Postdoc in single-cell cancer omics bioinformatics (Scholarship) - Hiring in process/Finished, not possible to apply

Do you want to contribute to improving human health?

A postdoc fellowship in single-cell cancer omics bioinformatics is immediately available in the Foukakis Lab at Karolinska University Hospital (https://staff.ki.se/orgid/5207635) jointly with the Bienko-Crosetto Lab at Science for Life Laboratory (www.bienkocrosettolabs.org).

Division

The Foukakis Lab at Oncology/Pathology department 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.

Duties

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 attend 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 attend alongside clinicians and scientists from different fields and backgrounds.

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.

Entry requirements

Scholarships for postdoctoral qualification can be established for foreign researchers who place their qualifications in Sweden. The purpose of scholarships for postdoctoral qualification is to promote internationalization and contribute to research qualification after a doctorate or equivalent.
A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four year period following the receipt of a doctoral degree or equivalent.
To be eligible for a postdoctoral scholarship, the person must have obtained a doctorate or a foreign degree deemed to be equivalent to a doctorate. Applicants who have not completed a doctorate at the end of the application period may also apply, provided that all requirements for a completed degree are met before the (intended) start date of the post doctoral education.

The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish doctorate or higher.

Your profile

You have:

• 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.

Location: Solna, SciLifeLab

Type of scholarship

The amount is tax free and it is set for twelve months at a time, paid out on a six months basis.
In exceptional cases, shorter periods may be acceptable.

Application process

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

• A complete curriculum vitae, 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)

The application is to be submitted on the Varbi recruitment system. At the latest 3 November.

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