PhD scholarship in Bioinformatics Applied to Pangenome Graphs

DTU Health Tech is looking for a qualified candidate for a PhD position in Bioinformatics applied to pangenome graphs.

Responsibilities and qualifications
In this position, you will develop algorithms and computational methods to deal with the analysis of large datasets from modern and ancient sources. More specifically, these algorithms will be aimed at developing novel methods using pangenomes graphs.

Traditionally, sequencing projects used a single linear reference genome to conduct analyses. Recently, groups have proposed replacing this single reference with a graph encompassing all known diversity within a species. While this approach has yielded exciting results, a lot of work remains to fully exploit the power of pangenomic graphs. The Modern and Ancient Genomes group at DTU are pioneers in terms of developing probabilistic inference methods on pangenome graphs. The position involves computational methods development which means that a large portion of time will be dedicated to algorithm development and coding, likely in C++.

You 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 and a bacherlor's degree. Ideally, your degree should be in computer science, mathematics or biological science with a focus on quantitative and mathematical aspects.

More specifically you should ideally have the following qualifications:

• Knowledge of a programming language like Python, Perl, C++ and/or Java
• Ability to work in a UNIX environment, ideally in a high-performance computing environment
• Thorough understanding of basic algorithms and data structures used in computer science
• Knowledge of probabilities and statistics
• Firm grasp of first-year university mathematics (differential calculus/linear algebra)
• Experience in bioinformatics and knowledge of metagenomics are a plus
• Expertise in next-generation sequencing data generation and processing are also a plus but not required

The language of communication at DTU is English.

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 DTU's rules for the PhD education .   

Assessment
The assessment of the applicants will be made by  Prof. Gabriel Renaud.

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.

Starting date is as soon as possible (or according to mutual agreement). The position is a full-time position.

You can read more about career paths at DTU here .

Further information
Further information may be obtained from Prof. Gabriel Renaud (gabre [at sign here] dtu.dk). 

You can read more about DTU Health Tech at www.healthtech.dtu.dk/english .  

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark . Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar ” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

Application procedure
Your complete online application must be submitted no later than15 December 2022 (Danish 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 (in English) including official description of grading scale
• A link to a code portfolio like GitHub or GitLab.

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

Applications 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 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 210 persons, 140 PhD students and a technical/administrative support staff of about 160 persons, of which a large majority contributes to our research infrastructure and related commercial activities.

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 mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,400 students and 5,800 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.