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lastModificationDate: 1547728998100

stillingsbetegnelse:
PhD scholarship in Plasmid Biology and Bioinformatics

jobbeskrivelse:

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 the Technical University of Denmark, DTU, is together with several partners worldwide and funded by the Novo Nordisk Foundation 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 (http://www.genomicepidemiology.org, http://www.globalmicrobialidentifier.org, http://www.compare-europe.eu).

Plasmids are known to be very important for the transfer of antimicrobial resistance between different bacterial species and we have already during our initial investigations identified several novel plasmids and would like to increase our focus with a new PhD-student.

While plasmids often serve as mediators of gene transfer, the process is also considered to be a strong evolutionary force in microbial environments. The group recently developed a procedure for the isolation of plasmid DNA from various sources, and subjected it to deep sequencing using the Oxford Nanopore long-read sequencing, Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. For this project we aim to characterize the plasmidome in various environments: e.g., waste water, animal faeces, which house complex yet dense microbial communities, and hold enormous significance for health including AMR research.

Plasmids are important for the transmission of AMR genes between bacterial species. We are seeking a candidate that can study the occurrence and abundance of plasmids in our global metagenomics data using bioinformatics approaches, as well as combing this with 'wet lab' investigations isolating and studying these plasmids.

The successful student will work in close collaboration with other PhD-students and post docs studying other aspects of antimicrobial resistance and involving expertise in conventional and molecular microbiology, bioinformatics and epidemiology.

• You will contribute to the improvement of plasmid extraction from complex samples.
• You will analyse the NGS data using bioinformatics methods.
• You will be mainly responsible for studying the occurrence of plasmids and their correlation to AMR in global metagenomic data-sets.
• You will contribute to build a global distribution of plasmidome occurrence and interaction.
• You will contribute to understanding the global transmission of AMR.
• Your research could include identifying plasmids, metagenomic mining, isolation and sequencing of plasmids, studying host-range of plasmids and determining associations between AMR, plasmids, bacterial composition and global epidemiological drivers.

Qualifications

It is expected that applicants have a master degree where there has been a major inclusion of bioinformatics, computer science or similar.

Beneficial:

• Expertise with analysing metagenomics data
• Expertise with assemblies (metagenomics and isolates)
• Working with long-read sequencing data
• Knowledge of statistical methods
• Experience with laboratory work

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. http://www.dtu.dk/english/Education/PhD/Rules/PhDguide

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. http://www.dtu.dk/english/about/job-and-career/working-at-dtu/career-paths

Further information


Further information may be obtained from Frank Aarestrup, professor, tel.+45 3588 6281 or Saria Otani, Post doc, E-mail: saot (at) food.dtu.dk

You can read more about the Departmentat

http://www.food.dtu.dk/english/research/genomic-epidemiology Application http://www.food.dtu.dk/english/research/genomic-epidemiology

Please submit your online application no later than 5 February 2019

To apply, please open the link "Apply online", fill out the online application form. The following must be attached in English:

• 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) http://www.dtu.dk/english/Education/phd/Applicant/Pre_acceptance-1-

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, 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.


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jobCategoriesCodes_0: http://data.europa.eu/esco/isco/C2310

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positionTypeCode: directhire

contractTypeCodes_0: fulltime

Arbejdsgiver Navn: Danmarks Tekniske Universitet

source: DK-STAR