Postdoctoral Researcher in Single-Cell Epigenetics

Karolinska Institutet; Solna kommun; On-site; SEK 446,000 - 625,000; Full time

Job summary

Karolinska Institutet seeks a postdoctoral researcher in Solna to study single-cell DNA methylation in pediatric cancers, especially acute myeloid leukemia. You will set up and advance scalable methylation methods, analyze large datasets, and develop new computational approaches with experimental collaborators to test hypotheses.

The role entails designing studies, interpreting results, and contributing to publications, with opportunities for cutting-edge AI-assisted analyses and

Qualifications

• PhD (or foreign degree equivalent) in a relevant field.
• Experience analyzing single-cell, epigenetic datasets.
• Strong programming skills in R and/or Python.
• Ability to handle large, complex biological datasets.
• Experience disseminating research at conferences.
• Good English communication for interdisciplinary work.

Responsibilities

• Set up and optimize single-cell methylation workflows.
• Process and analyze large sequencing datasets.
• Develop computational methods for cell-state characterization from DNA methylation.
• Identify biologically relevant mechanisms from methylation data.
• Collaborate with experimental biologists to form and test hypotheses.
• Integrate multimodal data and interpret results.
• Lead study design, methods, visualization, and manuscript preparation.

Skills

Single-cell analysis

R

Python

Data handling

Communication in English

Education

PhD or foreign degree equivalent to Swedish PhD

Tools

R

Python

Job description

Do you want to contribute to top quality medical research?

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.

• 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

Your profile

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

Additional merits:

• 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.

What do we offer?

A creative and inspiring environment with wide-ranging expertise and interests. Karolinska Institutet is one of the world's leading medical universities. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. At KI, you get to meet researchers working with a wide range of specialisms and methods, giving you ample opportunity to exchange knowledge and experience with the various scientific fields within medicine and health. It is the crossover collaborations, which have pushed KI to where it is today, at the forefront of global research. Several of the people you meet in healthcare are educated at KI. A close relationship with the health care providers is important for creating groundbreaking top quality education and research. Karolinska Institutet is also a state university, which entitles you to several benefits through our collective agreement.

KI applies individual and differentiated salary setting in accordance with our collective agreements RALS and RALS-T

This position is for 2 years with the possibility of extension.

Type of employment

Type of employment Temporary position

Contract type

Contract type Full time

First day of employment

First day of employment According to agreement

Salary Monthly salary

Number of positions

Number of positions 1

Full-time equivalent 100%

City

City Solna

County

Country

Country Sweden

Reference number

Contact

Union representative

• Robert Lindberg, Seko, [e-mail]