Postdoc position in single-cell cancer omics bioinformatics

Do you want to contribute to improving human health?

A postdoc position in single-cell cancer omics bioinformatics is immediately available in the Foukakis Lab at Karolinska University Hospital, employed by Karolinska Institutet. Jointly with the Bienko-Crosetto Lab at Science for Life Laboratory.

The Foukakis Lab at Oncology/Pathology department, Karolinska Institutet focuses on clinical and translational studies on breast cancer. The aim is to better understand and predict an individual patient's unique drug sensitivity, improve breast cancer survival, and avoid treatment-related toxicity. Tumor tissue and liquid biopsies are available from patients enrolled in multiple academic prospective randomized trials, as well as from retrospective patient cohorts. A translational research platform has been set up using a multitude of pathology and genomic methods in a concerted effort to identify prognostic and predictive biomarkers. The group has a significant national and international presence and collaborations.

The Bienko-Crosetto Lab develops and leverages cutting-edge genomic technologies to study the interplay between 3D genome architecture and genome stability, with a strong focus on understanding how somatic copy number alterations and structural variants form and evolve in cancer cells and how they contribute to tumor progression.

As a single-cell cancer omics bioinformatician, you will lead the analysis and interpretation of scDNA-seq and single-cell multi-omic data that we are generating from patient samples collected in the frame of large multi-center clinical trials and develop/apply advanced computational approaches to model how tumors evolve under the continuous selective pressure of anti-cancer therapies.

You will work at the crossroad between the clinic and the research lab where sequencing data are being generated, embedded in a culturally diverse and dynamic research environment where you will work alongside clinicians and scientists from different fields and backgrounds.

Your mission

Your main tasks will be:

• Processing single-cell whole genome and whole exome sequencing data to generate copy number alteration (CNA) profiles of single tumor cells and detect single nucleotide variants (SNV)
• Applying phylogenetic analysis to reconstruct tumor evolution utilizing data generated by time-course single-cell DNA sequencing
• Analyzing scATAC/RNA-seq and spatial transcriptomics data generated by single-cell sequencing of tumor biopsies
• Integrating single-cell and spatial omics datasets with clinical information to improve patient stratification and better predict therapy outcomes.

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:

• A PhD in Computational biology/Genomics/Bioinformatics or equivalent.
• A proven experience in analyzing next-generation sequencing data, preferably WGS/WES data from tumor samples
• Prior work in the field of tumor evolution and/or analysis of single-cell sequencing data from tumor samples is a strong advantage.
• A keen interest in tumor biology and application of genomic technologies to improve the diagnosis, classification and management of cancer patients.
• At least two publications in which the Applicant played a leading or major role in the analysis of sequencing data.
• Ability to independently organize your own work routine and flexibly adapt your weekly schedule to emerging requests.
• A problem-solving and forward-looking personality, i.e., you are motivated to solve obstacles that might present on the path to achieving a goal, you enjoy troubleshooting, you are not afraid of seeking for help, and you are able to find solutions even if this means revising the original goal/plan (never compromising scientific rigor and quality).
• A strong collaborative attitude, i.e., you are a strong team player and want to contribute to the success of the whole team.
• Fluency in oral and written English. 

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.

Location: Solna, SciLifeLab.

Choose to work at KI – Ten reasons why

Application

An employment application must contain the following documents in English or Swedish:

• PhD certificate
• A complete resumé, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
• A complete list of publications
• A summary of current work (no more than one page)

Welcome to apply at the latest 3^th February. 

The application is to be submitted through the Varbi recruitment system.

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

Want to make a difference? Join us and contribute to better health for all!