Postdoc in large scale microbial bioinformatics - DTU Food

Complex microbial communities (e.g., microbiomes) harbour an enormous amount of diverse and rich species, with equally rich gene reservoir for various functions. An increasing amount of data sets from various sources are becoming available also in public databases, but are drastically underutilized. This includes our understanding of the abundance and genomic context of antimicrobial resistance genes (ARGs). 

We are seeking a candidate for a vacant postdoc position in bioinformatics with a focus on analysing large number of partly public metagenomics datasets, especially focusing on ARGs and provide a better understanding of the evolution and ecology of AMR globally.

The postdoc will be affiliated with the Genomic Epidemiology Research Group, which primary task is to conduct targeted research with the aim of predicting and preventing infectious diseases in humans and animals, and supporting global detection, surveillance and control. The research group combines expertise in conventional and molecular microbiology with epidemiology and bioinformatics.

Responsibilities and qualifications:

• Your main responsibility will be to analyse, study and visualize large numbers of metagenomics datasets. 
• You will be responsible for downloading and analysing public metagenomes for presence and genomic context of antimicrobial resistance genes.
• You will also improve internal pipelines when newer methods become available. 
• With assistant from other group members, you will analyse the output, draw conclusions and present the outputs. 
• You will communicate research results by presenting data at project meetings and international conferences, and write reports and manuscripts for publication.
• You will engage in the general work carried out by the research group, including discussions and planning of strategies and projects, drafting research grant proposals, etc.
• If your interest lies here and time allows, you will also supervise students and contribute to the group’s teaching activities.
• Daily work will be in close collaboration with other researchers in the Genomic Epidemiology group and national and international partners.

Skills: 

• Proficiency in bioinformatics.

Essential:

• Should be fluent in BASH (unix command line) and possess strong python coding as well as visualization skills.
• Should be familiar with HPC environments.
• Familiarity with metagenomic workflows (read mapping, genomic assemblies, genome assessment, phylogeny).

Desirable:

• Familiarity with SQL databases and how to query them.
• Deep knowledge of publicly available microbial/genomic databases (ncbi refseq/ENA/JGI/marker gene databases) and able to query the latter.

As a formal qualification, you must hold a PhD degree (or equivalent). 

The ideal candidate:

• Holds a PhD degree within one of the following areas: microbiology, biochemistry, computational biology or similar. 
• Has documented experience with large scale metagenomics analyses.
• Preferably, has experience with antimicrobial resistance and bacterial pathogens and is familiar with genetic epidemiology.
• Is able to work independently and able to plan and carry out complex tasks, while having the ability to engage constructively in a large, international and cross-disciplinary research group. 
• Has good English communication skills, oral and written.
• Is ambitious and has a strong drive for obtaining high-quality results.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility. 

Salary and terms of employment 
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.

The period of employment is 2 years and starting date is according to mutual agreement. 

You can read more about career paths at DTU here .

Further information 
Further information may be obtained fromHead of Research Group, Professor Frank M. Aarestrup, fmaa@food.dtu.dk.

You can read more about the Genomic Epidemiology Research Group at http://www.food.dtu.dk/english/Research/Genomic-Epidemiology

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark .

Application procedure 
Your complete online application must be submitted no later than 2 October 2023 (23:59 Danish time). 

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• Application (cover letter)
• CV
• Academic Diplomas (MSc/PhD – in English)
• List of publications 

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

The National Food Institute (DTU Food) works within six technical focus areas: Biotechnology, nutrition, food quality, food safety, food technology and environment & human health. Activities cover a wide range of food products throughout the entire food chain from farm to table, comprising both research activities and research-based consulting and teaching. Read more at www.food.dtu.dk. 

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DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.