Postdoc in Microbiome Bioinformatics Workflows

Syddansk Universitet; Odense; On-site; DKK 480,000 - 560,000; Full time

Job summary

Syddansk Universitet in Odense invites applications for a 3-year Postdoc in Microbiome Bioinformatics Workflows. You will develop scalable computational workflows for large-scale multi-omics microbiome data and contribute to AMR-related consortia and EU projects.

The role requires a PhD and strong programming skills in Python/R, plus experience with Snakemake/Nextflow and UNIX. Collaboration with international partners is encouraged.

Qualifications

• PhD in bioinformatics or biology with strong experience in software development.
• Academic preparation as well as experience in biological statistics.
• Strong programming skills in Python and/or R.
• Experience with bioinformatics workflow environments such as snakemake, NextFlow or CWL.
• Experience in a high-performance computing environment using UNIX.
• Demonstrated capacity for effective teamwork.
• Proven track record showing scientific productivity in peer-reviewed journals.
• Excellent English communication skills, both written and oral.

Responsibilities

• Improve and expand workflows in the current MIntO pipeline and develop new workflows.
• Participate in and lead existing projects within the consortia and initiate new research projects.
• Interact with clinicians, veterinarians, biologists, and bioinformaticians to ensure proper interpretation of results.

Skills

Bioinformatics

Biology

Software development

Python

R

Snakemake

Nextflow

CWL

UNIX

Teamwork

Publications

English

Education

PhD in bioinformatics or biology

Tools

Snakemake

Nextflow

CWL

UNIX

Job description

Postdoc in Microbiome Bioinformatics Workflows

The position is limited to 3 years with the possibility of extension.

Research tasks

The position as a postdoc consists of research, teaching, professional development, and guidance in Microbiome Bioinformatics Workflows

We seek a bioinformatician to develop computational workflows to analyze large-scale microbiome multi-omics data in multiple projects studying human and animal health, including the consortium project PIG-PARADIGM to combat antimicrobial resistance (AMR) in pig production (http://pig-paradigm.net ) and EU Horizon 2020 project MICROB-PREDICT (https://microb-predict.eu/ ). We strive to implement efficient and scalable workflows to analyze and integrate these data derived from metagenomics, metatranscriptomics, viral metagenomics, metabolomics, and metaproteomics in collaboration with international data science partners (e.g., EMBL-Heidelberg; University of California, Davis) and other project partners. We have developed the MIntO package (https://github.com/arumugamlab/MIntO ) that integrates microbiome metagenomic and metatranscriptomic data. Our ambition is to develop new workflows that expand MIntO’s features (e.g., novel analysis types) as well as datatypes (e.g., metabolomic data).

In this position, you will be:

Responsible for improving and expanding workflows in our current MIntO pipeline, while also having a chance to create your own novel workflows.

Expected to participate in and lead existing projects within these consortia and other projects in the Arumugam group; and are highly encouraged to initiate new cutting-edge research projects.

Expected to interact and collaborate with other clinical researchers, veterinarians, biologists, and bioinformaticians in these consortia, to enhance and ensure proper interpretation of experimental results.

Expectations of qualifications

The applicant who is hired must have a Ph.D. degree and documented research experience in one or more of the areas/fields mentioned below:

• Bioinformatics
• Biology

The Postdoc fellowship is aimed at early-career researchers with a background in basic science. We are particularly interested in candidates with solid experience in analyzing large volumes of next-generation sequencing data, who are aware of challenges in scalability and efficiency

Required qualifications:

• PhD in bioinformatics or biology with strong experience in software development.
• Academic preparation as well as experience in biological statistics.
• Strong programming skills in Python and/or R.
• Experience with bioinformatics workflow environments such as snakemake, NextFlow or CWL.
• Experience in a high-performance computing environment using any flavor of UNIX.
• Demonstrated capacity for effective teamwork.
• Proven track record showing scientific productivity in peer-reviewed journals.
• Excellent English communication skills, both written and oral.

The following qualifications are highly preferred, but not required. Candidates who possess any of these qualifications are encouraged to highlight them in the application:

• Basic understanding of disease biology and/or microbiology.
• Experience in analyzing metagenomic datasets from host-associated microbiota.
• Experience in handling multi-omics data, including metabolomics and proteomics.
• Experience in distributed and cloud computing technologies.
• Experience in supervising other researchers at different levels.
• International mobility

Research strategy for OUH and the Department of Clinical Research

For further information, please contactGroup Leader Mani Arumugam, Department of Clinical Research, e-mail:[e-mail] ,phone: [phone]or Head of Department at the Department of Clinical ResearchRikke Leth-Larsen, e-mail:[e-mail] , phone: [phone]

Salary and terms of employment

The applicant will be employed in accordance withthe agreement between the Ministry of Finance and AC (the Danish Confederation of Professional Associations).

The position asPostdocis placed within salary steps 4–8 of the Danish state salary scale, depending on seniority.In addition, a centrally agreed postdoc allowance is paid, and further qualification- and function-related allowances may be negotiated.

The work location will be atCampusvej 55, 5230 Odense M.

Assessment

Shortlisting will be used as part of the initial selection process.

Assessment of shortlisted applications will be done under the existing Appointment Order for universities. Shortlisted applications will be assessed by an assessment committee. The committee may request additional information, and, if so, it is the responsibility of the applicant to provide the necessary material.

When the assessment committee has submitted its report, the applicants will receive part of the evaluation that concerns themselves.

References will be obtained for the preferred candidate from their current and previous employers. Applicants invited for interview should expect to complete a work-related personality assessment.

TheInternational Staff Office (ISO) at SDU provides a variety of services for new employees, guests and people who consider applying for a job at the University of Southern Denmark.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.