Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology

Division/ Department
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. CTMR aims to better understand the contribution of the human microbiome to physiology and pathophysiology with the goal of opening opportunities for the development of novel therapies in the area of gastroenterology, reproductive health and neonatology. The center is also part of the Horizon 2020 initiative on microbiological research, where the ONCOBIOME project gathers 17 partners from 10 countries to do research on four different types of cancer: gastrointestinal, breast, prostate, and melanoma. The focus of CTMR in the ONCOBIOME project is processing microbiome samples from a large screening program for colorectal cancer (30k individuals).

Duties
We are looking for an experienced postdoc-level researcher to join the CTMR team as a full-time bioinformatician. The applicant will take on a leading role in CTMR’s responsibilities in the large-scale ONCOBIOME project, which studies the connection between different types of cancer and the human microbiome. The position involves bioinformatics workflow development, as well as computational and biostatistical analyses of large-scale shotgun DNA sequencing data. The tasks include analysis and integration of human microbiome data with clinical metadata to identify biomarkers in clinical patient material. The bioinformatician will be heavily involved in design and implementation of the infrastructure configuration for establishing an efficient and sustainable sequencing workflow.The development work includes automating the majority of the sequence data analysis workflow. The successful applicant will also be working closely together with wet lab research engineers, to ensure high quality sample processing at all steps: DNA extraction, sequencing library preparation, sequencing, and finally data analysis.

This bioinformatics research position concerns the following main tasks:

  • Taking responsibility for the bioinformatics analysis effort of the microbiome samples of the ONCOBIOME project
  • Taking responsibility for implementing the bioinformatics analysis workflow of these samples, automating sequencing data processing and setting up reliable and robust downstream bioinformatic analyses.
  • Producing sample profiles (e.g. taxonomic, functional) by combining data across multiple sequencing runs (including performing routine quality control of sequencing data).
  • Performing biostatistical analyses of microbiome profiles in relation to cancer types and available sample metadata.
  • Being involved in the design and planning of wet lab processing

Qualifications / Requirements
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 is not afraid of 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. 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, applicants must have:

  • 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
  • Excellent oral and written communication skills
  • Fluency in English

Furthermore, it is beneficial if the applicant has:

  • 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 workflow management systems such as Snakemake and/or Nextflow, as well as working on HPC cluster systems
  • Experience of microbiome and/or cancer research

We place great emphasis on personal suitability.

Entry requirements
Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent scientific competence.

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

  1. 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
  2. A complete list of publications
  3. A summary of current work (no more than one page)

Interviews will be held continously during the application period. The application is to be submitted through the Varbi recruitment system.

Type of employment Visstidsanställning längre än 6 månader
Contract type Full time
Number of positions 1
Working hours 100%
City Solna
County Stockholms län
Country Sweden
Reference number 2-2138/2019
Contact
  • Fredrik Boulund, PhD, fredrik.boulund@ki.se
Union representative
  • Niklas Andersson, OFR, niklas.andersson@ki.se
  • Henry Wölling, SEKO, 08-524 840 80
  • Biborka Bereczky Veress, SACO, 46 70-173 85 75
Published 04.Apr.2019
Last application date 04.May.2019 11:59 PM CET

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