Postdoc in Microbiome Bioinformatics Workflows
Novo Nordisk Foundation Center for Basic Metabolic Research
Faculty of Health and Medical Sciences
University of Copenhagen
The University of Copenhagen is seeking a highly motivated and talented Postdoc fellow to commence on October 1, 2023, in the Arumugam Group at the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), University of Copenhagen.
The Novo Nordisk Foundation Center for Basic Metabolic Research’s vision is to strengthen interdisciplinary research that transforms our basic understanding of the mechanisms that underlie cardiometabolic health and disease, and to accelerate this knowledge toward new prevention and treatment strategies. We were established in 2010, and in 2017, we moved into new laboratories and offices in the Maersk Tower.
The Center has around 260 employees who work in an international, highly collaborative research environment across a range of biomedical disciplines. For more information, visit www.cbmr.ku.dk.
The Arumugam Group uses data science to investigate how health and diseases are influenced by our gut microbiome; how the gut microbiome interacts with the host and environmental factors, and how we can therapeutically modulate the gut microbiome to improve health. You can read more about the Arumugam Group here.
In the Arumugam Group, we strive for an inclusive and social work environment where support and constructive feedback is offered within the group. We are an interdisciplinary and multicultural team consisting of wet lab scientists and data analysts who work together towards a common goal. We have a large network of international collaborators, especially via international consortium projects.
We seek a bioinformatician to develop computational workflows to analyse largescale microbiome multi-omics data in multiple consortium projects studying human and animal health, including GALAXY/MicrobLiver studying liver fibrosis (https://www.sdu.dk/en/forskning/galaxy), MICROB-PREDICT studying late-stage liver cirrhosis (https://microb-predict.eu/) and PIG-PARADIGM to combat antimicrobial resistance (AMR) in pig production (http://pig-paradigm.net). 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 recently published the MIntO package (https://github.com/arumugamlab/MIntO) that integrates bacterial 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.
The Postdoc fellowship is aimed at early-career researchers with a basic science background. We are particularly interested in candidates with solid experience in analysing large volumes of next generation sequencing data, who are aware of challenges in scalability and efficiency.
- PhD in bioinformatics; or in 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 or CWL.
- Experience in analysing next generation sequencing datasets.
- Experience in high performance computing environment using any flavour 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 human disease biology and/or microbiology.
- Experience in analysing 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.
The Postdoc fellowships are open for applicants that hold a PhD degree obtained before October 1, 2023.
Terms of employment
The employment as Postdoc is a full-time position for 3 years. Starting date is October 1, 2023.
Salary, pension, and terms of employment will be in accordance with the agreement between the Danish Ministry of Finance and AC (Danish Confederation of Professional Associations). Depending on qualifications, a supplement may be negotiated.
Non-Danish and Danish applicants may be eligible for tax reductions if they hold a PhD degree and have not been tax liable to Denmark for the last 10 years.
The position is covered by the Job Structure for Academic Staff at Universities 2020.
For further information about the position, please contact Associate Professor Mani Arumugam at email@example.com. For questions regarding the recruitment procedure, please contact HR at firstname.lastname@example.org.
The University of Copenhagen International Staff Mobility office offers support and assistance to all international researchers on all issues related to moving to and settling in Denmark.
Your online application must be submitted in English via the ‘Apply now’ link below. Furthermore, your application must include the following documents/attachments – all in PDF format:
- Cover letter expressing the motivation and previous research experience of the applicant (max. one page)
- Curriculum vitae
- Copy of the PhD degree certificate and the master’s degree certificate. In case the PhD has not yet been completed, a written statement from the supervisor is acceptable, confirming it will be obtained before October 1, 2023.
- List of publications
- References (name and contact details of at least two references)
Application deadline: June 18, 2023, 23.59pm CET.
We reserve the right not to consider material received after the deadline and not to consider applications that do not live up to the abovementioned requirements.
The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work has been completed, each applicant can comment on the part of the assessment that relates to the applicant him/herself.
You can read about the recruitment process at www.employment.ku.dk/faculty/recruitment-process.
The applicant will be assessed according to Ministerial Order No. 242 of March 13, 2012, on the Appointment of Academic Staff at Universities.
The University of Copenhagen wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of their personal backgrounds.
Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.