The University of Greifswald´s Institute for Mathematics and Computer Science offers subject to the budgetary authority for the period from 01/02/2018 limited for 30 months two part-time positions (50 %) as a Research Assistant.
Payment will be made according to pay group 13 TV-L Wissenschaft if the personal and pay group specific qualifications can be provided.
The project "Scalable Genome Graph Data Structures for Metagenomics and Genome Annotation" is funded by the Swiss National Science Foundation (SNF) and will be carried out in close collaboration with project partners at the ETH Zürich. The aim is to design and implement a distributed graph data structure that can be used to efficiently encode thousands of genome sequences. The k-mer based data structure can be efficiently used as an alignment target for high throughput sequencing reads. One important application of the graph and aim of the applicants project is the accurate gene structure annotation of closely related species, e.g. of vertebrate clades, by taking phylogenetic relationships into account and using the graph.
There position at University of Greifswald advertised here is associated with another position at ETH Zürich in the group of Prof. Dr. Gunnar Rätsch. The candidate will be able to begin working on this project at ETH Zürich starting in or after August 2017 for up to six months, regulated by a separate contract. Within the group of Prof. Gunnar Rätsch, the core data structure and algorithms are being developed.
Job Description: One major task is the development and implementation of efficient methods to extract syntenic (homologous) regions from the graph. This could be via the identification of "bundles" of paths through the graph that represent homologous regions of different genomes that share many k-mers. Another major task is the development and implementation of a multi-species gene annotation algorithm directly utilizing the graph structure and its attached taxonomic annotation and building on top of the AUGUSTUS code base.
The candidate shall have a Master of Science or "Diplom" in Bioinformatics, Biomathematics, Mathematics, Computer Science or a related field. She or he must have experience in the implementation of efficient algorithms for large data. In particular, experience in C++ in a Linux environment is desired. He or she should have a good knowledge of tools for sequence analysis and molecular evolution, both in practice and on the algorithmic background.
The University would like to increase the proportion of women in areas in which they are underrepresented and thus applications from women are particularly welcome and will be treated with priority if they have the same qualifications and as long as there are no clear reasons which make a fellow applicant more suitable.
Severly disabled applicants with the same qualifications will be considered with preference.
This announcement is directed at all persons, no matter which gender.
The costs for applying cannot be reimbursed by the state of Mecklenburg-Vorpommern.