The price of genome sequencing is already so low that whole genome sequencing will also find worldwide application in human and veterinary practices as well as many other places where bacteria are handled. In Denmark alone this equals more than 1 million isolates annually in 15-20 laboratories and globally up to 1-2 billion isolates per year. The limiting factor will therefore in the future not be the cost of the sequencing, but how to assemble, process and handle the large amount of data in a standardized way that will make the information useful, especially for diagnostic and surveillance. The aim of the Center for Genomic Epidemiology is to provide the scientific foundation for future internet-based solutions that enable simplification of total genome sequence information and comparison to all other sequenced including spatial-temporal analysis. We will develop algorithms for rapid analyses of whole genome DNA-sequences, tools for analyses and extraction of information from the sequence data and internet/web-interfaces for using the tools in the global scientific and medical community. The activity is being expanded to also include other microorganisms, such as vira and parasites as well as metagenomic samples.
Responsibilities and tasks : The PhD student will work in the areas of:
- Developing new methods for automatic internet based upload and storage of genomic data and associated meta data, super computer driven analysis of the data, and storage of the results
- Developing new concepts for complex user searches and presentation of the results to the user
- Developing solutions for big data storage and analysis
- Establishing methods for outbreak detection based on whole genome sequencing
- Developing machine learning tools for geno- to pheno type prediction
- The sucessfull candidate will have bahelor level knowledge of biology, or Biochemistry as well as proficiency in several programming languages, prefarably including C, Java, JavaScript, HTML5 and PHP.
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.
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 of DTU. For information about the general requirements for enrolment and the general planning of the scholarship studies, please see the DTU PhD Guide.
Assessment : The assessment of the applicants will be made by Professor Ole Lund.
We offer : We offer an interesting and challenging job in an international environment focusing on education, research, public-sector consultancy and innovation, which contribute to enhancing the economy and improving social welfare. We strive for academic excellence, collegial respect and freedom tempered by responsibility. The Technical University of Denmark (DTU) is a leading technical university in northern Europe and benchmarks with the best universities in the world.
Salary and appointment terms : The salary and appointment terms are consistent with the current rules for PhD degree students. The period of employment is 3 years.
Applications must be submitted as one pdf file containing all materials to be given consideration. To apply, please open the link "Apply online," fill in 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
Deadline : 15.03.14
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