Four PhD scholarship in bioinformatics of metagenomics and global surveillance of antimicrobial resistance

DTU Fødevareinstituttet
mandag 30 apr 18

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Frist 25. maj 2018
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Antimicrobial resistance (AMR) is one of the largest threats against global health and obtaining information about the global prevalence and emergence is essential to guide interventions. The Research Group for Genomic Epidemiology at DTU Food is together with DTU Bioinformatics and several partners worldwide trying to establish a global surveillance of infectious diseases and antimicrobial resistance based on metagenomic sequencing of urban sewage, and data are now rolling in (www.genomicepidemiology.org, www.globalmicrobialidentifier.org, www.compare-europe.eu).

As part of this global endeavour, we are seeking 3-4 qualified PhD-candidates for analysing specific parts of the data, as outlined below.

Candidates are invited to apply for a specific project from the list below.

  • Importance of mobile elements for global transmission of AMR (Frank Aarestrup)
    Horisontal transmissible elements such as transposons and IS-elements are important for the transmission of AMR genes within and between bacterial species. We are seeking a candidate that can study the occurrence and abundance of such elements in combination with AMR genes in our global metagenomic data.
  • Metagenomic phylogeny (Ole Lund)
    Methods have been developed for constructing accurate phylogenies from isolates. The project is to develop and test methods for construction phylogenies for metagenomic samples, and for strains existing in these samples. Another part of the project is to correlate these phylogenies with epidemiological data such as AMR usage, geography, time, and wealth.
  • Machine learning and identification of chromosomal mutations (Ole Lund)
    Because urban sewage data represents a mix of metagenomics samples and bacterial species it can be difficult to predict AMR. The aim of the project is therefore to improve on the state-of-the art in AMR prediction by applying machine learning approaches. Additionally, we will try to develop machine leaning approaches for identifying which bacterial species carry individual AMR genes.
  • Human microbiome interaction (Simon Rasmussen)
    Worldwide metagenomic data of urban sewage gives us a unique possibility to identify differences between human gut bacteria across the world. If we combine this with immune information from the humans living in the different cities we can identify co-evolution between the bacteria in our gut and our immune system. We can then answer questions such as which bacteria are co-evolving with us, which are not? Are specific genes or peptides under selection in these bacteria? Can we correlate this with incidence of human disease?

Responsibilities and tasks
All candidates are expected to actively engage with other people, have good skills in collaboration and are openly sharing their results and knowledge.

For the specific positions:

Importance of mobile elements for global transmission of AMR
  • You will be responsible for studying the occurrence of transposons, IS-elements and other horizontally transferable elements and their correlation to AMR in global metagenomic data sets.
  • You will contribute to understanding the global transmission of AMR.
  • Your research could include identifying mobile elements, metagenomic mining, and determining associations between AMR, mobile elements, bacterial composition and global epidemiological drivers.
Metagenomic phylogeny
  • You will be responsible for constructing bacterial phylogeny from global metagenomic data sets and correlating this to AMR and global epidemiological variables.
  • You will contribute to the understanding of the global evolution and transmission of bacteria and AMR.
  • Your research could include use and development of phylogenetic methods and modelling.
Machine learning and identification of chromosomal mutations
  • You will be responsible for using machine learning approaches for identifying AMR genes, including chromosomal mutations in global metagenomic data sets.
  • You will contribute to improved detection of AMR.
  • Your research could include the use of machine learning for prediction.
Human microbiome interaction
  • You will be responsible for studying the correlation of specific genes or peptides detected in global metagenomic data sets to global human populations.
  • You will contribute to our understanding of association between human populations, bacterial composition and AMR.
  • Your research could include data mining, prediction of peptides and correlation to global epidemiological data.

Qualifications
Candidates should have a master's degree in engineering or a similar degree with an academic level equivalent to the master's degree in engineering.

It is expected that applicants have a master degree in bioinformatics, computer science or similar.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and the candidate 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.

Assessment
The assessment of the applicants will be made by:

  • Professor Frank M. Aarestrup, DTU Food
  • Associate professor Thomas Nordahl Petersen, DTU Food
  • Professor Ole Lund, DTU Bioinformatics
  • Associate professor Simon Rasmussen, DTU Bioinformatics

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 Professor Frank M. Aarestrup, fmaa@food.dtu.dk, tel.: +45 3588 6281.

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

Application
Please submit your online application no later than 25 May 2018 (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)

If relevant, you may add additional documents to the list above, e.g., a Research Statement

In the field “Please indicate which position you are applying for”, please indicate which project you are applying for.

Candidates may apply prior to obtaining their master's degree but cannot begin before having received it.

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

DTU Food (The National Food Institute, Technical University of Denmark) 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.

DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 6,000 advance science and technology to create innovative solutions that meet the demands of society, and our 11,200 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government and public agencies.