Postdoc - Multi-omics Bioinformatics

Karolinska Institutet, Department of Oncology-Pathology, Lehtiö research group

At the Department of Oncology-Pathology basic, translational and clinical research and educational activities related to cancer are carried out. Approximately 300 people from over 40 nations are currently working at the department. About 30 research groups with various cancer research profiles are involved and we have around 110 PhD students. The Department of Oncology-Pathology is responsible for undergraduate courses in Pathology, Oncology and Forensic Medicine for medical students, as well as for Tumor biology courses for biomedicine students and Pathology courses for opticians.

Do you want to contribute to improving human health?

The position will be placed in the Cancer proteomics Mass spectrometry research group headed by Professor Janne Lehtiö at Science for Life Laboratory (SciLifeLab). Karolinska Institutet is one of the four founding universities for SciLifeLab which is today national infrastructure and research center in technology driven life sciences. Lehtiö group is a translational group of scientists with a drive to improve human proteome analysis by developing new methods that can be applied to improve personalized cancer treatment. At present we seek to strengthen our research group with an outstanding scientist with proven expertise in interpretation and integration of cancer omics data and in generating value in both research and in translational settings. This is a postdoctoral position for 2 years (extendable up to a maximum of 4 years). We offer a very stimulating and diverse work in a team of very motivated co-workers with expertise in cutting-edge technology.

Your mission

We are seeking a highly motivated bioinformatician with a strong background in multi-omics data analysis to join our research team focused on cancer biology. This role offers the opportunity to contribute to cutting-edge investigations into tumor genomics, transcriptomics, and proteomics, with the goal of uncovering novel biological insights and informing the development of next-generation cancer therapies.

The successful candidate will lead the development and maintenance of robust computational pipelines for the integration of high-throughput sequencing data, including de novo transcriptome assembly and open reading frame (ORF) prediction. A key aspect of the work involves translating transcriptomic data into custom protein databases to support mass spectrometry-based proteomics, enabling the discovery of tumor-specific antigens.

This position is ideal for a scientist who thrives in a collaborative, interdisciplinary environment and is passionate about applying computational approaches to complex biological questions. The role also includes the development of tools and resources to support the clinical translation of research findings, particularly in the context of targeted immunotherapies.

Tasks for the position:

• Guide the development of proteogenomics through implementation of novel algorithms and computational analysis infrastructureDesign, maintain, and refine multi-omics bioinformatics pipelines, with a focus on transcriptome reconstruction from sequencing data and the subsequent translation of predicted open reading frames (ORFs) into custom protein sequence databases.
• Downstream from the previous point, design, maintain and refine the proteomic analyses pipelines that facilitate the discovery of novel tumor-associated proteins.
• With the previous two points, the key objective is to enable the exploration of the dark proteome—uncharacterized or non-canonical protein products that may hold untapped potential for understanding tumor biology and identifying novel therapeutic targets.
• Development of tools to support clinical initiatives in applications of genomics and proteomics
• Integrate sequencing data from external and public resources to improve clinical research outcome
• Supervise postdocs, graduate students and technical personnel in bioinformatics and proteogenomics analysis
• Apply for external funding - both national and international
• Actively participate in academic, industry and health care collaborations involving omics -based methods to improve cancer therapy

Your 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.

Qualifications

• PhD in bioinformatics, computer science, biology, medicine, or mathematical statistics.
• Experience in cancer research and analyses of large-scale multi-omics cancer data.
• Proven experience in development of bioinformatics tools and software packages.
• In-depth knowledge in NGS data processing from whole genome sequencing and RNA-seq, knowledge in single cell RNA-seq and spatial transcriptomics is a plus.
• Knowledge in Mass-spec proteomics and proteogenomics data analysis and interpretation.
• Acquaintance with immunotherapy concepts and neoantigen targeting.
• Substantial experience working in bash scripting and HPC Linux/Unix environment.
• Proficiency in programming (preferably Python, SQL, groovy, R, html, JavaScript, and bash).
• Good knowledge of cancer biology and translational cancer research.
• Experience of collaboration between different disciplines and providing bioinformatics support.
• Experience of implementational research.
• A proven academic track record, including high-impact and highly cited publications.
• Good knowledge in English, oral and written.

Additional merits

• Expertise in web programming and web application development.
• Expertise in managing large amounts of data by designing structured databases (PostgreSQL, MySQL).
• Machine learning methods such deep learning for analysis of proteomics data and classification of cancer profiles.

Since the position involves close interaction with several researchers, emphasis is placed on personal skills such as:

• Very good collaborative skills
• Excellent communication skills and analytical skills.

Bases of assessment

In assessing the candidates, suitability for the position, experience in the above-specified methods, and experience in the field, will form the basis for the selection of this recruitment.

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: Science for Life Laboratory, SciLifeLab in Solna

Choose to work at KI – Ten reasons why
Lehtiö Lab

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 17^th August.

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!