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Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik

Humboldt-Universität zu Berlin | Mathematisch-Naturwissenschaftliche Fakultät | Institut für Informatik | Wissensmanagement in der Bioinformatik | Stellenausschreibungen | Research Position: Biomedical Data Integration, Information Extraction, and Variant Assessment

Research Position: Biomedical Data Integration, Information Extraction, and Variant Assessment

The research group for „Knowledge Management in Bioinformatics“ at the Institute for Computer Science, Humboldt-Universität zu Berlin, has an open 3-year research position in the area of biomedical data integration and biomedical information extraction (text mining).


The position is part of the DFG-funded research unit Beyond the Exome, a collaboration between the Charite Berlin, the MDC Berlin, and Humboldt-Universität. The research unit investigates the role of non-coding variations for rare diseases. It encompasses experts from Medicine to Bioinformatics. The position is paid according to TVL-E13 (100%), at the earliest possible start date and will run for three years. Our prime interest is to find a highly motivated PhD student, but applications from PostDocs might also be eligible.


Applicants are expected to pursue independent research in the fields of biomedical data integration and biomedical information integration. We will build an integrated resource of information on non-coding variations and their relationships to diseases. An important source of information will be the scientific literature, for which we develop semi-automated methods for information extraction and normalization. The gathered information will be used to predict the clinical relevance of variations. The holder of this position will be able to chose its own focus within these topics (integration, extraction, prediction). A short description of our project can be found here.

Teaching Duties

There are no teaching duties.

The Environment

The holders of this position will work in an interdisciplinary team from computer science, medical informatics, and bioinformatics currently consisting of app. 10 full-time researchers plus students. We are engaged in a number of collaborative projects related to statistical analysis of -omics data, biomedical text mining, translational bioinformatics, and eScience infrastructures. The group is, for instance, part of the DFG-funded graduate school SOAMED on service-oriented architectures for medical applications, the two BMBF funded projects PREDICT and PERSONS on knowledge infrastructures for precision oncology, and the DFG Excellence Graduate school BSIO (Berlin School of Integrative Oncology).

Further information on the group may be found at WBI. Please also see our recent publications and currently funded projects.

Formal requirements

  • (Very) good Diploma or Master in Computer Science, Bioinformatics, Computational Linguistics, or equivalent qualifications
  • Good knowledge in databases and in machine learning and/or statistical Natural Language Processing
  • Experience in software programming and the development of user-friendly tools
  • Ambition to pursue high-profile research
  • Strong interest in interdisciplinary research and in pursuing a PhD
  • Fluent English


Please send applications containing the usual documents (certificates, summary of Master thesis, list of publications, at least one scientific reference) by email to Prof. Leser. Please also send all questions directly to him.

Deadline for applications is 31.12.2019. Applications arriving later might be excluded from consideration.

Humboldt-Universität is an equal-opportunity employer. Applications from disabled persons are, if equally qualified, handled with preference. We strongly encourage applications by females.

Note: This text is an informal description of the open position. The official announcement (only in German) can be found here.