1 Doctoral Researcher Position on Extraction of unstructured information related to gene regulatory interactions in human pathogenic fungi from biological research papers in Germany | Jena School for Microbial Communication (JSMC)

The project aims at automatically building up a literature-derived database of transcription factors (TFs) and their target genes for two fungi, Candida albicans and Aspergillus fumigatus. Crucial for this work will be to properly adapt already existing and create new language technology tools, such a named entity recognizers (for genes/proteins, species, diseases, etc.) and relation extractors (including and extending ones for protein-protein interactions). Challenging research questions to be solved here relate to discourse phenomena in full texts (e.g. anaphora) as well as expressions of different degrees of credibility of assertions (e.g. due to hedging and other varieties of uncertainty and vagueness in natural language).

We expect:

• a Master’s degree (or equivalent) at the intersection of Computer Science, Biology, Bioinformatics or Computational Linguistics. Candidates about to earn their degree are welcome to apply.
• desirable methodological skills: natural language technology, machine learning, statistics, programming experience (in JAVA), expandable biological background knowledge
• high motivation and interest to join one of the interdisciplinary research areas of JSMC
• creativity and interest to shape your own thesis project
• an integrative and cooperative personality with enthusiasm for actively participating in the lively JSMC Community
• very good communication skills in English (instruction language at JSMC)

We offer:

• a highly communicative atmosphere within a scientific network providing top-level research facilities
• a doctoral researcher position (TV-L E13, 65%) funded for three years based on the regulations of the German Research Foundation as well as generous research funding
• a comprehensive mentoring program with supervision by a team of advisors
• a top-level PhD training program with courses in state-of-the-art research technologies and soft skills
• Jena – the German City of Science 2008: a young and lively town with dynamic business activities, successful scientific centers of innovation and a vibrant cultural scene around the famous

Friedrich Schiller University Jena is an equal opportunity employer.