Postdoctoral Researcher in bioinformatics, cancer immunology and spatial transcriptomics

Do you want to contribute to top quality medical research?

Come join the Engblom lab! We are seeking a skilled bioinformatician or computational biologist for projects in the intersection of immunology, cancer, and spatial transcriptomics, with the goal to understand tumor-associated immune responses and harness these for therapy. The successful candidate would be employed by KI and affiliated with SciLifeLab, world leaders in spatial biology. The Engblom lab recently developed a new method to study B cells and B cell receptors within their tissue microenvironment using spatial transcriptomics. The Engblom lab is committed to cutting-edge research in spatially resolving immune responses during tumor progression and anti-cancer therapy.

Your mission

The applicant is expected to run and develop analysis pipelines to analyze high dimensional spatial and single-cell data of cancer and immune tissue from patients and pre-clinical studies and should have a strong background in both computational and statistical methods, with demonstrated experience in reproducible and scalable bioinformatics environments. The applicant will work in close collaboration with other Engblom lab team members who will generate the data in-house. The applicant is expected to be highly engaged, curious, and a team player. The candidate is expected to present results to general and specialized audiences, with a biological basis, through technological processes and mathematical support.

Your profile

We are looking for a candidate with proficiency and documented research experience particularly in immunology and/or bioinformatics, with a particular emphasis on performing analysis of high-dimensional data, which can be sequencing and/or imaging-based. Experience working with AI and machine learning approaches are considered a strong merit. We are seeking a post-doc candidate who is passionate about answering biological questions related to cancer immunology using cutting edge technology in close collaboration with experimental scientists. The Engblom lab works as a team and is dedicated to fostering the next generation of scientists, so we welcome candidates who are interested to teach and mentor budding scientists.

Requirements

• PhD degree in relevant fields (bioinformatics, immunology, computational biology, mathematics, and/or statistics).
• Strong programming skills in R and/or Python
• Demonstrated strong ability in analyzing high-dimensional data.
• Familiarity with Linux/Unix environments and shell scripting
• Demonstrated ability to present and analyze results orally and in writing
• Documented scientific publications in relevant fields
• Fluency in oral and written English

It is meritorious that the applicant has

• Prior involvement in interdisciplinary projects combining computational and biological sciences.
• Familiarity with data management tools, version control (Git), and collaborative coding (strong merit)
• Strong understanding of statistics and machine learning for high-dimensional data (strong merit)
• Experience with workflow management systems (e.g., Snakemake, Nextflow, or equivalent)
• Prior experience with interactive data visualization frameworks
• Experience analyzing spatial transcriptomics data (e.g. 10x Visium, image-based)
• Experience working with IgBLAST or similar immunogenomics tools
• Expertise in B and/or T cell receptor data analysis
• Documented experience in teaching and scientific communication
• Understanding of data security principles and compliance with data protection regulations (e.g. GDPR)
• Proficiency in containerization tools (e.g., Docker, Singularity)
• Experience developing reusable libraries or packages in R or Python.

The position will require independent work as well as extensive collaboration with other scientists. The research requires highly interdisciplinary work involving teams of contributors; therefore, team players that are motivated to help each other are highly encouraged to apply. Please describe in your summary of current work what type of analysis and tools you would like to develop in the lab, based on your previous experience and the lab’s profile.

To be eligible for employment as a postdoctor, 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.

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

The position is located within the Department of Medicine, Solna. The department consists of ten divisions and each division consists of several research groups. The position is located within division of Allergy and Respiratory within the lab of Dr. Camilla Engblom (SciLifeLab Fellow), hosted by Dr. Eduardo Villablanca which is physically located at CMM and SciLifeLab. The overall goal for the lab is to understand fundamental mechanisms of B cell-related immune responses in cancer (and beyond) to identify new avenues for B-cell mediated therapy. To do this, we interrogate the spatial relationships between B cell clones and their immediate niches within tissues using our in-house developed spatial transcriptomics-based technology (Spatial VDJ). Using established and newly developed algorithms, we map B cell evolution within tissues, including class switching and somatic hypermutation, and identify putative candidate tumor-regulatory antibody sequences for functional testing. In addition to the lab’s focus area, our research group has national and international collaborative projects within host-microbe interactions, vaccine research, technological development, and mucosal immunology. The lab is strongly affiliated to SciLifeLab, the birthplace for and continued world leaders in spatial transcriptomics research, which offers a unique scientific niche to spatially reconstruct B cell lineage evolution in tissues. We work closely with multiple SciLifeLab infrastructure and facilities to answer our scientific questions, resulting in a multidisciplinary research environment. Our lab aims to foster a creative, diverse, and inclusive work environment with the goal for all lab members to answer ambitious and exciting scientific questions. The lab is located at within a vibrant immunology community with expertise in inflammation, infection, allergy and autoimmune diseases.

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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)

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

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

1. Camilla Engblom, [email protected]

1. Louisa Cheung, SACO, [email protected]
2. Farzad Hedayaty, SACO-s, [email protected]
3. Maria Eldh, ST-OFR, [email protected]