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PhD Scholarship in Metagenomics

Danmarks Tekniske Universitet (DTU)

Frist 27. maj 2020

DTU seeks qualified candidates for a vacant PhD position in the Metagenomics group within the Section for Bioinformatics. The scholarship will start as soon as possible.

Metagenomics is the study of genetic material recovered from a wide range of environments including everything from the human lung microbiome to river bed sediments. Not only can metagenomics study microbiome composition and functionality, but novel algorithms allow us to assemble individual genomes from complex communities and even estimate the replication rate of these microbes.

We know that viruses and plasmids are present in large numbers in most microbiomes and we know their strong evolutionary role in bacterial evolution. Their ability to horizontally transfer genes between bacteria is behind the virulence and antibiotic resistance of many otherwise easily curable diseases. Despite these facts, they are still an often overlooked part of metagenomics studies.

Our group has a strong focus on the importance of extrachromosomal elements such as viruses and plasmids in bacterial evolution and also how they affect human health. We incorporate the latest knowledge in microbiology with the newest sequencing technology and novel informatics approaches to explore bacterial evolution using our developed bioinformatics tools and databases. We try to always have our projects done in close collaboration with clinicians, industry and wet-lab researchers to ensure that our research is applicable in the real world.

The goal of the PhD project will be to shed light on different aspects of the importance of viruses and/or plasmids in bacterial evolution and develop necessary tools in the process. The scholarship recipient will be able to work in collaboration with clinicians, industrial and/or wet-lab researchers and will be expected to take part in the project design to get a sense of project ownership.

Examples of projects could be:

  • Develop a sequence assembler specialized in extracting viruses from metagenomes in collaboration with clinical human gut microbiome specialists
  • Develop a Machine Learning Model to identify clinically relevant antibiotic resistance genes in metagenomes in collaboration with international experts
  • Explore the role of horizontal gene transfer in general microbiome evolution

In terms of education, candidates must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree, ideally in computer, mathematics or biological science.

Ideally, the candidate should have some of the following qualifications:

  • The language of communication at DTU is English.
  • Excellent problem-solving skills
  • Proficiency in a programming language (C++, Ruby, Python etc.)
  • Experience in bioinformatics and knowledge of genomics
  • Expertise in next-generation sequencing
  • Expertise in machine learning
  • Expertise in viruses, plasmids and/or mobile genetic elements

Approval and Enrolment
The scholarships for the PhD degree are subject to academic approval, and the candidates will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see the DTU PhD Guide.

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 appointment terms
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 3 years.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Gisle Vestergaard at gisves@dtu.dk.

You can read more about bioinformatics research at DTU Health Tech at Section for Bioinformatics.

Please submit your online application no later than 27 May 2020 (23:59 local 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:

  • A letter motivating the application (cover letter)
  • Curriculum vitae
  • Grade transcripts and BSc/MSc diploma
  • Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)

Incomplete applications will not be considered. Candidates may apply prior to obtaining their master's degree but cannot begin before having received it.

Applications and enclosures 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.

DTU Health Tech engages in research, education, and innovation base on technical and natural science for the healthcare sector. The Healthcare sector is a globally expanding market with demands for the most advanced technological solutions. DTU Health Tech creates the foundation for companies to develop new and innovative services and products which benefit people and create value for society. DTU Health Techs expertise spans from imaging and biosensor techniques, across digital health and biological modelling, to biopharma technologies. The department has a scientific staff of about 175 persons, 130 PhD students and a technical/administrative support staff of about 80 persons.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 vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 11,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.

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Danmarks Tekniske Universitet (DTU) - hurtigt overblik

Danmarks Tekniske Universitet (DTU)
Danmarks Tekniske Universitet (DTU)
DTU er et teknisk eliteuniversitet med international rækkevidde og standard. Vores mission er at udvikle og nyttiggøre naturvidenskab og teknisk videnskab til gavn for samfundet. 11.200 studerende uddanner sig her til fremtiden, og 6.000 medarbejdere har hver dag fokus på uddannelse, forskning, myndighedsrådgivning og innovation, som bidrager til øget vækst og velfærd.

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