Multi-omics Bioinformatician

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 better health for all?

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 bioinformatician with proven expertise in interpretation and integration of cancer omics data and in generating value in both research and in translational settings. The employment is a permanent position with a 6-month probation period). 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 looking for an outstanding multi-omics bioinformatician with strong analytical and programming skills working on cancer omics data. The candidate should develop, set up, maintain and update bioinformatics pipelines to integrate tumor data from different technologies (including genomics, transcriptomics and proteomics). Particular emphasis is placed on HPC-supported computing of sequencing data into assembled transcripts (de novo assembly is a frequent need), and further downstream translation of the ORFs of said transcripts into protein databases (FASTA) to be used in mining raw Mass Spectrometry Proteomics data. The aim is to generate novel knowledge about the tumor biology, discover tumor antigens, and associate the findings with emerging anti-cancer therapies, particularly towards targeted immunotherapies. The bioinformatician is also expected to develop tools to facilitate the translation of the work into new clinical initiatives.

Tasks for the position:

• Maintain, support, and update multiomics bioinformatics pipelines, with a particular focus on assembling sequencing data into transcripts and subsequently translating the ORFS in these transcripts into protein sequence databases.
• Guide the development of proteogenomics through implementation of novel algorithms and computational analysis infrastructure
• 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

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. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. Karolinska Institutet is also a state university, which entitles you to several good benefits through our collective agreement. And you get to practice freely in our modern wellness facilities, where trained staff are on site.

Location: Science for Life Laboratory, SciLifeLab in Solna

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Lehtiö Lab

Application

Welcome to apply at the latest 17^th August.

The application is to be submitted through the Varbi recruitment system.In this recruitment, you will apply with your CV without a personal letter. Instead, you will answer some questions about why you are applying for the job in the application form. 

Permanent position is initiated by a six months trial period.

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