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PhD position in Computational Systems Biology (f/m) open

Construction of a biochemical reaction network model to predict the chemical patterns arising from complex processing steps in cocoa Jacobs University Bremen is a private, state-recognized, English-language research university, offering Bachelor, Master or PhD programs in the focus areas Health, Mobility and Diversity. The guiding principles are first class research and teaching, international diversity and transdisciplinary cooperation. Jacobs University's goal is to prepare young talents from all around the world to take on the new challenges in today's globalized workplace. Currently, more than 1,300 students from over 100 nations live and study on the residential campus. 

Subject 
The collaborative project COMETA (COcoa METAbolism) analyzes the precise chemical composition of cocoa beans from various origins. The overarching goal is to develop new rapid quality tests for cocoa classification, processing, and planning requirements for raw material. This project bridges cutting edge research areas, including Microbiology, Analytical Chemistry, and Systems Biology, with direct industrial applications in a unique, highly interdisciplinary framework. The aim of the PhD project is the elucidation of chemical and metabolic reactions of industrial processing steps, such as fermentation and roasting to determine quality indicators for flavor and other relevant chocolate characteristics. Solely considering intermediates of the cocoa metabolism is insufficient as these processing steps are performed under non-physiological conditions, e.g., high temperature. Within this PhD project, a metabolic model of the cocoa bean will be reconstructed and interfaced with chemical databases, in order to predict the chemical scope of the system under diverse conditions. Mapping the identified quality indicators back to the assembled cocoa processing model allows an a priori assessment of the chocolate quality, for instance for a quality test directly on the plantation. 

Tasks and responsibilities 
 Statistical analysis of various high-throughput data sets for predicting quality indicators 
 Development of software tools for data integration and management 
 Identification of processing step-specific chemical and metabolic markers 
 Reconstruction of a processing model including the relevant chemical and metabolic reactions for the quality indicators starting from the identified markers 

Profile 
 MSc degree (or equivalent) in Bioinformatics, Applied Mathematics, Computer Science or a similar field 
 Solid knowledge of biochemistry and molecular biology 
 Strong programming skills including Python and R 
 Experience in mathematical modeling 
 Experience in handling high-throughput data 
 Knowledge of analytical chemistry and structure elucidation would be beneficial 
 Ability to work in an interdisciplinary environment and good communication skills including fluent in spoken and written English 
 Willingness to travel 

What we offer 
We offer an innovative, multidisciplinary, and dynamic research environment with a strong international profile and close connections to industry partners. The PhD position is available for a period of three years. 

How to apply 
Letters of application must be received by August 31st, 2015, for consideration. Interested candidates are encouraged to submit a CV, contact details of two references and a short letter of motivation electronically to: Prof. Dr. Marc-Thorsten Hütt (m.huett@jacobs-university.de) and Dr. Sergio Grimbs (s.grimbs@jacobs-university.de). Please, feel free to contact us for informal inquiries and additional information. For further information about Jacobs University please see www.jacobs-university.de. Jacobs University is an equal opportunity employer.

posted 2015.08.24