stillingsbetegnelse: PhD scholarship in B cell immunoinformatics

jobbeskrivelse:
Identification of B cell epitopes plays a major role in several biotechnological and clinical tasks and is central to our understanding of the immune system. Sequence and structure based B-cell epitope predictions have improved in the last decade, but their reliability is still not sufficient for many practical applications. In particular, most of the prediction methods do not take into account relevant information, such as the sequence and structural characteristic of the potential binding antibodies. This piece of information can not only improve the predictions, but generate more focused results in many clinical and pharmaceutical scenarios (e.g. antibody drug development or humanization). CBS (Center for Biological Sequence Analysis) is leading the field of immunoinformatics and the methods developed at CBS for prediction of B cell epitopes have in many independent benchmark calculations been demonstrated to be among the best available. Responsibilities and tasks A central part of the PhD will be dedicated to implement and develop improved methods for prediction B cell epitope prediction, continuing on a successful track of work started more than 10 years ago. The development of improved methods will include the training of last generation machine learning tools (such as random forests and deep neural networks), and the creation of novel structure and sequence based tools for the prediction, the analysis and the engineering of antibody-antigen interaction. As a central part of this project, the candidate will develop pipelines to automatically retrieve and store epitope data that will be used to train the methods and to assess the state-of-the-art performance by comparing all the epitope prediction method publicly available. Moreover, the PhD will in collaborations with research partners be working on applying the developed method to investigate and provide solutions to frontier clinical and biological problems including cancer- and auto-immunology. The successful candidate will have a bioinformatics, biology, or computer science background and must have strong computational skills and prior experience with Unix/Linux command line environments, as well as either C, Perl, Python or a comparable scripting language. The applicant must have prior experience with bioinformatics and high-performance machine learning methods. Knowledge of systems biology, immunology, and structural biology is considered a plus. 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 Morten Nielsen. 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. Further information Further information may be obtained from Morten Nielsen, mniel (at) cbs.dtu.dk Please do not send applications to this e-mail address, instead apply online as described below. You can read more about Center for Biological Sequence Analysis at http://www.cbs.dtu.dk and Department of Systems Biology at http://www.bio.dtu.dk Applicatio

Arbejdsgiver Navn: Danmarks Tekniske Universitet

Arbejdsgiver telefonnummer: 45252525

Arbejdsgiver faxnummer: 45881799

Job kort beskrivelse:
Undervisning og forskning på universiteter og højere læreranstalter

land: Danmark

region: Hovedstaden

krævede uddannelse: Ikke angivet

Kilde til jobtilbud: AMS, Offentlige arbejdsformidlinger, Danmark