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PhD in Computational Chemical Biology and Immunological Bioinformatics, DTU 2011

Two PhD positions are available for immediate start in the Computational Chemical Biology group and the Immunological Bioinformatics group at the Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark.

The Center for Biological Sequence Analysis conducts basic research in the field of bioinformatics, chemoinformatics and systems biology and employs a staff of +100 with a highly multi-disciplinary profile (molecular biologists, biochemists, chemists, medical doctors, physicists, computer scientists, and technical staff). The center represents one of the largest bioinformatics and systems biology groups in academia in Europe.

Projects
One of the major challenges in drug discovery is the accessibility of a standard and shared concept identifier from the large and disparate chemical and biomedical data sources. Such data-driven research with a careful assembly, overlay and comparison of data from many sources of information should provide a comprehensible framework of chemical, biological and pharmacological profiles of drugs.

The computational Chemical Biology group is involved in a European initiative (Open PHACTS) for the development of an open source Systems Chemical Biology Analysis platform. One of the main tasks of one PhD project will be to develop a “polypharmacology browser” to map the coverage of the chemical-biological space, allowing the detection of significant gaps and therefore facilitating the pharmacological profiling of small molecules. Such a profiler will include pharmacokinetics and toxicology data as well as pathways in order to address drug action across multiple levels of complexity from molecular and cellular levels to tissue and biological systems levels. The second project will be in association with the Immunological Bioinformatics group at CBS. The candidate will work on the development of a tool for predicting binding specificities for drug-targets based on receptor pocket similarities.

The applicants should have a strong computational background with experience in building pipelines, managing large data, and for the first project knowledge of web services such as Java or Flex. Background in biology and programming skills in UNIX, perl/python and MySQL will be an advantage. For the second project experience with working with molecular structures is a prerequisite. The applicant must be a good communicator and fluent in written as well as spoken English.

Qualifications

  • MSc degree in bioinformatics, chemoinformatics, computer science or information technology. Excellent programming skills. Experience in Java is preferred. Experience in Perl or Python or a similar programming language is appreciated
  • Familiar with working on UNIX platforms
  • Able to work independently and to plan and carry out complicated tasks, while also being part of a large and dynamic group
  • Good communication skills in English, both written and spoken
  • Interest in software development for chemical and biological purpose

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.

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.

The successful candidates will be based at the Technical University of Denmark in Lyngby.

Further information
Further information may be obtained from Olivier Taboureau (+ 45 45 25 24 89), or from center administrator Dorthe Kjærsgaard (+ 45 45 25 24 80).

Application
We must have your online application by 19 May 2011. Please open the link "apply for this job online", fill in the application form and attach the following documents:

  • 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 (see guidelines and excel spreadsheet here)

Please DO NOT include reprints of already published papers in your application.

Candidates may apply prior to obtaining their master's degree, but cannot begin before having received it.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

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