Postdoctor in microbiome research with bioinformatics experience - Hiring in process/Finished, not possible to apply

Do you want to contribute to improving human health?

The institution for microbiology, tumor- and cell biology (MTC) at Karolinska Institutet performs research and teaching within immunology, infection biology, cellular biology, and cancer. The Center for Translational Microbiome Research (CTMR) was started in January 2016 as a collaboration between Karolinska Institutet, Science for Life Laboratory (SciLifeLab) and Ferring Pharmaceuticals. The center 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. CTMR 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 area of gastroenterology, reproductive health and neonatology.

Your mission

As a postdoc in microbiome research, you will focus on analysis work concerning the role of the microbiome in several different projects all focusing on studying the microbiome and its interaction with the human host. A central component of the role is to assume responsibility for bioinformatics analysis work in assigned studies, e.g. establish analysis plans combining microbiome data with additional metadata such as omics-data, questionnaires, etc. in order to perform the analysis work in collaboration with other colleagues at CTMR and external research partners with the ambition to generate scientific publications. The successful candidate will be working in close collaboration with several different teams within CTMR such as clinical epidemiology, bioinformatics, wet lab, as well as external collaborators outside of CTMR. The working language is English.

Your profile

Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent scientific competence. It is considered as an advantage if you have completed your doctoral degree within the last three years, if there are special reasons, your degree may have been completed earlier. 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) date of employment. This must be substantiated by the applicant's main supervisor, director or equivalent.

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

• Demonstrated ability to communicate both verbally and in text
• Demonstrated ability to author scientific articles
• Demonstrated ability to analyze microbiome data sets
• Experience working in interdisciplinary teams
• Experience with at least one commonly used programming language (Python or R)

Additional skills that are especially meritorious for the position:

• Experience of research concerning the human vaginal and/or gastrointestinal microbiome
• An understanding of the unique properties that microbiome data exhibits and which statistical challenges arise from this
• Experience working with metadata for microbiome studies according to available standards, ontologies, and formatting (e.g. MIxS)
• Experience analyzing both marker gene and metagenome data from DNA or RNA using scientifically established methods
• Experience with bacterial isolate assembly and annotation, using short read and/or long read sequencing
• Experience with metagenome assembly and binning
• Insight into epidemiological approaches and study design with a special focus on microbiome data
• Experience working on HPC-systems using bash and Slurm
• Experience working with version management systems (git/github)
• Experience working with containers for bioinformatics work (Docker, Singularity)
• Experience with techniques and frameworks for reproducible bioinformatics analyses, e.g. Snakemake or Nextflow

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. 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. 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. Karolinska Institutet is also a state university, which entitles you to several benefits through our collective agreement.

Location: Solna

Application

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

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.

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

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