Research assistant/PostDoc for WGS data analysis in the field of AMR - DTU Food

Antimicrobial resistance is among the biggest challenges for human and animal health. The GloCaB Research Group at the National Food Institute acts as reference laboratory – you can become part of this!
Do you have experience with whole genome sequencing (WGS) data quality control and analysis from bacterial isolates? Are you also interested in genomics and antimicrobial resistance (AMR)?

The Research Group for Global Capacity Building (GloCaB) is looking for a bioinformatician. We provide, as part of the responsibilities as reference laboratory for AMR for EU, WHO and FAO:

• Advisory services to other national reference laboratories and authorities, international and supranational institutions, and agencies
• Verification of phenotypic and genotypic antimicrobial susceptibility testing
• External quality assurance (EQA) and genomic proficiency test (PT) schemes.

In GloCaB, we collaborate globally with researchers, clinicians, veterinarians and food laboratories, supporting them with for example, WGS, genomic analysis and expertise in AMR and we build capacity related to surveillance of AMR in multiple low- and middle-income countries.

Responsibilities and qualifications
As our new colleague, your primary areas of responsibility will include to:

• Construct and maintain pipelines on a HPC cluster and extend the current ones for short read technology (Illumina) to include long read technology (Oxford Nanopore)
• Handle and analyse WGS (long and short read technologies) and metagenomics (occasionally) data
• Organize data analysis, write reports/manuscripts and produce plots summarizing main findings
• Present results orally to a wider audience
• Assist in the evaluation of WGS data quality for and from EQAs and genomic PTs
• Perform benchmarking of tools outputting WGS analysis results
• Provide bioinformatics support related to single isolate genomes and AMR annotation
• Support and assist in organizing teaching and training in person and online in WGS, including sequencing quality control, genomic analysis, phylogenetic analysis, and other ad-hoc tasks related to building capacity in bioinformatics for our international network
• Some travel activities may be expected.

As a formal qualification, you must have a master’s degree in bioinformatics or equivalent (for a research assistant) or a PhD degree in bioinformatics or equivalent (for a postdoc). Preferably you have a strong background in microbiology, molecular biology, genetics, and genomics.

Essential expertise includes:

• Documented experience in WGS of bacterial isolates, and further bioinformatics analysis
• Experience with next and third generation sequencing data quality control
• Experience with bacterial AMR (including gene annotation) and typing
• Experience working on HPC clusters, preferably with Computerome
• Proficiency in either Bash, R or Python
• Proficiency working in a Unix environment
• Experience in providing bioinformatics support to non-bioinformaticians
• Experience in providing bioinformatics and WGS data analysis training
• Ability to plan and execute complex tasks according to formal requirements and timelines
• Ability to engage constructively in a large, international, and cross-disciplinary environment
• Experience in writing scientific manuscripts for peer-reviewed journals
• Excellent communication skills and fluent in English, oral and written
• Familiarity with analysis of metagenomic data and machine learning techniques is a plus but not essential.
• Experience with data management, visualization, and interpretation, including proficiency in statistical analysis

What we offer in return
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 and the opportunity to work with colleagues who are experts in their field.

We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

You can read more about the Institute at www.food.dtu.dk and about the research group at www.food.dtu.dk/english/research/global-capacity-building

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 position will be customized according to the preferred candidate's profile (Research Assistant or Postdoc).

We offer a full-time position for a period of employment of 3 years starting on 1 September 2024 or by mutual agreement.

The workplace is DTU Lyngby Campus, Building 204, Henrik Dams Alle, 2800 Kgs. Lyngby.

You can read more about career paths at DTU here.

Further information
Further information on the position may be obtained from Professor Rene S. Hendriksen on +45 2245 0763.

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 12 July 2024 (23:59 Danish time).

Interviews will take place in August.

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", 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)

Please indicate if you apply for a Postdoc or a Research Assistant.
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.

Technology for people
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.

Adresse:

Henrik Dams Allé
2800 Kgs. Lyngby