Postdoctoral Researcher in Bioinformatics Karolinska Institute Center for Translational Microbiome Research

Postdoctoral Researcher in Bioinformatics 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: 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) Interviews will be held continously during the application period. The application is to be submitted through the Varbi recruitment system. Karolinska Institutet is one of the world’s leading medical universities. Its vision is to significantly contribute to the improvement of human health. Karolinska Institutet accounts for the single largest share of all academic medical research conducted in Sweden and offers the country’s broadest range of education in medicine and health sciences. The Nobel Assembly at Karolinska Institutet selects the Nobel laureates in Physiology or Medicine. Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published. Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone. For temp agencies and recruiters, and to salespersons: We politely, yet firmly, decline direct contact with temp agencies and recruiters, as well as those selling additional job announcements. Type of employment Temporary position longer than 6 months Contract type Full time First day of employment enl. ök Salary månadslön 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 If you apply for this position please say you saw it on Medicinoxy Apply

Postdoctoral Researcher in Bioinformatics

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:

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)

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

Karolinska Institutet is one of the world’s leading medical universities. Its vision is to significantly contribute to the improvement of human health. Karolinska Institutet accounts for the single largest share of all academic medical research conducted in Sweden and offers the country’s broadest range of education in medicine and health sciences. The Nobel Assembly at Karolinska Institutet selects the Nobel laureates in Physiology or Medicine.

Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published.

Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone.

For temp agencies and recruiters, and to salespersons: We politely, yet firmly, decline direct contact with temp agencies and recruiters, as well as those selling additional job announcements.

Type of employment Temporary position longer than 6 months

Contract type Full time

First day of employment enl. ök

Salary månadslön

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