 35 research groups form a dynamic and strong research environment with a common goal to improve diagnostics, treatments, and quality of life for patients with cancer. Our facilities are located at Bioclinicum within the Karolinska University Hospital while part of the department is located within the Science for Life Laboratory. This provides access to advanced technologies including genomics, proteomics, metabolomics, spatial biology, cellular and molecular imaging, and bioinformatics. Our close connection with The Swedish Childhood Tumor Biobank, The Theranostic Trial Center, and The Karolinska Comprehensive Cancer Center, enable pre-clinical and clinical scientists to engage in collaborative projects for early clinical testing of precision therapies, to enhance cancer diagnostics, to facilitate early detection and to develop innovative clinical trials in cancer patients.

Your mission
The position involves generating, processing and analyzing single cell methylation data for pediatric cancers, in particular pediatric acute myeloid leukemia. The postdoc will be involved in setting up a recently developed method for generating single cell DNA methylation at scale and use the resulting data to study pediatric tumor evolution. Because of the novelty of the data type there are opportunities to develop and publish new computational approaches to work with this data and study tumor biology.

Key Responsibilities

• Facilitate setting up single cell methylation at scale
• Processing and maintaining large sequencing datasets
• Developing new computational approaches for characterizing cell states and shifts in cell states based on DNA methylation
• Developing new computational approaches for identifying biologically relevant mechanisms
• Working together as a team with experimental biologists to guide the generation hypotheses, place biological findings in context and to validate findings
• Performing multimodal integration using other data modalities
• Data interpretation and generating new testable hypotheses
• Be responsible for study design, computational methods, writing, data visualization, manuscript preparation, presenting and managing of data involved in publications

Qualifications

• To be eligible for employment as a postdoctoral researcher, a PhD or a foreign degree deemed to be equivalent to a Swedish PhD is required. This eligibility requirement must be fulfilled at the latest at the time of the employment decision. Completion of your doctoral degree within the last three years is considered an advantage. If there are special reasons, your degree may have been completed earlier.
• Qualifications and experience:
• Documented experience in analyzing single-cell, single-nucleus and/or epigenetic datasets
• Strong programming skills in R and/or Python
• Experience handling large and complex biological datasets
• Experience with key analytical tasks including alignment, quality control, data integration, and biological interpretation
• The ability to develop and troubleshoot computational approaches, ensure reproducibility and critically interpret results
• Documented experience of being able to successfully disseminate research i.e. through national/ international conferences
• Good communication skills in English and the ability to work in an interdisciplinary environment

Skills Required

• Experience in generating single cell sequencing libraries
• Experience working in the wet lab
• Experience working with pediatric cancer data
• Documented experience in working with/studying DNA methylation
• Knowledge/experience in epigenetic regulation of developmental biology
• Documented experience in generating computational workflows i.e. published packages or bioinformatic tools
• Applicants having a multidisciplinary background (both wet lab and computational experience) are prioritized for this position. Having experience with pediatric cancer and DNA methylation is preferred but not required.

Additional Information

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