Postdoc in Host-Microbiome Multi-omic Data Science

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.

About us
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.

Our research
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.

Job description
We seek a data scientist to derive insights from host-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 integrate and interpret these data derived from microbiome (e.g., metagenomics, metatranscriptomics, viral metagenomics, metabolomics, metaproteomics) and host (e.g., genetics, proteomics, circulating metabolomics) in collaboration with international data science partners (e.g., EMBL-Heidelberg; University of California, Davis) and other project partners. The current state-of-the-art for multi-omics integration and interpretation leaves much to be desired. Fortunately, our ongoing work leveraging a deep learning approach (autoencoders) integrates multi-omics data and generates biologically relevant insights using a biologically informed machine learning framework. Our ambition is to strengthen this research direction using expertise in data science and machine learning.

In this position, you will be:

• Responsible for improving and expanding our current deep learning approaches, while also having a chance to create your own novel approaches.
• Expected to participate in and lead existing data science projects within these consortia and 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.

Profile
The Postdoc fellowship is aimed at early-career researchers with a basic science background. We are particularly interested in candidates with strong analytical skills and interdisciplinary experience. Candidates with solid data science background but lacking biological training are strongly encouraged to apply and include a statement about their motivation for this position and how they anticipate addressing this.

Required qualifications:

• PhD in computer science (informatics), mathematics, physics, or bioinformatics; or in biology with strong experience in software development.
• Academic preparation as well as experience in machine learning and statistical analysis.
• Strong programming skills in and experience using deep learning frameworks (e.g., PyTorch, TensorFlow).
• Experience in 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:

• Experience in applying deep learning to biological problems.
• 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.

Eligibility
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.

Questions
For further information about the position, please contact Associate Professor Mani Arumugam at [email protected]. For questions regarding the recruitment procedure, please contact HR at [email protected].

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.

Application procedure
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.

Kilde: Jobnet.dk