Postdoc in Microbiome Bioinformatics Workflows

Freelio; Odense; On-site; DKK 420,000 - 500,000; Full time

Job summary

University of Southern Denmark invites applications for a Postdoc (100% time) in the Arumugam Group, Department of Clinical Research, Faculty of Health Sciences. The role focuses on microbiome bioinformatics, developing scalable workflows to analyze multi-omics data across large projects, including AMR and Horizon 2020 initiatives.

The fellow will contribute to research, teaching, and professional development, with opportunities to lead new research directions and collaborate with international

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 analyzing next-generation sequencing datasets.
• 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.

Responsibilities

• Improve and expand workflows in the current MIntO pipeline and develop new workflows.
• Participate in and lead projects within the consortia and other projects.
• Interact and collaborate with clinical researchers, veterinarians, biologists, and bioinformaticians to ensure proper interpretation of results.

Skills

Python

R

Bioinformatics

Snakemake

Nextflow

CWL

NGS data analysis

Unix

HPC

Teamwork

English

Publications

Education

PhD in bioinformatics or biology

Tools

MIntO

Job description

Om stillingenA position as a postdoc (100% time) is vacant at the the Arumugam Group, Research unit of Medical Gastroenterology ,the Department of Clinical Research , Faculty of Health Sciences , University of Southern Denmark .

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).

• 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 analyzing next-generation sequencing datasets.
• 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

The joint research strategy for the Department of Clinical Research and Odense University Hospital sets the direction for our shared research efforts in the years ahead. Rooted in the vision – We conduct research together to shape the patient care of the future – it focuses in particular on: cross-disciplinary research – with people at the centre; strong research environments – as drivers of development; and the research journey – from idea to impact. Further information on the joint research strategy of the Department of Clinical Research and Odense University Hospital is available here.

Further information

Group Leader Mani Arumugam, Department of Clinical Research, e‑mail: [email] ,phone: + [telefon] or Head of Department at the Department of Clinical ResearchRikke Leth-Larsen, e‑mail: [email] , phone: [telefon]

Application deadline September 09, 2026, at 23.59 hrs. (CET/CEST).

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 at Campusvej 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.

Living and working in Denmark

Foreign applicants will be offered Danish language training as part of the employment.

The International 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.