PhD in Computational Systems Biology (Life Science, Applied Mathematics, Computer Science and Chemistry) Germany

The department of Life Science & Chemistry in the focus area Health at Jacobs University invites applications for a PhD position in Computational Systems Biology .

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.

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.

 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


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

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 ( and Dr. Sergio Grimbs ( Please, feel free to contact us for informal inquiries and additional information.

For further information about Jacobs University please see

Jacobs University is an equal opportunity employer.

(Full-time and limited for three years)