Thesis / Internships

  • For a BSc or MSc thesis project in our group, you can choose from one of the available research projects or research themes. There is no substitute for learning research than by doing research. So join our lab, and contact one of the responsible SSB staff members for their ideas on exciting thesis projects (both BSc and MSc), be it computational (dry) or experimental (wet). Check out the publications and different researc areas/projects for topics that are currently being studied. Be aware that to start a thesis project you should already have gained sufficient background knowledge and that your study advisor has to sign for approval.

Computational Systems Biology

Our research focus is on deriving a deeper understanding of microbial systems by uncovering biological meaning from genome scale data and through multiscale data integration. All of our projects are in close collaborations with experimental partners. To answer biological questions we use a broad range of bioinformatics, computational, analytical mathematics  and statistical methods.

Contact person: dr. Robert Smith,

Example projects:

Systems Health is an interdisciplinary field of study that looks at the systems of the human body as part of an integrated whole, incorporating biochemical, physiological, and environment interactions. Systems Health draws on systems science and systems biology, and considers complex interactions within the human body in light of a patient’s molecular profiles (genomics, metabolomics, proteomics, metagenomics),  behavior and environment. This entails application to both Human and Animals: while research question may differ concerning the organism considered, experimental and data analysis tools are often the same.
We investigate complex biomedical problems by developing, integrating and applying mathematical models (bottom-up approaches) in conjunction with statistical and machine learning methods (Top-down approaches). We have several ongoing projects and MSC thesis and internship on both theoretical/methodological and applicative aspects of System Health and Medicine concerning both humans and animals. If interested send a message!
Contact person: dr. Edoardo Saccenti, / Dr. Robert Smith,
Available Projects:
Example of Past Projects:

Microbial engineering

A main goal of the Laboratory of Systems and Synthetic Biology is to gain a systems understanding of industrially relevant microorganisms and to translate this knowledge to high-added value applications.

Filamentous fungi such as Aspergillus niger form a class of relatively simple eukaryotic organisms that are popular in the bioproduction industry. We aim to develop fungal cell factories using genomics, synthetic biology and metabolic modeling approaches. Whenever necessary, we use Saccharomyces cerevisiae as a model system or host for the analysis of fungal processes.

Pseudomonas putida is another industrially relevant organism that we are making ready for a life as cell factory. We are developing methods to make easy re-programming of the lifestyle of P. putida towards production of bulk and specialty chemicals possible. We are also aiming towards P. putida strains that are able to withstand the harsh conditions that are often met in industrial bioprocesses. Since we don’t want our strains to escape to the environment, we are designing and producing P. putida strains that will not be able to survive outside the lab or the factory.

Every now and then, we are performing projects involving other organisms than the two mentioned above. For details about these projects and the ones involving A. niger and P. putida please send an email.

Contact person: Dr. Robert Smith,

Example projects:


Subject choice, planning, and thesis contract

Finding a suitable thesis project requires some groundwork. Start by reading the research themes and research projects pages. Identify research ideas that interest you. Next contact the contact person of the research project(s) of your choice, agree with your supervisor(s) on the research topic, the duration (i.e. credit points) and starting date. Optimally do all of this at least 3 months in advance. Upon agreement fill in the BSc or MSc thesis contract, obtain a copy of the BSc or MSc thesis evaluation form and send a copy of the signed thesis contract to your study advisor for approval and send in the undersigned filled-in thesis contract to the SSB secretary.

On your first day, visit the SSB secretary to:

  • Sign-off for having read the (VSNU) Netherlands Code of Conduct for Scientific Practice 2012, rules for appropriate storage of data, bio- and other research materials and rules on safety and Other lab-rules as laid down in the short guide for employees and guests of the Laboratory.

Thesis Evaluation

Normally there are two intermediate evaluations: A 10-min introductory presentation of the project is given for the workgroup within 3 weeks. After approximately 1.5 months, the thesis-project will be evaluated with your supervisor.

The thesis project ends with handing in the report and giving a 20-min oral presentation. Writing the thesis report is an important part of the research project and you should reserve enough time for this activity. Three weeks before the final date, at least an outline of thesis should be ready. A draft version (digital word version) should be handed in to the supervisor for suggestion and comments before giving the final presentation. Grading will be done after your final examination, which normally will take place directly after your final presentation.

Once you have completed all the required activities and have handed in the final version of the thesis by E-mail as pdf file to the secretary the grade will be submitted.