Postdoctoral studies in Microbiome (scholarship)

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. MTC has about 40 research groups and our key words are multidisciplinary, bridging, national and international collaborations.

Both the main and co-supervisor laboratories maintain close collaborations with clinical doctors, epidemiologists, microbiologists, immunologists, and other groups studying the genetic aspects of the human microbiome. Associate Professor Du's laboratory focuses on clinical microbiome studies and microbe-host interactions, fostering a friendly and interactive environment for learning, discussion, and teamwork.

Team

Du's laboratory is part of the microbe-host division, which comprises professors and experts dedicated to studying microbes from the gut, vagina, and oral cavity, as well as their mechanisms of interaction with the host and the development of diseases.

Duties

The candidate is expected to play a major role in bioinformatics analysis, scientific hypothesis generation, presentation of results and manuscript preparation. The candidate will work on several projects regarding roles of microbiota in cancer development related HPV infection, cancer immune therapy and women’s health. The position involves bioinformatics workflow development, as well as computational and biostatistical analyses of large-scale shotgun DNA sequencing data. The successful candidate will also be working closely together with wet lab research engineers, to ensure high quality sample processing at all steps.

This bioinformatics research position concerns the following main tasks:

• Taking responsibility for the bioinformatics analysis effort of several microbiota related projects
• Taking responsibility for performing reproducible and robust bioinformatics analyses of samples
• Performing biostatistical analyses of microbiome profiles in relation to available sample metadata
• Being involved in the design and planning of wet lab processing

Entry requirements

Postdoctoral scholarships may be established for foreign researchers who pursue their merit in Sweden. A foreign researcher is a person living in another country who comes to Sweden with the intention of only staying in Sweden for all or part of their postdoctoral education at KI. Persons who are resident in Sweden and/or have carried out all or part of their academic education at KI or some other educational institution in Sweden cannot be considered for scholarships. The purpose of scholarships for postdoctoral qualification is to promote internationalization and contribute to research qualification after a doctorate or equivalent.

A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four-year period following the receipt of a doctoral degree or equivalent.

To be eligible for a postdoctoral scholarship, the person must have obtained a doctorate, or a foreign degree deemed to be equivalent to a doctorate. 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) start date of the post-doctoral education.

We are looking for an experienced postdoc-level candidate that completed his/her PhD within the last few years. You are a careful and detail-oriented person who likes to take responsibility. You enjoy working together in teams and are capable of close internal cooperation, as well as interacting with external collaborators that are experts in a wide variety of fields connected to our research. For this, excellent communication skills are required. You have a strong desire to deliver high quality work, on time, and have experience working independently. We expect great familiarity with bioinformatics work in a Linux environment.

In addition to the aforementioned requirements for the position:

• Experience in working with bioinformatics tools for large-scale metagenomic (DNA) analysis
• Experience producing feature count tables from raw unprocessed shotgun sequencing data using a variety of techniques
• High familiarity with at least one scripting language, e.g. Python
• Experience with statistical analysis of shotgun metagenomics data in R, Python, or similar
• Experience in utilizing natural language models for host prediction of bacteriophages and their specific proteins
• Experience in virome analysis using metagenomic data. Experience in transcriptomic and proteomic analysis
• Excellent oral and written communication skills
• Fluency in English

Meritorious for the position:

• Experience of microbiome bioinformatics research
• Experience of molecular biology lab work, including troubleshooting
• A medical or biomedical background
• Experience working with case/control or population-based studies (not necessarily human)
• Experience with conda dependency and environment management
• Experience with workflow management systems such as Snakemake and/or Nextflow, as well as working on HPC cluster systems
• Experience with container tools such as Docker or Singularity

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 innovative medical research and provide the largest range of biomedical 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. Students and employees have free access to our modern gym facilities with trained staff on site.

Location: Solna

Type of scholarship

The amount is tax free and it is set for twelve months at a time, paid out on a six months basis. In exceptional cases, shorter periods may be acceptable.

Application process

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

• A complete curriculum vitae, 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 on the Varbi recruitment system.

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