Technical University of Denmark (DTU)

PhD scholarship in AI for Immunological Molecules

Technical University of Denmark (DTU)

2800 Kgs. Lyngby, Denmark

The Bioinformatics section at DTU Health Technology has its main research and teaching activities in bio-medical and bio-technological informatics, metagenomics, epidemiology, integrative systems biology and machine learning. The research at the Bioinformatics section 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 within the Bioinformatics section 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.

A PhD scholarship is available in the AI for Immunological Molecules group headed by Associate Professor Paolo Marcatili, at the Department Health Technology.

Structural and functional characterization of proteins and peptides is of paramount importance in several biotechnological and clinical tasks and is central to many industrial processes. In particular, the local structure of peptides, either free or embedded in proteins, is often the key to understand or engineer their function, but it is often hard to determine experimentally. On the other hand, available computational tools are often not reliable nor time efficient.

As a part of existing projects (PROVIDE) and collaborations, we are looking for a highly motivated and talented candidate to carry out a PhD project on “Improved structural and functional characterisation of proteins and peptides by deep learning”.

The project will focus on the development of deep learning and generative tools to predict the local structure of peptides of industrial (food production) or biological relevance (antibodies, TCRs, pMHCs), and to exploit these tools to uncover their function (antimicrobial, emulsification, gelation, immunogenicity among others).

Responsibilities and tasks
The PhD student will primarily be:

  • Identifying and collecting structural and functional data on peptides and proteins
  • Developing tools for the prediction of protein and peptide structure
  • Exploit these data and tools to identify molecules with industrial or biologically interesting function


The tools used in the project will by focused around conventional, deep, and generative adversarial networks.

Qualifications
Candidates should have a master’s degree in bioinformatics, biology, computer science, engineering, or a similar degree with an academic level equivalent to the master’s degree in engineering.

In addition, you 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.
  • Background within machine learning, bioinformatics and structural biology.
  • In depth understanding of the basic concepts in protein structure and molecular biology
  • 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


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.

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.

Further information
Further information may be obtained from Associate Professor Paolo Marcatili, tel.: +45 4525 2477 or by email pamar@dtu.dk

You can read more about Department of Health Technology at www.healthtech.dtu.dk/english

Application
Please submit your online application no later than 4 July 2019 (local time).

Apply online at www.career.dtu.dk.

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 (an official translation into English)
  • 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 master’s degree 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.

Please apply via recruiter’s website.

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