Research Specialist in Human Microbiome Research with Bioinformatics competence Full-time NEW

Research Specialist in Human Microbiome Research with Bioinformatics Competence

Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology

Do you want to contribute to improving human health?

The Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet conducts research and teaching within immunology, infection biology, cell biology and cancer. Our key words are multidisciplinary, bridging, national and international collaborations.

Description of the Subject Area

The multidisciplinary team of Cultureomics builds on a deep understanding of translational microbiome research and has established a broad technical, biological, clinical and epidemiological platform for studying complex microbiological communities in well-defined human materials. The group aims to better understand the contribution of the human microbiome to physiology and pathophysiology with the goal to open opportunities for development of novel therapies in the field of women's health, reproductive health and neonatology.

Your Mission

As a Research Specialist in microbiome bioinformatics and computational analysis, you will lead the design and execution of advanced analytical strategies for complex, heterogeneous datasets across multiple projects investigating the role of the microbiome in human health and disease. A central component of the role is to assume substantial responsibility for assigned studies, including the development of analysis plans that integrate metagenomics data with complex and heterogeneous metadata such as clinical variables, questionnaires, and registry data.

The role requires working with real-world datasets that may be incomplete, noisy, and longitudinal in nature, and therefore demands critical evaluation of data quality, appropriate preprocessing, and careful consideration of confounding and bias.

Analysis work will be performed in close collaboration with colleagues at Karolinska and external research partners, with the goal of generating high-quality scientific publications. The successful candidate is expected to contribute to analytical strategy, interpretation of results, and scientific writing.

The position involves close collaboration with multiple teams, including clinical epidemiology, bioinformatics, and wet lab groups, as well as external clinical collaborators. The working language is English.

Eligibility Requirements

For employment as Research Specialist at Karolinska Institutet, the eligibility requirements stated in the Guidelines for non-teaching positions at Karolinska Institutet are applied in relation to the established profile of employment.

To be eligible for employment as a Research Specialist, in addition to holding a Degree of Doctor, PhD, or having a foreign degree deemed equivalent to a Swedish doctoral degree, the applicant must have demonstrated research expertise as well as have documented postdoctoral research experience.

In addition to the aforementioned requirements for the position, the application must have:

• Demonstrated ability to independently design, implement, and interpret analyses of complex biological datasets
• Demonstrated ability to communicate scientific results effectively both verbally and in writing
• Demonstrated ability to author scientific articles, including leading or contributing substantially to manuscripts
• Demonstrated experience analyzing human microbiome datasets
• Experience working in interdisciplinary teams involving computational, laboratory and clinical collaborators
• Experience with at least one commonly used programming language (Python or R), with emphasis on reproducible and maintainable code
• Experience working with large-scale, longitudinal cohort data and registry-linked datasets
• Experience handling complex, heterogeneous, and partially incomplete datasets, including data integration across multiple sources.
• Strong understanding of statistical and computational challenges specific to microbiome data (e.g. compositionality, sparsity, batch effects)
• Experience analyzing both marker gene and shotgun metagenomic data, including taxonomic and functional profiling
• Experience integrating microbiome data with clinical, epidemiological, and registry data in a hypothesis-driven or data-driven framework
• Experience applying machine learning methods to biological or clinical datasets, including appropriate validation strategies and awareness of potential data leakage
• Insight into epidemiological study design, confounding, and bias in observational data
• Experience working on HPC systems using bash and job scheduling systems (e.g. SLURM)
• Ability to critically evaluate analytical approaches and adapt methods to evolving data structures and research questions

Meritorious for the position:

• Previous experience working as a postdoctoral researcher or in a role requiring equivalent analytical independence
• Experience working with version control systems (git/GitHub)
• Experience working with containerization tools (Docker, Singularity)
• Experience developing reproducible analysis workflows (e.g. Snakemake, Nextflow)

Assessment Criteria

After an overall assessment of the expertise and merits of the applicants in relation to the subject area, Karolinska Institutet will determine which of them has the best potential to contribute to a positive development of the activities at KI.

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. Here, 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.

Choose to work at KI – Ten reasons why Location : Solna

Application

We prefer that Your application is written in English, but You can also apply in Swedish. An application must contain the following documents: PhD certificate, resumé, qualifications and description of planned research, presented in accordance with Karolinska Institutet's qualifications portfolio.

The application must be submitted through the Varbi recruitment system.

Permanent position is initiated by a six months trial period.