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PhD Scholarship in Improved Immunoinformatic Methods for Rational T Cell Epitope Discovery

International students are invited for a PhD scholarship in computer science at Technical University of Denmark. This position is available for 5 years. This position is closed on July 01, 2019.

The Bioinformatics section at the Department of Health Technology has its main research and teaching activities in bio-medical and bio-technological informatics, metagenomics, epidemiology, integrative systems biology and machine learning. Our research at DTU Bioinformatics is focused on bioinformatics and computational analyses of large amounts of data generated within biological, biomedical and biotechnological and life sciences area.

We strive to gain new knowledge and drive innovation in human, animal, plant and food science and collaborate with all relevant industries. A cornerstone in achieving this is the dedicated effort to develop bioinformatics, immuno-informatics, metagenomics and systems biology methods and solutions to the challenge of handling and interpreting large scale and heterogeneous big data. We run projects combining big data and laboratory research via the national supercomputing center (Computerome) and molecular genomics laboratories.

A PhD scholarship is available in the Immunoinformatics and Machine-Learning group headed by Professor Morten Nielsen.

Identification of T cell epitopes plays a major role in several biotechnological and clinical tasks and is central to our understanding of the immune system. When T cells scrutinize the surface of cells for foreign peptides presented in complex with MHC (Major histocompatibility complex) molecules, MHC merely presents a minor proportion of the peptides produced within a cell on the cell surface, and only a minor proportion of these is recognized by T cells. While the rules of MHC antigen presentation to a high degree are now understood, very limited knowledge exists regarding the rules defining the role of the T cell and the interaction of the T cell receptor with its cognate pMHC target.

To continue on a successful track of work started more than 15 years ago, we are looking for a highly motivated and talented candidate to carry out a PhD project in Improved immunoinformatic methods for rational T cell epitope discovery.

The project will focus on further advancing our understanding of the rules associated with the process of MHC antigen presentation and T receptor recognition of their cognate epitope targets, with the aim of developing improved methods for rational epitope discovery, and T cell repertoire profiling. The project will be centered around MHC MS eluted ligand data, and single cell T cell sequence data available from collaborators and the public domain.

Responsibilities and tasks

The PhD student will primarily be: Using the knowledge to develop improved methods for rational epitope discovery The tools used in the project will by focused around conventional and deep neural networks. Qualifications

Candidates should hold a MSc in bioinformatics, biology, computer science, engineering, or a similar degree with an academic level equivalent to the MSc in engineering.

In addition, the successful candidate should be able to exhibit the following personal and professional qualifications: Strong computational skills and experience with Unix/Linux command line environments, as well as Python, Perl, R, C or a comparable scripting language. In depth understanding of the basic concepts of the cellular immune system Strong communication skills in written as well as spoken English. Flexibility and a general positive attitude to changes Capability of taking personal responsibility for your work and your results 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

Assessment

An assessment panel will assess the applicants based on both personal and academic qualifications.

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 from 1 August 2019 or as soon as possible hereafter.

You can read more about

Further information

Further information may be obtained from Professor Morten Nielsen, tel.: +45 4525 2425 or by email

You can read more about us at

Application

Please submit your online application no later than 1 July 2019 (local time). 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 An assessment panel will assess the applicants based on both personal and academic qualifications.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.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 from 1 August 2019 or as soon as possible hereafter.You can read more about career paths at DTU here Further information may be obtained from Professor Morten Nielsen, tel.: +45 4525 2425 or by email mniel@dtu.dk You can read more about us at www.healthtech.dtu.dk/english Please submit your online application no later than 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: Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here) Names and contact details of two referees Candidates may apply prior to obtaining their MSc but cannot begin before having received it.

All interested candidates irrespective of age, gender, disability, race, 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.

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 university collaborating globally with business, industry, government and public agencies.


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