PhD scholarship in Whole Genome Sequencing and Machine Learning for Improving Food Safety

Thursday 13 Feb 20

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Identification of bacteria is crucial, as different measures and actions will be taken whether food pathogens are detected, mostly at genus or species level. However, the identification techniques used today are time-consuming, and more importantly lack the resolution to differentiate between strains of the same species. Such strain-level diversity could affect the recognition of the risk level and decision of consequent actions. Certainly, these limitations can be resolved by whole-genome sequencing (WGS) technology. The lack of genetic insight and access to advanced computing facilities is a major hurdle for food industry to apply WGS technology in practice. A smart tool to predict virulence level and resistance to disinfectants is needed for frontline safety/quality assurance practice.

 

Considering the importance of Listeria monocytogenes to the food industry especially dairy industry, this project aims to incorporate WGS data of clinical and dairy isolates in machine-learning predictors to identify the virulence level and disinfectant-resistance of L. monocytogenes strains in real-time. With the developed tool, the food industrial users only need to upload raw read sequences data to the server hosted at DTU via a freely accessible web-based interface, in order to receive easily interpretable output. This project will improve and speed up the decision-making and food safety management of the dairy industry.


For this, the Research Group for Genomic Epidemiology, National Food Institute, DTU seeks a candidate for a vacant PhD position in whole genome sequencing and machine learning for improving food safety.  

 

Responsibilities and tasks

  • You will be responsible for characterization and analysis of Listeria monocytogenes genomes and developing machine learning model to predict virulence level and disinfectant-resistance in L. monocytogenes strains.
  • You will engage in developing web-based tool for food industrial users to predict the virulence and disinfectant-resistance of L. monocytogenes genomes in real-time.
  • You will communicate research results by presenting data at project meetings and international conferences, and write manuscripts for publication. The day-to-day work will be performed in close collaboration with other researchers in the Genomic Epidemiology group and with national and international partners including food industrial partner associated with the project. Collaboration includes active participation in national and international meetings and conferences, sharing of data and results, contribution to joint publications.

Qualifications
Candidates should have a two-year master's degree (120 ECTS points) in bioinformatics or a similar degree with an academic level equivalent to a two-year master's degree. Preferably the candidates with machine learning experience or similar. 


Research Group for Genomic Epidemiology, National Food Institute, DTU is the WHO Collaborating Centre for Antimicrobial Resistance and the EU Reference Laboratory for Antimicrobial Resistance (AMR), which ensures large international collaborative networks.

 

The research group has been working on genomic epidemiology of various foodborne bacteria including Listeria monocytogenes to predict and prevent infectious diseases in humans and to support global detection and control with an emphasis on AMR and foodborne infections. The group has developed online WGS tools for bacterial genome analysis, which have been accessed by users around the world. The group has full access to Computerome (Danish National Supercomputer for Life Sciences). In addition, the group ensures availability of intellectual expertise and technology to execute the project, including all facilities for molecular biology experiments, bioinformatics facilities, and expertise in whole genome sequencing, metagenomics, and machine learning.

 

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.


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 Researcher Pimlapas Leekitcharoenphon, pile@food.dtu.dk, +45 2876 9522.


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


Application
Please submit your online application no later than 26 March 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)

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.


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 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.

https://www.food.dtu.dk/english/service/about-the-institute/vacant-positions/job?id=c3fd0dd0-6f03-462e-9356-2c9a9e2233db
23 FEBRUARY 2020